Showing papers on "Potential energy surface published in 2019"

PhysNet: A Neural Network for Predicting Energies, Forces, Dipole Moments, and Partial Charges.

Abstract: In recent years, machine learning (ML) methods have become increasingly popular in computational chemistry. After being trained on appropriate ab initio reference data, these methods allow for accurately predicting the properties of chemical systems, circumventing the need for explicitly solving the electronic Schrodinger equation. Because of their computational efficiency and scalability to large data sets, deep neural networks (DNNs) are a particularly promising ML algorithm for chemical applications. This work introduces PhysNet, a DNN architecture designed for predicting energies, forces, and dipole moments of chemical systems. PhysNet achieves state-of-the-art performance on the QM9, MD17, and ISO17 benchmarks. Further, two new data sets are generated in order to probe the performance of ML models for describing chemical reactions, long-range interactions, and condensed phase systems. It is shown that explicitly including electrostatics in energy predictions is crucial for a qualitatively correct description of the asymptotic regions of a potential energy surface (PES). PhysNet models trained on a systematically constructed set of small peptide fragments (at most eight heavy atoms) are able to generalize to considerably larger proteins like deca-alanine (Ala10): The optimized geometry of helical Ala10 predicted by PhysNet is virtually identical to ab initio results (RMSD = 0.21 A). By running unbiased molecular dynamics (MD) simulations of Ala10 on the PhysNet-PES in gas phase, it is found that instead of a helical structure, Ala10 folds into a "wreath-shaped" configuration, which is more stable than the helical form by 0.46 kcal mol-1 according to the reference ab initio calculations.

Exploration of Chemical Compound, Conformer, and Reaction Space with Meta-Dynamics Simulations Based on Tight-Binding Quantum Chemical Calculations.

Abstract: The semiempirical tight-binding based quantum chemistry method GFN2-xTB is used in the framework of meta-dynamics (MTD) to globally explore chemical compound, conformer, and reaction space. The biasing potential given as a sum of Gaussian functions is expressed with the root-mean-square-deviation (RMSD) in Cartesian space as a metric for the collective variables. This choice makes the approach robust and generally applicable to three common problems (i.e., conformer search, chemical reaction space exploration in a virtual nanoreactor, and for guessing reaction paths). Because of the inherent locality of the atomic RMSD, functional group or fragment selective treatments are possible facilitating the investigation of catalytic processes where, for example, only the substrate is thermally activated. Due to the approximate character of the GFN2-xTB method, the resulting structure ensembles require further refinement with more sophisticated, for example, density functional or wave function theory methods. However, the approach is extremely efficient running routinely on common laptop computers in minutes to hours of computation time even for realistically sized molecules with a few hundred atoms. Furthermore, the underlying potential energy surface for molecules containing almost all elements ( Z = 1-86) is globally consistent including the covalent dissociation process and electronically complicated situations in, for example, transition metal systems. As examples, thermal decomposition, ethyne oligomerization, the oxidation of hydrocarbons (by oxygen and a P450 enzyme model), a Miller-Urey model system, a thermally forbidden dimerization, and a multistep intramolecular cyclization reaction are shown. For typical conformational search problems of organic drug molecules, the new MTD(RMSD) algorithm yields lower energy structures and more complete conformer ensembles at reduced computational effort compared with its already well performing predecessor.

LASP: Fast global potential energy surface exploration

Abstract: Here we introduce the LASP code, which is designed for large‐scale atomistic simulation of complex materials with neural network (NN) potential. The software architecture and functionalities of LASP will be overviewed. LASP features with the global neural network (G‐NN) potential that is generated by learning the first principles dataset of global PES from stochastic surface walking (SSW) global optimization. The combination of the SSW method with global NN potential facilitates greatly the PES exploration for a wide range of complex materials. Not limited to SSW‐NN global optimization, the software implements standard interfaces to dock with other energy/force evaluation packages and can also perform common tasks for computing PES properties, such as single‐ended and double‐ended transition state search, the molecular dynamics simulation with and without restraints. A few examples are given to illustrate the efficiency and capabilities of LASP code. Our ongoing efforts for code developing and G‐NN potential library building are also presented.

