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This work follows a companion article, which will be referred to as Paper I [Campeggio et al., J. Chem. Phys. 158, 244104 (2023)] in which a quantum-stochastic Liouville equation for the description of the quantum–classical dynamics of a molecule in a dissipative bath has been formulated in curvilinear internal coordinates. In such an approach, the coordinates of the system are separated into three subsets: the quantum coordinates, the classical relevant nuclear degrees of freedom, and the classical irrelevant (bath) coordinates. The equation has been derived in natural internal coordinates, which are bond lengths, bond angles, and dihedral angles. The resulting equation needs to be parameterized. In particular, one needs to compute the potential energy surfaces, the friction tensor, and the rate constants for the nonradiative jumps among the quantum states. While standard methods exist for the calculation of energy and dissipative properties, an efficient evaluation of the transition rates needs to be developed. In this paper, an approximated treatment is introduced, which leads to a simple explicit formula with a single adjustable parameter. Such an approximated expression is compared with the exact calculation of transition rates obtained via molecular dynamics simulations. To make such a comparison possible, a simple sandbox system has been used, with two quantum states and a single internal coordinate (together with its conjugate momentum). Results show that the adjustable parameter, which is an effective decoherence time, can be parameterized from the effective relaxation times of the autocorrelation functions of the conjugated momenta of the relevant nuclear coordinates. [ABSTRACT FROM AUTHOR]

Hybrid methods that combine molecular dynamics methods capable of analyzing dynamics with Monte Carlo (MC) methods that can efficiently treat thermodynamically stable states are valuable for understanding complex chemical processes in which an equilibrium state is reached through many elementary processes. The hybrid MC (HMC) method is one such promising method; however, it often fails to sample configurations properly from the canonical multimodal distribution due to the rugged potential energy surfaces. In this paper, we extend the HMC method to overcome this difficulty. The new method, which is termed potential scaling HMC (PS-HMC), makes use of an artificially modulated trajectory to propose a new configuration. The trajectory is generated from Hamilton's equations, but the potential energy surface is scaled to be gradually flattened and then recovered to the original surface, which facilitates barrier-crossing processes. We apply the PS-HMC method to three kinds of molecular processes: the thermal motion of argon particles, butane isomerization, and an atom transfer chemical reaction. These applications demonstrate that the PS-HMC method is capable of correctly constructing the canonical ensemble with a multimodal distribution. The sampling efficiency and accepted trajectories are examined to clarify the features of the PS-HMC method. Despite the potential scaling, many reactive atom transfer trajectories (elementary processes) pass through the vicinity of the minimum energy path. Furthermore, we demonstrate that the method can properly imitate the relaxation process owing to the inherent configurational continuity. By comparing the PS-HMC method with other relevant methods, we can conclude that the new method is a unique approach for studying both the dynamic and thermodynamic aspects of chemical processes. [ABSTRACT FROM AUTHOR]

The mechanism of vibrational relaxation and dissociation in the O2–O system at elevated temperatures is investigated by means of molecular dynamics. The most recent O3 potential energy surfaces (PESs), obtained from the first principles quantum mechanical calculations [Varga et al., J. Chem. Phys. 147, 154312 (2017)], are used to derive a complete set of state-specific rate coefficients of vibrational energy transfer and dissociation. Unlike most of the previous efforts that utilize only the lowest and supposedly most reactive 11A′ O3 PES [A. Varandas and A. Pais, Mol. Phys. 65, 843 (1988)], this paper demonstrates the necessity to account for a complete ensemble of all excited O3 PESs that correlate with O2(X) and O(3P) when high-temperature kinetics is of interest. At the same time, it is found that the Varandas 11A′ O3 PES adequately describes vibrational energy transfer and dissociating dynamics when compared to the most recent 11A′ O3 PES by Varga et al. [J. Chem Phys. 147, 154312 (2017)]. The differences between this new dataset and previous rate coefficients are quantified by the master equation model. [ABSTRACT FROM AUTHOR]

In the companion paper [T. S. Ingebrigtsen, S. Toxvaerd, O. J. Heilmann, T. B. Schro\der, and J. C. Dyre, 'NVU dynamics. I. Geodesic motion on the constant-potential-energy hypersurface,' J. Chem. Phys. (in press)] an algorithm was developed for tracing out a geodesic curve on the constant-potential-energy hypersurface. Here, simulations of NVU dynamics are compared to results for four other dynamics, both deterministic and stochastic. First, NVU dynamics is compared to the standard energy-conserving Newtonian NVE dynamics by simulations of the Kob-Andersen binary Lennard-Jones liquid, its WCA version (i.e., with cut-off's at the pair potential minima), and the Lennard-Jones Gaussian liquid. We find identical results for all quantities probed: radial distribution functions, incoherent intermediate scattering functions, and mean-square displacement as function of time. Arguments are presented for the equivalence of NVU and NVE dynamics in the thermodynamic limit; in particular, to leading order in 1/N these two dynamics give identical time-autocorrelation functions. In the final part of the paper, NVU dynamics is compared to Monte Carlo dynamics, to a diffusive dynamics of small-step random walks on the constant-potential-energy hypersurface, and to Nosé-Hoover NVT dynamics. If time is scaled for the two stochastic dynamics to make single-particle diffusion constants identical to that of NVE dynamics, the simulations show that all five dynamics are equivalent at low temperatures except at short times. [ABSTRACT FROM AUTHOR]

In a previous paper [J. L. McAfee and B. Poirier, J. Chem. Phys. 130, 064701 (2009)], using spin-polarized density functional theory (DFT), the authors reported a binding energy of 0.755 eV, for a single hydrogen atom adsorbed on a pristine (unrelaxed) (5,5) single-walled carbon nanotube (SWNT) substrate. A full three-dimensional (3D) potential energy surface (PES) for the SWNT-H system was also developed, and used in a quantum dynamics calculation to compute all rovibrational bound states, and associated equatorial and longitudinal adsorbate migration rates. A highly pronounced preference for the latter migration pathway at ambient temperatures was observed. In this work, we extend the aforementioned study to include multiple H-atom adsorbates. Extensive DFT calculations are performed, in order to ascertain the most relevant dynamical pathways. For two adsorbates, the SWNT-H-H system is found to exhibit highly site-specific binding, as well as long-range correlation and pronounced binding energy enhancement. The latter effect is even more pronounced in the full-hydrogenation limit, increasing the per-adsorbate binding energy to 2.6 eV. To study migration dynamics, a single-hole model is developed, for which the binding energy drops to 2.11 eV. A global 3D PES is developed for the hole migration model, using 40 radial × 18 cylindrical ab initio geometries, fit to a Fourier basis with radially dependent expansion coefficients (rms error 4.9 meV). As compared with the single-adsorbate case, the hole migration PES does not exhibit separate chemisorption and physisorption wells. The barrier to longitudinal migration is also found to be much lower. Quantum dynamics calculations for all rovibrational states are then performed (using a mixed spectral basis/phase-space optimized discrete variable representation), and used to compute longitudinal migration rates. Ramifications for the use of SWNTs as potential hydrogen storage materials are discussed. [ABSTRACT FROM AUTHOR]

