Physics and Astronomy › Atomic and Molecular Physics, and Optics

Spectroscopy and Quantum Chemical Studies

Works Count: 118134

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This cluster of papers explores the role of quantum coherence in photosynthetic energy transfer, as well as its effects on energy migration, ion interactions, hydrogen bonding, and vibrational dynamics in aqueous systems. The research also delves into the impact of ions on surface interfaces and the behavior of molecular systems under quantum coherence.

Keywords

Quantum Coherence; Photosynthesis; Aqueous Systems; Energy Transfer; Vibrational Spectroscopy; Ion Effects; Hydrogen Bonding; Electronic Excitations; Surface Interfaces; Molecular Dynamics

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

2012-07-25

Bill R. Miller , T. Dwight McGee , Jason M. Swails +3 more

MM-PBSA is a post-processing end-state method to calculate free energies of molecules in solution. MMPBSA.py is a program written in Python for streamlining end-state free energy calculations using ensembles derived … MM-PBSA is a post-processing end-state method to calculate free energies of molecules in solution. MMPBSA.py is a program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics (MD) or Monte Carlo (MC) simulations. Several implicit solvation models are available with MMPBSA.py, including the Poisson–Boltzmann Model, the Generalized Born Model, and the Reference Interaction Site Model. Vibrational frequencies may be calculated using normal mode or quasi-harmonic analysis to approximate the solute entropy. Specific interactions can also be dissected using free energy decomposition or alanine scanning. A parallel implementation significantly speeds up the calculation by dividing frames evenly across available processors. MMPBSA.py is an efficient, user-friendly program with the flexibility to accommodate the needs of users performing end-state free energy calculations. The source code can be downloaded at http://ambermd.org/ with AmberTools, released under the GNU General Public License.

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

2008-07-01

In Suk Joung , Thomas E. Cheatham

Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular … Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular structure, to influence on biomolecular dynamics, to key physiological influence on homeostasis and signaling. To properly model ionic interaction and stability in atomistic simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model or representation of the monovalent ions is critically necessary. A good model needs to simultaneously reproduce many properties of ions, including their structure, dynamics, solvation, and moreover both the interactions of these ions with each other in the crystal and in solution and the interactions of ions with other molecules. At present, the best force fields for biomolecules employ a simple additive, nonpolarizable, and pairwise potential for atomic interaction. In this work, we describe our efforts to build better models of the monovalent ions within the pairwise Coulombic and 6-12 Lennard-Jones framework, where the models are tuned to balance crystal and solution properties in Ewald simulations with specific choices of well-known water models. Although it has been clearly demonstrated that truly accurate treatments of ions will require inclusion of nonadditivity and polarizability (particularly with the anions) and ultimately even a quantum mechanical treatment, our goal was to simply push the limits of the additive treatments to see if a balanced model could be created. The applied methodology is general and can be extended to other ions and to polarizable force-field models. Our starting point centered on observations from long simulations of biomolecules in salt solution with the AMBER force fields where salt crystals formed well below their solubility limit. The likely cause of the artifact in the AMBER parameters relates to the naive mixing of the Smith and Dang chloride parameters with AMBER-adapted Åqvist cation parameters. To provide a more appropriate balance, we reoptimized the parameters of the Lennard-Jones potential for the ions and specific choices of water models. To validate and optimize the parameters, we calculated hydration free energies of the solvated ions and also lattice energies (LE) and lattice constants (LC) of alkali halide salt crystals. This is the first effort that systematically scans across the Lennard-Jones space (well depth and radius) while balancing ion properties like LE and LC across all pair combinations of the alkali ions and halide ions. The optimization across the entire monovalent series avoids systematic deviations. The ion parameters developed, optimized, and characterized were targeted for use with some of the most commonly used rigid and nonpolarizable water models, specifically TIP3P, TIP4PEW, and SPC/E. In addition to well reproducing the solution and crystal properties, the new ion parameters well reproduce binding energies of the ions to water and the radii of the first hydration shells.

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Brownian dynamics with hydrodynamic interactions

1978-08-15

D.L. Ermak , J. Andrew McCammon

A method for simulating the Brownian dynamics of N particles with the inclusion of hydrodynamic interactions is described. The particles may also be subject to the usual interparticle or external … A method for simulating the Brownian dynamics of N particles with the inclusion of hydrodynamic interactions is described. The particles may also be subject to the usual interparticle or external forces (e.g., electrostatic) which have been included in previous methods for simulating Brownian dynamics of particles in the absence of hydrodynamic interactions. The present method is derived from the Langevin equations for the N particle assembly, and the results are shown to be consistent with the corresponding Fokker–Planck results. Sample calculations on small systems illustrate the importance of including hydrodynamic interactions in Brownian dynamics simulations. The method should be useful for simulation studies of diffusion limited reactions, polymer dynamics, protein folding, particle coagulation, and other phenomena in solution.

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Infrared spectroscopy of proteins

2007-06-29

Andreas Barth

Continuum solvation models: A new approach to the problem of solute’s charge distribution and cavity boundaries

1997-03-22

Benedetta Mennucci , Jacopo Tomasi

In continuum solvation models the definition of a cavity that embeds the solute molecule leads to problems related to the portion of solute’s electronic charge lying outside its boundaries (charge … In continuum solvation models the definition of a cavity that embeds the solute molecule leads to problems related to the portion of solute’s electronic charge lying outside its boundaries (charge tails). The correction strategies developed so far can be shown to work insufficiently, since they only correct the global charge defect, but lead to considerable local errors. The present paper will be focused on the theoretical and technical aspects of this problem, and it will present in detail a new method which allows a very refined treatment of solute’s charge tails in the outer space; some numerical results of solutes in water will be shown and discussed. As further analyses, the introduction of Pauli repulsion term will be considered, and the implications all these effects have on molecular properties, such as (hyper)polarizabilities, numerically evaluated. The new approach has been implemented within the framework of the polarizable continuum model (PCM).

Quantum Mechanical Continuum Solvation Models

2005-07-26

Jacopo Tomasi , Benedetta Mennucci , Roberto Cammi

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuantum Mechanical Continuum Solvation ModelsJacopo Tomasi, Benedetta Mennucci, and Roberto CammiView Author Information Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, … ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuantum Mechanical Continuum Solvation ModelsJacopo Tomasi, Benedetta Mennucci, and Roberto CammiView Author Information Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy, and Dipartimento di Chimica, Università di Parma, Viale delle Scienze 17/A, 43100 Parma, Italy Cite this: Chem. Rev. 2005, 105, 8, 2999–3094Publication Date (Web):July 26, 2005Publication History Received6 January 2005Published online26 July 2005Published inissue 1 August 2005https://pubs.acs.org/doi/10.1021/cr9904009https://doi.org/10.1021/cr9904009research-articleACS PublicationsCopyright © 2005 American Chemical SocietyRequest reuse permissionsArticle Views40539Altmetric-Citations13824LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Cavities,Molecules,Solution chemistry,Solvation,Solvents Get e-Alerts

Second-order perturbation theory with a CASSCF reference function

1990-07-01

Kerstin Andersson , Per Aake. Malmqvist , Bjoern O. Roos +2 more

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSecond-order perturbation theory with a CASSCF reference functionKerstin. Andersson, Per Aake. Malmqvist, Bjoern O. Roos, Andrzej J. Sadlej, and Krzysztof. WolinskiCite this: J. Phys. Chem. 1990, 94, … ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSecond-order perturbation theory with a CASSCF reference functionKerstin. Andersson, Per Aake. Malmqvist, Bjoern O. Roos, Andrzej J. Sadlej, and Krzysztof. WolinskiCite this: J. Phys. Chem. 1990, 94, 14, 5483–5488Publication Date (Print):July 1, 1990Publication History Published online1 May 2002Published inissue 1 July 1990https://pubs.acs.org/doi/10.1021/j100377a012https://doi.org/10.1021/j100377a012research-articleACS PublicationsRequest reuse permissionsArticle Views4704Altmetric-Citations2852LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts

Die Berechnung optischer und elektrostatischer Gitterpotentiale

1921-01-01

P. P. Ewald

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P<scp>ACKMOL</scp>: A package for building initial configurations for molecular dynamics simulations

2009-02-19

Leandro Martı́nez , Ricardo Andrade , E. G. Birgin +1 more

Abstract Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that … Abstract Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules must keep safe pairwise distances. Obtaining such a molecular arrangement can be considered a packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules must be greater than some specified tolerance. We have developed a code able to pack millions of atoms, grouped in arbitrarily complex molecules, inside a variety of three‐dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straightforward. In addition, different atoms belonging to the same molecule may also be restricted to different spatial regions, in such a way that more ordered molecular arrangements can be built, as micelles, lipid double‐layers, etc. The packing time for state‐of‐the‐art molecular dynamics systems varies from a few seconds to a few minutes in a personal computer. The input files are simple and currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and can be downloaded from http://www.ime.unicamp.br/∼martinez/packmol/ . © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009

Solution of the Schrödinger Equation with a Hamiltonian Periodic in Time

1965-05-24

J.H. Shirley

The interaction of a quantum system with an oscillating field is studied in a formalism which replaces the semiclassical time-dependent Hamiltonian with a time-independent Hamiltonian represented by an infinite matrix. … The interaction of a quantum system with an oscillating field is studied in a formalism which replaces the semiclassical time-dependent Hamiltonian with a time-independent Hamiltonian represented by an infinite matrix. The formalism is developed as a mathematical equivalent to the semiclassical treatment, and interpreted as a classical approximation to the quantum treatment of the field. Combined with a perturbation theory for two nearly degenerate states, the formalism provides a convenient method for determining resonance transition probabilities including frequency shifts and multiple quantum transitions. The theory is illustrated by a detailed study of the simple case of a two-state system excited by a strong oscillating field.

Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions

2009-04-14

Aleksandr V. Marenich , Christopher J. Cramer , Donald G. Truhlar

We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called … We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the "D" stands for "density" to denote that the full solute electron density is used without defining partial atomic charges. "Continuum" denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where "universal" denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which a few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonhomogeneous Poisson equation for electrostatics in terms of the integral-equation-formalism polarizable continuum model (IEF-PCM). The cavities for the bulk electrostatic calculation are defined by superpositions of nuclear-centered spheres. The second component is called the cavity-dispersion-solvent-structure term and is the contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. This contribution is a sum of terms that are proportional (with geometry-dependent proportionality constants called atomic surface tensions) to the solvent-accessible surface areas of the individual atoms of the solute. The SMD model has been parametrized with a training set of 2821 solvation data including 112 aqueous ionic solvation free energies, 220 solvation free energies for 166 ions in acetonitrile, methanol, and dimethyl sulfoxide, 2346 solvation free energies for 318 neutral solutes in 91 solvents (90 nonaqueous organic solvents and water), and 143 transfer free energies for 93 neutral solutes between water and 15 organic solvents. The elements present in the solutes are H, C, N, O, F, Si, P, S, Cl, and Br. The SMD model employs a single set of parameters (intrinsic atomic Coulomb radii and atomic surface tension coefficients) optimized over six electronic structure methods: M05-2X/MIDI!6D, M05-2X/6-31G, M05-2X/6-31+G, M05-2X/cc-pVTZ, B3LYP/6-31G, and HF/6-31G. Although the SMD model has been parametrized using the IEF-PCM protocol for bulk electrostatics, it may also be employed with other algorithms for solving the nonhomogeneous Poisson equation for continuum solvation calculations in which the solute is represented by its electron density in real space. This includes, for example, the conductor-like screening algorithm. With the 6-31G basis set, the SMD model achieves mean unsigned errors of 0.6-1.0 kcal/mol in the solvation free energies of tested neutrals and mean unsigned errors of 4 kcal/mol on average for ions with either Gaussian03 or GAMESS.