Elucidating the Nuclear Quantum Dynamics of Intramolecular Double Hydrogen Transfer in Porphycene.

Abstract: We address the double hydrogen transfer (DHT) dynamics of the porphycene molecule, a complex paradigmatic system in which the making and breaking of H-bonds in a highly anharmonic potential energy surface require a quantum mechanical treatment not only of the electrons but also of the nuclei. We combine density functional theory calculations, employing hybrid functionals and van der Waals corrections, with recently proposed and optimized path-integral ring-polymer methods for the approximation of quantum vibrational spectra and reaction rates. Our full-dimensional ring-polymer instanton simulations show that below 100 K the concerted DHT tunneling pathway dominates but between 100 and 300 K there is a competition between concerted and stepwise pathways when nuclear quantum effects are included. We obtain ground-state reaction rates of 2.19 × 1011 s-1 at 150 K and 0.63 × 1011 s-1 at 100 K, in good agreement with experiment. We also reproduce the puzzling N-H stretching band of porphycene with very good accuracy from thermostated ring-polymer molecular dynamics simulations. The position and line shape of this peak, centered at around 2600 cm-1 and spanning 750 cm-1, stem from a combination of very strong H-bonds, the coupling to low-frequency modes, and the access to cis-like isomeric conformations, which cannot be appropriately captured with classical-nuclei dynamics. These results verify the appropriateness of our general theoretical approach and provide a framework for a deeper physical understanding of hydrogen transfer dynamics in complex systems.

Ultrafast X-Ray Scattering Measurements of Coherent Structural Dynamics on the Ground-State Potential Energy Surface of a Diplatinum Molecule.

Abstract: We report x-ray free electron laser experiments addressing ground-state structural dynamics of the diplatinum anion Pt2POP4 following photoexcitation. The structural dynamics are tracked with <100 fs time resolution by x-ray scattering, utilizing the anisotropic component to suppress contributions from the bulk solvent. The x-ray data exhibit a strong oscillatory component with period 0.28 ps and decay time 2.2 ps, and structural analysis of the difference signal directly shows this as arising from ground-state dynamics along the PtPt coordinate. These results are compared with multiscale Born-Oppenheimer molecular dynamics simulations and demonstrate how off-resonance excitation can be used to prepare a vibrationally cold excited-state population complemented by a structure-dependent depletion of the ground-state population which subsequently evolves in time, allowing direct tracking of ground-state structural dynamics. (Less)

Decomposition kinetics for HONO and HNO2

Abstract: This work presents a detailed investigation into the isomerization and decomposition of HONO and HNO2. State-of-the-art electronic structure theory is used to compute the HNO2 potential energy surface. Temperature and pressure dependent rate coefficients are computed using microcanonical rate theory and the master equation. The electronic structure theory properties are optimized against the relevant experimental data. A novel strategy was developed to incorporate uncertainty in the minimum energy pathway into the optimized mechanism. The new mechanism is in excellent agreement with all available experimental data for H + NO2 → OH + NO and OH + NO → HONO. The calculations identify OH + NO as the dominant products for HNO2, which were neglected from all previous mechanisms in the literature.

Exact Potential Energy Surface for Molecules in Cavities

Abstract: We find and analyze the exact time-dependent potential energy surface driving the proton motion for a model of cavity-induced suppression of proton-coupled electron transfer. We show how, in contrast to the polaritonic surfaces, its features directly correlate to the proton dynamics and we discuss cavity modifications of its structure responsible for the suppression. The results highlight the interplay between nonadiabatic effects from coupling to photons and coupling to electrons and suggest caution is needed when applying traditional dynamics methods based on polaritonic surfaces.

Strong Vibrational Relaxation of NO Scattered from Au(111): Importance of the Adiabatic Potential Energy Surface

Abstract: Experimental observations of multiquantum relaxation of highly vibrationally excited NO scattering from Au(111) are a benchmark for the breakdown of the Born-Oppenheimer approximation in molecule-surface systems. This remarkable vibrational inelasticity was long thought to be almost exclusively mediated by electron transfer; however, no theories have quantitatively reproduced various experimental data. This was suggested to be due to errors in the adiabatic potential energy surface (PES) used in those studies. Here, we investigate electronically adiabatic molecular dynamics of this system with a globally accurate high-dimensional PES that is newly developed with neural networks from first principles. The NO vibrational energy loss is much larger than that on the earlier adiabatic PES. Additionally, the translational inelasticity and translational energy dependence of vibrational inelasticity are also more accurately reproduced. There is reason to be optimistic that electronically nonadiabatic theories using this adiabatic PES as a starting point might accurately reproduce experimental results on this important system.

