Potential energy surfaces governing chemical reactions involving carbon, oxygen and hydrogen

The lowest singlet states of O[subscript]3 in C[subscript] 2v are studied in the Full Optimized Reaction Space (FORS) MCSCF level of theory with an extended atomic basis set plus polarization functions. The [superscript]1A\u27 ground state potential energy surface contains two minima. The upper minimum lies 29.8 kcal/mole above the ground state minimum and most importantly above the O[subscript]2([superscript]3[sigma][subscript]g[superscript]-) + O([superscript]3P) dissociation limit. It resembles a ring structure having D[subscript] 3h symmetry. The potential energy surface governing the C[subscript] 2v restricted ring opening of the cyclic O[subscript]3 to the ground state is also computed. A conical intersection is found between the 1-[superscript]1A[subscript]1 and 2-[superscript]1A[subscript]1 potential energy surfaces. This first case of an intersection of two states of the same symmetry in a real system is definitively proved by monitoring the sign of the wavefunction on a closed loop around it;Ab-initio calculations elucidating the structure, the ring opening and the dissociation process of the cyclic CO[subscript]2 isomer are reported. The optimal isosceles-triangle (C[subscript] 2v) geometries corresponding to the C[subscript] 2v constraint dissociation OCO → C + O[subscript]2 are determined. The entire C[subscript] 2v surface is computed, revealing the existence of a metastable cyclic carbene-type species corresponding to a local minimum 137.6 kcal/mole above the linear total minimum. Finally, energies are determined for various relevant cross sections with lower symmetry (C[subscript] s), i.e. for asymmetric bond lengths;Extended basis set calculations for the key regions of the ground state [superscript]1A[subscript]1 cyclopropylidene (C[subscript] 2v) to allene (D[subscript] 2d) ring opening reaction surface are performed within the FORS MCSCF framework. Optimized geometries of the reactant, product, transition state and allene isomerization transition state as well as the barrier for the ring opening and the allene isomerization together with the overall exothermicity are reported in the various levels of MCSCF approximation incorporating FORS spaces ranging from 20 to 1764 configurations. The reaction path from the transition state passes from a point where the two surfaces corresponding to the [superscript]1A\u27 and [superscript]1A\u27\u27 states intersect each other. Explanations for the various features of the potential energy surface governing the ring opening of cyclopropylidene to allene are obtained through localized quasi-atomic FORS MO\u27s. ftn*Performed under Contract No. W-7405-Eng-82 for the U.S. Dept. of Energ

Helical Organic and Inorganic Polymers

Despite being a staple of synthetic plastics and biomolecules, helical polymers are scarcely studied with Gaussian-basis-set {\it ab initio} electron-correlated methods on an equal footing with molecules. This article introduces an {\it ab initio} second-order many-body Green's-function [MBGF(2)] method with nondiagonal, frequency-dependent Dyson self-energy for infinite helical polymers using screw-axis-symmetry-adapted Gaussian-spherical-harmonics basis functions. Together with the Gaussian-basis-set density-functional theory for energies, analytical atomic forces, translational-period force, and helical-angle force, it can compute correlated energy, quasiparticle energy bands, structures, and vibrational frequencies of an infinite helical polymer, which smoothly converge at the corresponding oligomer results. These methods can handle incommensurable structures, which have an infinite translational period and are hard to characterize by any other method, just as efficiently as commensurable structures. We apply these methods to polyethylene ($2/1$ helix), polyacetylene (Peierls' system), and polytetrafluoroethylene ($13/6$ helix) to establish the quantitative accuracy of MBGF(2)/cc-pVDZ in simulating their (angle-resolved) ultraviolet photoelectron spectra, and of B3LYP/cc-pVDZ or 6-31G** in reproducing their structures, infrared and Raman band positions, phonon dispersions, and (coherent and incoherent) inelastic neutron scattering spectra. We then predict the same properties for infinitely catenated chains of nitrogen or oxygen and discuss their possible metastable existence under ambient conditions. They include planar zigzag polyazene (N$_2$)$_x$ (Peierls' system), $11/3$-helical isotactic polyazane (NH)$_x$, $9/4$-helical isotactic polyfluoroazane (NF)$_x$, and $7/2$-helical polyoxane (O)$_x$ as potential high-energy-density materials

The Melting Temperature of Liquid Water with the Effective Fragment Potential

The direct simulation of the solid–liquid water interface with the effective fragment potential (EFP) via the constant enthalpy and pressure (NPH) ensemble was used to estimate the melting temperature (Tm) of ice-Ih. Initial configurations and velocities, taken from equilibrated constant pressure and temperature (NPT) simulations at P = 1 atm and T = 305 K, 325 K and 399 K, respectively, yielded corresponding Tm values of 378 ± 16 K, 382 ± 14 K and 384 ± 15 K. These estimates are consistently higher than experiment, albeit to the same degree as previously reported estimates using density functional theory (DFT)-based Born–Oppenheimer simulations with the Becke-Lee–Yang–Parr functional plus dispersion corrections (BLYP-D)

