References of "Journal of Chemical Physics"
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See detailQuantum machine learning corrects classical forcefields: Stretching DNA base pairs in explicit solvent
Berryman, Josh UL; Taghavi, Amirhossein UL; Mazur, Florian UL et al

in Journal of Chemical Physics (2022), 157(6),

In order to improve the accuracy of molecular dynamics simulations, classical forcefields are supplemented with a kernel-based machine learning method trained on quantum-mechanical fragment energies. As ... [more ▼]

In order to improve the accuracy of molecular dynamics simulations, classical forcefields are supplemented with a kernel-based machine learning method trained on quantum-mechanical fragment energies. As an example application, a potential-energy surface is generalized for a small DNA duplex, taking into account explicit solvation and long-range electron exchange–correlation effects. A long-standing problem in molecular science is that experimental studies of the structural and thermodynamic behavior of DNA under tension are not well confirmed by simulation; study of the potential energy vs extension taking into account a novel correction shows that leading classical DNA models have excessive stiffness with respect to stretching. This discrepancy is found to be common across multiple forcefields. The quantum correction is in qualitative agreement with the experimental thermodynamics for larger DNA double helices, providing a candidate explanation for the general and long-standing discrepancy between single molecule stretching experiments and classical calculations of DNA stretching. The new dataset of quantum calculations should facilitate multiple types of nucleic acid simulation, and the associated Kernel Modified Molecular Dynamics method (KMMD) is applicable to biomolecular simulations in general. KMMD is made available as part of the AMBER22 simulation software. [less ▲]

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See detailFrom predicting to learning dissipation from pair correlations of active liquids
Rassolov, Gregory; Tociu, Laura; Fodor, Etienne UL et al

in Journal of Chemical Physics (2022)

Active systems, which are driven out of equilibrium by local non-conservative forces, can adopt unique behaviors and configurations. An important challenge in the design of novel materials, which utilize ... [more ▼]

Active systems, which are driven out of equilibrium by local non-conservative forces, can adopt unique behaviors and configurations. An important challenge in the design of novel materials, which utilize such properties, is to precisely connect the static structure of active systems to the dissipation of energy induced by the local driving. Here, we use tools from liquid-state theories and machine learning to take on this challenge. We first analytically demonstrate for an isotropic active matter system that dissipation and pair correlations are closely related when driving forces behave like an active temperature. We then extend a nonequilibrium mean-field framework for predicting these pair correlations, which unlike most existing approaches is applicable even for strongly interacting particles and far from equilibrium, to predicting dissipation in these systems. Based on this theory, we reveal a robust analytic relation between dissipation and structure, which holds even as the system approaches a nonequilibrium phase transition. Finally, we construct a neural network that maps static configurations of particles to their dissipation rate without any prior knowledge of the underlying dynamics. Our results open novel perspectives on the interplay between dissipation and organization out of equilibrium. [less ▲]

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See detailMean-field theory for the structure of strongly interacting active liquids
Tociu, Laura; Rassolov, Gregory; Fodor, Etienne UL et al

in Journal of Chemical Physics (2022)

Active systems, which are driven out of equilibrium by local non-conservative forces, exhibit unique behaviors and structures with potential utility for the design of novel materials. An important and ... [more ▼]

Active systems, which are driven out of equilibrium by local non-conservative forces, exhibit unique behaviors and structures with potential utility for the design of novel materials. An important and difficult challenge along the path toward this goal is to precisely predict how the structure of active systems is modified as their driving forces push them out of equilibrium. Here, we use tools from liquid-state theories to approach this challenge for a classic minimal active matter model. First, we construct a nonequilibrium mean-field framework that can predict the structure of systems of weakly interacting particles. Second, motivated by equilibrium solvation theories, we modify this theory to extend it with surprisingly high accuracy to systems of strongly interacting particles, distinguishing it from most existing similarly tractable approaches. Our results provide insight into spatial organization in strongly interacting out-of-equilibrium systems. [less ▲]

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See detailInformation thermodynamics for deterministic chemical reaction networks
Penocchio, Emanuele UL; Avanzini, Francesco UL; Esposito, Massimiliano UL

in Journal of Chemical Physics (2022), 157(3), 034110

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See detailSample size dependence of tagged molecule dynamics in steady-state networks with bimolecular reactions: Cycle times of a light-driven pump
Asnicar, Daniele; Penocchio, Emanuele UL; Frezzato, Diego

in Journal of Chemical Physics (2022), 156(18), 184116

Here, steady-state reaction networks are inspected from the viewpoint of individual tagged molecules jumping among their chemical states upon the occurrence of reactive events. Such an agent-based ... [more ▼]