Behavior of the Electronic Dielectric Constant in Covalent and Ionic Materials

1971-02-15

S. H. Wemple , M. DiDomenico

Refractive-index dispersion data below the interband absorption edge in more than 100 widely different solids and liquids are analyzed using a single-effective-oscillator fit of the form ${n}^{2}\ensuremath{-}1=\frac{{E}_{d}{E}_{0}}{({E}_{0}^{2}\ensuremath{-}{\ensuremath{\hbar}}^{2}{\ensuremath{\omega}}^{2})}$, where $\ensuremath{\hbar}\ensuremath{\omega}$ is … Refractive-index dispersion data below the interband absorption edge in more than 100 widely different solids and liquids are analyzed using a single-effective-oscillator fit of the form ${n}^{2}\ensuremath{-}1=\frac{{E}_{d}{E}_{0}}{({E}_{0}^{2}\ensuremath{-}{\ensuremath{\hbar}}^{2}{\ensuremath{\omega}}^{2})}$, where $\ensuremath{\hbar}\ensuremath{\omega}$ is the photon energy, ${E}_{0}$ is the single oscillator energy, and ${E}_{d}$ is the dispersion energy. The parameter ${E}_{d}$, which is a measure of the strength of interband optical transitions, is found to obey the simple empirical relationship ${E}_{d}=\ensuremath{\beta}{N}_{c}{Z}_{a}{N}_{e}$, where ${N}_{c}$ is the coordination number of the cation nearest neighbor to the anion, ${Z}_{a}$ is the formal chemical valency of the anion, ${N}_{e}$ is the effective number of valence electrons per anion (usually ${N}_{e}=8$), and $\ensuremath{\beta}$ is essentially two-valued, taking on the "ionic" value ${\ensuremath{\beta}}_{i}=0.26\ifmmode\pm\else\textpm\fi{}0.04$ eV for halides and most oxides, and the "covalent" value ${\ensuremath{\beta}}_{c}=0.37\ifmmode\pm\else\textpm\fi{}0.05$ eV for the tetrahedrally bonded ${A}^{N}{B}^{8\ensuremath{-}N}$ zinc-blende- and diamond-type structures, as well as for scheelite-structure oxides and some iodates and carbonates. Wurtzite-structure crystals form a transitional group between ionic and covalent crystal classes. Experimentally, it is also found that ${E}_{d}$ does not depend significantly on either the bandgap or the volume density of valence electrons. The experimental results are related to the fundamental ${\ensuremath{\epsilon}}_{2}$ spectrum via appropriately defined moment integrals. It is found, using relationships between moment integrals, that for a particularly simple choice of a model ${\ensuremath{\epsilon}}_{2}$ spectrum, viz., constant optical-frequency conductivity with high- and low-frequency cutoffs, the bandgap parameter ${E}_{a}$ in the high-frequency sum rule introduced by Hopfield provides the connection between the single-oscillator parameters (${E}_{0},{E}_{d}$) and the Phillips static-dielectric-constant parameters (${E}_{g},\ensuremath{\hbar}{\ensuremath{\omega}}_{p}$), i.e., ${(\ensuremath{\hbar}{\ensuremath{\omega}}_{p})}^{2}={E}_{a}{E}_{d} \mathrm{and} {E}_{g}^{2}={E}_{a}{E}_{0}$. Finally, it is suggested that the observed dependence of ${E}_{d}$ on coordination number and valency implies that an understanding of refractive-index behavior may lie in a localized molecular theory of optical transitions.

A unified formulation of the constant temperature molecular dynamics methods

1984-07-01

Shūichi Nosé

Three recently proposed constant temperature molecular dynamics methods by: (i) Nosé (Mol. Phys., to be published); (ii) Hoover et al. [Phys. Rev. Lett. 48, 1818 (1982)], and Evans and Morriss … Three recently proposed constant temperature molecular dynamics methods by: (i) Nosé (Mol. Phys., to be published); (ii) Hoover et al. [Phys. Rev. Lett. 48, 1818 (1982)], and Evans and Morriss [Chem. Phys. 77, 63 (1983)]; and (iii) Haile and Gupta [J. Chem. Phys. 79, 3067 (1983)] are examined analytically via calculating the equilibrium distribution functions and comparing them with that of the canonical ensemble. Except for effects due to momentum and angular momentum conservation, method (1) yields the rigorous canonical distribution in both momentum and coordinate space. Method (2) can be made rigorous in coordinate space, and can be derived from method (1) by imposing a specific constraint. Method (3) is not rigorous and gives a deviation of order N−1/2 from the canonical distribution (N the number of particles). The results for the constant temperature–constant pressure ensemble are similar to the canonical ensemble case.

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Rationale for mixing exact exchange with density functional approximations

1996-12-08

John P. Perdew , Matthias Ernzerhof , Kieron Burke

Density functional approximations for the exchange-correlation energy EDFAxc of an electronic system are often improved by admixing some exact exchange Ex: Exc≊EDFAxc+(1/n)(Ex−EDFAx). This procedure is justified when the error in … Density functional approximations for the exchange-correlation energy EDFAxc of an electronic system are often improved by admixing some exact exchange Ex: Exc≊EDFAxc+(1/n)(Ex−EDFAx). This procedure is justified when the error in EDFAxc arises from the λ=0 or exchange end of the coupling-constant integral ∫10 dλ EDFAxc,λ. We argue that the optimum integer n is approximately the lowest order of Görling–Levy perturbation theory which provides a realistic description of the coupling-constant dependence Exc,λ in the range 0≤λ≤1, whence n≊4 for atomization energies of typical molecules. We also propose a continuous generalization of n as an index of correlation strength, and a possible mixing of second-order perturbation theory with the generalized gradient approximation.

A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations

1990-07-01

Martin J. Field , Paul A. Bash , Martin Karplus

Abstract A combined quantum mechanical (QM) and molecular mechanical (MM) potential has been developed for the study of reactions in condensed phases. For the quantum mechanical calculations semiempirical methods of … Abstract A combined quantum mechanical (QM) and molecular mechanical (MM) potential has been developed for the study of reactions in condensed phases. For the quantum mechanical calculations semiempirical methods of the MNDO and AM1 type are used, while the molecular mechanics part is treated with the CHARMM force field. Specific prescriptions are given for the interactions between the QM and MM portions of the system; cases in which the QM and MM methodology is applied to parts of the same molecule or to different molecules are considered. The details of the method and a range of test calculations, including comparisons with ab initio and experimental results, are given. It is found that in many cases satisfactory results are obtained. However, there are limitations to this type of approach, some of which arise from the AM1 or MNDO methods themselves and others from the present QM/MM implementation. This suggests that it is important to test the applicability of the method to each particular case prior to its use. Possible areas of improvement in the methodology are discussed.

Ab initio study of solvated molecules: a new implementation of the polarizable continuum model

1996-06-01

Maurizio Cossi , Vincenzo Barone , Roberto Cammi +1 more

Continuous surface charge polarizable continuum models of solvation. I. General formalism

2010-03-17

Giovanni Scalmani , Michael J. Frisch

Continuum solvation models are appealing because of the simplified yet accurate description they provide of the solvent effect on a solute, described either by quantum mechanical or classical methods. The … Continuum solvation models are appealing because of the simplified yet accurate description they provide of the solvent effect on a solute, described either by quantum mechanical or classical methods. The polarizable continuum model (PCM) family of solvation models is among the most widely used, although their application has been hampered by discontinuities and singularities arising from the discretization of the integral equations at the solute-solvent interface. In this contribution we introduce a continuous surface charge (CSC) approach that leads to a smooth and robust formalism for the PCM models. We start from the scheme proposed over ten years ago by York and Karplus and we generalize it in various ways, including the extension to analytic second derivatives with respect to atomic positions. We propose an optimal discrete representation of the integral operators required for the determination of the apparent surface charge. We achieve a clear separation between “model” and “cavity” which, together with simple generalizations of modern integral codes, is all that is required for an extensible and efficient implementation of the PCM models. Following this approach we are now able to introduce solvent effects on energies, structures, and vibrational frequencies (analytical first and second derivatives with respect to atomic coordinates), magnetic properties (derivatives with respect of magnetic field using GIAOs), and in the calculation more complex properties like frequency-dependent Raman activities, vibrational circular dichroism, and Raman optical activity.

Molecular dynamics with coupling to an external bath

1984-10-15

Herman J. C. Berendsen , Johan P. M. Postma , Wilfred F. van Gunsteren +2 more

In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties … In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD. A method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling. The method is easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints. The influence of coupling time constants on dynamical variables is evaluated. A leap-frog algorithm is presented for the general case involving constraints with coupling to both a constant temperature and a constant pressure bath.

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Constant pressure molecular dynamics simulation: The Langevin piston method

1995-09-15

Scott E. Feller , Yuhong Zhang , Richard W. Pastor +1 more

A new method for performing molecular dynamics simulations under constant pressure is presented. In the method, which is based on the extended system formalism introduced by Andersen, the deterministic equations … A new method for performing molecular dynamics simulations under constant pressure is presented. In the method, which is based on the extended system formalism introduced by Andersen, the deterministic equations of motion for the piston degree of freedom are replaced by a Langevin equation; a suitable choice of collision frequency then eliminates the unphysical ‘‘ringing’’ of the volume associated with the piston mass. In this way it is similar to the ‘‘weak coupling algorithm’’ developed by Berendsen and co-workers to perform molecular dynamics simulation without piston mass effects. It is shown, however, that the weak coupling algorithm induces artifacts into the simulation which can be quite severe for inhomogeneous systems such as aqueous biopolymers or liquid/liquid interfaces.

Energies, structures, and electronic properties of molecules in solution with the C‐PCM solvation model

2003-03-11

Maurizio Cossi , Nadia Rega , Giovanni Scalmani +1 more

The conductor-like solvation model, as developed in the framework of the polarizable continuum model (PCM), has been reformulated and newly implemented in order to compute energies, geometric structures, harmonic frequencies, … The conductor-like solvation model, as developed in the framework of the polarizable continuum model (PCM), has been reformulated and newly implemented in order to compute energies, geometric structures, harmonic frequencies, and electronic properties in solution for any chemical system that can be studied in vacuo. Particular attention is devoted to large systems requiring suitable iterative algorithms to compute the solvation charges: the fast multipole method (FMM) has been extensively used to ensure a linear scaling of the computational times with the size of the solute. A number of test applications are presented to evaluate the performances of the method.

Electronegativity: The density functional viewpoint

1978-04-15

Robert G. Parr , Robert A. Donnelly , Mel Levy +1 more

Precision is given to the concept of electronegativity. It is the negative of the chemical potential (the Lagrange multiplier for the normalization constraint) in the Hohenberg–Kohn density functional theory of … Precision is given to the concept of electronegativity. It is the negative of the chemical potential (the Lagrange multiplier for the normalization constraint) in the Hohenberg–Kohn density functional theory of the ground state: χ=−μ=−(∂E/∂N)v. Electronegativity is constant throughout an atom or molecule, and constant from orbital to orbital within an atom or molecule. Definitions are given of the concepts of an atom in a molecule and of a valence state of an atom in a molecule, and it is shown how valence-state electronegativity differences drive charge transfers on molecule formation. An equation of Gibbs–Duhem type is given for the change of electronegativity from one situation to another, and some discussion is given of certain relations among energy components discovered by Fraga.

Semianalytical treatment of solvation for molecular mechanics and dynamics

1990-08-01

W. Clark Still , Anna Tempczyk , Ronald C. Hawley +1 more

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSemianalytical treatment of solvation for molecular mechanics and dynamicsW. Clark Still, Anna Tempczyk, Ronald C. Hawley, and Thomas HendricksonCite this: J. Am. Chem. Soc. 1990, 112, 16, … ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSemianalytical treatment of solvation for molecular mechanics and dynamicsW. Clark Still, Anna Tempczyk, Ronald C. Hawley, and Thomas HendricksonCite this: J. Am. Chem. Soc. 1990, 112, 16, 6127–6129Publication Date (Print):August 1, 1990Publication History Published online1 May 2002Published inissue 1 August 1990https://pubs.acs.org/doi/10.1021/ja00172a038https://doi.org/10.1021/ja00172a038research-articleACS PublicationsRequest reuse permissionsArticle Views4856Altmetric-Citations3186LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts

Single-Reference ab Initio Methods for the Calculation of Excited States of Large Molecules

2005-10-06

Andreas Dreuw , Martin Head‐Gordon

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSingle-Reference ab Initio Methods for the Calculation of Excited States of Large MoleculesAndreas Dreuw and Martin Head-GordonView Author Information Institut für Physikalische und Theoretische Chemie, Johann Wolfgang … ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSingle-Reference ab Initio Methods for the Calculation of Excited States of Large MoleculesAndreas Dreuw and Martin Head-GordonView Author Information Institut für Physikalische und Theoretische Chemie, Johann Wolfgang Goethe-Universität, Marie Curie-Strasse 11, 60439 Frankfurt am Main, Germany Department of Chemistry, University of California, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720-1470 Cite this: Chem. Rev. 2005, 105, 11, 4009–4037Publication Date (Web):October 6, 2005Publication History Received8 April 2005Published online6 October 2005Published inissue 1 November 2005https://doi.org/10.1021/cr0505627Copyright © 2005 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views15996Altmetric-Citations2060LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (478 KB) Get e-AlertsSUBJECTS:Electrical energy,Electron density,Energy,Excited states,Time dependant density functional theory Get e-Alerts

Efficacious Form for Model Pseudopotentials

1982-05-17

Leonard Kleinman , D. M. Bylander

A simple way has been discovered to put model pseudopotentials, $V(\stackrel{\ensuremath{\rightarrow}}{\mathrm{r}})={\ensuremath{\Sigma}}_{\mathrm{lm}}|{Y}_{\mathrm{lm}}〉{V}_{l}(r)\ifmmode\times\else\texttimes\fi{}〈{Y}_{\mathrm{lm}}|$, into a form which reduces the number of integrals of $V(\stackrel{\ensuremath{\rightarrow}}{\mathrm{r}})$ required for an energyband calculation from $\frac{\mathrm{mn}(n+1)}{2}$ to … A simple way has been discovered to put model pseudopotentials, $V(\stackrel{\ensuremath{\rightarrow}}{\mathrm{r}})={\ensuremath{\Sigma}}_{\mathrm{lm}}|{Y}_{\mathrm{lm}}〉{V}_{l}(r)\ifmmode\times\else\texttimes\fi{}〈{Y}_{\mathrm{lm}}|$, into a form which reduces the number of integrals of $V(\stackrel{\ensuremath{\rightarrow}}{\mathrm{r}})$ required for an energyband calculation from $\frac{\mathrm{mn}(n+1)}{2}$ to $\mathrm{mn}$ for each $l$ in the sum (where $n$ is the number of plane waves used in the expansion and $m$ the number of points in the Brillouin zone at which the calculation is performed). The new form may be chosen to improve the accuracy of the pseudopotential when used in other chemical environments.