Trajectory-adjusted electronic zero point energy in classical Meyer-Miller vibronic dynamics: Symmetrical quasiclassical application to photodissociation.

Abstract: An electronic zero-point energy (ZPE) adjustment protocol is presented within the context of the symmetrical quasiclassical (SQC) quantization of the electronic oscillator degrees of freedom (DOF) in classical Meyer-Miller (MM) vibronic dynamics for the molecular dynamics treatment of electronically nonadiabatic processes. The “adjustment” procedure maintains the same initial and final distributions of coordinates and momenta in the electronic oscillator DOF as previously given by the SQC windowing protocol but modifies the ZPE parameter in the MM Hamiltonian, on a per trajectory basis, so that the initial nuclear forces are precisely those corresponding to the initial electronic quantum state. Examples demonstrate that this slight modification to the standard SQC/MM approach significantly improves treatment of the multistate nonadiabatic dynamics following a Franck-Condon type vertical excitation onto a highly repulsive potential energy surface as is typical in the photodissociation context.

Low dimensional representations along intrinsic reaction coordinates and molecular dynamics trajectories using interatomic distance matrices

Abstract: Most chemical transformations (reactions or conformational changes) that are of interest to researchers have many degrees of freedom, usually too many to visualize without reducing the dimensionality of the system to include only the most important atomic motions. In this article, we describe a method of using Principal Component Analysis (PCA) for analyzing a series of molecular geometries (e.g., a reaction pathway or molecular dynamics trajectory) and determining the reduced dimensional space that captures the most structural variance in the fewest dimensions. The software written to carry out this method is called PathReducer, which permits (1) visualizing the geometries in a reduced dimensional space, (2) determining the axes that make up the reduced dimensional space, and (3) projecting the series of geometries into the low-dimensional space for visualization. We investigated two options to represent molecular structures within PathReducer: aligned Cartesian coordinates and matrices of interatomic distances. We found that interatomic distance matrices better captured non-linear motions in a smaller number of dimensions. To demonstrate the utility of PathReducer, we have carried out a number of applications where we have projected molecular dynamics trajectories into a reduced dimensional space defined by an intrinsic reaction coordinate. The visualizations provided by this analysis show that dynamic paths can differ greatly from the minimum energy pathway on a potential energy surface. Viewing intrinsic reaction coordinates and trajectories in this way provides a quick way to gather qualitative information about the pathways trajectories take relative to a minimum energy path. Given that the outputs from PCA are linear combinations of the input molecular structure coordinates (i.e., Cartesian coordinates or interatomic distances), they can be easily transferred to other types of calculations that require the definition of a reduced dimensional space (e.g., biased molecular dynamics simulations).

Analysis of acetic acid gas phase reactivity: Rate constant estimation and kinetic simulations

Abstract: The gas phase reactivity of acetic acid was investigated combining first principle calculations with kinetic simulations Rate constants for the unimolecular decomposition of acetic acid were determined integrating the 1D master equation over a Potential Energy Surface (PES) investigated at the M06-2X/aug-cc-pVTZ level Energies were computed at the CCSD(T)/aug-cc-pVTZ level using a basis set size correction factor determined at the DF-MP2/aug-cc-pVQZ level Three decomposition channels were considered: CO2 + CH4, CH2CO + H2O, and CH3 + COOH Rate constants were computed in the 700–2100 K and 01–100 atm temperature and pressure ranges The simulations show that the reaction is in fall off above 1200 K at pressures smaller than 10 atm Successively, the PESs for acetic acid H-abstraction by H, OH, OOH, O2, and CH3 were investigated at the same level of theory Rate constants were computed accounting explicitly for the formation of entrance and exit van der Waals wells and their collisional stabilization Energy barriers were determined at the CASPT2 level for H-abstraction by OH of the acidic H, since it has a strong multireference character The calculated rate constant is in good agreement with experiments and supports the experimental finding that at low temperatures it is pressure dependent The calculated rate constants were used to update the POLIMI kinetic model and to simulate the pyrolysis and combustion of acetic acid It was found that acetic acid decomposition and the formation of its direct decomposition products can be reasonably predicted The formation of secondary products, such as H2 and C2 hydrocarbons, is underpredicted This suggests that reaction routes not incorporated in the model may be active Some hypotheses are formulated on which these may be

