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We present the results of experimental and computational studies of the physicochemical properties and structure of a newly synthesized tripropylammonium 2-sulfobenzoate (TPrA/SBA) protic ionic liquid (PIL). Quantum-chemical methods were used to evaluate the hydrogen-donor properties of the SBA molecule and to model the proton transfer between the acid and base molecules. The results revealed that the ionic liquid was formed through an acid-base interaction between the proton of the –SO3H group in the acid and the nitrogen atom in the amine. Additionally, we conducted a molecular dynamics simulation to determine the hydrogen bond topology in the PIL bulk as well as the average number of hydrogen bonds between the ions. To provide further insights, we compared the structural parameters and properties of the TPrA/SBA ionic liquid with the data on the two other tripropylammonium-based PILs with hydrogen sulfate (SA) and triflate (TfO) anions. [ABSTRACT FROM AUTHOR]

When studying physical properties of highly toxic chemicals, such as chemical warfare agents (CWAs), molecular dynamics (MD) simulations can serve as an alternative to experimental measurements. We performed MD simulations to calculate viscosity of four organophosphorus liquids, CWAs, sarin, and soman, as well as their simulants, DMMP and DIMP, in the temperature range from 0 to 60∘C. The molecules were represented with Transferable Potentials for Phase Equilibria United Atom (TraPPE‐UA) force field; the calculations were performed using the Green–Kubo method. The results for sarin and DMMP are in good agreement with previously published experimental data, which justifies the use of the TraPPE‐UA force field for other organophosphorus compounds. Therefore we predicted viscosity of DIMP and soman, for which the experimental data were unavailable. Our results suggest that for applications where liquid viscosity is important, DMMP is a suitable simulant for sarin, and DIMP is a suitable simulant for soman. [ABSTRACT FROM AUTHOR]

Diffusion quantum Monte Carlo (DMC) provides a powerful approach for obtaining the ground state energy and wave function of molecules, ions, and molecular clusters. The approach is uniquely well suited for studies of fluxional molecules, which undergo large amplitude vibrational motions even in their ground state. In contrast to the electronic structure problem, where the wave function must be antisymmetric with respect to exchange of any pair of electrons, the wave function for the ground vibrational state is nodeless. This greatly simplifies the application of DMC for vibrational problems. Because there is not a single potential function that can be used to describe the intramolecular and intermolecular interactions in all molecular systems, most methods that are used to describe nuclear quantum effects rely on a carefully chosen zero‐order description of the molecular vibrations. In contrast, DMC calculations can be performed in Cartesian coordinates, making the DMC algorithm easily transferable between different chemical systems. In this contribution, the theory that underlies DMC will be discussed along with important considerations for performing DMC calculations. Extensions for evaluating vibrationally excited states and molecular properties are also discussed. Insights that can be obtained from DMC calculations are illustrated in the context of the protonated water clusters. This article is categorized under:Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo MethodsTheoretical and Physical Chemistry > Spectroscopy [ABSTRACT FROM AUTHOR]

Correlations of the shear viscosity of quartz nanofluids with particle concentration, particle size, and temperature were investigated with molecular dynamics simulations and density functional theory (DFT) calculations. A new understanding to the experimentally concluded correlations was addressed in terms of microscopic particle–water interfacial interaction in three aspects. First, the viscosity of quartz nanofluids at different particle concentrations, particle sizes, and temperatures were simulated using the equilibrium molecular dynamics simulations method to reproduce the experimental observations. At the same particle size, the nanofluid viscosity decreases significantly with temperature and increases with nanoparticle volume concentration, and at the same volume concentration, the nanofluid viscosity increases with the decrease of particle size. Second, DFT calculations confirm a stronger particle–water interaction than that among water molecules. The important role of particle–water interaction in the viscosity determination of nanofluids was revealed. Finally, a correlation was proposed to fit the simulated results and compared with earlier two-parameter correlations. One parameter in the correlation is indeed a constant, while the other is a function of SiO2–water interaction energy. Our study proposes a physical basis for the experimentally concluded correlations on the viscosity of nanofluids. [ABSTRACT FROM AUTHOR]

