Search

This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar's development in more than thirty years of its existence. [ABSTRACT FROM AUTHOR]

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.

A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

We report a fragment-based electronic structure method, intended for the study of clusters and molecular liquids, that incorporates electronic polarization (induction) in a self-consistent fashion but treats intermolecular exchange and dispersion interactions perturbatively, as post-self-consistent field corrections, using a form of pairwise symmetry-adapted perturbation theory. The computational cost of the method scales quadratically as a function of the number of fragments (monomers), but could be made to scale linearly by exploiting distance-dependent thresholds. Extensive benchmark calculations are reported using the S22 database of high-level ab initio binding energies for dimers, and we find that average errors can be reduced to <1 kcal/mol with a suitable choice of basis set. Comparison to ab initio benchmarks for water clusters as large as (H2O)20 demonstrates that the method recovers >=90% of the binding energy in these systems, at a tiny fraction of the computational cost. As such, this approach represents a promising path toward accurate, systematically improvable, and parameter-free simulation of molecular liquids. [ABSTRACT FROM AUTHOR]

Previously, we reported an electron-water pseudopotential designed to be used in conjunction with a polarizable water model, in order to describe the hydrated electron [L. D. Jacobson et al., J. Chem. Phys. 130, 124115 (2009)]. Subsequently, we found this model to be inadequate for the aqueous electron in bulk water, and here we report a reparametrization of the model. Unlike the previous model, the current version is not fit directly to any observables; rather, we use an ab initio exchange-correlation potential, along with a repulsive potential that is fit to reproduce the density maximum of the excess electron's wave function within the static-exchange approximation. The new parametrization performs at least as well as the previous model, as compared to ab initio benchmarks for (H2O)n- clusters, and also predicts reasonable values for the diffusion coefficient, radius of gyration, and absorption maximum of the bulk species. The new model predicts a vertical electron binding energy of 3.7 eV in bulk water, which is 1.4 eV smaller than the value obtained using nonpolarizable models; the difference represents the solvent's electronic reorganization energy following electron detachment. We find that the electron's first solvation shell is quite loose, which may be responsible for the electron's large, positive entropy of hydration. Many-body polarization alters the electronic absorption line shape in a qualitative way, giving rise to a high-energy tail that is observed experimentally but is absent in previous simulations. In our model, this feature arises from spatially diffuse excited states that are bound only by electronic reorganization (i.e., solvent polarization) following electronic excitation. [ABSTRACT FROM AUTHOR]

Previously, Turi and Borgis [J. Chem. Phys. 117, 6186 (2002)] parametrized an electron-water interaction potential, intended for use in simulations of hydrated electrons, by considering H2O- in the “static exchange” (essentially, frozen-core Hartree–Fock) approximation, then applying an approximate Phillips–Kleinman procedure to construct a one-electron pseudopotential representing the electron-water interaction. To date, this pseudopotential has been used exclusively in conjunction with a simple point charge water model that is parametrized for bulk water and yields poor results for small, neutral water clusters. Here, we extend upon the work of Turi and Borgis by reparametrizing the electron-water pseudopotential for use with the AMOEBA water model, which performs well for neutral clusters. The result is a one-electron model Hamiltonian for (H2O)n-, in which the one-electron wave function polarizes the water molecules, and vice versa, in a fully self-consistent fashion. The new model is fully variational and analytic energy gradients are available. We have implemented the new model using a modified Davidson algorithm to compute eigenstates, with the unpaired electron represented on a real-space grid. Comparison to ab initio electronic structure calculations for (H2O)n- cluster isomers ranging from n=2 to n=35 reveals that the new model is significantly more accurate than the Turi–Borgis model, for both relative isomer energies and for vertical electron detachment energies. Electron-water polarization interactions are found to be much more significant for cavity states of the unpaired electron than for surface states. [ABSTRACT FROM AUTHOR]

The electronic absorption spectrum of the aqueous electron in bulk water is simulated by using long-range-corrected time-dependent density functional theory as well as mixed quantum/classical molecular dynamics based on a one-electron model in which electron-water polarization is treated self-consistently. Both methods have shown that the high-energy Lorentzian tail has come from delocalized bound-state excitations of the electron rather than bound-to-continuum excitations and excited states in the blue tail are bound only by polarization of the solvent electron density.