We propose a modification to the nonadiabatic surface hopping calculation method formulated in a paper by Yu et al. [Phys. Chem. Chem. Phys. 16, 25883 (2014)], which is a multidimensional extension of the Zhu-Nakamura theory with a practical diabatic gradient estimation algorithm. In our modification, their diabatic gradient estimation algorithm, which is based on a simple interpolation of the adiabatic potential energy surfaces, is replaced by an algorithm using the numerical derivatives of the adiabatic gradients. We then apply the algorithm to several models of nonadiabatic dynamics, both analytic and ab initio models, to numerically demonstrate that our method indeed widens the applicability and robustness of their method. We also discuss the validity and limitations of our new nonadiabatic surface hopping method while considering in mind potential applications to excited-state dynamics of biomolecules or unconventional nonadiabatic dynamics such as radiation decay processes in ultraintense X-ray fields. [ABSTRACT FROM AUTHOR]

We compute four-dimensional diabatic potential energy surfaces and transition dipole moment surfaces of O2-O2, relevant for the theoretical description of collision-induced absorption in the forbidden X3∑-g → a1Δg and X3∑-g →b1∑+g bands at 7883 cm-1 and 13 122 cm-1, respectively. We compute potentials at the multi-reference configuration interaction (MRCI) level and dipole surfaces at the MRCI and complete active space self-consistent field (CASSCF) levels of theory. Potentials and dipole surfaces are transformed to a diabatic basis using a recent multiple-property-based diabatization algorithm. We discuss the angular expansion of these surfaces, derive the symmetry constraints on the expansion coefficients, and present working equations for determining the expansion coefficients by numerical integration over the angles. We also present an interpolation scheme with exponential extrapolation to both short and large separations, which is used for representing the O2-O2 distance dependence of the angular expansion coefficients. For the triplet ground state of the complex, the potential energy surface is in reasonable agreement with previous calculations, whereas global excited state potentials are reported here for the first time. The transition dipole moment surfaces are strongly dependent on the level of theory at which they are calculated, as is also shown here by benchmark calculations at high symmetry geometries. Therefore, ab initio calculations of the collision-induced absorption spectra cannot become quantitatively predictive unless more accurate transition dipole surfaces can be computed. This is left as an open question for method development in electronic structure theory. The calculated potential energy and transition dipole moment surfaces are employed in quantum dynamical calculations of collision-induced absorption spectra reported in Paper II [T. Karman et al., J. Chem. Phys. 147, 084307 (2017)]. [ABSTRACT FROM AUTHOR]

The multiscale coarse-graining (MS-CG) method is a method for constructing a coarse-grained (CG) model of a system using data obtained from molecular dynamics simulations of the corresponding atomically detailed model. The formal statistical mechanical derivation of the method shows that the potential energy function extracted from an MS-CG calculation is a variational approximation for the true potential of mean force of the CG sites, one that becomes exact in the limit that a complete basis set is used in the variational calculation if enough data are obtained from the atomistic simulations. Most applications of the MS-CG method have employed a representation for the nonbonded part of the CG potential that is a sum of all possible pair interactions. This approach, despite being quite successful for some CG models, is inadequate for some others. Here we propose a systematic method for including three body terms as well as two body terms in the nonbonded part of the CG potential energy. The current method is more general than a previous version presented in a recent paper of this series [L. Larini, L. Lu, and G. A. Voth, J. Chem. Phys. 132, 164107 (2010)], in the sense that it does not make any restrictive choices for the functional form of the three body potential. We use hierarchical multiresolution functions that are similar to wavelets to develop very flexible basis function expansions with both two and three body basis functions. The variational problem is solved by a numerical technique that is capable of automatically selecting an appropriate subset of basis functions from a large initial set. We apply the method to two very different coarse-grained models: a solvent free model of a two component solution made of identical Lennard-Jones particles and a one site model of SPC/E water where a site is placed at the center of mass of each water molecule. These calculations show that the inclusion of three body terms in the nonbonded CG potential can lead to significant improvement in the accuracy of CG potentials and hence of CG simulations. [ABSTRACT FROM AUTHOR]

Dynamics is essential to the biological functions of many bio-molecules, yet our knowledge of dynamics remains fragmented. Experimental techniques for studying bio-molecules either provide high resolution information on static conformations of the molecule or provide low-resolution, ensemble information that does not shed light on single molecule dynamics. In parallel, bio-molecular dynamics occur at time scale that are not yet attainable through detailed simulation methods. These limitations are especially noticeable when studying transition paths. To address this issue, we report in this paper two methods that derive meaningful trajectories for proteins between two of their conformations. The first method, MinActionPath, uses approximations of the potential energy surface for the molecule to derive an analytical solution of the equations of motion related to the concept of minimum action path. The second method, RelaxPath, follows the same principle of minimum action path but implements a more sophisticated potential, including a mixed elastic potential and a collision term to alleviate steric clashes. Using this new potential, the equations of motion cannot be solved analytically. We have introduced a relaxation method for solving those equations. We describe both the theories behind the two methods and their implementations, focusing on the specific techniques we have used that make those implementations amenable to study large molecular systems. We have illustrated the performance of RelaxPath on simple 2D systems. We have also compared MinActionPath and RelaxPath to other methods for generating transition paths on a well suited test set of large proteins, for which the end points of the trajectories as well as an intermediate conformation between those end points are known. We have shown that RelaxPath outperforms those other methods, including MinActionPath, in its ability to generate trajectories that get close to the known intermediates. We have also shown that the structures along the RelaxPath trajectories remain protein-like. Open source versions of the two programs MinActionPath and RelaxPath are available by request. [ABSTRACT FROM AUTHOR]

Classical transition state theory (TST) provides the rigorous basis for the application of molecular dynamics (MD) to infrequent events, i.e., reactions that are slow due to a high energy barrier. The TST rate is simply the equilibrium flux through a surface that divides reactants from products. In order to apply MD to infrequent events, corrections to the TST rate that account for recrossings of the dividing surface are computed by starting trajectories at the dividing surface and integrating them backward and forward in time. Both classical TST and conventional MD invoke the adiabatic approximation, i.e., the assumption that nuclear motion evolves on a single potential energy surface. Many chemical rate processes involve multiple potential energy surfaces, however, and a number of ‘‘surface-hopping’’ MD methods have been developed in order to incorporate nonadiabatic transitions among the potential energy surfaces. In this paper we generalize TST to processes involving multiple potential energy surfaces. This provides the framework for a new method for MD simulation of infrequent events for reactions that evolve on multiple potential energy surfaces. We show how this method can be applied rigorously even in conjunction with phase-coherent surface-hopping methods, where the probability of switching potential energy surfaces depends on the history of the trajectory, so integrating trajectories backward to calculate the recrossing correction is problematic. We illustrate this new method by applying it in conjunction with the ‘‘molecular dynamics with quantum transitions’’ (MDQT) surface-hopping method to a one-dimensional two-state barrier crossing problem. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Trajectory-based Gaussian basis sets have been tremendously successful in describing highdimensional quantum molecular dynamics. In this paper, we introduce a pseudospectral Gaussianbased method that achieves accurate quantum dynamics using efficient, real-space sampling of the time-dependent basis set. As in other Gaussian basis methods, we begin with a basis set expansion using time-dependent Gaussian basis functions guided by classical mechanics. Unlike other Gaussian methods but characteristic of the pseudospectral and collocation methods, the basis set is tested with N Dirac delta functions, where N is the number of basis functions, rather than using the basis function as test functions. As a result, the integration for matrix elements is reduced to function evaluation. Pseudospectral Gaussian dynamics only requires O(N) potential energy calculations, in contrast to O(N²) evaluations in a variational calculation. The classical trajectories allow small basis sets to sample high-dimensional potentials. Applications are made to diatomic oscillations in a Morse potential and a generalized version of the Henon-Heiles potential in two, four, and six dimensions. Comparisons are drawn to full analytical evaluation of potential energy integrals (variational) and the bra-ket averaged Taylor (BAT) expansion, an O(N) approximation used in Gaussian-based dynamics. In all cases, the pseudospectral Gaussian method is competitive with full variational calculations that require a global, analytical, and integrable potential energy surface. Additionally, the BAT breaks down when quantum mechanical coherence is particularly strong (i.e., barrier reflection in the Morse oscillator). The ability to obtain variational accuracy using only the potential energy at discrete points makes the pseudospectral Gaussian method a promising avenue for on-the-fly dynamics, where electronic structure calculations become computationally significant. [ABSTRACT FROM AUTHOR]

