642 research outputs found
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 ( helix),
polyacetylene (Peierls' system), and polytetrafluoroethylene ( 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) (Peierls'
system), -helical isotactic polyazane (NH), -helical isotactic
polyfluoroazane (NF), and -helical polyoxane (O) as potential
high-energy-density materials
Ewald methods for polarizable surfaces with application to hydroxylation and hydrogen bonding on the (012) and (001) surfaces of alpha-Fe2O3
We present a clear and rigorous derivation of the Ewald-like method for
calculation of the electrostatic energy of the systems infinitely periodic in
two-dimensions and of finite size in the third dimension (slabs) which is
significantly faster than existing methods. Molecular dynamics simulations
using the transferable/polarizable model by Rustad et al. were applied to study
the surface relaxation of the nonhydroxylated, hydroxylated, and solvated
surfaces of alpha-Fe2O3 (hematite). We find that our nonhydroxylated structures
and energies are in good agreement with previous LDA calculations on
alpha-alumina by Manassidis et al. [Surf. Sci. Lett. 285, L517, 1993]. Using
the results of molecular dynamics simulations of solvated interfaces, we define
end-member hydroxylated-hydrated states for the surfaces which are used in
energy minimization calculations. We find that hydration has a small effect on
the surface structure, but that hydroxylation has a significant effect. Our
calculations, both for gas-phase and solution-phase adsorption, predict a
greater amount of hydroxylation for the (012) surface than for the (001)
surface. Our simulations also indicate the presence of four-fold coordinated
iron ions on the (001) surface.Comment: 23 pages, REVTeX (LaTeX), 8 figures not included, e-mail to
[email protected], paper accepted in Surface Scienc
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)
Extreme Acceleration of Graph Neural Network-based Prediction Models for Quantum Chemistry
Molecular property calculations are the bedrock of chemical physics.
High-fidelity \textit{ab initio} modeling techniques for computing the
molecular properties can be prohibitively expensive, and motivate the
development of machine-learning models that make the same predictions more
efficiently. Training graph neural networks over large molecular databases
introduces unique computational challenges such as the need to process millions
of small graphs with variable size and support communication patterns that are
distinct from learning over large graphs such as social networks. This paper
demonstrates a novel hardware-software co-design approach to scale up the
training of graph neural networks for molecular property prediction. We
introduce an algorithm to coalesce the batches of molecular graphs into fixed
size packs to eliminate redundant computation and memory associated with
alternative padding techniques and improve throughput via minimizing
communication. We demonstrate the effectiveness of our co-design approach by
providing an implementation of a well-established molecular property prediction
model on the Graphcore Intelligence Processing Units (IPU). We evaluate the
training performance on multiple molecular graph databases with varying degrees
of graph counts, sizes and sparsity. We demonstrate that such a co-design
approach can reduce the training time of such molecular property prediction
models from days to less than two hours, opening new possibilities for
AI-driven scientific discovery
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
Anomalously Strong Effect of the Ion Sign on the Thermochemistry of Hydrogen Bonded Aqueous Clusters of Identical Chemical Composition
The sign preference of hydrogen bonded aqueous ionic clusters X±(H2O)i (n =1–5, X = F; Cl; Br) has been investigated using the Density Functional Theory and ab initio MP2 method. The present study indicates the anomalously large difference in formation free energies between cations and anions of identical chemical composition. The effect of vibrational anharmonicity on stepwise Gibbs free energy changes has been investigated, and possible uncertainties associated with the harmonic treatment of vibrational spectra have been discussed
- …