Canonical sampling through velocity rescaling

2007-01-03

Giovanni Bussi , Davide Donadio , Michele Parrinello

The authors present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. … The authors present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. The authors illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liquid phases. Its performance is excellent and largely independent of the thermostat parameter also with regard to the dynamic properties.

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Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems

2007-04-01

Gregory S. Engel , Tessa R. Calhoun , Elizabeth L. Read +5 more

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Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model

1998-02-20

Vincenzo Barone , Maurizio Cossi

A new implementation of the conductor-like screening solvation model (COSMO) in the GAUSSIAN94 package is presented. It allows Hartree−Fock (HF), density functional (DF) and post-HF energy, and HF and DF … A new implementation of the conductor-like screening solvation model (COSMO) in the GAUSSIAN94 package is presented. It allows Hartree−Fock (HF), density functional (DF) and post-HF energy, and HF and DF gradient calculations: the cavities are modeled on the molecular shape, using recently optimized parameters, and both electrostatic and nonelectrostatic contributions to energies and gradients are considered. The calculated solvation energies for 19 neutral molecules in water are found in very good agreement with experimental data; the solvent-induced geometry relaxation is studied for some closed and open shell molecules, at HF and DF levels. The computational times are very satisfying: the self-consistent energy evaluation needs a time 15−30% longer than the corresponding procedure in vacuo, whereas the calculation of energy gradients is only 25% longer than in vacuo for medium size molecules.

Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K

2001-10-06

Pekka Mark , Lennart Nilsson

Molecular dynamics simulations of five water models, the TIP3P (original and modified), SPC (original and refined), and SPC/E (original), were performed using the CHARMM molecular mechanics program. All simulations were … Molecular dynamics simulations of five water models, the TIP3P (original and modified), SPC (original and refined), and SPC/E (original), were performed using the CHARMM molecular mechanics program. All simulations were carried out in the microcanonical NVE ensemble, using 901 water molecules in a cubic simulation cell furnished with periodic boundary conditions at 298 K. The SHAKE algorithm was used to keep water molecules rigid. Nanosecond trajectories were calculated with all water models for high statistical accuracy. The characteristic self-diffusion coefficients D and radial distribution functions, gOO, gOH, and gHH for all five water models were determined and compared to experimental data. The effects of velocity rescaling on the self-diffusion coefficient D were examined. All these empirical water models used in this study are similar by having three interaction sites, but the small differences in their pair potentials composed of Lennard-Jones (LJ) and Coulombic terms give significant differences in the calculated self-diffusion coefficients, and in the height of the second peak of the radial distribution function gOO.

A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP)

2004-07-01

Takeshi Yanai , David P. Tew , Nicholas C. Handy

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The ORCA program system

2011-06-28

Frank Neese

Abstract ORCA is a general‐purpose quantum chemistry program package that features virtually all modern electronic structure methods (density functional theory, many‐body perturbation and coupled cluster theories, and multireference and semiempirical … Abstract ORCA is a general‐purpose quantum chemistry program package that features virtually all modern electronic structure methods (density functional theory, many‐body perturbation and coupled cluster theories, and multireference and semiempirical methods). It is designed with the aim of generality, extendibility, efficiency, and user friendliness. Its main field of application is larger molecules, transition metal complexes, and their spectroscopic properties. ORCA uses standard Gaussian basis functions and is fully parallelized. The article provides an overview of its current possibilities and documents its efficiency. © 2011 John Wiley & Sons, Ltd. This article is categorized under: Software > Quantum Chemistry

Analysis of Macromolecular Polydispersity in Intensity Correlation Spectroscopy: The Method of Cumulants

1972-12-01

Dennis E. Koppel

The first order electric field correlation function of laser light scattered by polydisperse solutions of macromolecules can be written as a sum or distribution of exponentials, with decay rates proportional … The first order electric field correlation function of laser light scattered by polydisperse solutions of macromolecules can be written as a sum or distribution of exponentials, with decay rates proportional to the diffusion coefficients of the solute molecules. It is shown that the logarithm of this correlation function is formally equivalent to a cumulant generating function. A method is described by which the distribution function of the decay rates (and thus the extent of polydispersity) can be characterized, in a light scattering experiment, by calculation of the moments or cumulants. The systematic and random statistical errors in the calculated cumulants are discussed.

Ab initiomolecular dynamics for liquid metals

1993-01-01

Georg Kresse , J. Häfner

We present ab initio quantum-mechanical molecular-dynamics calculations based on the calculation of the electronic ground state and of the Hellmann-Feynman forces in the local-density approximation at each molecular-dynamics step. This … We present ab initio quantum-mechanical molecular-dynamics calculations based on the calculation of the electronic ground state and of the Hellmann-Feynman forces in the local-density approximation at each molecular-dynamics step. This is possible using conjugate-gradient techniques for energy minimization, and predicting the wave functions for new ionic positions using subspace alignment. This approach avoids the instabilities inherent in quantum-mechanical molecular-dynamics calculations for metals based on the use of a fictitious Newtonian dynamics for the electronic degrees of freedom. This method gives perfect control of the adiabaticity and allows us to perform simulations over several picoseconds.

Exchange functionals with improved long-range behavior and adiabatic connection methods without adjustable parameters: The mPW and mPW1PW models

1998-01-08

Carlo Adamo , Vincenzo Barone

Starting from an analysis of the low-density and large gradient regions which dominate van der Waals interactions, we propose a modification of the exchange functional introduced by Perdew and Wang, … Starting from an analysis of the low-density and large gradient regions which dominate van der Waals interactions, we propose a modification of the exchange functional introduced by Perdew and Wang, which significantly enlarges its field of applications. This is obtained without increasing the number of adjustable parameters and retaining all the asymptotic and scaling properties of the original model. Coupling the new exchange functional to the correlation functional also proposed by Perdew and Wang leads to the mPWPW model, which represents the most accurate generalized gradient approximation available until now. We next introduce an adiabatic connection method in which the ratio between exact and density functional exchange is determined a priori from purely theoretical considerations and no further parameters are present. The resulting mPW1PW model allows to obtain remarkable results both for covalent and noncovalent interactions in a quite satisfactory theoretical framework encompassing the free electron gas limit and most of the known scaling conditions. The new functionals have been coded with their derivatives in the Gaussian series of programs, thus allowing fully self-consistent computations of energy and properties together with analytical evaluation of first and second geometry derivatives.

Theory of open quantum systems

2002-05-09

Rui‐Xue Xu , YiJing Yan

A quantum dissipation theory is constructed with the system–bath interaction being treated rigorously at the second-order cumulant level for both reduced dynamics and initial canonical boundary condition. The theory is … A quantum dissipation theory is constructed with the system–bath interaction being treated rigorously at the second-order cumulant level for both reduced dynamics and initial canonical boundary condition. The theory is valid for arbitrary bath correlation functions and time-dependent external driving fields, and satisfies correlated detailed-balance relation at any temperatures. The general formulation assumes a particularly simple form in driven Brownian oscillator systems in which the correlated driving-dissipation effects can be accounted for exactly in terms of local-field correction. Remarks on a class of widely used phenomenological quantum master equations that neglects the bath dispersion-induced dissipation are also made in contact with the present theory.

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DREIDING: a generic force field for molecular simulations

1990-12-01

Stephen L. Mayo , Barry D. Olafson , William A. Goddard

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDREIDING: a generic force field for molecular simulationsStephen L. Mayo, Barry D. Olafson, and William A. GoddardCite this: J. Phys. Chem. 1990, 94, 26, 8897–8909Publication Date (Print):December … ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDREIDING: a generic force field for molecular simulationsStephen L. Mayo, Barry D. Olafson, and William A. GoddardCite this: J. Phys. Chem. 1990, 94, 26, 8897–8909Publication Date (Print):December 1, 1990Publication History Published online1 May 2002Published inissue 1 December 1990https://pubs.acs.org/doi/10.1021/j100389a010https://doi.org/10.1021/j100389a010research-articleACS PublicationsRequest reuse permissionsArticle Views24094Altmetric-Citations5225LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts

Nosé–Hoover chains: The canonical ensemble via continuous dynamics

1992-08-15

Glenn Martyna , Michael L. Klein , Mark E. Tuckerman

Nosé has derived a set of dynamical equations that can be shown to give canonically distributed positions and momenta provided the phase space average can be taken into the trajectory … Nosé has derived a set of dynamical equations that can be shown to give canonically distributed positions and momenta provided the phase space average can be taken into the trajectory average, i.e., the system is ergodic [S. Nosé, J. Chem. Phys. 81, 511 (1984), W. G. Hoover, Phys. Rev. A 31, 1695 (1985)]. Unfortunately, the Nosé–Hoover dynamics is not ergodic for small or stiff systems. Here a modification of the dynamics is proposed which includes not a single thermostat variable but a chain of variables, Nosé–Hoover chains. The ‘‘new’’ dynamics gives the canonical distribution where the simple formalism fails. In addition, the new method is easier to use than an extension [D. Kusnezov, A. Bulgac, and W. Bauer, Ann. Phys. 204, 155 (1990)] which also gives the canonical distribution for stiff cases.

Reaction-rate theory: fifty years after Kramers

1990-04-01

Peter Hänggi , Peter Talkner , Michal Borkovec

The calculation of rate coefficients is a discipline of nonlinear science of importance to much of physics, chemistry, engineering, and biology. Fifty years after Kramers' seminal paper on thermally activated … The calculation of rate coefficients is a discipline of nonlinear science of importance to much of physics, chemistry, engineering, and biology. Fifty years after Kramers' seminal paper on thermally activated barrier crossing, the authors report, extend, and interpret much of our current understanding relating to theories of noise-activated escape, for which many of the notable contributions are originating from the communities both of physics and of physical chemistry. Theoretical as well as numerical approaches are discussed for single- and many-dimensional metastable systems (including fields) in gases and condensed phases. The role of many-dimensional transition-state theory is contrasted with Kramers' reaction-rate theory for moderate-to-strong friction; the authors emphasize the physical situation and the close connection between unimolecular rate theory and Kramers' work for weakly damped systems. The rate theory accounting for memory friction is presented, together with a unifying theoretical approach which covers the whole regime of weak-to-moderate-to-strong friction on the same basis (turnover theory). The peculiarities of noise-activated escape in a variety of physically different metastable potential configurations is elucidated in terms of the mean-first-passage-time technique. Moreover, the role and the complexity of escape in driven systems exhibiting possibly multiple, metastable stationary nonequilibrium states is identified. At lower temperatures, quantum tunneling effects start to dominate the rate mechanism. The early quantum approaches as well as the latest quantum versions of Kramers' theory are discussed, thereby providing a description of dissipative escape events at all temperatures. In addition, an attempt is made to discuss prominent experimental work as it relates to Kramers' reaction-rate theory and to indicate the most important areas for future research in theory and experiment.

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Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects

1981-02-01

Stanislav Miertuš , Eolo Scrocco , J. Tomasi

Review of second-order models for adsorption systems

2006-02-08

Y HO

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Dynamics of the dissipative two-state system

1987-01-01

A. J. Leggett , Sudip Chakravarty , Alan T. Dorsey +3 more

This paper presents the results of a functional-integral approach to the dynamics of a two-state system coupled to a dissipative environment. It is primarily an extended account of results obtained … This paper presents the results of a functional-integral approach to the dynamics of a two-state system coupled to a dissipative environment. It is primarily an extended account of results obtained over the last four years by the authors; while they try to provide some background for orientation, it is emphatically not intended as a comprehensive review of the literature on the subject. Its contents include (1) an exact and general prescription for the reduction, under appropriate circumstances, of the problem of a system tunneling between two wells in the presence of a dissipative environment to the "spin-boson" problem; (2) the derivation of an exact formula for the dynamics of the latter problem; (3) the demonstration that there exists a simple approximation to this exact formula which is controlled, in the sense that we can put explicit bounds on the errors incurred in it, and that for almost all regions of the parameter space these errors are either very small in the limit of interest to us (the "slow-tunneling" limit) or can themselves be evaluated with satisfactory accuracy; (4) use of these results to obtain quantitative expressions for the dynamics of the system as a function of the spectral density $J(\ensuremath{\omega})$ of its coupling to the environment. If $J(\ensuremath{\omega})$ behaves as ${\ensuremath{\omega}}^{s}$ for frequencies of the order of the tunneling frequency or smaller, the authors find for the "unbiased" case the following results: For $s<1$ the system is localized at zero temperature, and at finite $T$ relaxes incoherently at a rate proportional to $\mathrm{exp}\ensuremath{-}{(\frac{{T}_{0}}{T})}^{1\ensuremath{-}s}$. For $s>2$ it undergoes underdamped coherent oscillations for all relevant temperatures, while for $1<s<2$ there is a crossover from coherent oscillation to overdamped relaxation as $T$ increases. Exact expressions for the oscillation and/or relaxation rates are presented in all these cases. For the "ohmic" case, $s=1$, the qualitative nature of the behavior depends critically on the dimensionless coupling strength $\ensuremath{\alpha}$ as well as the temperature $T$: over most of the ($\ensuremath{\alpha}$,$T$) plane (including the whole region $\ensuremath{\alpha}>1$) the behavior is an incoherent relaxation at a rate proportional to ${T}^{2\ensuremath{\alpha}\ensuremath{-}1}$, but for low $T$ and $0<\ensuremath{\alpha}<\frac{1}{2}$ the authors predict a combination of damped coherent oscillation and incoherent background which appears to disagree with the results of all previous approximations. The case of finite bias is also discussed.