In the past two decades, machine learning potentials (MLPs) have reached a level of maturity that now enables applications to large-scale atomistic simulations of a wide range of systems in chemistry, physics, and materials science. Different machine learning algorithms have been used with great success in the construction of these MLPs. In this review, we discuss an important group of MLPs relying on artificial neural networks to establish a mapping from the atomic structure to the potential energy. In spite of this common feature, there are important conceptual differences among MLPs, which concern the dimensionality of the systems, the inclusion of long-range electrostatic interactions, global phenomena like nonlocal charge transfer, and the type of descriptor used to represent the atomic structure, which can be either predefined or learnable. A concise overview is given along with a discussion of the open challenges in the field. [ABSTRACT FROM AUTHOR]

The parallel-tempering molecular dynamics (PTMD) method is a key computational tool to explore complex potential energy surfaces. As a result of its computational cost, it has mainly been coupled to force-field approaches despite the interest it could also represent for ab initio studies. In this article, we present the native implementation of the PTMD algorithm in the deMon2k code which is the first implementation of this approach in a DFT code based on localized basis set. To take advantage of the intrinsic parallel nature of the PTMD algorithm without modifying the Message Passing Interface (MPI) scheme dedicated to the calculation of the electronic structure, a two-layer MPI architecture was implemented. Both synchronous and asynchronous communications between processes for configuration exchanges were implemented in order to test the parallel efficiency of the code. This article presents the implementation details and their application to describe phase changes in the water hexamer (H 2 O) 6 at the DFT level. [ABSTRACT FROM AUTHOR]

This review is dedicated to the application of the self-consistent-charge density-functional-based tight-binding (SCC-DFTB) approach to describe the structures, energetics, thermodynamic and spectral properties of water clusters, in the context of both fundamental and applied studies. We first present modifications implemented in the parametrisation of the potential that is mandatory to describe molecular aggregates as well as methods for global optimisation and determination of macroscopic properties. Then a number of applications of atmospherical and astrophysical interest, involving collaborations between theoreticians and experimentalists, are discussed to exemplify past and present contributions of SCC-DFTB to those two domains. Most applications presented in this review take advantage of the computational efficiency of SCC-DFTB to conduct extensive molecular dynamics simulations to obtain spectral and thermodynamic properties of water clusters. We also show some new results related to ongoing studies on both water clusters with impurities and liquid water. [ABSTRACT FROM AUTHOR]

Nanometer‐size particles such as ultrafine aerosol particles, ice nanoparticles, water nanodroplets, etc, play an important, however, not yet fully understood role in the atmospheric chemistry and physics. These species are often composed of water with admixture of other atmospherically relevant molecules. To mimic and investigate such particles in laboratory experiments, mixed water clusters with atmospherically relevant molecules can be generated in molecular beams and studied by various mass spectrometric methods. The present review demonstrates that such experiments can provide unprecedented details of reaction mechanisms, and detailed insight into the photon‐, electron‐, and ion‐induced processes relevant to the atmospheric chemistry. After a brief outline of the molecular beam preparation, cluster properties, and ionization methods, we focus on the mixed clusters with various atmospheric molecules, such as hydrated sulfuric acid and nitric acid clusters, NxOy and halogen‐containing molecules with water. A special attention is paid to their reactivity and solvent effects of water molecules on the observed processes. [ABSTRACT FROM AUTHOR]