Comparisons are presented of experimental and theoretical studies of the rotationally inelastic scattering of CD3 radicals with H2 and D2 collision partners at respective collision energies of 680 ± 75 and 640 ± 60 cm-1. Close-coupling quantum-mechanical calculations performed using a newly constructed ab initio potential energy surface (PES) provide initial-to-final CD3 rotational level (n, k → n', k') integral and differential cross sections (ICSs and DCSs). The DCSs are compared with crossed molecular beam and velocity map imaging measurements of angular scattering distributions, which serve as a critical test of the accuracy of the new PES. In general, there is very good agreement between the experimental measurements and the calculations. The DCSs for CD3 scattering from both H2 and D2 peak in the forward hemisphere for n' = 2-4 and shift more to sideways and backward scattering for n' = 5. For n' = 6-8, the DCSs are dominated by backward scattering. DCSs for a particular CD3 n→n' transition have a similar angular dependence with either D2 or H2 as collision partner. Any differences between DCSs or ICSs can be attributed to mass effects because the PES is unchanged for CD3-H2 and CD3-D2 collisions. Further comparisons are drawn between the CD3-D2 scattering and results for CD3-He presented in our recent paper [O. Tkáč, A. G. Sage, S. J. Greaves, A. J. Orr-Ewing, P. J. Dagdigian, Q. Ma, and M. H. Alexander, Chem. Sci. 4, 4199 (2013)]. These systems have the same reduced mass, but are governed by different PESs. [ABSTRACT FROM AUTHOR]

This paper shows how a compact finite difference Hessian approximation scheme can be proficiently implemented into semiclassical initial value representation molecular dynamics. Effects of the approximation on the monodromy matrix calculation are tested by propagating initial sampling distributions to determine power spectra for analytic potential energy surfaces and for 'on the fly' carbon dioxide direct dynamics. With the approximation scheme the computational cost is significantly reduced, making ab initio direct semiclassical dynamics computationally more feasible and, at the same time, properly reproducing important quantum effects inherent in the monodromy matrix and the pre-exponential factor of the semiclassical propagator. [ABSTRACT FROM AUTHOR]

The dynamics of complex systems often involve thermally activated barrier crossing events that allow these systems to move from one basin of attraction on the high dimensional energy surface to another. Such events are ubiquitous, but challenging to simulate using conventional simulation tools, such as molecular dynamics. Recently, E and Zhou [Nonlinearity 24(6), 1831 (2011)] proposed a set of dynamic equations, the gentlest ascent dynamics (GAD), to describe the escape of a system from a basin of attraction and proved that solutions of GAD converge to index-1 saddle points of the underlying energy. In this paper, we extend GAD to enable finite temperature simulations in which the system hops between different saddle points on the energy surface. An effective strategy to use GAD to sample an ensemble of low barrier saddle points located in the vicinity of a locally stable configuration on the high dimensional energy surface is proposed. The utility of the method is demonstrated by studying the low barrier saddle points associated with point defect activity on a surface. This is done for two representative systems, namely, (a) a surface vacancy and ad-atom pair and (b) a heptamer island on the (111) surface of copper. [ABSTRACT FROM AUTHOR]

Markov state models of molecular kinetics (MSMs), in which the long-time statistical dynamics of a molecule is approximated by a Markov chain on a discrete partition of configuration space, have seen widespread use in recent years. This approach has many appealing characteristics compared to straightforward molecular dynamics simulation and analysis, including the potential to mitigate the sampling problem by extracting long-time kinetic information from short trajectories and the ability to straightforwardly calculate expectation values and statistical uncertainties of various stationary and dynamical molecular observables. In this paper, we summarize the current state of the art in generation and validation of MSMs and give some important new results. We describe an upper bound for the approximation error made by modeling molecular dynamics with a MSM and we show that this error can be made arbitrarily small with surprisingly little effort. In contrast to previous practice, it becomes clear that the best MSM is not obtained by the most metastable discretization, but the MSM can be much improved if non-metastable states are introduced near the transition states. Moreover, we show that it is not necessary to resolve all slow processes by the state space partitioning, but individual dynamical processes of interest can be resolved separately. We also present an efficient estimator for reversible transition matrices and a robust test to validate that a MSM reproduces the kinetics of the molecular dynamics data. [ABSTRACT FROM AUTHOR]

The hydrogen storage system LiH + NH3 ↔ LiNH2 + H2 is one of the most promising hydrogen storage systems, where the reaction yield can be increased by replacing Li in LiH with other alkali metals (Na or K) in order of Li < Na < K. In this paper, we have studied the alkali metal M (M = Li, Na, K) dependence of the reactivity of MH with NH3 by calculating the potential barrier of the H2 desorption process from the reaction of an M2H2 cluster with an NH3 molecule based on the ab initio structure optimization method. We have shown that the height of the potential barrier becomes lower in order of Li, Na, and K, where the difference of the potential barrier in Li and Na is relatively smaller than that in Na and K, and this tendency is consistent with the recent experimental results. We have also shown that the H-H distance of the H2 dimer at the transition state takes larger distance and the change of the potential energy around the transition state becomes softer in order of Li, Na, and K. There are almost no M dependence in the charge of the H atom in NH3 before the reaction, while that of the H atom in M2H2 takes larger negative value in order of Li, Na, and K. We have also performed molecular dynamics simulations on the M2H2-NH3 system and succeeded to reproduce the H2 desorption from the reaction of Na2H2 with NH3. [ABSTRACT FROM AUTHOR]