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A New Two-Constant Equation of State

1976-02-01

Ding‐Yu Peng , Donald B. Robinson

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA New Two-Constant Equation of StateDing-Yu Peng and Donald B. RobinsonCite this: Ind. Eng. Chem. Fundamen. 1976, 15, 1, 59–64Publication Date (Print):February 1, 1976Publication History Published online1 … ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA New Two-Constant Equation of StateDing-Yu Peng and Donald B. RobinsonCite this: Ind. Eng. Chem. Fundamen. 1976, 15, 1, 59–64Publication Date (Print):February 1, 1976Publication History Published online1 May 2002Published inissue 1 February 1976https://pubs.acs.org/doi/10.1021/i160057a011https://doi.org/10.1021/i160057a011research-articleACS PublicationsRequest reuse permissionsArticle Views21168Altmetric-Citations9849LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts

Relaxation Effects in Nuclear Magnetic Resonance Absorption

1948-04-01

N. Bloembergen , Edward M. Purcell , R. V. Pound

The exchange of energy between a system of nuclear spins immersed in a strong magnetic field, and the heat reservoir consisting of the other degrees of freedom (the "lattice") of … The exchange of energy between a system of nuclear spins immersed in a strong magnetic field, and the heat reservoir consisting of the other degrees of freedom (the "lattice") of the substance containing the magnetic nuclei, serves to bring the spin system into equilibrium at a finite temperature. In this condition the system can absorb energy from an applied radiofrequency field. With the absorption of energy, however, the spin temperature tends to rise and the rate of absorption to decrease. Through this "saturation" effect, and in some cases by a more direct method, the spin-lattice relaxation time ${T}_{1}$ can be measured. The interaction among the magnetic nuclei, with which a characteristic time $T_{2}^{}{}_{}{}^{\ensuremath{'}}$ is associated, contributes to the width of the absorption line. Both interactions have been studied in a variety of substances, but with the emphasis on liquids containing hydrogen.Magnetic resonance absorption is observed by means of a radiofrequency bridge; the magnetic field at the sample is modulated at a low frequency. A detailed analysis of the method by which ${T}_{1}$ is derived from saturation experiments is given. Relaxation times observed range from ${10}^{\ensuremath{-}4}$ to ${10}^{2}$ seconds. In liquids ${T}_{1}$ ordinarily decreases with increasing viscosity, in some cases reaching a minimum value after which it increases with further increase in viscosity. The line width meanwhile increases monotonically from an extremely small value toward a value determined by the spin-spin interaction in the rigid lattice. The effect of paramagnetic ions in solution upon the proton relaxation time and line width has been investigated. The relaxation time and line width in ice have been measured at various temperatures.The results can be explained by a theory which takes into account the effect of the thermal motion of the magnetic nuclei upon the spin-spin interaction. The local magnetic field produced at one nucleus by neighboring magnetic nuclei, or even by electronic magnetic moments of paramagnetic ions, is spread out into a spectrum extending to frequencies of the order of $\frac{1}{{\ensuremath{\tau}}_{c}}$, where ${\ensuremath{\tau}}_{c}$ is a correlation time associated with the local Brownian motion and closely related to the characteristic time which occurs in Debye's theory of polar liquids. If the nuclear Larmor frequency $\ensuremath{\omega}$ is much less than $\frac{1}{{\ensuremath{\tau}}_{c}}$, the perturbations caused by the local field nearly average out, ${T}_{1}$ is inversely proportional to ${\ensuremath{\tau}}_{c}$, and the width of the resonance line, in frequency, is about $\frac{1}{{T}_{1}}$. A similar situation is found in hydrogen gas where ${\ensuremath{\tau}}_{c}$ is the time between collisions. In very viscous liquids and in some solids where $\ensuremath{\omega}{\ensuremath{\tau}}_{c}>1$, a quite different behavior is predicted, and observed. Values of ${\ensuremath{\tau}}_{c}$ for ice, inferred from nuclear relaxation measurements, correlate well with dielectric dispersion data.Formulas useful in estimating the detectability of magnetic resonance absorption in various cases are derived in the appendix.

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Escaping free-energy minima

2002-09-23

Alessandro Laio , Michele Parrinello

We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined … We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates. A characteristic feature of these dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the FES, allowing the efficient exploration and accurate determination of the FES as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution.

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10th Spiers Memorial Lecture. Transfer mechanisms of electronic excitation

1959-01-01

Th. Förster

The first page of this article is displayed as the abstract. The first page of this article is displayed as the abstract.

Charge equilibration for molecular dynamics simulations

1991-04-01

Anthony K. Rappé , William A. Goddard

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCharge equilibration for molecular dynamics simulationsAnthony K. Rappe and William A. Goddard IIICite this: J. Phys. Chem. 1991, 95, 8, 3358–3363Publication Date (Print):April 1, 1991Publication History Published … ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCharge equilibration for molecular dynamics simulationsAnthony K. Rappe and William A. Goddard IIICite this: J. Phys. Chem. 1991, 95, 8, 3358–3363Publication Date (Print):April 1, 1991Publication History Published online1 May 2002Published inissue 1 April 1991https://doi.org/10.1021/j100161a070RIGHTS & PERMISSIONSArticle Views11733Altmetric-Citations2479LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (1 MB) Get e-Alerts

GROMACS: Fast, flexible, and free

2005-10-06

David van der Spoel , Erik Lindahl , Berk Hess +3 more

Abstract This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written … Abstract This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum‐chemical packages (MOPAC, GAMES‐UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org . © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1701–1718, 2005

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

2013-08-06

Romelia Salomón–Ferrer , Andreas W. Götz , Duncan Poole +2 more

We present an implementation of explicit solvent all atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA-enabled GPUs. First released publicly in April 2010 … We present an implementation of explicit solvent all atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA-enabled GPUs. First released publicly in April 2010 as part of version 11 of the AMBER MD package and further improved and optimized over the last two years, this implementation supports the three most widely used statistical mechanical ensembles (NVE, NVT, and NPT), uses particle mesh Ewald (PME) for the long-range electrostatics, and runs entirely on CUDA-enabled NVIDIA graphics processing units (GPUs), providing results that are statistically indistinguishable from the traditional CPU version of the software and with performance that exceeds that achievable by the CPU version of AMBER software running on all conventional CPU-based clusters and supercomputers. We briefly discuss three different precision models developed specifically for this work (SPDP, SPFP, and DPDP) and highlight the technical details of the approach as it extends beyond previously reported work [Götz et al., J. Chem. Theory Comput. 2012, DOI: 10.1021/ct200909j; Le Grand et al., Comp. Phys. Comm. 2013, DOI: 10.1016/j.cpc.2012.09.022].We highlight the substantial improvements in performance that are seen over traditional CPU-only machines and provide validation of our implementation and precision models. We also provide evidence supporting our decision to deprecate the previously described fully single precision (SPSP) model from the latest release of the AMBER software package.

Phenomenological Theory of Ion Solvation. Effective Radii of Hydrated Ions

1959-09-01

E. R. Nightingale

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhenomenological Theory of Ion Solvation. Effective Radii of Hydrated IonsE. R. Nightingale Jr.Cite this: J. Phys. Chem. 1959, 63, 9, 1381–1387Publication Date (Print):September 1, 1959Publication History Published … ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhenomenological Theory of Ion Solvation. Effective Radii of Hydrated IonsE. R. Nightingale Jr.Cite this: J. Phys. Chem. 1959, 63, 9, 1381–1387Publication Date (Print):September 1, 1959Publication History Published online1 May 2002Published inissue 1 September 1959https://pubs.acs.org/doi/10.1021/j150579a011https://doi.org/10.1021/j150579a011research-articleACS PublicationsRequest reuse permissionsArticle Views16704Altmetric-Citations2506LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts

CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations

2020-05-19

Thomas D. Kühne , Marcella Iannuzzi , Mauro Del Ben +7 more

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel … CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post–Hartree–Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.

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Cotunneling assisted nonequilibrium thermodynamics of a photosynthetic junction

2025-06-25

D. Ganpath Ram Sharma , Manash Jyoti Sarmah , Mriganka Sandilya +1 more | The Journal of Chemical Physics

We theoretically investigate a photosystem II-based reaction center modeled as a nonequilibrium quantum junction. We specifically focus on the electron–electron interactions that enable cotunneling events to be captured through quantum … We theoretically investigate a photosystem II-based reaction center modeled as a nonequilibrium quantum junction. We specifically focus on the electron–electron interactions that enable cotunneling events to be captured through quantum mechanical rates due to the inclusion of a negatively charged many-body state. Using a master equation framework with realistic spectral profiles, we analyze the cotunneling assisted current, power, and work. Amplification of the cotunneling assisted current and power occurs over a narrower bias range, reflecting a trade-off where a higher flux is compensated by a reduced work window. We further report that the cotunneling-enhanced thermodynamic variables, particularly within specific bias windows, depend on the interplay between cotunneling amplitudes, electron transition rates, and interaction energy. Both attractive and repulsive electronic interactions can enhance cotunneling, but this effect is sensitive to the energy balance between states and the tunneling strength asymmetries.

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Phase transition of a chiral molecular model over the complete graph

2025-06-25

J. Hernández , Anna Sikov , Alberto Ramos +1 more | The Journal of Chemical Physics

This paper presents a mean-field approximation of the two-dimensional lattice chiral molecular model introduced by Lombardo et al., Proc. Natl. Acad. Sci. U. S. A. 106(36), 15131–15135 (2009) and simplified … This paper presents a mean-field approximation of the two-dimensional lattice chiral molecular model introduced by Lombardo et al., Proc. Natl. Acad. Sci. U. S. A. 106(36), 15131–15135 (2009) and simplified by Cruz-Simbron et al., J. Chem. Phys. 160, 084502 (2024), obtained by defining a chiral system over a complete graph. Using thermodynamic formalism, we derive a closed-form expression for the free energy of the system fβ; we establish its analyticity for all β &gt; 0 and its convexity over an interval depending on the Hamiltonian of the system. Our findings confirm the existence of first- and second-order phase transitions within this mean-field framework, confirming the first-order phase transition previously proposed by Lombardo et al., Proc. Natl. Acad. Sci. U. S. A. 106(36), 15131–15135 (2009) in the mean-field approximation. Furthermore, we construct a comprehensive phase diagram for the proposed model, providing a deeper understanding of its thermodynamic behavior.

Nuclear quantum effects at the liquid/vapor interface from neural-network based path integral molecular dynamics simulations

2025-06-25

Elias Eingang , Christoph Dellago , Marcello Sega | The Journal of Chemical Physics

Nuclear quantum effects (NQEs) significantly influence the properties of water, including its structure, dynamics, and phase behavior. While their impact on bulk water has been extensively studied, their role at … Nuclear quantum effects (NQEs) significantly influence the properties of water, including its structure, dynamics, and phase behavior. While their impact on bulk water has been extensively studied, their role at the liquid–vapor interface remains largely unexplored. In this work, we employ machine-learned neural network potentials trained on ab initio data to conduct large-scale path-integral molecular dynamics simulations at the RPBE-D3 level. Our results reveal that NQEs increase the surface tension, albeit marginally, shift the critical point to higher temperatures, and alter the orientational preferences of interfacial water molecules. This study provides the first direct quantification of the effect of NQEs on the surface tension of water. These findings highlight the fundamental role of quantum fluctuations in interfacial physics and underscore the necessity of including NQEs in accurate simulations of aqueous systems.