A fragmented, permutationally invariant polynomial approach for potential energy surfaces of large molecules: Application to N-methyl acetamide

Abstract: We describe and apply a method to extend permutationally invariant polynomial (PIP) potential energy surface (PES) fitting to molecules with more than 10 atoms. The method creates a compact basis of PIPs as the union of PIPs obtained from fragments of the molecule. An application is reported for trans-N-methyl acetamide, where B3LYP/cc-pVDZ electronic energies and gradients are used to develop a full-dimensional potential for this prototype peptide molecule. The performance of several fragmented bases is verified against a benchmark PES using all (66) Morse variables. The method appears feasible for much larger molecules.

A master equation simulation for the •OH + CH3OH reaction.

Abstract: A combined (fixed-J) two-dimensional master-equation/semi-classical transition state theory/variational Rice-Ramsperger-Kassel-Marcus approach has been used to compute reaction rate coefficients of •OH with CH3OH over a wide range of temperatures (10–2500 K) and pressures (10−1–104 Torr) based on a potential energy surface that has been constructed using a modification of the high accuracy extrapolated ab initio thermochemistry (HEAT) protocol. The calculated results show that the title reaction is nearly pressure-independent when T > 250 K but depends strongly on pressure at lower temperatures. In addition, the preferred mechanism and rate constants are found to be very sensitive to temperature. The reaction pathway CH3OH + •OH → CH3O• + H2O proceeds exclusively through tunneling at exceedingly low temperatures (T ≤ 50 K), typical of those established in interstellar environments. In this regime, the rate constant is found to increase with decreasing temperature, which agrees with low-temperature experimental results. The thermodynamically favored reaction pathway CH3OH + •OH → •CH2OH + H2O becomes dominant at higher temperatures (T ≥ 200 K), such as those found in Earth’s atmosphere as well as combustion environments. By adjusting the ab initio barrier heights slightly, experimental rate constants from 200 to 1250 K can be satisfactorily reproduced.

Two-dimensional electronic-vibrational spectroscopic study of conical intersection dynamics: an experimental and electronic structure study

Abstract: The relaxation from the lowest singlet excited state of the triphenylmethane dyes, crystal violet and malachite green, is studied via two-dimensional electronic-vibrational (2DEV) spectroscopy. After excitation of the dyes at their respective absorption maxima, the ensuing excited state dynamics are tracked by monitoring the C[double bond, length as m-dash]C aromatic stretch. With the aid of electronic structure calculations, the observed transitions in the 2DEV spectra are assigned to specific geometries and a detailed story of the evolution of the nuclear wavepacket as it diffuses on the excited state potential energy surface (PES) and ultimately passes through the conical intersection is developed. Notably, it is revealed that the relaxation of the lowest singlet excited state involves intramolecular charge transfer while the nuclear wavepacket is on the excited state PES. Finally, through analyzing the center line slopes of the measured peaks, we show how both solvent motions and changes in the molecular dipole moment affect the correlation between electronic and vibrational degrees of freedom. This work clearly demonstrates the usefulness of 2DEV spectroscopy in following the motion of nuclear wavepackets after photoexcitation and in studying the interactions between the molecular dipole moment and surrounding solvent environment.

Six-dimensional potential energy surface for NaK-NaK collisions: Gaussian process representation with correct asymptotic form.