The important role of liquid water in many areas of science from chemistry, physics, biology, geology to climate research, etc., has motivated numerous theoretical studies of its structure and dynamics. The significance of quantum effects on the properties of water, however, has not yet been fully resolved. In this paper we focus on quantum dynamical effects in liquid water based on the linearized semiclassical initial value representation (LSC-IVR) with a quantum version of the simple point charge/flexible (q-SPC/fw) model [Paesani et al., J. Chem. Phys. 125, 184507 (2006)] for the potential energy function. The infrared (IR) absorption spectrum and the translational diffusion constants have been obtained from the corresponding thermal correlation functions, and the effects of intermolecular and intramolecular correlations have been studied. The LSC-IVR simulation results are compared with those predicted by the centroid molecular dynamics (CMD) approach. Although the LSC-IVR and CMD results agree well for the broadband for hindered motions in liquid water, the intramolecular bending and O–H stretching peaks predicted by the LSC-IVR are blueshifted from those given by CMD; reasons for this are discussed. We also suggest that the broadband in the IR spectrum corresponding to restricted translation and libration gives more information than the diffusion constant on the nature of quantum effects on translational and rotational motions and should thus receive more attention in this regard. [ABSTRACT FROM AUTHOR]

The multiscale coarse-graining (MS-CG) method, proposed by Izvekov and Voth [J. Phys. Chem. B 109, 2469 (2005); Izvekov and VothJ. Chem. Phys. 123, 134105 (2005)], is a method for determining the effective potential energy function for a coarse-grained model of a fluid using data obtained from molecular dynamics (MD) simulation of the corresponding atomically detailed model. The method has been given a rigorous statistical mechanical basis [Noid et al. J. Chem. Phys. 128, 244114 (2008); Noid et al.,J. Chem. Phys. 128, 244115 (2008)]. The coarse-grained (CG) potentials obtained using the MS-CG method are an approximate variational solution for the exact many-body potential of mean force for the coarse-grained sites. In this paper we apply this method to study the many-body potential of mean force among solutes in a simple model of a solution of Lennard-Jones particles. We use a new set of basis functions for the variational calculation that is useful when the coarse-grained potential is approximately equal to an arbitrarily complicated pairwise additive, central interaction among the sites of the coarse-grained model. For this model, pairwise additivity of the many-body potential of mean force is a very good approximation when the solute concentration is low, and it becomes less accurate for high concentrations, indicating the importance of many-body contributions to the coarse-grained potential. The best possible pairwise additive CG potential of the solute particles is found to be quite long ranged for all concentrations except those for which the mole fraction of solute is very close to unity. We discuss strategies for construction of short-ranged potentials for efficient but accurate CG MD simulation. We also discuss how the choice of basis functions for the variational calculation can be used to provide smoothing of the calculated CG potential function to overcome statistical sampling error in the atomistic simulation data used for the generation of the potential. [ABSTRACT FROM AUTHOR]

We describe an atomistic method for computing the viscosity of highly viscous liquids based on activated state kinetics. A basin-filling algorithm allowing the system to climb out of deep energy minima through a series of activation and relaxation is proposed and first benchmarked on the problem of adatom diffusion on a metal surface. It is then used to generate transition state pathway trajectories in the potential energy landscape of a binary Lennard-Jones system. Analysis of a sampled trajectory shows the system moves from one deep minimum to another by a process that involves high activation energy and the crossing of many local minima and saddle points. To use the trajectory data to compute the viscosity we derive a Markov Network model within the Green–Kubo formalism and show that it is capable of producing the temperature dependence in the low-viscosity regime described by molecular dynamics simulation, and in the high-viscosity regime (102–1012 Pa s) shown by experiments on fragile glass-forming liquids. We also derive a mean-field-like description involving a coarse-grained temperature-dependent activation barrier, and show it can account qualitatively for the fragile behavior. From the standpoint of molecular studies of transport phenomena this work provides access to long relaxation time processes beyond the reach of current molecular dynamics capabilities. In a companion paper we report a similar study of silica, a representative strong liquid. A comparison of the two systems gives insight into the fundamental difference between strong and fragile temperature variations. [ABSTRACT FROM AUTHOR]

In this paper, we present the results of a theoretical investigation on the dynamics of the title reaction at collision energies below 1.2 kcal/mol using rigorous quantum reactive scattering calculations. Vibrationally resolved integral and differential cross sections, as well as product rotational distributions, have been calculated using two electronically adiabatic potential energy surfaces, developed by us on the basis of semiempirical modifications of the entrance channel. In particular, we focus our attention on the role of the exothermicity and of the exit channel region of the interaction on the experimental observables. From the comparison between the theoretical results, insight about the main mechanisms governing the reaction is extracted, especially regarding the bimodal structure of the HF(v=2) nascent rotational state distributions. A good overall agreement with molecular beam scattering experiments has been obtained. [ABSTRACT FROM AUTHOR]

A new semiempirical exchange-Coulomb model potential energy surface for the N2–He interaction was reported recently [A. K. Dham et al., J. Chem. Phys. 127, 054302 (2007)] and, using it, the temperature dependence of bulk gas properties of N2–He mixtures, such as the second virial coefficient and traditional transport phenomena, most of which depend primarily on the isotropic component of the interaction potential energy surface, was determined. Values of these properties, along with values calculated using two high-quality ab initio potential energy surfaces [C.-H. Hu and A. J. Thakkar, J. Chem. Phys. 104, 2541 (1996); K. Patel et al., ibid 119, 909 (2003)] were compared critically to available experimental data. The present paper reports on the ability of the same three potential energy surfaces to predict state-to-state and total differential cross sections, total integral cross sections, and the temperature dependence of bulk gas relaxation phenomena (including magnetic field effects on transport coefficients). While all three potential energy surfaces give total differential and higher speed integral scattering results that fall within the experimental uncertainties, integral scattering results and state-to-state differential cross section measurements consistently exceed the calculated values. All three surfaces give similar agreement with the relaxation properties of N2–He binary mixtures, with the semiempirical exchange-Coulomb model potential energy surface giving slightly better overall agreement with experiment than the two ab initio potential energy surfaces. [ABSTRACT FROM AUTHOR]

For the charge transfer and vibrational and electronic deexcitations between O2/O2++CO+/CO, O/O++CO2+/CO2, and C/C++O3+/O3, multistep reaction pathways are discussed in light of the theoretical data of this and previous paper together with close comparison with the experimental observations. Our calculations show that these pathways involve both the long range and molecular region ranges of the potential energy surfaces of the electronic states of the stable isomers of OOCO+ and mostly those of the weakly bound charge transfer complex OOCO+. The couplings between these electronic states such as vibronic, Renner-Teller, Jahn-Teller, and spin orbit are viewed to play crucial roles here. Moreover, the initial orientation of the reactants, in the entrance channels, strongly influences the reaction mechanisms undertaken. We propose for the first time a mechanism for the widely experimentally studied spin-forbidden exothermic O+(4Su)+CO2(X 1Σg+)→O2+(X 2Πg)+CO(X 1Σ+) reaction where the O turns around the OCO molecule. [ABSTRACT FROM AUTHOR]