Reducing Down(stream)time: Pretraining Molecular GNNs using Heterogeneous AI Accelerators

The demonstrated success of transfer learning has popularized approaches that involve pretraining models from massive data sources and subsequent finetuning towards a specific task. While such approaches have become the norm in fields such as natural language processing, implementation and evaluation of transfer learning approaches for chemistry are in the early stages. In this work, we demonstrate finetuning for downstream tasks on a graph neural network (GNN) trained over a molecular database containing 2.7 million water clusters. The use of Graphcore IPUs as an AI accelerator for training molecular GNNs reduces training time from a reported 2.7 days on 0.5M clusters to 1.2 hours on 2.7M clusters. Finetuning the pretrained model for downstream tasks of molecular dynamics and transfer to a different potential energy surface took only 8.3 hours and 28 minutes, respectively, on a single GPU.Comment: Machine Learning and the Physical Sciences Workshop at the 36th conference on Neural Information Processing Systems (NeurIPS

The Effective Fragment Potential: Small Clusters and Radial Distribution Functions

The effective fragment potential (EFP) method for treating solventeffects provides relative energies and structures that are in excellent agreement with the analogous fully quantum [i.e., Hartree-Fock (HF), density functional theory(DFT), and second order perturbation theory (MP2)] results for small water clusters. The ability of the method to predict bulk water properties with a comparable accuracy is assessed by performing EFP molecular dynamics simulations. The resulting radial distribution functions (RDF) suggest that as the underlying quantum method is improved from HF to DFT to MP2, the agreement with the experimental RDF also improves. The MP2-based EFP method yields a RDF that is in excellent agreement with experiment

Efficient and Accurate Fragmentation Methods

Three novel fragmentation methods that are available in the electronic structure program GAMESS (general atomic and molecular electronic structure system) are discussed in this Account. The fragment molecular orbital (FMO) method can be combined with any electronic structure method to perform accurate calculations on large molecular species with no reliance on capping atoms or empirical parameters. The FMO method is highly scalable and can take advantage of massively parallel computer systems. For example, the method has been shown to scale nearly linearly on up to 131 000 processor cores for calculations on large water clusters. There have been many applications of the FMO method to large molecular clusters, to biomolecules (e.g., proteins), and to materials that are used as heterogeneous catalysts. The effective fragment potential (EFP) method is a model potential approach that is fully derived from first principles and has no empirically fitted parameters. Consequently, an EFP can be generated for any molecule by a simple preparatory GAMESS calculation. The EFP method provides accurate descriptions of all types of intermolecular interactions, including Coulombic interactions, polarization/induction, exchange repulsion, dispersion, and charge transfer. The EFP method has been applied successfully to the study of liquid water, π-stacking in substituted benzenes and in DNA base pairs, solvent effects on positive and negative ions, electronic spectra and dynamics, non-adiabatic phenomena in electronic excited states, and nonlinear excited state properties. The effective fragment molecular orbital (EFMO) method is a merger of the FMO and EFP methods, in which interfragment interactions are described by the EFP potential, rather than the less accurate electrostatic potential. The use of EFP in this manner facilitates the use of a smaller value for the distance cut-off (Rcut). Rcut determines the distance at which EFP interactions replace fully quantum mechanical calculations on fragment–fragment (dimer) interactions. The EFMO method is both more accurate and more computationally efficient than the most commonly used FMO implementation (FMO2), in which all dimers are explicitly included in the calculation. While the FMO2 method itself does not incorporate three-body interactions, such interactions are included in the EFMO method via the EFP self-consistent induction term. Several applications (ranging from clusters to proteins) of the three methods are discussed to demonstrate their efficacy. The EFMO method will be especially exciting once the analytic gradients have been completed, because this will allow geometry optimizations, the prediction of vibrational spectra, reaction path following, and molecular dynamics simulations using the method

Ab initio molecular dynamics of liquid water using embedded-fragment second-order many-body perturbation theory towards its accurate property prediction

A direct, simultaneous calculation of properties of a liquid using an ab initio electron-correlated theory has long been unthinkable. Here we present structural, dynamical, and response properties of liquid water calculated by ab initio molecular dynamics using the embedded-fragment spin-component-scaled second-order many-body perturbation method with the aug-cc-pVDZ basis set. This level of theory is chosen as it accurately and inexpensively reproduces the water dimer potential energy surface from the coupled-cluster singles, doubles, and noniterative triples with the augcc-pVQZ basis set, which is nearly exact. The calculated radial distribution function, self-diffusion coefficient, coordinate number, and dipole moment, as well as the infrared and Raman spectra are in excellent agreement with experimental results. The shapes and widths of the OH stretching bands in the infrared and Raman spectra and their isotropic-anisotropic Raman noncoincidence, which reflect the diverse local hydrogen-bond environment, are also reproduced computationally. The simulation also reveals intriguing dynamic features of the environment, which are difficult to probe experimentally, such as a surprisingly large fluctuation in the coordination number and the detailed mechanism by which the hydrogen donating water molecules move across the first and second shells, thereby causing this fluctuationopen