Particle dynamics in biconical cavities: First-passage, direct-transit, and looping time distributions

2025-06-25

Alexander M. Berezhkovskii , Leonardo Dagdug , Sergey M. Bezrukov | The Journal of Chemical Physics

Earlier, we analyzed the effects of monotonically changing entropy potentials imposed by expanding or narrowing tubes on particle diffusion in such tubes [Berezhkovskii et al., J. Chem. Phys. 147, 134104 … Earlier, we analyzed the effects of monotonically changing entropy potentials imposed by expanding or narrowing tubes on particle diffusion in such tubes [Berezhkovskii et al., J. Chem. Phys. 147, 134104 (2017)]. In the present study, we examine particle dynamics in biconical cavities, wherein particle motion is influenced by either an entropy potential well, as in a cavity composed of first expanding and then narrowing cones, or an entropy potential barrier, as in a cavity made up of first narrowing and then expanding identical cones. Both types of cavities are relevant to multiple technological and biological problems, where examples of such structures can be found at the micro- and nanoscales. We derive analytical expressions for the Laplace transforms of the distributions for the first-passage, direct-transit, and looping times in such structures. We find that not only the average values but also the distributions of the first-passage times in both cavities are indeed identical. However, the direct-transit and looping time distributions are drastically different. In particular, the mean direct-transit time for the expanding–narrowing cavity (entropy potential well) approaches a constant value with the increasing ratio of the cavity’s largest radius to the radius of its opening. In contrast, it goes to infinity in the case of the narrowing–expanding cavity (entropy potential barrier).

Charge transfer at air–water interfaces: A machine learning potential-based molecular dynamics study

2025-06-25

Zhiwei Wang , Zhaoan Chen , Jun‐Jie Fang +3 more | The Journal of Chemical Physics

Water at interfaces plays a crucial role in many natural processes and industrial applications. However, the relationship between water’s hydrogen bonding and charge transfer characteristics at these interfaces remains poorly … Water at interfaces plays a crucial role in many natural processes and industrial applications. However, the relationship between water’s hydrogen bonding and charge transfer characteristics at these interfaces remains poorly understood. Here, we develop machine learning potentials at near density functional theory accuracy based on datasets generated with ab initio molecular dynamics simulations, enabling us to explore the structure and charge transfer at air–water interfaces. Our simulations reveal a non-uniform charge distribution along the interfacial normal direction: water molecules in the outermost layer in direct contact with the air tend to be positively charged, while those in a thin sub-interface layer are negatively charged. We further demonstrate that this uneven charge distribution arises from the donor–acceptor asymmetry of H-bonds among interfacial water molecules. These findings provide a detailed atomic-level insight into the charge transfer behaviors of water at interfaces.

Wavefunction-based simulations of 2D electronic spectroscopy of conjugated polymers: Signatures of exciton transport and coherent vibronic dynamics at finite temperature

2025-06-25

Dominik Brey , Irène Burghardt | The Journal of Chemical Physics

Spectroscopic signatures of exciton transport and vibronic coupling in two-dimensional electronic spectroscopy (2DES) are studied for an oligothiophene chain as a minimal model for intra-chain exciton migration in poly-(3-hexylthiophene). Generalizing … Spectroscopic signatures of exciton transport and vibronic coupling in two-dimensional electronic spectroscopy (2DES) are studied for an oligothiophene chain as a minimal model for intra-chain exciton migration in poly-(3-hexylthiophene). Generalizing our previous approach [Brey et al., Faraday Discuss. 237, 148 (2022)], a first-principles parameterized Frenkel Hamiltonian is combined with a collective high-frequency lattice mode and a set of ring-torsional modes whose thermal fluctuations drive exciton migration. A wavefunction-based quantum–classical treatment is employed, where quantum Langevin friction via the Kostin equation acts on the collective lattice mode, while the torsional modes evolve under a classical Langevin equation at finite temperature. Single wavefunction realizations exhibit largely adiabatic, diffusive exciton motion across the 20-site lattice under periodic boundary conditions. 2DES spectra are computed using the equation-of-motion phase matching approach (EOM-PMA) within a wavefunction setting. In line with experimental observations, a pronounced vibronic fine structure is observed, which is modulated by spectral diffusion due to fluctuation-induced changes in the exciton extension and localization.

Stabilization Method as a Tool for Electronic State Spectroscopy

2025-06-24

Pedro A. S. Randi , P. Limão-Vieira , M. H. F. Bettega | The Journal of Physical Chemistry A

We propose a new systematic approach to distinguish valence and diffuse electronically excited states of polyatomic molecules. This method applies the stabilization technique of Hazi and Taylor [Phys. Rev. A … We propose a new systematic approach to distinguish valence and diffuse electronically excited states of polyatomic molecules. This method applies the stabilization technique of Hazi and Taylor [Phys. Rev. A 1970, 1 (1109)] to neutral excited states, using basis set diffuseness as the stabilization parameter. By monitoring how excited states behave under basis set contraction, one can differentiate valence states from Rydberg and mixed valence-Rydberg states, reducing the arbitrariness of previous strategies. Valence states remain stable, whereas the energies of Rydberg and mixed states vary. This approach is compatible with any electronic structure method. To illustrate its applicability, we characterize the singlet excited states of CCl4, HCOOH, and 2-chlorotoluene. This provides a valuable tool for investigating the nature of the electronically excited states.

Automated Selection of Nuclear Coordinates for Reduced Dimensionality Nonadiabatic Dynamics

2025-06-24

V. Delmas , Alessandro Nicola Nardi , Isabella C. D. Merritt +3 more | Journal of Chemical Theory and Computation

Poor scaling of dynamics simulations with number of dimensions is currently a major limiting factor in the simulation of photochemical processes. In this work, we investigate ways to reduce the … Poor scaling of dynamics simulations with number of dimensions is currently a major limiting factor in the simulation of photochemical processes. In this work, we investigate ways to reduce the dimensionality of many-atom systems with a view toward enhancing computational efficiency while maintaining accuracy. Using mixed quantum-classical Trajectory Surface Hopping (TSH) simulations of three photoreactive molecules─trans-azomethane (tAZM), butyrolactone (Bulac), and furanone (Fur)─we explore two different dimensionality reduction techniques: Principal Component Analysis (PCA) and Normal Mode Variance (NMV). Dynamics simulations are run in full dimensionality and reduced dimensionality, employing either PCA or NMV, and the impact of the dimensionality reduction on selected electronic and geometric properties of the dynamics is evaluated. For all three molecules, both PCA and NMV can be used to select lower-dimensional spaces in which the full-dimensionality dynamics results are reproduced. PCA reduction outperforms NMV in all systems, allowing for a more significant dimensionality reduction without loss of accuracy. The improved accuracy of PCA is, for tAZM, mostly seen in the electronic properties while for both Fur and Bulac the advantage is clear in the ring-opening reaction itself as well. The present approach opens routes to simulation of larger photochemically relevant systems, through the use of automated dimensionality reduction, avoiding human bias.

External Reorganization Energy upon Charge Transfer Reactions in Mildly Polar Media: The Case of Naphthalene in Tetrahydrofuran

2025-06-24

Francesco Ambrosio , Alessandro Landi , Michele Loriso +2 more | The Journal of Physical Chemistry Letters

External reorganization energy, λext, is of paramount importance in condensed-phase electron transfer (ET) processes, but its precise determination remains a challenge. We here combine classical molecular dynamics with advanced electronic-structure … External reorganization energy, λext, is of paramount importance in condensed-phase electron transfer (ET) processes, but its precise determination remains a challenge. We here combine classical molecular dynamics with advanced electronic-structure calculations and the thermodynamic integration technique to calculate λext for a mildly polar solvent, tetrahydrofuran (THF), in ET reactions involving the (NAP/NAP-) redox couple (NAP = naphthalene), a system widely studied in this context. First, we simulate the structural and electronic properties of liquid THF, as well as those of NAP and NAP- solutions, in excellent agreement with available measurements. Then, from the calculated vertical and adiabatic energy levels, we determine the values of λext associated with the reduction of NAP and the oxidation of NAP-. We observe a clear asymmetry in the solvent response for the two processes, which could not be captured by either the Marcus approximation or using standard implicit solvent models. Finally, we identify the different contributions to λext that are at the root of nonlinear solvent response, including dipole-charge interactions and effects arising from induced polarization. These interactions are found to be most significant in the first solvation shell, particularly for a limited number of solvent molecules closest to the solute.

Heisenberg dynamics of mixed quantum-classical systems

2025-06-24

David Martínez-Crespo , Cesare Tronci | The European Physical Journal Plus

The nature of water interactions and the molecular signatures of hydrophobicity

2025-06-24

N. Loubet , Alejandro R. Verde , Gustavo A. Appignanesi | The Journal of Chemical Physics

Despite being of utmost relevance in central fields ranging from biophysics to self-assembly processes in materials science, we still lack a precise comprehensive definition of hydrophobicity to replace the usual, … Despite being of utmost relevance in central fields ranging from biophysics to self-assembly processes in materials science, we still lack a precise comprehensive definition of hydrophobicity to replace the usual, merely qualitative descriptions that rely on water repellency or a lack of affinity. Building on recent findings regarding the structure and interactions of bulk water, we use a recently introduced water structural indicator to reach the following quantitative molecular elucidation: "hydrophobicity is the inability of a system to pay for the lacking hydrogen bonds (HBs) it produces in its hydration layer at least the same cost that this kind of defect imposes on bulk water, a defect interaction threshold whose magnitude is significantly lower than the HB energy." We will demonstrate that such a defect interaction threshold not only marks the transition to hydrophobicity that occurs at a contact angle of θ = 90° in surfaces with different polarity degrees (allowing for an absolute scale) but also accurately signals the onset of drying regimes in nanoconfined aqueous systems. This is relevant from a practical perspective, as the possibility of being (locally) wet or dry becomes crucial in many fields. Specifically, our approach allows for assessing local hydrophobicity with unprecedented resolution (suitable for regions of different sizes, even at the single-atom level), particularly for self-assembly processes in biology and materials science, which often entail patterned regions combining hydrophobic and hydrophilic sites, thus posing challenges (and opportunities) for rational design efforts.

Symmetry breaking as predicted by a phase space Hamiltonian with a spin Coriolis potential

2025-06-24

Nadine C. Bradbury , Titouan Duston , Zhen Tao +3 more | The Journal of Chemical Physics

We perform electronic structure calculations for a set of molecules with degenerate spin-dependent ground states (CH23, CH3•2, O23) going beyond the Born-Oppenheimer approximation and accounting for nuclear motion. According to … We perform electronic structure calculations for a set of molecules with degenerate spin-dependent ground states (CH23, CH3•2, O23) going beyond the Born-Oppenheimer approximation and accounting for nuclear motion. According to a phase space approach that parameterizes electronic states (|Φ⟩) and electronic energies (E) by nuclear position and momentum [i.e., |Φ(R, P)⟩ and E(R, P)], we find that the presence of degenerate spin degrees of freedom leads to broken symmetry ground states. More precisely, rather than a single degenerate minimum at (R, P) = (Rmin, 0), the ground state energy has two minima at (R,P)=(Rmin',±Pmin) (where Rmin' is close to Rmin), dramatically contradicting the notion that the total energy of the system can be written in separable form as E=P22M+Vel. Although we find that the broken symmetry solutions have small barriers between them for the small molecules, we hypothesize that the barriers should be macroscopically large for metallic solids, thus offering up a new phase-space potential energy surface for simulating the Einstein-de Haas effect.

Machine learning meets su(n) Lie algebra: Enhancing quantum dynamics learning with exact trace conservation

2025-06-24

Arif Ullah , Jeremy O. Richardson | The Journal of Chemical Physics

Machine learning has emerged as a promising tool for simulating quantum dissipative dynamics. However, existing methods often struggle to enforce key physical constraints, such as trace conservation, when modeling reduced … Machine learning has emerged as a promising tool for simulating quantum dissipative dynamics. However, existing methods often struggle to enforce key physical constraints, such as trace conservation, when modeling reduced density matrices (RDMs). While physics-informed neural networks (PINN) aim to address these challenges, they frequently fail to achieve full physical consistency. In this work, we introduce a novel approach that leverages the su(n) Lie algebra to represent RDMs as a combination of an identity matrix and n2 - 1 Hermitian, traceless, and orthogonal basis operators, where n is the system's dimension. By learning only the coefficients associated with the operators, our framework inherently ensures exact trace conservation, as the traceless nature of the operators restricts the trace contribution solely to the identity matrix. This eliminates the need for explicit trace-preserving penalty terms in the loss function, simplifying optimization and improving learning efficiency. We validate our approach on two benchmark quantum systems: the spin-boson model and the Fenna-Matthews-Olson complex. By comparing the performance of four neural network architectures-purely data-driven physics-uninformed neural networks (PUNN), su(n) Lie algebra-based PUNN (su(n)-PUNN), traditional PINN, and su(n) Lie algebra-based PINN (su(n)-PINN)-we highlight the limitations of conventional methods and demonstrate the superior accuracy, robustness, and efficiency of our approach in learning quantum dissipative dynamics.