Here, steady-state reaction networks are inspected from the viewpoint of individual tagged molecules jumping among their chemical states upon the occurrence of reactive events. Such an agent-based viewpoint is useful for selectively characterizing the behavior of functional molecules, especially in the presence of bimolecular processes. We present the tools for simulating the jump dynamics both in the macroscopic limit and in the small-volume sample where the numbers of reactive molecules are of the order of few units with an inherently stochastic kinetics. The focus is on how an ideal spatial “compartmentalization” may affect the dynamical features of the tagged molecule. Our general approach is applied to a synthetic light-driven supramolecular pump composed of ring-like and axle-like molecules that dynamically assemble and disassemble, originating an average ring-through-axle directed motion under constant irradiation. In such an example, the dynamical feature of interest is the completion time of direct/inverse cycles of tagged rings and axles. We find a surprisingly strong robustness of the average cycle times with respect to the system’s size. This is explained in the presence of rate-determining unimolecular processes, which may, therefore, play a crucial role in stabilizing the behavior of small chemical systems against strong fluctuations in the number of molecules. [less ▲]

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See detailActive matter in infinite dimensions: Fokker–Planck equation and dynamical mean-field theory at low density
Manacorda, Alessandro UL

in Journal of Chemical Physics (2021)

We investigate the behavior of self-propelled particles in infinite space dimensions by comparing two powerful approaches in many-body dynamics: the Fokker-Planck equation and dynamical mean-field theory ... [more ▼]

We investigate the behavior of self-propelled particles in infinite space dimensions by comparing two powerful approaches in many-body dynamics: the Fokker-Planck equation and dynamical mean-field theory. The dynamics of the particles at low densities and infinite persistence time is solved in the steady-state with both methods, thereby proving the consistency of the two approaches in a paradigmatic out-of-equilibrium system. We obtain the analytic expression for the pair distribution function and the effective self-propulsion to first order in the density, confirming the results obtained in a previous paper and extending them to the case of a non-monotonous interaction potential. Furthermore, we obtain the transient behavior of active hard spheres when relaxing from equilibrium to the nonequilibrium steady-state. Our results show how collective dynamics is affected by interactions to first order in the density, and point out future directions for further analytical and numerical solutions of this problem. [less ▲]

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See detailNonequilibrium thermodynamics of light-induced reactions
Penocchio, Emanuele UL; Rao, Riccardo; Esposito, Massimiliano UL

in Journal of Chemical Physics (2021), 155

Current formulations of nonequilibrium thermodynamics of open chemical reaction networks only consider chemostats as free-energy sources sustaining nonequilibrium behaviors. Here, we extend the theory to ... [more ▼]

Current formulations of nonequilibrium thermodynamics of open chemical reaction networks only consider chemostats as free-energy sources sustaining nonequilibrium behaviors. Here, we extend the theory to include incoherent light as a source of free energy. We do so by relying on a local equilibrium assumption to derive the chemical potential of photons relative to the system they interact with. This allows us to identify the thermodynamic potential and the thermodynamic forces driving light-reacting chemical systems out-of-equilibrium. We use this framework to treat two paradigmatic photochemical mechanisms describing light-induced unimolecular reactions—namely, the adiabatic and diabatic mechanisms—and highlight the different thermodynamics they lead to. Furthermore, using a thermodynamic coarse-graining procedure, we express our findings in terms of commonly measured experimental quantities, such as quantum yields. [less ▲]

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See detailSoftware for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package
Evgeny Epifanovsky; Andrew T. B Gilbert; Xintian Feng et al

in Journal of Chemical Physics (2021)

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See detailNonequilibrium thermodynamics of non-ideal chemical reaction networks
Avanzini, Francesco UL; Penocchio, Emanuele UL; Falasco, Gianmaria UL et al

in Journal of Chemical Physics (2021), 154

All current formulations of nonequilibrium thermodynamics of open chemical reaction networks rely on the assumption of non-interacting species. We develop a general theory that accounts for interactions ... [more ▼]

All current formulations of nonequilibrium thermodynamics of open chemical reaction networks rely on the assumption of non-interacting species. We develop a general theory that accounts for interactions between chemical species within a mean-field approach using activity coefficients. Thermodynamic consistency requires that rate equations do not obey standard mass-action kinetics but account for the interactions with concentration dependent kinetic constants. Many features of the ideal formulations are recovered. Crucially, the thermodynamic potential and the forces driving non-ideal chemical systems out of equilibrium are identified. Our theory is general and holds for any mean-field expression of the interactions leading to lower bounded free energies. [less ▲]