Cis, cis-peroxynitrous acid is known to be an intermediate in atmospheric reactions between OH and NO2 as well as HOO and NO. The infrared absorption spectra of matrix-isolated cc-HOONO and cc-DOONO in argon have been observed in the range of 500–8000 cm-1. Besides the seven fundamental vibrational modes that have been assigned earlier for this molecule [Zhang et al., J. Chem. Phys. 124, 084305 (2006)], more than 50 of the overtone and combination bands have been observed for cc-HOONO and cc-DOONO. Ab initio CCSD(T)/atomic natural orbital anharmonic force field calculations were used to help guide the assignments. Based on this study of the vibrational overtone transitions of cis, cis-HOONO that go as high as 8000 cm-1 and the earlier paper on the vibrational fundamentals, we conclude that the CCSD(T)/ANO anharmonic frequencies seem to correct to ±35 cm-1. The success of the theoretically predicted anharmonic frequencies {υ} in assigning overtone spectra of HOONO up to 8000 cm-1 suggests that the CCSD(T)/ANO method is producing a reliable potential energy surface for this reactive molecule. [ABSTRACT FROM AUTHOR]

The neural network (NN) procedure to interpolate ab initio data for the purpose of molecular dynamics (MD) simulations has been tested on the SiO2 system. Unlike other similar NN studies, here, we studied the dissociation of SiO2 without the initial use of any empirical potential. During the dissociation of SiO2 into Si+O or Si+O2, the spin multiplicity of the system changes from singlet to triplet in the first reaction and from singlet to pentet in the second. This paper employs four potential surfaces. The first is a NN fit [NN(STP)] to a database comprising the lowest of the singlet, triplet, and pentet energies obtained from density functional calculations in 6673 nuclear configurations. The other three potential surfaces are obtained from NN fits to the singlet, triplet, and pentet-state energies. The dissociation dynamics on the singlet-state and NN(STP) surfaces are reported. The results obtained using the singlet surface correspond to those expected if the reaction were to occur adiabatically. The dynamics on the NN(STP) surface represent those expected if the reaction follows a minimum-energy pathway. This study on a small system demonstrates the application of NNs for MD studies using ab initio data when the spin multiplicity of the system changes during the dissociation process. [ABSTRACT FROM AUTHOR]

In this paper we evaluate the use of higher order derivatives in the construction of an interpolated potential energy surface for the OH+H2→H2O+H reaction. The surface construction involves interpolating between local Taylor expansions about a set of known data points. We examine the use of first, second, third, and fourth order Taylor expansions in the interpolation scheme. The convergence of the various interpolated surfaces is evaluated in terms of the probability of reaction. We conclude that first order Taylor expansions (and by implication zeroth order expansions) are not suitable for constructing potential energy surfaces for reactive systems. We also conclude that it is inefficient to use fourth order derivatives. The factors differentiating between second and third order Taylor expansions are less clear. Although third order surfaces require substantially fewer data points to converge than second order surfaces, this faster convergence does not offset the large cost incurred in calculating numerical third derivatives. We therefore conclude that, without an efficient means for calculating analytic third derivatives, second order derivatives provide the most cost-effective means of constructing a global potential energy surface by interpolation. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The δ-target method proposed recently [Chem. Phys. Lett. 235, 309 (1995)] was shown to significantly simplify the task of optimal control of molecular localization. The present paper is intended to study the application of the δ-target technique to a practically interesting case of a diatomic molecule including rotation. Illustrative numerical examples are presented for the molecules NO and Na2. The δ-target method is shown to provide good control when the rotational temperature is not too high. The optimal control solution is very robust and insensitive to small changes in the potential curves and transition dipole moment functions. It is shown that the field obtained within the linearized δ-target optimal control technique can be successfully used in the nonlinear regime. The possibility of extending the δ-target technique is considered for treating strong field nonlinear optimal control tasks. The computational advantages of the method are discussed. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We present a new dual-level approach to representing potential energy surfaces in which a very small number of high-level electronic structure calculations are combined with a lower-level global surface, e.g., one defined implicitly by neglect-of-diatomic-differential-overlap calculations with specific reaction parameters, to generate the potential at any geometry where it may be needed. We interpolate the potential energy surface with a small number of accurate data points (the higher level) that are placed along the reaction path by using information on the global shape of the potential from less accurate calculations (the lower level). We confirm the findings of Ischtwan and Collins on the usefulness of single-level schemes including Hessians, and we delineate the regime of usefulness of single-level schemes based on gradients or even single-point energies. Furthermore we find that dual-level interpolation can offer cost savings over single-level schemes, and dual-level methods employing Hessians, gradients, or even only simple energy evaluations can yield reasonable potential energy surfaces with relatively low cost, with the potentials being more accurate along the reaction path. For all methods considered in this paper the accuracy of the interpolation for our test cases is lower when the potentials at points significantly removed from the reaction path are predicted from data that lie entirely on the reaction path. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Neural networks provide an efficient, general interpolation method for nonlinear functions of several variables. This paper describes the use of feed-forward neural networks to model global properties of potential energy surfaces from information available at a limited number of configurations. As an initial demonstration of the method, several fits are made to data derived from an empirical potential model of CO adsorbed on Ni(111). The data are error-free and geometries are selected from uniform grids of two and three dimensions. The neural network model predicts the potential to within a few hundredths of a kcal/mole at arbitrary geometries. The accuracy and efficiency of the neural network in practical calculations are demonstrated in quantum transition state theory rate calculations for surface diffusion of CO/Ni(111) using a Monte Carlo/path integral method. The network model is much faster to evaluate than the original potential from which it is derived. As a more complex test of the method, the interaction potential of H2 with the Si(100)-2×1 surface is determined as a function of 12 degrees of freedom from energies calculated with the local density functional method at 750 geometries. The training examples are not uniformly spaced and they depend weakly on variables not included in the fit. The neural net model predicts the potential at geometries outside the training set with a mean absolute deviation of 2.1 kcal/mole. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The routine location of the global minimum energy structures of a molecular system remains a challenging problem in chemical physics. Recently Straub and co-workers [J. Ma et al., J. Chem. Phys. 99, 4024 (1993) and 101, 533 (1994)] have introduced a number of novel dynamic simulated annealing algorithms for global optimization. Instead of using Newton’s equations, they are based on Liouville’s equation and the particles are described with phase space distributions. The methods were shown to have significantly enhanced effectiveness over traditional methods when used to locate the global minima of Lennard-Jones clusters. In this paper the extensions necessary to use these methods with ab initio quantum mechanical potentials are presented and their application is illustrated by the simulated annealing of a small lithium atom cluster. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

To improve the performance of the third-order density-functional tight-binding method (DFTB3) for non-covalent interactions involving organic and biological molecules, a chemical-potential equalization (CPE) approach was introduced [J. Phys. Chem. A, 116, 9131 (2012)] and parameterized for the H, C, N, O, and S chemical elements [J. Chem. Phys., 143, 084123 (2015)]. Based largely on equilibrium structures, the parameterized DFTB3/CPE models were shown to exhibit improvements in molecular polarizabilities and intermolecular interactions. With more extensive analyses, however, we observe here that the available DFTB3/CPE models have two critical limitations: (1) they lead to sharply varying potential energy surfaces, thus causing numerical instability in molecular dynamics (MD) simulations, and (2) they lead to spurious interactions at short distances for some dimer complexes. These shortcomings are attributed to the employed screening functions and the overfitting of CPE parameters. In this work, we introduce a new strategy to simplify the parameterization procedure and significantly reduce free parameters down to four global (i.e., independent of element type) ones. With this strategy, two new models, DFTB3/CPE(r) and DFTB3/CPE(r†) are parameterized. The new models lead to smooth potential energy surfaces, stable MD simulations, and alleviate the spurious interactions at short distances, thus representing consistent improvements for both neutral and ionic hydrogen bonds. [ABSTRACT FROM AUTHOR]