The effects of the molar ratio, temperature, and solvent on the formation of the cocrystal explosive DNP/CL-20 were investigated using molecular dynamics (MD) simulation. The cocrystal structure was predicted through Monte Carlo (MC) simulation and using first-principles methods. The results showed that the DNP/CL-20 cocrystal might be more stable in the molar ratio 1:1 near to 318 K, and the most probable cocrystal crystallizes in the triclinic crystal system with the space group P $$ \overline{1} $$ . Cocrystallization was more likely to occur in methanol and ethanol at 308 K as a result of solvent effects. The optimized structure and the reduced density gradient (RDG) of the DNP/CL-20 complex confirmed that the main driving forces for cocrystallization were a series of hydrogen bonds and van der Waals forces. Analyses of the trigger bonds, the charges on the nitro groups, the electrostatic surface potential (ESP), and the free space per molecule in the cocrystal lattice were carried out to further explore their influences on the sensitivity of CL-20. The results indicated that the DNP/CL-20 complex tended to be more stable and insensitive than pure CL-20. Moreover, an investigation of the detonation performance of the DNP/CL-20 cocrystal indicated that it possesses high power. [ABSTRACT FROM AUTHOR]

Hydrogen bond statistics, energy distributions of hydrogen bonds and hydrogen bond lifetimes for aqueous monoethylene glycol (MEG), diethylene glycol (DEG), and triethylene glycol (TEG) were investigated at temperatures ranging from 275 to 370 K at 101.325 kPa using molecular dynamics simulations. Each individual type of hydrogen bond were studied separately to better understand how each type of hydrogen bond affected the collective behavior often measured in experiments. We also studied the effects of glycols on water-water hydrogen bond structures and lifetimes. Decay constants for hydroxyl type hydrogen bonds, as well as for water based hydrogen bonds were in the same order, thus indicating that all these hydrogen bonds play an essential role in the process of dielectric relaxation. Correlations between water hydrogen bond distances and angles were not affected markedly by adding glycols. However, hydrogen bond lifetimes increased by 9, 29, and 62 times by adding MEG, DEG, and TEG, respectively. © 2016 American Institute of Chemical Engineers AIChE J, 63: 1674-1689, 2017 [ABSTRACT FROM AUTHOR]

This review focuses on papers published since 2000 on the topic of the properties of solutes in water. More specifically, it evaluates the state of the art of our understanding of the complex relationship between the shape of a hydrophobe and the hydrophobic effect. To highlight this, we present a selection of references covering both empirical and molecular dynamics studies of small (molecular-scale) solutes. These include empirical studies of small molecules, synthetic hosts, crystalline monolayers, and proteins, as well as in silico investigations of entities such as idealized hard and soft spheres, small solutes, hydrophobic plates, artificial concavity, molecular hosts, carbon nanotubes and spheres, and proteins. [ABSTRACT FROM AUTHOR]

A major portion (∼98%) of the quantum-classical molecular dynamics approach, namely, Time-Dependent Discrete Variable Representation (TDDVR) method, is recently parallelized using shared-memory parallelization scheme with the aim of performing dynamics on relatively large molecular systems. Therefore, we have chosen the furan as a model system for dynamical simulation. Four lowest singlet excited electronic states 1A2(3s), 1B2(V), 1A1(V*), and 1B1(3p) of furan are vibronically coupled through several conical intersections in the vicinity of Frank-Condon region. The major focus of the present paper is to explore the efficiency of our newly implemented parallelized TDDVR algorithm to perform dynamics on large dimensional quantum systems in vibronically coupled electronic manifold. The present version of parallelized TDDVR algorithm show closely linear speed up with increasing number of computing processors. As a significant speed up is achieved by cycling in the correct way over arrays, all dynamical simulations are performed within a reasonable wall clock time. The photoelectron spectra calculated by the TDDVR method show peak by peak correspondence with the experimental spectra. The TDDVR calculated quantum-classical dynamical outcomes, viz., population and photoelectron spectra, etc. show good agreement with the findings of the well-established quantum dynamical method, i.e. Multi Configuration Time-Dependent Hartree (MCTDH) approach. • A major portion (98%) of the quantum-classical molecular dynamics approach, namely, Time-Dependent Discrete Variable Representation (TDDVR) method, is parallelized using shared memory parallelization scheme with the aim of performing dynamics on relatively large molecular systems. • The latest parallel TDDVR shows almost linear scalability with corresponding serial code. • The photoelectron spectra simulated by the TDDVR method shows good agreement with the experimental UV photoelectron spectra of furan. [ABSTRACT FROM AUTHOR]