Abstract: Constructing accurate global potential energy surfaces (PESs) describing chemically reactive molecule-molecule collisions of alkali metal dimers presents a major challenge. To be suitable for quantum scattering calculations, such PESs must represent accurately three- and four-body interactions, describe conical intersections, and have a proper asymptotic form at the long range. Here, we demonstrate that such global potentials can be obtained by Gaussian Process (GP) regression merged with the analytic asymptotic expansions at the long range. We propose an efficient sampling technique, which allows us to construct an accurate global PES accounting for different chemical arrangements with <2500 ab initio calculations. We apply this method to (NaK)2 and obtain the first global PES for a system of four alkali metal atoms. The resulting surface exhibits a complex landscape including a pair and a quartet of symmetrically equivalent local minima and a seam of conical intersections. The dissociation energy found from our ab initio calculations is 4534 cm−1. This result is reproduced by the GP models with an error of less than 3%. The GP models of the PES allow us to analyze the features of the global PES, representative of general alkali metal four-atom interactions. Understanding these interactions is of key importance in the field of ultracold chemistry.Constructing accurate global potential energy surfaces (PESs) describing chemically reactive molecule-molecule collisions of alkali metal dimers presents a major challenge. To be suitable for quantum scattering calculations, such PESs must represent accurately three- and four-body interactions, describe conical intersections, and have a proper asymptotic form at the long range. Here, we demonstrate that such global potentials can be obtained by Gaussian Process (GP) regression merged with the analytic asymptotic expansions at the long range. We propose an efficient sampling technique, which allows us to construct an accurate global PES accounting for different chemical arrangements with <2500 ab initio calculations. We apply this method to (NaK)2 and obtain the first global PES for a system of four alkali metal atoms. The resulting surface exhibits a complex landscape including a pair and a quartet of symmetrically equivalent local minima and a seam of conical intersections. The dissociation energy found ...

A comparative test of different density functionals for calculations of NH3-SCR over Cu-Chabazite.

Abstract: A general challenge in density functional theory calculations is to simultaneously account for different types of bonds. One such example is reactions in zeolites where both van der Waals and chemical bonds should be described accurately. Here, we use different exchange-correlation functionals to explore O2 dissociation over pairs of Cu(NH3)2+ complexes in Cu-Chabazite. This is an important part of selective catalytic reduction of NOx using NH3 as a reducing agent. The investigated functionals are PBE, PBE+U, PBE+D, PBE+U+D, PBE-cx, BEEF and HSE06+D. We find that the potential energy landscape for O2 activation and dissociation depends critically on the choice of functional. However, the van der Waals contributions are similarly described by the functionals accounting for this interaction. The discrepancies in the potential energy surface are instead related to different descriptions of the Cu-O chemical bond. By investigating the electronic, structural and energetic properties of reference systems including bulk copper oxides and (Cu2O2)2+ enzymatic crystals, we find that the PBE+U approach together with van der Waals corrections provides a reasonable simultaneous accuracy of the different bonds in the systems.

Tunneling Splittings in Water Clusters from Path Integral Molecular Dynamics.

Abstract: We present calculations of tunneling splittings in selected small water clusters, based on a recently developed path integral molecular dynamics (PIMD) method. The ground-rotational-state tunneling motions associated with the largest splittings in the water dimer, trimer, and hexamer are considered, and we show that the PIMD predictions are in very good agreement with benchmark quantum and experimental results. As the tunneling spectra are highly sensitive to both the details of the quantum dynamics and the potential energy surface, our calculations are a validation of the MB-Pol surface as well as the accuracy of PIMD. The favorable scaling of PIMD with system size paves the way for calculations of tunneling splittings in large, nonrigid molecular systems with motions that cannot be treated accurately by other methods, such as the semiclassical instanton.

Anharmonic Vibrational States of Solids from DFT Calculations. Part I: Description of the Potential Energy Surface.

Abstract: A computational approach is presented to compute anharmonic vibrational states of solids from quantum-mechanical DFT calculations by taking into explicit account phonon–phonon couplings via the vib...