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See detailNumerical solution of the dynamical mean field theory of infinite-dimensional equilibrium liquids
Manacorda, Alessandro UL; Schehr, Grégory; Zamponi, Francesco

in Journal of Chemical Physics (2020)

We present a numerical solution of the dynamical mean field theory of infinite-dimensional equilibrium liquids established in [Phys. Rev. Lett. 116, 015902 (2016)]. For soft sphere interactions, we obtain ... [more ▼]

We present a numerical solution of the dynamical mean field theory of infinite-dimensional equilibrium liquids established in [Phys. Rev. Lett. 116, 015902 (2016)]. For soft sphere interactions, we obtain the numerical solution by an iterative algorithm and a straightforward discretization of time. We also discuss the case of hard spheres, for which we first derive analytically the dynamical mean field theory as a non-trivial limit of the soft sphere one. We present numerical results for the memory function and the mean square displacement. Our results reproduce and extend kinetic theory in the dilute or short-time limit, while they also describe dynamical arrest towards the glass phase in the dense strongly-interacting regime. [less ▲]

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See detailFirst-principles modeling of chemistry in mixed solvents: Where to go from here?
Maldonado, Alex; Basdogan, Yasemin; Berryman, Josh UL et al

in Journal of Chemical Physics (2020), 152

Mixed solvents (i.e., binary or higher order mixtures of ionic or nonionic liquids) play crucial roles in chemical syntheses, separations, and electrochemical devices because they can be tuned for ... [more ▼]

Mixed solvents (i.e., binary or higher order mixtures of ionic or nonionic liquids) play crucial roles in chemical syntheses, separations, and electrochemical devices because they can be tuned for specific reactions and applications. Apart from fully explicit solvation treatments that can be difficult to parameterize or computationally expensive, there is currently no well-established first-principles regimen for reliably modeling atomic-scale chemistry in mixed solvent environments. We offer our perspective on how this process could be achieved in the near future as mixed solvent systems become more explored using theoretical and computational chemistry. We first outline what makes mixed solvent systems far more complex compared to single-component solvents. An overview of current and promising techniques for modeling mixed solvent environments is provided. We focus on so-called hybrid solvation treatments such as the conductor-like screening model for real solvents and the reference interaction site model, which are far less computationally demanding than explicit simulations. We also propose that cluster-continuum approaches rooted in physically rigorous quasi-chemical theory provide a robust, yet practical, route for studying chemical processes in mixed solvents. [less ▲]

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See detailDFTB+, a software package for efficient approximate density functional theory based atomistic simulations
Hourahine, Ben; Aradi, Bálint; Blum, Volker et al

in Journal of Chemical Physics (2020), 152(12), 124101

DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various methods ... [more ▼]

DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various methods approximating density functional theory (DFT), such as the density functional based tight binding (DFTB) and the extended tight binding method, it enables simulations of large systems and long timescales with reasonable accuracy while being considerably faster for typical simulations than the respective ab initio methods. Based on the DFTB framework, it additionally offers approximated versions of various DFT extensions including hybrid functionals, time dependent formalism for treating excited systems, electron transport using non-equilibrium Green’s functions, and many more. DFTB+ can be used as a user-friendly standalone application in addition to being embedded into other software packages as a library or acting as a calculation-server accessed by socket communication. We give an overview of the recently developed capabilities of the DFTB+ code, demonstrating with a few use case examples, discuss the strengths and weaknesses of the various features, and also discuss on-going developments and possible future perspectives. [less ▲]

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See detailImproved description of ligand polarization enhances transferability of ion–ligand interactions
Wineman-Fisher, Vered; Al-Hamdani, Yasmine; Nagy, R Péter et al

in Journal of Chemical Physics (2020)

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See detailMolecular force fields with gradient-domain machine learning (GDML): Comparison and synergies with classical force fields
Sauceda, Huziel E; Gastegger, Michael; Chmiela, Stefan et al

in Journal of Chemical Physics (2020)

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See detailStrong current response to slow modulation: A metabolic case-study
Forastiere, Danilo UL; Falasco, Gianmaria UL; Esposito, Massimiliano UL

in Journal of Chemical Physics (2020), 152(13), 134101

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See detailOn the dynamics of reaction coordinates in classical, time-dependent, many-body processes
Meyer, Hugues UL; Voigtmann, Thomas; Schilling, Tanja

in Journal of Chemical Physics (2019), 150(17), 174118

Complex microscopic many-body processes are often interpreted in terms of so-called “reaction coordinates,” i.e., in terms of the evolution of a small set of coarse-grained observables. A rigorous method ... [more ▼]