ABSTRACT The propensity of backbone Cα atoms to engage in carbon-oxygen (CH···O) hydrogen bonding is well-appreciated in protein structure, but side chain CH···O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH···O hydrogen bonding is examined through a survey of neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, methyl groups were observed to form stabilizing CH···O hydrogen bonds within protein structure that are maintained through protein dynamics and participate in correlated motion. Collectively, these findings illustrate that side chain methyl CH···O hydrogen bonding contributes to the energetics of protein structure and folding. Proteins 2015; 83:403-410. © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Quasi-classical trajectory calculations were performed to investigate the stereodynamics of the reaction H(S) + ClO(Π) → HO(Π) + Cl(P) using the ground-state potential energy surface 1A′. The alignment and orientation of the product molecules as well as the four polarization-dependent differential cross-sections (PDDCSs) for this reaction across a wide range of collision energies (0.05-1.0 eV) and for the rovibrational state ClO( v = 0 and j = 0) were obtained and are reported here. It was found that the OH product rotational polarization is not very sensitive to the collision energy selected. We discuss this phenomenon in detail. The calculated results indicate that, for this system, the two deep wells in the potential energy surface are very likely to be powerful influences on the degree of product rotational polarization. In addition, the microscopic reaction mechanism that dictates the product angular momentum orientation was investigated. The forward peak in the PDDCS at θ = 0° in our study showed a strong dependence on the initial collision energy. [ABSTRACT FROM AUTHOR]

The semiclassical (SC) theory based on an initial value representation (IVR) methodology provides a practical way to describe quantum effects in complex molecular systems. The efficiency of SC-IVR calculations for time correlation functions depends heavily on how to perform the Monte Carlo sampling of initial conditions. Here, we compare a variety of possibilities of sampling initial conditions in the SC calculations by choosing the sampling function to be either time-dependent or time-independent (TI). The implementation of these importance sampling protocols to two benchmark system-bath models demonstrates its advantages over the standard sampling method. In particular, the recently developed TI importance sampling which incorporates path correlation in the bath degrees of freedom shows a great potential in describing many-body quantum dynamics efficiently and accurately. [ABSTRACT FROM AUTHOR]

Quasiclassical trajectory calculations have been performed for the OH + CO reaction at zero total angular momentum and collision energies up to 0.4 eV. Calculations have been carried out on the same potential energy surface which was used for full-dimensional state-to-state quantum dynamical calculation. The resulting quasiclassical total reaction probability as well as the product rotational and vibrational distributions have been analyzed and compared with the outcomes of a pseudo-quantization treatment of the product vibrational energy. Energy-conserving classical trajectories reproduce fairly well all the quantum features but the oscillatory patterns, whereas this does not apply to the energy non-conserving ones. Total reaction probabilities obtained from quasiclassical calculations at several fixed total angular momentum are also compared with centrifugal sudden quantum results. These results have also allowed to investigate the effect of the total angular momentum on the translational energy and angular distributions of the products. [ABSTRACT FROM AUTHOR]