Configurational sampling is central to characterize the equilibrium properties of complex molecular systems, but it remains a significant computational challenge. The conventional molecular dynamics (MD) simulations of limited duration often result in inadequate sampling and thus inaccurate equilibrium estimates. Replica exchange with nonequilibrium switches (RENS) is a collective variable-free computational technique to achieve extensive sampling from a sequence of equilibrium and nonequilibrium MD simulations without modifying the underlying potential energy surface of the system. Unlike the conventional replica exchange molecular dynamics (REMD) simulation, which demands a significant number of replicas for better accuracy, RENS employs nonequilibrium heating (forward) and cooling (reverse) work simulations prior to configurational swaps to improve the acceptance probability for replica exchange by using only a few replicas. Here, we have implemented the RENS algorithm on four model systems and examined its performance against the conventional MD and REMD simulations. The desired equilibrium distributions were generated by RENS for all the model systems, whereas REMD and MD simulations could not do so due to inadequate sampling on the same timescales. The calculated work distributions from RENS obeyed the expected nonequilibrium fluctuation theorem. The results indicate that the switching time of the nonequilibrium simulations can be systematically altered to optimize the acceptance probability and the reduced work of switching. The modular implementation of RENS algorithm not only enables us to readily extend it to multiple replicas but also paves the way for extension to larger molecular systems in the future. [ABSTRACT FROM AUTHOR]

Molecular rotations and vibrations have been extensively studied by chemists for decades, both experimentally using spectroscopic methods and theoretically with the help of quantum chemistry. However, the theoretical investigation of molecular rotations and vibrations in strong magnetic fields requires computationally more demanding tools. As such, proper calculations of rotational and vibrational spectra were not feasible up until very recently. In this work, we present rotational and vibrational spectra for two small linear molecules, H2 and LiH, in strong magnetic fields. By treating the nuclei as classical particles, trajectories for rotations and vibrations are simulated from ab initio molecular dynamics. Born–Oppenheimer potential energy surfaces are calculated at the Hartree–Fock and MP2 levels of theory using London atomic orbitals to ensure gauge origin invariance. For the calculation of nuclear trajectories, a highly efficient Tajima propagator is introduced, incorporating the Berry curvature tensor accounting for the screening of nuclear charges. [ABSTRACT FROM AUTHOR]

In this work, we present a general purpose deep neural network package for representing energies, forces, dipole moments, and polarizabilities of atomistic systems. This so-called recursively embedded atom neural network model takes advantages of both the physically inspired atomic descriptor based neural networks and the message-passing based neural networks. Implemented in the PyTorch framework, the training process is parallelized on both the central processing unit and the graphics processing unit with high efficiency and low memory in which all hyperparameters can be optimized automatically. We demonstrate the state-of-the-art accuracy, high efficiency, scalability, and universality of this package by learning not only energies (with or without forces) but also dipole moment vectors and polarizability tensors in various molecular, reactive, and periodic systems. An interface between a trained model and LAMMPs is provided for large scale molecular dynamics simulations. We hope that this open-source toolbox will allow for future method development and applications of machine learned potential energy surfaces and quantum-chemical properties of molecules, reactions, and materials. [ABSTRACT FROM AUTHOR]

Comparisons are presented of experimental and theoretical studies of the rotationally inelastic scattering of CD3 radicals with H2 and D2 collision partners at respective collision energies of 680 ± 75 and 640 ± 60 cm-1. Close-coupling quantum-mechanical calculations performed using a newly constructed ab initio potential energy surface (PES) provide initial-to-final CD3 rotational level (n, k → n', k') integral and differential cross sections (ICSs and DCSs). The DCSs are compared with crossed molecular beam and velocity map imaging measurements of angular scattering distributions, which serve as a critical test of the accuracy of the new PES. In general, there is very good agreement between the experimental measurements and the calculations. The DCSs for CD3 scattering from both H2 and D2 peak in the forward hemisphere for n' = 2-4 and shift more to sideways and backward scattering for n' = 5. For n' = 6-8, the DCSs are dominated by backward scattering. DCSs for a particular CD3 n→n' transition have a similar angular dependence with either D2 or H2 as collision partner. Any differences between DCSs or ICSs can be attributed to mass effects because the PES is unchanged for CD3-H2 and CD3-D2 collisions. Further comparisons are drawn between the CD3-D2 scattering and results for CD3-He presented in our recent paper [O. Tkáč, A. G. Sage, S. J. Greaves, A. J. Orr-Ewing, P. J. Dagdigian, Q. Ma, and M. H. Alexander, Chem. Sci. 4, 4199 (2013)]. These systems have the same reduced mass, but are governed by different PESs. [ABSTRACT FROM AUTHOR]

Hydrogen bonds are of paramount importance in the chemistry of clays, mediating the interaction between the clay surface and water, and for some materials between separate layers. It is well-established that the accuracy of a computational model for clays depends on the level of theory at which the electronic structure is treated. However, for hydrogen-bonded systems, the motion of light H nuclei on the electronic potential energy surface is often affected by quantum delocalization. Using path integral molecular dynamics, we show that nuclear quantum effects lead to a relatively small change in the structure of clays, but one that is comparable to the variation incurred by treating the clay at different levels of electronic structure theory. Accounting for quantum effects weakens the hydrogen bonds in clays, with H-bonds between different layers of the clay affected more than those within the same layer; this is ascribed to the fact that the confinement of an H atom inside a layer is independent of its participation in hydrogen-bonding. More importantly, the weakening of hydrogen bonds by nuclear quantum effects causes changes in the vibrational spectra of these systems, significantly shifting the O–H stretching peaks and meaning that in order to fully understand these spectra by computational modeling, both electronic and nuclear quantum effects must be included. We show that after reparameterization of the popular clay forcefield CLAYFF, the O–H stretching region of their vibrational spectra better matches the experimental one, with no detriment to the model's agreement with other experimental properties. [ABSTRACT FROM AUTHOR]

Hydrogen cyanide (HCN) and its isomer hydrogen isocyanide (HNC) are omnipresent in the interstellar medium (ISM). The ratio between the two isomers serves as an indicator of the physical conditions in different areas of the ISM. As such, the isomerization process between the two isomers has been extensively studied on the neutral potential energy surface. Moreover, HCN and HNC are thought to be precursors of important organic molecules, such as adenine. Here, we use quantum chemistry calculations and ab initio molecular dynamics simulations to focus on the chemistry that occurs upon ionization of pure HNC clusters. We demonstrate that upon ionization of HNC clusters, a distonic ion CN⋯HCNH+ is formed, and this formation is accompanied by HNC-to-HCN isomerization. Moreover, we show that the cluster environment and the network of hydrogen bonds are crucial for the isomerization process to occur and for the stabilization of the clusters. We demonstrate that, in contrast to HNC clusters, isomerization of ionized HCN clusters can occur only for the larger clusters. In addition, we discuss the formation of aminonitrile cation in the clusters and propose a barrierless route for diaminonitrile, a known precursor of amino acids and nucleobases, to form. [ABSTRACT FROM AUTHOR]