Extending the information-theoretic approach from the (one) electron density to the pair density

2025-06-24

Yilin Zhao , Dongbo Zhao , Chunying Rong +2 more | The Journal of Chemical Physics

Within the framework of chemical reactivity theory, information-theoretic descriptors have predominantly focused on global and local measures, while nonlocal descriptors beyond Shannon entropy remain largely unexplored. By extending the information … Within the framework of chemical reactivity theory, information-theoretic descriptors have predominantly focused on global and local measures, while nonlocal descriptors beyond Shannon entropy remain largely unexplored. By extending the information carrier from the one-electron density to the two-electron distribution function (pair density), this work introduces information-theoretic descriptors rooted in both one-electron and pair densities. This broadens the scope of the information-theoretic approach (ITA) and introduces new types of ITA descriptors, notably the joint, conditional, and mutual ITA quantities. To elucidate the interaction between electron correlation and localization, we compute and analyze a suite of ITA descriptors for one-electron and pair electrons, including the Shannon entropy, Fisher information, and Rényi entropy, for neutral atoms ranging from helium (He) to argon (Ar). The results demonstrate how the pair-density ITA enhances the interpretation of electronic correlations and its connection to spatial localization.

Localisation-delocalisation property of a particle in a quantum well disturbed by a uniform electric field

2025-06-24

Dehua Wang , Tian‐tian Tang | The Philosophical Magazine A Journal of Theoretical Experimental and Applied Physics

Interplay between Mixed and Pure Exciton States Controls Singlet Fission in Rubrene Single Crystals

2025-06-24

Dmitry R. Maslennikov , Marios Maimaris , Haoqing Ning +7 more | Journal of the American Chemical Society

Singlet fission (SF) is a multielectron process in which one singlet exciton S converts into a pair of separated triplet excitons T. SF is widely studied as it may help … Singlet fission (SF) is a multielectron process in which one singlet exciton S converts into a pair of separated triplet excitons T. SF is widely studied as it may help overcome the Shockley-Queisser efficiency limit for semiconductor photovoltaic cells. To elucidate and control the SF mechanism, great attention has been given to the identification of intermediate states in SF materials, which often appear elusive due to the complexity and fast time scales of the SF process. Here, we apply 14 fs-1 ms transient absorption techniques to high-purity rubrene single crystals to disentangle the intrinsic fission dynamics from the effects of defects and grain boundaries and to identify reliably the fission intermediates. Our data demonstrates that above-gap excitation directly generates a hybrid vibronically assisted mixture of singlet state and triplet-pair multiexciton [S/TT], which rapidly (<100 fs) and coherently branches into pure singlet or triplet excitations. The relaxation of [S/TT] to S is followed by a relatively slow and temperature-activated (48 meV activation energy) incoherent fission process. The SF competing pathways and intermediates revealed here unify the observations and models presented in previous studies of SF in rubrene and offer alternative strategies for the development of SF-enhanced photovoltaic materials.

Towards a robust approach to infer causality from molecular dynamics simulations

2025-06-24

Vittorio Del Tatto , Debarshi Banerjee , Ali Hassanali +1 more | The Journal of Chemical Physics

The ability to distinguish between correlation and causation of variables in molecular systems remains an interesting and open area of investigation. In this work, we probe causality in a molecular … The ability to distinguish between correlation and causation of variables in molecular systems remains an interesting and open area of investigation. In this work, we probe causality in a molecular system using two independent computational methods that infer the causal direction through the language of information transfer. Specifically, we demonstrate that a molecular dynamics simulation involving a single tryptophan in liquid water displays asymmetric information transfer between specific collective variables, such as solute and solvent coordinates. Analyzing a discrete Markov-state and Langevin dynamics on a 2D free energy surface, we show that the same kind of asymmetries can emerge even in extremely simple systems undergoing equilibrium and time-reversible dynamics. We use these model systems to rationalize the unidirectional information transfer in the molecular system in terms of asymmetries in the underlying free energy landscape and/or relaxation dynamics of the relevant coordinates. Finally, we propose a computational experiment that allows one to decide if an asymmetric information transfer between two variables corresponds to a genuine causal link.

A Phenomenological Symmetry Rule for Chemical Reactivity under Vibrational Strong Coupling

2025-06-24

Anjali Jayachandran , Bianca Patrahau , John G. Ricca +6 more | Angewandte Chemie International Edition

Symmetry is known to strongly influence the course of a chemical reaction. It has also been found to play a key role in vibrational strong coupling (VSC), where it can … Symmetry is known to strongly influence the course of a chemical reaction. It has also been found to play a key role in vibrational strong coupling (VSC), where it can influence the outcome of chemical reactions or alter chemical equilibria. However, the precise nature of this effect and its extent remains elusive. To further explore the role of vibrational symmetry, we have investigated the equilibrium constants of different charge transfer complexes, in particular of isomers of trimethyl benzene belonging to different point groups from which a general symmetry rule emerges. We describe the strongly coupled system by a direct product of irreducible representations associated with the complexes and the cavity. As a consequence, the coupled vibration is associated with a new irreducible representation that projects differently on the reaction coordinate of the charge transfer complexation, reflecting the changes in the equilibrium constants. This phenomenological symmetry rule points to a general underlying framework for predicting the outcome of chemical reactivity under VSC.

A first-principles approach to electromechanics in liquids

2025-06-24

Anna T. Bui , Stephen J. Cox | Journal of Physics Condensed Matter

Abstract Electromechanics in fluids describes the response of the number density to electric fields, and thus provides a powerful means by which to control the behavior of liquids. While continuum … Abstract Electromechanics in fluids describes the response of the number density to electric fields, and thus provides a powerful means by which to control the behavior of liquids. While continuum approaches have proven successful in describing electromechanical phenomena in macroscopic bodies, their use is questionable when relevant length scales become comparable to a system's natural correlation lengths, as commonly occurs in, e.g., biological systems, nanopores, and microfluidics. Here, we present a first-principles theory for electromechanical phenomena in fluids. Our approach is based on the recently proposed hyperdensity functional theory [Sammüller et al ., Phys. Rev. Lett. 133 , 098201 (2024)] in which we treat the charge density as an observable of the system, with the intrinsic Helmholtz free energy functional dependent upon both density and electrostatic potential. Expressions for the coupling between number and charge densities emerge naturally in this formalism, avoiding the need to construct density-dependent and spatially varying material parameters such as the dielectric constant. Furthermore, we make our theory practical by deriving a connection between hyperdensity functional theory and local molecular field theory, which facilitates the use of machine learning to obtain explicit representations for the free energy functionals of systems with short-ranged electrostatic interactions, with long-ranged effects accounted for in a well-controlled mean-field fashion.

Wavepacket and reduced-density approaches for high-dimensional quantum dynamics: Application to the nonlinear spectroscopy of asymmetrical light-harvesting building blocks

2025-06-23

Joachim Galiana , Michèle Desouter-Lecomte , Benjamin Lasorne | The Journal of Chemical Physics

Excitation-energy transfer (EET) and relaxation in an optically excited building block of poly(phenylene ethynylene) (PPE) dendrimers are simulated using wavepackets with the multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) method and reduced-density … Excitation-energy transfer (EET) and relaxation in an optically excited building block of poly(phenylene ethynylene) (PPE) dendrimers are simulated using wavepackets with the multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) method and reduced-density matrices with the hierarchical equations of motion (HEOM) approach. The dynamics of the ultrafast electronic funneling between the first two excited electronic states in the asymmetrically meta-substituted PPE oligomer with two rings on one branch and three rings on the other side, with a shared ring in between, is treated with 93-dimensional ab initio vibronic-coupling Hamiltonian (VCH) models, either linear or with bilinear and quadratic terms. The linear VCH model is also used to calibrate an open quantum system that falls in a computationally demanding non-perturbative non-Markovian regime. The linear-response absorption and emission spectra are simulated with both the ML-MCTDH and HEOM methods. The latter is further used to explore the nonlinear regime toward two-dimensional spectroscopy. We illustrate how a minimal VCH model with the two main active bright states and the impulsive-pulse limit in third-order response theory may provide at lower cost polarization-sensitive time-resolved signals that monitor the early EET dynamics. We also confirm the essential role played by the high-frequency acetylenic and quinoidal vibrational modes.

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A simulation study on Raman cross sections of OH and OD stretches in isotopically pure and diluted liquid water

2025-06-23

Tetsuyuki Takayama , Takuhiro Otosu , S. Yamaguchi | The Journal of Chemical Physics

The Raman scattering activity spectra of isotopically pure and diluted liquid water are theoretically calculated to examine the mole-fraction dependence of the OH- and OD-stretch cross sections. This mole-fraction dependence … The Raman scattering activity spectra of isotopically pure and diluted liquid water are theoretically calculated to examine the mole-fraction dependence of the OH- and OD-stretch cross sections. This mole-fraction dependence was once claimed to be anomalous and attributed to nuclear quantum correlations of protons and deuterons when it was discovered experimentally. The present study demonstrates that the experimental data of the mole-fraction dependence of the cross sections, as well as the Raman scattering activity spectra in the stretch region, are well reproduced by the theoretical calculations according to the quantum/classical mixed approach in which the nuclear quantum correlations are not taken into account. This suggests that the anomalous dependence does not serve as evidence of the nuclear quantum correlations. The present study provides a more plausible interpretation that the OH- and OD-stretch cross sections depend on the mole fraction because of the inter- and intra-molecular vibrational couplings.

A Reactive Explicit Electron Force Field for Hydrocarbons

2025-06-23

Zhimin Zhou , Hongqiang Cui , Hongjun Fan +2 more | Journal of Chemical Theory and Computation

The prevailing reactive force fields are typically based on the bond-order concept or other predefined chemical frameworks, along with implicit electronic treatments and the incorporation of intricate corrections, which severely … The prevailing reactive force fields are typically based on the bond-order concept or other predefined chemical frameworks, along with implicit electronic treatments and the incorporation of intricate corrections, which severely limit their further development. Explicit electron force fields introduce electrons as particles into the force field, and their ability to model electronically excited systems as well as electronic response properties has been demonstrated, yet the description of ground-state reactions for complex systems remains challenging. This study introduces a new explicit electron force field (EeFF) for modeling hydrocarbon ground-state reactions. The EeFF explicitly treats electrons as distinct wave packets with variable radii and variable spin properties, thus providing a more physically realistic description of electronic behavior. The model incorporates quantum kinetic energy, Coulomb integration, and Pauli repulsion of electrons by introducing specialized potential functions applicable to different types of wave packets, thereby superseding the traditional bond-order concept. The EeFF has been optimized using training sets of CH compounds with more than 10000 conformations covering a wide range of hydrocarbon systems and reactions. Compared with ReaxFF, EeFF reduces energy and force errors. A new molecular dynamics simulation method is used to realize the dynamic evolution of electron spin properties and allow the degrees of freedom of nuclei and electrons to change over time while approaching adiabatic conditions. Subsequent simulations of iso-octane thermal decomposition effectively reproduce the main product distributions as well as the key reaction pathways, and the motion trajectories of electrons provide unique insights into the reaction mechanisms at the electron level.

Real-time revealing of Triplet State evolution in Dibenzothiophene Derivatives Using Ultrafast Spectroscopy

2025-06-23

Tiantian Guan , Yonggang Yang , Yang Liu +3 more | Optics Express

Elucidation of the pH-Dependent Electric Double Layer Structure at the Positively Charged Amorphous Alumina/Water Interface Using Heterodyne-Detected Vibrational Sum-Frequency Generation

2025-06-22

Feng Wei , Satoshi Nihonyanagi , Tahei Tahara | Journal of the American Chemical Society

Alumina is one of the most abundant oxides in nature. Hence, the molecular-level elucidation of the alumina/water interface is important not only for a fundamental understanding of the oxide surface, … Alumina is one of the most abundant oxides in nature. Hence, the molecular-level elucidation of the alumina/water interface is important not only for a fundamental understanding of the oxide surface, but also for applications of oxide-related materials in extensive research fields. In the present study, the water structure in the electrical double layer (EDL) at the alumina-water interface is investigated through the interface-selective vibrational spectra (χ(2)) in the OH stretch region, measured with heterodyne-detected vibrational sum-frequency generation spectroscopy. The imaginary part of χ(2) (Imχ(2)) spectra is collected while salt concentrations are varied (0.01-5.0 M) in the acidic and neutral pH range (pH 2.0-8.0), where the alumina surface is positively charged. The spectral additivity of the Imχ(2) spectra enables the decomposition of the spectra into the contributions of the diffuse layer (DL) and Stern layer (SL) to discuss them separately. The surface charge density at each pH is evaluated from the salt-concentration dependence of the amplitude of the DL spectra using the modified Gouy-Chapman theory, providing a single pKa value of ∼3.7 ± 0.2 due to the Al2OH2+/Al2OH equilibrium at the alumina surface. Moreover, it is found that the spectra of the DL and SL are very similar to each other, indicating that the water in the SL is bulk-like water with highly concentrated salt, without specific interaction with the alumina surface. This implies that the water structure of the EDL at the alumina/water interface is much simpler than that at the silica/water interface, where the water molecule has specific interactions with the silica surface. These findings reveal that the alumina/water interface provides another distinct prototype of the EDL structure at oxide/water interfaces.