Quasi-classical trajectory (QCT) calculations are performed for the reaction F + OH → HF + O based on the adiabatic potential-energy surface (PES) of the 13A″ triplet state. The reaction probability as a function of incident angle has been presented. The differential cross sections (DCSs), the distribution of angle between k and j′, P(θr) and the distribution of dihedral angle denoting k - k′ - j′ correlation, P(ϕr) have also been calculated at the different incident angles in the center-of-mass (CM) frame, respectively. The effects of reactant alignment on stereodynamics of the reaction are firstly revealed, which provides the theoretical foundation for the related experiment and enriches the theories of the stereodynamics. [ABSTRACT FROM AUTHOR]

grid empowered molecular simulator (GEMS) embodying in a single workflow the ab initio treatment of elementary chemical processes has been extended to four atom reactions. GEMS has been used to carry out a massive quasiclassical investigation for the $$\hbox{OH} +\hbox{CO} \rightarrow\hbox{H} +\hbox{CO}_2$$ reaction on the most recently proposed potential energy surface. The type of potential energy surface used and the possibility of running the simulations on the grid have allowed us to keep the error of the order of a few percent at all values of the collision energy and to estimate accurately the dependence of the reaction cross section on the collision energy. The accuracy of the calculations has allowed to unequivocally single out the fact that the calculated center-of-mass angular distribution is clearly isotropic and radically differs from the asymmetric forward-backward structure obtained from the experiment. However, when the laboratory frame analogues are compared, the difference almost vanishes. [ABSTRACT FROM AUTHOR]

A current emphasis in empirical force fields is on the development of potential functions that explicitly treat electronic polarizability. In the present article, the commonly used methodologies for modeling electronic polarization are presented along with an overview of selected application studies. Models presented include induced point-dipoles, classical Drude oscillators, and fluctuating charge methods. The theoretical background of each method is followed by an introduction to extended Lagrangian integrators required for computationally tractable molecular dynamics simulations using polarizable force fields. The remainder of the review focuses on application studies using these methods. Emphasis is placed on water models, for which numerous examples exist, with a more thorough discussion presented on the recently published models associated with the Drude-based CHARMM and the AMOEBA force fields. The utility of polarizable models for the study of ion solvation is then presented followed by an overview of studies of small molecules (e.g., CCl4, alkanes, etc.) and macromolecule (proteins, nucleic acids and lipid bilayers) application studies. The review is written with the goal of providing a general overview of the current status of the field and to facilitate future application and developments. [ABSTRACT FROM AUTHOR]

The hyperspherical method is a widely used and successful approach for the quantum treatment of elementary chemical processes. It has been mostly applied to three-atomic systems, and current progress is here outlined concerning the basic theoretical framework for the extension to four-body bound state and reactive scattering problems. Although most applications only exploit the advantages of the hyperspherical coordinate systems for the formulation of the few-body problem, the full power of the technique implies representations explicitly involving quantum hyperangular momentum operators as dynamical quantities and hyperspherical harmonics as basis functions. In terms of discrete analogues of these harmonics one has a universal representation for the kinetic energy and a diagonal representation for the potential (hyperquantization algorithm). Very recently, advances have been made on the use of the approach in classical dynamics, provided that a hyperspherical formulation is given based on “classical” definitions of the hyperangular momenta and related quantities. The aim of the present paper is to offer a retrospective and prospective view of the hyperspherical methods both in quantum and classical dynamics. Specifically, regarding the general quantum hyperspherical approaches for three- and four-body systems, we first focus on the basis set issue, and then we present developments on the classical formulation that has led to applications involving the implementations of hyperspherical techniques for classical molecular dynamics simulations of simple nanoaggregates. [ABSTRACT FROM AUTHOR]

Focuses on a study which discussed progress in crossed-beam studies of neutral reactions. Experimental methodologies; Information on the bulb studies; Conclusion.

Focuses on a study which examined the state-to-state chemical reaction dynamics in polyatomic systems. Aim of the state-to-state chemical reaction dynamics; Domain in which the dynamics was developed; Conclusion.

Provides information on a study which examined the application of coincidence techniques to the study of the reaction dynamics of isolated molecules. Information on the molecular-frame photoelectron angular distributions; Details on the three-body dissociation dynamics; Coincidence studies of dissociative photodetachment.

Focuses on a study which examined molecular dynamics through a review of stimulated emission pumping. Development process of the simulated emission pumping; Information on the unimolecular dynamics; Details on the scattering dynamics.