An algorithm is derived for computer simulation of geodesics on the constant-potential-energy hypersurface of a system of N classical particles. First, a basic time-reversible geodesic algorithm is derived by discretizing the geodesic stationarity condition and implementing the constant-potential-energy constraint via standard Lagrangian multipliers. The basic NVU algorithm is tested by single-precision computer simulations of the Lennard-Jones liquid. Excellent numerical stability is obtained if the force cutoff is smoothed and the two initial configurations have identical potential energy within machine precision. Nevertheless, just as for NVE algorithms, stabilizers are needed for very long runs in order to compensate for the accumulation of numerical errors that eventually lead to 'entropic drift' of the potential energy towards higher values. A modification of the basic NVU algorithm is introduced that ensures potential-energy and step-length conservation; center-of-mass drift is also eliminated. Analytical arguments confirmed by simulations demonstrate that the modified NVU algorithm is absolutely stable. Finally, we present simulations showing that the NVU algorithm and the standard leap-frog NVE algorithm have identical radial distribution functions for the Lennard-Jones liquid. [ABSTRACT FROM AUTHOR]

We present a kinetic analysis of the nonadiabatic decay mechanism of an excited state hydrated electron to the ground state. The theoretical treatment is based on a quantized, gap dependent golden rule rate constant formula which describes the nonadiabatic transition rate between two quantum states. The rate formula is expressed in terms of quantum time correlation functions of the energy gap and of the nonadiabatic coupling. These gap dependent quantities are evaluated from three different sets of mixed quantum-classical molecular dynamics simulations of a hydrated electron equilibrated (a) in its ground state, (b) in its first excited state, and (c) on a hypothetical mixed potential energy surface which is the average of the ground and the first excited electronic states. The quantized, gap dependent rate results are applied in a phenomenological kinetic equation which provides the survival probability function of the excited state electron. Although the lifetime of the equilibrated excited state electron is computed to be very short (well under 100 fs), the survival probability function for the nonequilibrium process in pump-probe experiments yields an effective excited state lifetime of around 300 fs, a value that is consistent with the findings of several experimental groups and previous theoretical estimates. [ABSTRACT FROM AUTHOR]

We consider the clustering of Lennard-Jones particles by using an energetic connectivity criterion proposed long ago by Hill [J. Chem. Phys. 32, 617 (1955)] for the bond between pairs of particles. The criterion establishes that two particles are bonded (directly connected) if their relative kinetic energy is less than minus their relative potential energy. Thus, in general, it depends on the direction as well as on the magnitude of the velocities and positions of the particles. An integral equation for the pair connectedness function, proposed by two of the authors [Phys. Rev. E 61, R6067 (2000)], is solved for this criterion and the results are compared with those obtained from molecular dynamics simulations and from a connectedness Percus-Yevick-type integral equation for a velocity-averaged version of Hill’s energetic criterion. [ABSTRACT FROM AUTHOR]

A representation of the three-dimensional potential energy surface (PES) of the H2O–H van der Waals dimer is presented. The H2O molecule is treated as a rigid body held at its experimentally determined equilibrium geometry, with the OH bond length set to 1.809 650 34 a0 and the HOH bond angle set to 1.824 044 93 radians. Ab initio calculations are carried out at the coupled-cluster single, double, and perturbative triple level, with scalar relativistic effects included using the second-order Douglas–Kroll–Hess approximation. The ab initio calculations employ the aug-cc-pVnZ-DK series of basis sets (n = D, T, Q), which are recontracted versions of the aug-cc-pVnZ basis sets that are appropriate for relativistic calculations. The counterpoise method is used to reduce the basis set superposition error; in addition, results obtained using the aug-cc-pVTZ-DK and aug-cc-pVQZ-DK basis sets were extrapolated to the complete basis set (CBS) limit. The PES is based on calculations carried out at 1054 symmetry-unique H2O–H geometries for which the distance R between the H-atom and the H2O center of mass ranges from R = 2.5–9.0 Å. The reproduction of the PES along the orientational degrees of freedom was performed using Lebedev quadrature and an expansion in spherical harmonics. The mean absolute error of the reproduced PES is <0.02 cm−1 for R ≥ 3.0 Å and <0.21 cm−1 for R between 2.5 and 3.0 Å. The global minimum for the CBS PES is a coplanar H2O–H geometry, with R = 3.41 Å, in which the angle formed between the H2O C2 symmetry axis and the H-atom is 122.25°; the CBS binding energy for this geometry is 61.297 cm−1. In addition, by utilizing the symmetry of the H2O molecule, the spherical harmonic expansion was simplified with no loss in accuracy and a speedup of ∼1.8 was achieved. The reproduced PES can be used in future molecular dynamics simulations. [ABSTRACT FROM AUTHOR]

Ab initio molecular dynamics (AIMD) is a valuable technique for studying molecules and materials at finite temperatures where the nuclei evolve on potential energy surfaces obtained from accurate electronic structure calculations. In this work, we present an approach to running AIMD simulations on noisy intermediate-scale quantum (NISQ)-era quantum computers. The electronic energies are calculated on a quantum computer using the variational quantum eigensolver (VQE) method. Algorithms for computation of analytical gradients entirely on a quantum computer require quantum fault-tolerant hardware, which is beyond NISQ-era. Therefore, we compute the energy gradients numerically using finite differences, the Hellmann–Feynman theorem, and a correlated sampling technique. This method only requires additional classical calculations of electron integrals for each degree of freedom without any additional computations on a quantum computer beyond the initial VQE run. As a proof of concept, AIMD simulations are demonstrated for the H2 molecule on IBM quantum devices. In addition, we demonstrate the validity of the method for larger molecules using full configuration interaction wave functions. As quantum hardware and noise mitigation techniques continue to improve, the method can be utilized for studying larger molecular systems. [ABSTRACT FROM AUTHOR]

In this work, a first-principles systematic study of (Pt3Cu)n, n = 1–9, clusters was performed employing the linear combination of Gaussian-type orbital auxiliary density functional theory approach. The growth of the clusters has been achieved by increasing the previous cluster by one Pt3Cu unit at a time. To explore in detail the potential energy surface of these clusters, initial structures were obtained from Born–Oppenheimer molecular dynamics trajectories generated at different temperatures and spin multiplicities. For each cluster size, several dozens of structures were optimized without any constraints. The most stable structures were characterized by frequency analysis calculations. This study demonstrates that the obtained most stable structures prefer low spin multiplicities. To gain insight into the growing pattern of these systems, average bond lengths were calculated for the lowest stable structures. This work reveals that the Cu atoms prefer to be together and to localize inside the cluster structures. Moreover, these systems tend to form octahedra moieties in the size range of n going from 4 to 9 Pt3Cu units. Magnetic moment per atom and spin density plots were obtained for the neutral, cationic, and anionic ground state structures. Dissociation energies, ionization potential, and electron affinity were calculated, too. The dissociation energy and the electron affinity increase as the number of Pt3Cu units grows, whereas the ionization potential decreases. [ABSTRACT FROM AUTHOR]