General Quantum Alchemical Free Energy Simulations via Hamiltonian Interpolation

2025-06-20

Chenghan Li , Xing Zhang , Garnet Kin‐Lic Chan | Journal of Chemical Theory and Computation

We present an implementation of alchemical free energy simulations at the quantum mechanical level by directly interpolating the electronic Hamiltonian. The method is compatible with any level of electronic structure … We present an implementation of alchemical free energy simulations at the quantum mechanical level by directly interpolating the electronic Hamiltonian. The method is compatible with any level of electronic structure theory and requires only one quantum calculation for each molecular dynamics step in contrast to multiple energy evaluations that would be needed when interpolating the ground-state energies. We demonstrate the correctness and applicability of the technique by computing alchemical free energy changes of gas-phase molecules, with both nuclear and electron creation/annihilation. We also show an initial application to first-principles pKa calculation for solvated molecules where we quantum mechanically annihilate a bonded proton.

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Modulation of Electric Field and Interface on Competitive Reaction Mechanisms

2025-06-20

Pengchao Zhang , Xuefei Xu | Journal of Chemical Theory and Computation

Recently, much evidence has accumulated, showing that electric fields and water interfaces influence the characteristics and alignment of biomolecules and greatly boost reaction rates. The prototropic tautomerism is a fundamental … Recently, much evidence has accumulated, showing that electric fields and water interfaces influence the characteristics and alignment of biomolecules and greatly boost reaction rates. The prototropic tautomerism is a fundamental process in biological systems; however, a comprehensive understanding of the electric field effects and interfacial effects on it is still lacking. In this work, we performed a theoretical study of the modulation of the electric field and the interface on the tautomerism dynamics of solvated glycine by using deep potential molecular dynamics technology with enhanced sampling. The deep learning potentials used were trained to integrate long-range electrostatic interactions in order to better describe the electric field effect. We observed that an external electric field of 10 mV/Å barely changed the key structures involved in tautomerism reactions but significantly influenced their relative free energies and consequently made the transformation from zwitterionic ([Z]) to neutral ([N]) glycine more achievable both thermodynamically and dynamically and altered the optimal reaction mechanism from intramolecular proton transfer (Intra-PT) to intermolecular proton transfer (Inter-PT) involving a separate cationic-glycine-hydroxide ion pair. The detailed analysis revealed that the electric field increased the thermodynamical stability of [N] relative to [Z] by 7 kJ/mol due to the entropy effect and promoted the Inter-PT pathway by electrostatically facilitating the separation of ion pairs, causing the free-energy-barrier decrease of the rate-determined step by approximately 10 kJ/mol. Interestingly, in the air-water interface, due to the interfacial propensity of the glycine and water self-ions, the separation of ion pairs is restricted, slowing the Inter-PT pathways. Nevertheless, the interfacial interconversion between the [Z] and [N] forms of glycine is dynamically accelerated via the Intra-PT pathway due to partial solvation. These findings provide new insights into how the electric field and interfaces modulate thermodynamics, kinetics, and the mechanism of chemical reactions.

Molecular Insights into the Influence of Ions on the Water Structure. II. Halide Ions in Solution

2025-06-20

Henry Agnew , Roya Savoj , Richa Rashmi +2 more | The Journal of Physical Chemistry B

Understanding how halide ions affect the structure and dynamics of water at the molecular level is essential for a wide range of chemical, biological, and environmental processes. In this study, … Understanding how halide ions affect the structure and dynamics of water at the molecular level is essential for a wide range of chemical, biological, and environmental processes. In this study, we use molecular dynamics simulations with MB-nrg data-driven many-body potential energy functions to investigate the hydration properties of halide ions in bulk water. The results reveal distinct trends in hydration structure, residence times, dipole moment distributions, and infrared spectral signatures, reflecting variations in ion size, charge density, and polarizability. In particular, fluoride promotes uniquely strong and more directional hydrogen bonds with the surrounding water molecules, which leads to substantial spectral shifts and slower water exchange dynamics. In contrast, heavier halides induce only minimal perturbations on the water hydrogen-bond network, even within the first hydration shell. These insights provide a quantitative framework for understanding ion-specific effects in aqueous systems and set the stage for future studies of more complex environments such as aqueous interfaces and confined systems.

Quantum versus semiclassical signatures of correlated triple ionization in Dalitz plots

2025-06-20

NULL AUTHOR_ID | Physical review. A/Physical review, A

Intensity-Calibrated Variable-Angle Surface Spectroscopy Provides the Electrostatic Potential at the Interface between Bonded and Diffuse Regions of the Electrical Double Layer

2025-06-20

Md. Mosfeq Uddin , Dennis K. Hore | Langmuir

Second-order nonlinear optical spectroscopy is capable of separating contributions of water molecules bonded to a charged surface from those in the diffuse portion of the electrical double layer on account … Second-order nonlinear optical spectroscopy is capable of separating contributions of water molecules bonded to a charged surface from those in the diffuse portion of the electrical double layer on account of the phase-matching considerations that dictate how signals are accumulated over a finite distance. One of the most characteristic features of this interfacial water structure is the electrical potential at the distance from the surface that separates these two regions. Here we describe a scheme for calibrating the absolute second-order susceptibility of the silica-aqueous interface and thereby provide the first account of intensity-based on-resonance sum-frequency generation to measure the potential at the interface between the bonded and diffuse water structures at low ionic strength. Our finding that the magnitude of the potential is slightly greater than the ζ-potential suggests that the structural influence of the surface silanol groups does not extend quite to the slipping plane.

Formally exact fluorescence spectroscopy simulations for mesoscale molecular aggregates with N0 scaling

2025-06-20

Tarun Gera , Alexia Hartzell , Lipeng Chen +2 more | The Journal of Chemical Physics

We present a size-invariant (i.e., N0) scaling algorithm for simulating fluorescence spectroscopy in large molecular aggregates. We combine the dyadic adaptive hierarchy of pure states (DadHOPS) equation-of-motion with an operator … We present a size-invariant (i.e., N0) scaling algorithm for simulating fluorescence spectroscopy in large molecular aggregates. We combine the dyadic adaptive hierarchy of pure states (DadHOPS) equation-of-motion with an operator decomposition scheme and an efficient Monte Carlo sampling algorithm to enable a formally exact, local description of the fluorescence spectrum in large molecular aggregates. Furthermore, we demonstrate that the ensemble average inverse participation ratio of DadHOPS wave functions reproduces the delocalization extent extracted from fluorescence spectroscopy of J-aggregates with strong vibronic transitions. This work provides a computationally efficient framework for fluorescence simulations, offering a new tool for understanding the optical properties of mesoscale molecular systems.

Extracting Coupling-Mode Spectral Densities with Two-Dimensional Electronic Spectroscopy

2025-06-19

R. Wit , Jonathan Keeling , Brendon W. Lovett +1 more | The Journal of Physical Chemistry Letters

Methods for reconstructing the spectral density of a vibrational environment from experimental data can yield key insights into the impact of the environment on molecular function. Although such experimental methods … Methods for reconstructing the spectral density of a vibrational environment from experimental data can yield key insights into the impact of the environment on molecular function. Although such experimental methods exist, they generally only access vibrational modes that couple diagonally to the electronic system. Here we present a method for extracting the spectral density of modes that couple to the transition between electronic states, using two-dimensional electronic spectroscopy. To demonstrate this, we use a process-tensor method that can simulate two-dimensional electronic spectroscopy measurements in a numerically exact way. To explain how the extraction works, we also derive an approximate analytical solution, which illustrates that the non-Markovianity of the environment plays an essential role in the existence of the simulated signal.

Excitation Energy Transfer between Porphyrin Dyes on a Clay Surface: A Study Employing Multifidelity Machine Learning

2025-06-19

Dongyu Lyu , V.V. Vinod , Matthias Holzenkamp +5 more | Advanced Theory and Simulations

Abstract Natural light‐harvesting antenna complexes efficiently capture solar energy mostly using chlorophyll molecules, i.e., magnesium porphyrin pigments, embedded in a protein matrix. Inspired by this natural configuration, artificial clay‐porphyrin antenna … Abstract Natural light‐harvesting antenna complexes efficiently capture solar energy mostly using chlorophyll molecules, i.e., magnesium porphyrin pigments, embedded in a protein matrix. Inspired by this natural configuration, artificial clay‐porphyrin antenna structures have experimentally been synthesized and demonstrated to exhibit remarkable excitation energy transfer properties. The current study presents a computational design and simulations of a synthetic light‐harvesting system that emulates natural mechanisms by arranging cationic free‐base porphyrin molecules on an anionic clay surface. The transfer of excitation energy among the porphyrin dyes is investigated using a multiscale quantum mechanics/molecular mechanics (QM/MM) approach based on the semi‐empirical density functional‐based tight‐binding theory for the ground state dynamics. To improve the accuracy of the results, an innovative multifidelity machine learning approach is incorporated, which allows the prediction of excitation energies at the numerically demanding time‐dependent density functional theory level together with the def2‐SVP basis set. This approach is applied to an extensive dataset of 640 k geometries for the 90‐atom porphyrin structures, facilitating a thorough analysis of the excitation energy diffusion among the porphyrin molecules adsorbed to the clay surface. The insights gained from this study, inspired by natural light‐harvesting complexes, demonstrate the potential of porphyrin‐clay systems as effective energy transfer systems.

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Second harmonic generation of nonpoled polyurea thin film prepared via vapor deposition polymerization method

2025-06-19

Atsushi Sugita , Shusaku Nandate , Tatsumi KITAMURA +4 more | Japanese Journal of Applied Physics

Abstract This study reports the second-order nonlinear optical properties of polyurea thin film synthesized from 4,4′-diphenyl methane diisocyanate and 2,7-diaminofluorene via a vapor deposition polymerization. Second harmonic generation (SHG) effect … Abstract This study reports the second-order nonlinear optical properties of polyurea thin film synthesized from 4,4′-diphenyl methane diisocyanate and 2,7-diaminofluorene via a vapor deposition polymerization. Second harmonic generation (SHG) effect was observed in the as-deposited polyurea thin film on a SiO2 substrate, even without conventional poling. The SHG operation remained stable at temperatures up to 140°C. SHG signal were resolved as functions of pump light wavelength, incidence angle of the pump light and rotation angle of around the surface normal of the sample. The electronic and structural properties of the polyurea were also studied using quantum chemical calculations based on a density functional theory, revealing molecular orientation and electronic features that trigger the second-order nonlinear susceptibility of this material.

Nonadiabatic Dynamics with Constrained Nuclear-Electronic Orbital Theory

2025-06-18

Zhe Liu , Zehua Chen , Yang Yang | The Journal of Physical Chemistry Letters

Incorporating nuclear quantum effects into nonadiabatic dynamics remains a significant challenge. Herein we introduce new nonadiabatic dynamics approaches based on the recently developed constrained nuclear-electronic orbital (CNEO) theory. The CNEO … Incorporating nuclear quantum effects into nonadiabatic dynamics remains a significant challenge. Herein we introduce new nonadiabatic dynamics approaches based on the recently developed constrained nuclear-electronic orbital (CNEO) theory. The CNEO approach integrates nuclear quantum effects, particularly quantum nuclear delocalization effects, into effective potential energy surfaces. When combined with Ehrenfest dynamics and surface hopping, it effectively captures both nonadiabaticity and quantum nuclear delocalization effects. We apply these new approaches to a one-dimensional proton-coupled electron transfer model and find that they outperform conventional Ehrenfest dynamics and surface hopping, particularly in accurately predicting proton transfer dynamics and proton transmission probabilities in the low-momentum regime.

Ultrafast Coherent Electron Transfer through Intermolecular Quantum Well States

2025-06-18

Xintong Li , Linjie Chen , Zehua Wang +7 more | Journal of the American Chemical Society

Molecular materials offer a boundless design palette for light absorption and charge transport in both natural photosynthesis and engineered photovoltaics. They function in combination as chromophores, donors, conductors, and acceptors, … Molecular materials offer a boundless design palette for light absorption and charge transport in both natural photosynthesis and engineered photovoltaics. They function in combination as chromophores, donors, conductors, and acceptors, enabling the excitation and charge carrier transport through space and wire-like intramolecular pathways. Although quantum coherence is believed to enhance photoexcitation and photoinduced charge transfer, fluctuating and inhomogeneous environments accelerate decoherence. Here, we assemble a nanoporous medium consisting of a templated bipyridyl ethylene (BPE) molecule array on a Ag(111) surface that functions as an exceptional intermolecular nonnuclear quantum well conductor of coherent electron waves spanning over 20 Å length. Time-periodic driving of the Ag/BPE interface by femtosecond pulses promotes electrons into a ladder of Floquet quasi-energy donor states, where intermolecular quantum well states act as a resonant doorway for coherent electron transport into BPE/vacuum image potential acceptor states. The bifurcation of electron passage between the Floquet donor ladder and the charge transfer acceptor channel is recorded by projecting the active electrons into the photoemission continuum in an interferometric time- and angle-resolved multiphoton photoemission experiment. We find that exceptional decoupling of electrons from the metal substrate by the molecule-dressed vacuum preserves the coherence on the ∼150 fs time scale. This offers a new paradigm for quantum state design where a molecule-dressed vacuum mediates coherent electron transport in nanoporous molecular architectures.