Complex microscopic many-body processes are often interpreted in terms of so-called “reaction coordinates,” i.e., in terms of the evolution of a small set of coarse-grained observables. A rigorous method to produce the equation of motion of such observables is to use projection operator techniques, which split the dynamics of the observables into a main contribution and a marginal one. The basis of any derivation in this framework is the classical Heisenberg equation for an observable. If the Hamiltonian of the underlying microscopic dynamics and the observable under study do not explicitly depend on time, this equation is obtained by a straightforward derivation. However, the problem is more complicated if one considers Hamiltonians which depend on time explicitly as, e.g., in systems under external driving, or if the observable of interest has an explicit dependence on time. We use an analogy to fluid dynamics to derive the classical Heisenberg picture and then apply a projection operator formalism to derive the nonstationary generalized Langevin equation for a coarse-grained variable. We show, in particular, that the results presented for time-independent Hamiltonians and observables in the study by Meyer, Voigtmann, and Schilling, J. Chem. Phys. 147, 214110 (2017) can be generalized to the time-dependent case. [less ▲]

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See detailMolecular force fields with gradient-domain machine learning: Construction and application to dynamics of small molecules with coupled cluster forces
Sauceda, Huziel; Chmiela, Stefan; Poltavsky, Igor et al

in Journal of Chemical Physics (2019), 150

We present the construction of molecular force fields for small molecules (less than 25 atoms) using the recently developed symmetrized gradient-domain machine learning (sGDML) approach [Chmiela et al ... [more ▼]

We present the construction of molecular force fields for small molecules (less than 25 atoms) using the recently developed symmetrized gradient-domain machine learning (sGDML) approach [Chmiela et al., Nat. Commun. 9, 3887 (2018) and Chmiela et al., Sci. Adv. 3, e1603015 (2017)]. This approach is able to accurately reconstruct complex high-dimensional potential-energy surfaces from just a few 100s of molecular conformations extracted from ab initio molecular dynamics trajectories. The data efficiency of the sGDML approach implies that atomic forces for these conformations can be computed with high-level wavefunction-based approaches, such as the “gold standard” coupled-cluster theory with single, double and perturbative triple excitations [CCSD(T)]. We demonstrate that the flexible nature of the sGDML model recovers local and non-local electronic interactions (e.g., H-bonding, proton transfer, lone pairs, changes in hybridization states, steric repulsion, and n → π* interactions) without imposing any restriction on the nature of interatomic potentials. The analysis of sGDML molecular dynamics trajectories yields new qualitative insights into dynamics and spectroscopy of small molecules close to spectroscopic accuracy. [less ▲]

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See detailUnderstanding non-covalent interactions in larger molecular complexes from first principles
Al-Hamdani, Yasmine; Tkatchenko, Alexandre UL

in Journal of Chemical Physics (2019), 150

Non-covalent interactions pervade all matter and play a fundamental role in layered materials, biological systems, and large molecular complexes. Despite this, our accumulated understanding of non ... [more ▼]

Non-covalent interactions pervade all matter and play a fundamental role in layered materials, biological systems, and large molecular complexes. Despite this, our accumulated understanding of non-covalent interactions to date has been mainly developed in the tens-of-atoms molecular regime. This falls considerably short of the scales at which we would like to understand energy trends, structural properties, and temperature dependencies in materials where non-covalent interactions have an appreciable role. However, as more reference information is obtained beyond moderately sized molecular systems, our understanding is improving and we stand to gain pertinent insights by tackling more complex systems, such as supramolecular complexes, molecular crystals, and other soft materials. In addition, accurate reference information is needed to provide the drive for extending the predictive power of more efficient workhorse methods, such as density functional approximations that also approximate van der Waals dispersion interactions. In this perspective, we discuss the first-principles approaches that have been used to obtain reference interaction energies for beyond modestly sized molecular complexes. The methods include quantum Monte Carlo, symmetry-adapted perturbation theory, non-canonical coupled cluster theory, and approaches based on the random-phase approximation. By considering the approximations that underpin each method, the most accurate theoretical references for supramolecular complexes and molecular crystals to date are ascertained. With these, we also assess a handful of widely used exchange-correlation functionals in density functional theory. The discussion culminates in a framework for putting into perspective the accuracy of high-level wavefunction-based methods and identifying future challenges. [less ▲]

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