Anharmonic Vibrational States of Solids from DFT Calculations. Part II: Implementation of the VSCF and VCI Methods

Abstract: Two methods are implemented in the Crystal program for the calculation of anharmonic vibrational states of solids: the vibrational self-consistent field (VSCF) and the vibrational configuration-interaction (VCI). While the former is a mean-field approach, where each vibrational mode interacts with the average potential of the others, the latter allows for an explicit and complete account of mode-mode correlation. Both schemes are based on the representation of the adiabatic potential energy surface (PES) discussed in Part I, where the PES is expanded in a Taylor's series so as to include up to cubic and quartic terms. The VSCF and VCI methods are formally presented and their numerical parameters discussed. In particular, the convergence of computed anharmonic vibrational states, within the VCI method, is investigated as a function of the truncation of the expansion of the nuclear wave function. The correctness and effectiveness of the implementation is discussed by comparing with available theoretical and experimental data on both molecular and periodic systems. The effect of the adopted basis set and exchange-correlation functional in the description of the PES on computed anharmonic vibrational states is also addressed.

Anomalous kinetics of the reaction between OH and HO2 on an accurate triplet state potential energy surface.

Abstract: The reaction OH + HO2 → H2O + O2 is of great significance in interstellar media, the atmosphere, and combustion. In addition, it presents a prototypical reaction between two non-atom radical species. However, the temperature dependence of its rate coefficients has been debated for several decades. In this work, the rate coefficients are revisited by the quasi-classical trajectory (QCT) approach. To this end, a globally accurate full-dimensional potential energy surface of the ground triplet state for the title reaction is constructed using the permutation invariant polynomial-neural network (PIP-NN) method based on 108 000 points calculated at the level of CCSD(T)-F12a/AVTZ, in which particular attention is paid to the initial guess in the preceding Hartree–Fock procedure to obtain reliable ab initio energies. The QCT rate coefficients are compared to available experimental and theoretical results. It has been found that not only the trend, but also the magnitude, i.e. the large negative temperature dependence at low temperatures, and slightly positive temperature dependence at high temperatures, are consistent with some experiments.

Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations.

Abstract: Quantum mechanics/molecular mechanics (QM/MM) calculations are applied for anharmonic vibrational analyses of biomolecules and solvated molecules. The QM/MM method is implemented into a molecular dynamics (MD) program, GENESIS, by interfacing with external electronic structure programs. Following the geometry optimization and the harmonic normal-mode analysis based on a partial Hessian, the anharmonic potential energy surface (PES) is generated from QM/MM energies and gradients calculated at grid points. The PES is used for vibrational self-consistent field (VSCF) and post-VSCF calculations to compute the vibrational spectrum. The method is first applied to a phosphate ion in solution. With both the ion and neighboring water molecules taken as a QM region, IR spectra of representative hydration structures are calculated by the second-order vibrational quasi-degenerate perturbation theory (VQDPT2) at the level of B3LYP/cc-pVTZ and TIP3P force field. A weight-average of IR spectra over the structures reproduces the experimental spectrum with a mean absolute deviation of 16 cm-1. Then, the method is applied to an enzyme, P450 nitric oxide reductase (P450nor), with the NO molecule bound to a ferric (FeIII) heme. Starting from snapshot structures obtained from MD simulations of P450nor in solution, QM/MM calculations have been carried out at the level of B3LYP-D3/def2-SVP(D). The spin state of FeIII(NO) is likely a closed-shell singlet state based on a ratio of N-O and Fe-NO stretching frequencies (νN-O and νFe-NO) calculated for closed- and open-shell singlet states. The calculated νN-O and νFe-NO overestimate the experimental ones by 120 and 75 cm-1, respectively. The electronic structure and solvation of FeIII(NO) affect the structure around the heme of P450nor leading to an increase in νN-O and νFe-NO.

Near dissociation states for H$_2^+$-He on MRCI and FCI potential energy surfaces

Abstract: A new analytical potential energy surface (PES) has been constructed for H$_2^+$-He using a reproducing kernel Hilbert space (RKHS) representation from an extensive number of $ab initio$ energies computed at the multi-reference and full configuration interaction level of theory. For the MRCI PES the long-range interaction region of the PES is described by analytical functions and is connected smoothly to the short-range interaction region, represented as a RKHS. All ro-vibrational states for the ground electronic state of H$_2^+$-He are calculated using two different methods to determine quantum bound states. Comparing transition frequencies for the near-dissociation states for $ortho$- and $para$-H$_2^+$-He allows assignment of the 15.2 GHz line to a $J=2$ $e/f$ parity doublet of $ortho$-H$_2^+$-He whereas the experimentally determined 21.8 GHz line is only consistent with a $(J=0)$ $\rightarrow$ $(J=1)$ $e/e$ transition in $para$-H$_2^+$-He.