A new potential energy surface (PES) and dynamical study of the reactive process of H2CO + OH toward the formation of HCO + H2O and HCOOH + H are presented. In this work, a source of spurious long range interactions in symmetry adapted neural network (NN) schemes is identified, which prevents their direct application for low temperature dynamical studies. For this reason, a partition of the PES into a diabatic matrix plus a NN many-body term has been used, fitted with a novel artificial neural network scheme that prevents spurious asymptotic interactions. Quasi-classical trajectory (QCT) and ring polymer molecular dynamics (RPMD) studies have been carried on this PES to evaluate the rate constant temperature dependence for the different reactive processes, showing good agreement with the available experimental data. Of special interest is the analysis of the previously identified trapping mechanism in the RPMD study, which can be attributed to spurious resonances associated with excitations of the normal modes of the ring polymer. [ABSTRACT FROM AUTHOR]

Thermal dissociation reaction into polyatomic molecules on the ground state no-barrier potential energy surface is studied by classical molecular dynamics simulations of N2O4⇋2NO2. A phase space surface ET=Veff(Rl)>=0 is identified as the transition state (TS), where ET is the sum of the potential and kinetic energies of interfragment motion and Veff(Rl) is the orbital angular momentum-dependent effective barrier. By dividing the motion of the system into fragments’ vibrational (V), rotational (R), and interfragment (T) modes, where the T mode is composed of translational (TT) and orbital (TL) modes, a scheme of reactive energy transfer for fragmentation is presented. The present energy condition for the TS is in accord with the one of phase space theory (PST). The observed photofragmentation rates of NCNO and CH2CO which increase with energy slower than predicted by PST suggest that intrareactant energy redistribution may influence the rate. Dissociation is found to occur by energy redistribution among T-R-V modes followed by the one among TT-TL-R modes, which determine the product vibrational and rotational distributions, respectively. This scheme supports separate statistical ensemble method in reproducing the nascent distributions from unimolecular photofragmentation at excess energies above the vibrational threshold. © 1996 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The vibrational quenching cross sections and corresponding low-temperature rate constants for the ν = 1 and ν = 2 states of CN−(1Σ+) colliding with He and Ar atoms have been computed ab initio using new three-dimensional potential energy surfaces. Little work has been carried out so far on low-energy vibrationally inelastic collisions for anions with neutral atoms. The cross sections and rates calculated at energies and temperatures relevant for both ion traps and astrochemical modeling are found by the present calculations to be even smaller than those of the similar C 2 − /He and C 2 − /Ar systems, which are in turn of the order of those existing for the collisions involving neutral diatom–atom systems. The implications of our finding in the present case mainly focus on the possible role of small computed rate constants in the dynamics of molecular cooling and the evolution of astrochemical modeling networks. [ABSTRACT FROM AUTHOR]

Extended Lagrangian Born–Oppenheimer molecular dynamics (XL-BOMD) [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for orbital-free Hohenberg–Kohn density-functional theory and for charge equilibration and polarizable force-field models that can be derived from the same orbital-free framework. The purpose is to introduce the most recent features of orbital-based XL-BOMD to molecular dynamics simulations based on charge equilibration and polarizable force-field models. These features include a metric tensor generalization of the extended harmonic potential, preconditioners, and the ability to use only a single Coulomb summation to determine the fully equilibrated charges and the interatomic forces in each time step for the shadow Born–Oppenheimer potential energy surface. The orbital-free formulation has a charge-dependent, short-range energy term that is separate from long-range Coulomb interactions. This enables local parameterizations of the short-range energy term, while the long-range electrostatic interactions can be treated separately. The theory is illustrated for molecular dynamics simulations of an atomistic system described by a charge equilibration model with periodic boundary conditions. The system of linear equations that determines the equilibrated charges and the forces is diagonal, and only a single Ewald summation is needed in each time step. The simulations exhibit the same features in accuracy, convergence, and stability as are expected from orbital-based XL-BOMD. [ABSTRACT FROM AUTHOR]

In this article, we present a systematic study on developing machine learning force fields (MLFFs) for crystalline silicon. While the main-stream approach of fitting a MLFF is to use a small and localized training set from molecular dynamics simulations, it is unlikely to cover the global features of the potential energy surface. To remedy this issue, we used randomly generated symmetrical crystal structures to train a more general Si-MLFF. Furthermore, we performed substantial benchmarks among different choices of material descriptors and regression techniques on two different sets of silicon data. Our results show that neural network potential fitting with bispectrum coefficients as descriptors is a feasible method for obtaining accurate and transferable MLFFs. [ABSTRACT FROM AUTHOR]

The 2D-Raman-THz response in all possible time-orderings (Raman-THz-THz, THz-Raman-THz, and THz-THz-Raman) of amorphous water ice is calculated in two ways: from atomistic molecular dynamics simulations and with the help of a Feynman diagram model, the latter of which power-expands the potential energy surface and the dipole and polarizability surfaces up to leading order. Comparing both results allows one to dissect the 2D-Raman-THz response into contributions from mechanical anharmonicity, as well as electrical dipole and polarizability anharmonicities. Mechanical anharmonicity dominates the 2D-Raman-THz response of the hydrogen-bond stretching and hydrogen-bond bending bands of water, and dipole anharmonicity dominates that of the librational band, while the contribution of polarizability anharmonicity is comparably weak. A distinct echo of the hydrogen-bond stretching band is observed for the THz-Raman-THz pulse sequence, again dominated by mechanical anharmonicity. A peculiar mechanism is discussed, which is based on the coupling between the many normal modes within the hydrogen-bond stretching band and which will inevitably generate such an echo for an amorphous structure. [ABSTRACT FROM AUTHOR]

Ring polymer molecular dynamics (RPMD) has proven to be an accurate approach for calculating thermal rate coefficients of various chemical reactions. For wider application of this methodology, efficient ways to generate the underlying full-dimensional potential energy surfaces (PESs) and the corresponding energy gradients are required. Recently, we have proposed a fully automated procedure based on combining the original RPMDrate code with active learning for PES on-the-fly using moment tensor potential and successfully applied it to two representative thermally activated chemical reactions [I. S. Novikov et al., Phys. Chem. Chem. Phys. 20, 29503–29512 (2018)]. In this work, using a prototype insertion chemical reaction S + H2, we show that this procedure works equally well for another class of chemical reactions. We find that the corresponding PES can be generated by fitting to less than 1500 automatically generated structures, while the RPMD rate coefficients show deviation from the reference values within the typical convergence error of the RPMDrate. We note that more structures are accumulated during the real-time propagation of the dynamic factor (the recrossing factor) as opposed to the previous study. We also observe that a relatively flat free energy profile along the reaction coordinate before entering the complex-formation well can cause issues with locating the maximum of the free energy surface for less converged PESs. However, the final RPMD rate coefficient is independent of the position of the dividing surface that makes it invulnerable to this problem, keeping the total number of necessary structures within a few thousand. Our work concludes that, in the future, the proposed methodology can be applied to realistic complex chemical reactions with various energy profiles. [ABSTRACT FROM AUTHOR]