Free Energies of Solvation in Benzene and Hexafluorobenzene: Is Explicit Polarization Needed?

2025-06-18

William L. Jorgensen , Julian Tirado‐Rives | The Journal of Physical Chemistry B

Free energies of solvation in liquid benzene and hexafluorobenzene have been computed for 42 uncharged solutes. Monte Carlo statistical mechanics was used with the free-energy perturbation theory and the OPLS-AA … Free energies of solvation in liquid benzene and hexafluorobenzene have been computed for 42 uncharged solutes. Monte Carlo statistical mechanics was used with the free-energy perturbation theory and the OPLS-AA force field. The results address the transferability of the potential functions developed for pure liquids to mixed systems and the potential importance of explicit polarization for neutral organic molecules in aromatic solvents. Although the free-energy results cover an 11 kcal/mol range, the average error in comparison with experimental data points is only 0.4 kcal/mol. There is no systematic pattern to the discrepancies, so the need to add explicit treatment of solute-solvent polarization effects is not supported. This contrasts the situation with cationic solutes as reflected in cation-π interactions. Results for free energies of hydration are also provided for the 42 solutes in TIP4P water and give an average error of 0.49 kcal/mol. Implications for modeling biomolecular systems with standard force fields are considered. It is also interesting to note the overall similar values for free energies of solvation in benzene and hexafluorobenzene despite the reversal of polarity for the aromatic rings; the most significant exception is the more favorable solvation of perfluoroalkanes in the perfluoro solvent. Alternative accommodations of solutes in the two solvents are illustrated.

First-Principles Prediction of Vibrational Sum Frequency Generation Features of Phenyl Groups at the 2D Interface with C∞ Symmetry

2025-06-18

Jihyeong Ryu , Yiwen Guo , Sibing Chen +3 more | Langmuir

Vibrational sum frequency generation (SFG) spectroscopy is capable of probing the orientation of the interfacial molecules. A conventional approach assumes that hyperpolarizability tensors governing the SFG signal intensity can be … Vibrational sum frequency generation (SFG) spectroscopy is capable of probing the orientation of the interfacial molecules. A conventional approach assumes that hyperpolarizability tensors governing the SFG signal intensity can be determined based on the point group symmetry of individual functional groups. However, vibrational coupling among neighboring groups breaks the normal mode symmetry. This makes it difficult to accurately interpret SFG spectra, particularly for phenyl (C6H5-) groups. In this study, we employed density functional theory (DFT) calculations to predict the SFG spectral features of C6H5 groups at two-dimensional interfaces with C∞ symmetry. Using model compounds such as iodobenzene (C6H5-I) and various substituted phenyl derivatives, we systematically investigated the effect of vibrational coupling with neighboring atoms on the aromatic C-H stretching modes presented in the 3000-3100 cm-1 region. If the substituent group lacks C-H bonds capable of coupling with the phenyl ring vibrations, the computed polarizability and dipole derivative tensors align well with the A1 and B1 symmetries expected from the C2v point group. However, when the substituent contains C-H groups in the nearest or next-nearest positions to the phenyl ring, significant deviations from C2v symmetry arise, leading to shifts in peak positions and intensity variations in SFG spectra. These findings underscore the limitations of conventional C2v-based SFG analyses in determining the tilt angle of phenyl groups at polymer interfaces and emphasize the necessity of incorporating vibrational coupling effects for accurate SFG spectral interpretation. The approach presented in this work provides a more rigorous framework for accurately predicting and characterizing interfacial molecular orientations and can be extended to other complex systems, where vibrational interactions play a crucial role.

A time averaged semiclassical approach to the computation of nonadiabatic vibronic absorption spectra

2025-06-17

Davide Moscato , Michele Gandolfi , Michele Ceotto | The Journal of Chemical Physics

In this work, we propose a method to compute semiclassical absorption spectra of nonadiabatic systems. We first report the working formula for the absorption cross section for diabatically coupled systems … In this work, we propose a method to compute semiclassical absorption spectra of nonadiabatic systems. We first report the working formula for the absorption cross section for diabatically coupled systems and review the main features of the Meyer–Miller–Stock–Thoss Hamiltonian and its semiclassical propagation. Then, by combining the mapped Hamiltonian and the initial value representation formalism, we introduce a time-averaged semiclassical method for the calculation of the absorption spectrum, which also accounts for nonadiabatic effects in vibronic spectroscopy. After improving an already existing symplectic algorithm for the symplectic phase space propagation, we consider a model system to benchmark our semiclassical approach against exact quantum mechanical calculations. Finally, we test our method on the four mode model of pyrazine—a fundamental benchmark in the field of nonadiabatic vibronic spectroscopy—for understanding the potentiality and limitations of our semiclassical approach.

Correlation between monolayer water structures and dynamics: A two-stage phase transition in terahertz electric fields

2025-06-17

Zi Wang , Yunzhen Zhao , Jiaye Su | International Communications in Heat and Mass Transfer

Sensitivity-Enhanced Pure Shift Spectroscopy Empowered by Deep Learning and PSYCHE

2025-06-17

Xiaoxu Zheng , Wen Zhu , Xiaoqi Shi +6 more | Analytical Chemistry

Proton nuclear magnetic resonance (NMR) is the most used NMR technique. However, the limited range of chemical shifts and the complicated multiplet splitting often lead to severe spectral overlapping, making … Proton nuclear magnetic resonance (NMR) is the most used NMR technique. However, the limited range of chemical shifts and the complicated multiplet splitting often lead to severe spectral overlapping, making spectral analysis complex. Pure shift methods convert multiplets into singlets to greatly improve the spectral resolution but lead to severe sensitivity loss, aggravating the issue of low sensitivity of NMR compared to that of other spectroscopic techniques. Pure shift yielded by the chirp excitation (PSYCHE) method is currently the most popular pure shift method. But relatively small flip angles of chirp pulses are used to achieve a balance between the sensitivity and purity, leading to relatively low spectral sensitivity. In this work, the flip angle of 60° is utilized in the PSYCHE experiment to increase the sensitivity by four times but with strong recoupling artifacts. Then, a deep neural network model is employed to remove recoupling artifacts to obtain a clean spectrum. The model can correctly recognize all peaks, remove recoupling artifacts and chunking sidebands, and retain the desired pure shift peaks. The processed spectra are clean and free of recoupling artifacts. This method is applicable for semiquantitative analysis with high accuracy, allowing the monitoring of concentration changes of different substances in the mixture. This method will promote wider NMR applications, especially on low-concentration samples.

Vibrational dynamics of iron pentacarbonyl [Fe(CO)5] in liquid alkanes revisited

2025-06-17

Armel Jouan , Mindaugas Jonušas , Julien Vincent +6 more | The Journal of Chemical Physics

We explore the solvent-dependence of the vibrational dynamics of Fe(CO)5 (IPC) using a novel 2D-IR setup. A 320 pixel MCT camera allows us to achieve high spectral resolution within a … We explore the solvent-dependence of the vibrational dynamics of Fe(CO)5 (IPC) using a novel 2D-IR setup. A 320 pixel MCT camera allows us to achieve high spectral resolution within a large detection window, which can be matched in excitation by scanning coherence times of up to 250 ps. The dynamics of the IR active modes of IPC in the C≡O stretching range are probed in a series of alkanes of different chain lengths and viscosities. 2D-IR maps at short waiting times reveal the detailed anharmonic structure of the modes at play: we determined the cross-anharmonicity between the A2″ and E′ modes (δ = −0.8 ± 0.1 cm−1), and we are able to differentiate the diagonal anharmonicity of the doubly degenerate mode (ΔE ≃ 18 cm−1) from its non-diagonal anharmonicity (ΔEE ≃ 11 cm−1). Our analysis of the polarization dependence of the 2D-IR signals strongly confirms an exchange mechanism between the IR-active modes due to Berry pseudo-rotation, which shows very little dependence on solvent viscosity, in contrast to the anisotropy loss. The implications of our findings for the exchange mechanism are discussed.

Direct Measurement of the Effect of Cholesterol and 7-Dehydrocholesterol on Membrane Dipole Electric Field in Single and Mixed Sterol Vesicles Using Vibrational Stark Effect Spectroscopy

2025-06-16

Sydney C. Povilaitis , Jason Hector , Morgan E. Mantsch +1 more | The Journal of Physical Chemistry B

Cholesterol is an important contributor to the properties, structure, and function of biological membranes. An immediate biosynthetic precursor to cholesterol, 7-dehydrocholesterol (7DHC), differs only in a single double bond, yet … Cholesterol is an important contributor to the properties, structure, and function of biological membranes. An immediate biosynthetic precursor to cholesterol, 7-dehydrocholesterol (7DHC), differs only in a single double bond, yet defects in the conversion of 7DHC to cholesterol result in metabolic disorders. The membrane dipole field, F⃗d, is the greatest contributor to the total membrane electric field and arises from the alignment of interfacial lipids and water molecules. We have previously shown, using vibrational stark effect (VSE) spectroscopy, that the magnitude of membrane dipole field decreases with increasing cholesterol content and that sterol structure can differentially affect F⃗d. Here, we employ VSE spectroscopy to directly measure F⃗d in small unilamellar vesicles (SUVs) composed of DMPC and 0-40% cholesterol or 7DHC. Our results show that cholesterol and 7DHC influence F⃗d in a similar way, reducing the magnitude of F⃗d with increasing sterol content in a trimodal manner corresponding to phase transitions in DMPC/sterol bilayers. To probe F⃗d in membranes that better model diseased states, VSE measurements were performed on SUVs with 40% total sterol, but mixed compositions of cholesterol and 7DHC. F⃗d was bimodal in these systems, reflecting a 7DHC-like field at 10% cholesterol/30% 7DHC but a cholesterol-like content at 15% cholesterol (25% 7DHC) and above. We propose possible sources of these trimodal and bimodal effects and discuss the implications on our understanding of membrane electrostatics and cholesterol-related metabolic disorders.

Broadband shot-to-shot transient absorption anisotropy

2025-06-16

Maximilian Binzer , František Šanda , Lars Mewes +2 more | The Journal of Chemical Physics

Transient absorption (TA) is the most widespread method to follow ultrafast dynamics in molecules and materials. The related method of TA anisotropy (TAA) reports on the ultrafast reorientation dynamics of … Transient absorption (TA) is the most widespread method to follow ultrafast dynamics in molecules and materials. The related method of TA anisotropy (TAA) reports on the ultrafast reorientation dynamics of transition dipole moments, reporting on phenomena ranging from electronic dephasing to orientational diffusion. While these are fundamental aspects complementary to TA, TAA is generally less widely used. The main reason is that TAA signals are usually not measured directly but are retrieved from two consecutive TA measurements with parallel (R‖) and perpendicular (R⊥) polarization of pump and probe pulses. This means that even minor systematic errors in these measurements lead to drastic changes in the TAA signal. In this work, the authors demonstrate alternating shot-to-shot detection of R‖ and R⊥, minimizing systematic errors due to laser fluctuations. The employed broadband detection lets us discuss effects dependent on detection wavelength in the ultrafast anisotropy decay of 2,3-naphthalocyanine, a system previously scrutinized by David Jonas and co-workers. In particular, we compare timescales of population relaxation and decoherence and support the proposals for isotropic type of relaxation in square symmetric molecules.

Significant Effects of Excitonic Coupling and Charge Transfer on the Circular Dichroism Spectrum of Photosynthetic Light-Harvesting I Complex

2025-06-16

Rio Tsuji , Kazuhiro J. Fujimoto , Nobuo Hiwatashi +2 more | The Journal of Physical Chemistry B

Spectral properties of light-harvesting (LH) complexes are key to understanding excitation-energy transfer in photosynthesis. This study examines the physicochemical factors that shape the circular dichroism (CD) spectrum of LH1 in … Spectral properties of light-harvesting (LH) complexes are key to understanding excitation-energy transfer in photosynthesis. This study examines the physicochemical factors that shape the circular dichroism (CD) spectrum of LH1 in Rhodospirillum rubrum. Calculations using four computational models reveal that intermolecular electronic interactions, particularly excitonic coupling, primarily determine the LH1 CD spectrum shape, while charge transfer effects contribute significantly to the redshift of the peaks. Another finding is that the LH1-specific spectrum shape arises from excitonic coupling extending over 12 bacteriochlorophyll (BChl) a molecules. Further computational analysis additionally identified an anticlockwise rotation of the transition dipole moments of the BChl a assembly as a contributing factor. Our results demonstrate how slight variations in intermolecular orientation influence CD spectrum shape, offering insight into the mechanisms governing the optical properties of light-harvesting antennas. Our computational approach advances the systematic study of CD spectrum shapes associated with chromophore aggregation.