Theoretical study of the decomposition mechanism of C4F7N

Abstract: Investigations into alternative gases to reduce the usage of SF6 have great benefits on global warming issues and the health of maintenance personnel. C4F7N is one of the most remarkable replacements for SF6 owing to its good insulating performance, low global warming potential and non-toxicity. The decomposition mechanism of C4F7N is important in evaluating the insulation performance but it is still not clear. Therefore, the B3LYP/6-311G(d,p) method in conjunction with transition state theory is used to study the decomposition mechanism of C4F7N. Sixteen reactions are found in the decomposition pathways of C4F7N. The optimized configurations and harmonic vibrational frequencies of selected species are very consistent with experimental data to verify the method adopted in this paper. The potential energy surface of these reactions are obtained and the reaction mechanisms are analyzed. The rate constants over 300 K–3500 K relevant to the insulation breakdown temperature are computed based on the above quantum chemistry calculations and dominant reactions in different temperature regions are selected. For example, reaction R5 (C4F7N → TS2 → FCN + CF2CFCF3) is the most important reaction leading to the dissociation of C4F7N below 600 K, while reaction R2 (C4F7N → C2F4CN + CF3) takes the place of reaction R5 over 600 K to 3300 K and reaction R3 (C4F7N → TS1 → CF2CFCN + CF4) becomes dominant above 700 K; reaction R15 (CF2CFCNCF3 → CF2CFCN + CF3) plays the major role in the generation of CF3 with the overwhelming contribution rate. The results obtained here are expected to construct a relatively complete C4F7N decomposition scheme, including the main byproduct formation processes and to lay a theoretical basis for the investigation of its insulation performance.

Reduced rovibrational coupling Cartesian dynamics for semiclassical calculations: Application to the spectrum of the Zundel cation

Abstract: We study the vibrational spectrum of the protonated water dimer, by means of a divide-and-conquer semiclassical initial value representation of the quantum propagator, as a first step in the study of larger protonated water clusters. We use the potential energy surface from the work of Huang et al. [J. Chem. Phys. 122, 044308 (2005)]. To tackle such an anharmonic and floppy molecule, we employ fully Cartesian dynamics and carefully reduce the coupling to global rotations in the definition of normal modes. We apply the time-averaging filter and obtain clean power spectra relative to suitable reference states that highlight the spectral peaks corresponding to the fundamental excitations of the system. Our trajectory-based approach allows for the physical interpretation of the very challenging proton transfer modes. We find that it is important, for such a floppy molecule, to selectively avoid initially exciting lower energy modes, in order to obtain cleaner spectra. The estimated vibrational energies display a mean absolute error (MAE) of ∼29 cm-1 with respect to available multiconfiguration time-dependent Hartree calculations and MAE ∼ 14 cm-1 when compared to the optically active experimental excitations of the Ne-tagged Zundel cation. The reasonable scaling in the number of trajectories for Monte Carlo convergence is promising for applications to higher dimensional protonated cluster systems.

Intramolecular stretching vibrational states and frequency shifts of (H2)2 confined inside the large cage of clathrate hydrate from an eight-dimensional quantum treatment using small basis sets

Abstract: We report the results of calculations pertaining to the HH intramolecular stretching fundamentals of (p-H2)2 encapsulated in the large cage of structure II clathrate hydrate. The eight-dimensional (8D) quantum treatment assumes rotationless (j = 0) H2 moieties and a rigid clathrate structure but is otherwise fully coupled. The (H2)2-clathrate interaction is constructed in a pairwise-additive fashion, by combining the ab initio H2-H2O pair potential for flexible H2 and rigid H2O [D. Lauvergnat et al., J. Chem. Phys. 150, 154303 (2019)] and the six-dimensional (6D) H2-H2 potential energy surface [R. J. Hinde, J. Chem. Phys. 128, 154308 (2008)]. The calculations are performed by first solving for the eigenstates of a reduced-dimension 6D "intermolecular" Hamiltonian extracted from the full 8D Hamiltonian by taking the H2 moieties to be rigid. An 8D contracted product basis for the solution of the full problem is then constructed from a small number of the lowest-energy 6D intermolecular eigenstates and two discrete variable representations covering the H2-monomer internuclear distances. Converged results are obtained already by including just the two lowest intermolecular eigenstates in the final 8D basis of dimension 128. The two HH vibrational stretching fundamentals are computed for three hydrate domains having an increasing number of H2O molecules. For the largest domain, the two fundamentals are found to be site-split by ∼0.5 cm-1 and to be redshifted by about 24 cm-1 from the free-H2 monomer stretch frequency, in excellent agreement with the experimental value of 26 cm-1. A first-order perturbation theory treatment gives results that are nearly identical to those of the 8D quantum calculations.

Mapping the polymorphic transformation gateway vibration in crystalline 1,2,4,5-tetrabromobenzene

Abstract: The thermosalient behavior of 1,2,4,5-tetrabromobenzene (TBB) is related to a temperature-induced polymorphic structural change. The mechanism behind the phase transition has been investigated in this work using low-frequency (10–250 cm−1) Raman spectroscopy and solid-state density functional theory simulations. Careful adjustments of the probing laser power permitted thermal control of the polymorph populations and enabled high-quality Raman vibrational spectra to be obtained for both the β (low temperature) and γ (high temperature) forms of TBB. Numerous well-defined vibrational features appear in the Raman spectra of both polymorphs which could be assigned to specific motions of the solid-state TBB molecules. It was discovered that the lowest-frequency vibration at 15.5 cm−1 in β-TBB at 291 K is a rotational mode that functions as a gateway for inducing the polymorphic phase transition to γ-TBB, and serves as the initiating step in the storage of mechanical strain for subsequent macroscopic release. Computationally mapping the potential energy surface along this vibrational coordinate reveals that the two TBB polymorphs are separated by a 2.40 kJ mol−1 barrier and that γ-TBB exhibits an enhanced cohesion energy that stabilizes its structure.

Stereodynamical control of product branching in multi-channel barrierless hydrogen abstraction of CH3OH by F.

Abstract: Hydrogen abstraction from methanol (CH3OH) by F atoms presents an ideal proving ground to investigate dynamics of multi-channel reactions, because two types of hydrogen can be abstracted from the methanol molecule leading to the HF + CH3O and HF + CH2OH products. Using the quasi-classical trajectory approach on a globally accurate potential energy surface based on high-level ab initio calculations, this work reports a comprehensive dynamical investigation of this multi-channel reaction, yielding measurable attributes including integral and differential cross sections, as well as branching ratios. It is shown that while complex-forming and direct mechanisms coexist at low collision energies, these barrierless reaction channels are dominated at high energies by the direct mechanism, in which the reaction is only possible for trajectories entering into the respective dynamical cones of acceptance. Perhaps more importantly, the non-statistical product branching is found to be dictated by unique stereodynamics in the entrance channels.

Vibrational Spectroscopy of N3- in the Gas and Condensed Phase.

Abstract: Azido-derivatized amino acids are potentially useful, positionally resolved spectroscopic probes for studying the structural dynamics of proteins and macromolecules in solution. To this end, a computational model for the vibrational modes of N3– based on accurate electronic structure calculations and a reproducing kernel Hilbert space representation of the potential energy surface for the internal degrees of freedom is developed. Fully dimensional quantum bound state calculations yield the antisymmetric stretch vibration at 1974 cm–1 compared with 1986 cm–1 from experiment. This mode shifts by 64 cm–1 (from the frequency distribution) and 74 cm–1 (from the IR line shape) to the blue, respectively, compared with 61 cm–1 from experiment for N3– in water. The decay time of the frequency fluctuation correlation function is 1.1 ps, which is in good agreement with experiment (1.2–1.3 ps) and the full width at half maximum of the asymmetric stretch in solution is 18.5 cm–1 compared with 25.2 cm–1 from experiment...