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]

A pseudospectral implementation of nonadiabatic derivative couplings in the Tamm–Dancoff approximation is reported, and the accuracy and efficiency of the pseudospectral nonadiabatic derivative couplings are studied. Our results demonstrate that the pseudospectral method provides mean absolute errors of 0.2%–1.9%, while providing a significant speedup. Benchmark calculations on fullerenes (Cn, n up to 100) using B3LYP achieved 10- to 15-fold, 8- to 17-fold, and 43- to 75-fold speedups for 6-31G**, 6-31++G**, and cc-pVTZ basis sets, respectively, when compared to the conventional spectral method. [ABSTRACT FROM AUTHOR]

The accuracy and efficiency of time-dependent density functional theory (TDDFT) excited state gradient calculations using the pseudospectral method are presented. TDDFT excited state geometry optimizations of the G2 test set molecules, the organic fluorophores with large Stokes shifts, and the Pt-complexes show that the pseudospectral method gives average errors of 0.01–0.1 kcal/mol for the TDDFT excited state energy, 0.02–0.06 pm for the bond length, and 0.02–0.12° for the bond angle when compared to the results from conventional TDDFT. TDDFT gradient calculations of fullerenes (Cn, n up to 540) with the B3LYP functional and 6-31G** basis set show that the pseudospectral method provides 8- to 14-fold speedups in the total wall clock time over the conventional methods. The pseudospectral TDDFT gradient calculations with a diffuse basis set give higher speedups than the calculations for the same basis set without diffuse functions included. [ABSTRACT FROM AUTHOR]

This paper describes an empirical localized orbital correction model which improves the accuracy of density functional theory (DFT) methods for the prediction of thermochemical properties for molecules of first and second row elements. The B3LYP localized orbital correction version of the model improves B3LYP DFT atomization energy calculations on the G3 data set of 222 molecules from a mean absolute deviation (MAD) from experiment of 4.8 to 0.8 kcal/mol. The almost complete elimination of large outliers and the substantial reduction in MAD yield overall results comparable to the G3 wave-function-based method; furthermore, the new model has zero additional computational cost beyond standard DFT calculations. The following four classes of correction parameters are applied to a molecule based on standard valence bond assignments: corrections to atoms, corrections to individual bonds, corrections for neighboring bonds of a given bond, and radical environmental corrections. Although the model is heuristic and is based on a 22 parameter multiple linear regression to experimental errors, each of the parameters is justified on physical grounds, and each provides insight into the fundamental limitations of DFT, most importantly the failure of current DFT methods to accurately account for nondynamical electron correlation. [ABSTRACT FROM AUTHOR]

We have developed an algorithm based upon pseudospectral (PS) ab initio electronic structure methods for evaluating nuclear magnetic shielding constants using gauge-including atomic orbitals (GIAOs) in the spin-restricted and spin-unrestricted formalisms of Hartree–Fock (HF) theory and density-functional theory (DFT). The nuclear magnetic shielding constants for both 1H and 13C calculated using PS methodology for 21 small molecules have absolute mean errors of less than 0.3 ppm in comparison with analytic integral results. CPU timing comparisons between PS methods and conventional methods carried out for seven large molecules ranging from 510 to 1285 basis functions demonstrate that the PS methods are an order of magnitude more efficient than the conventional methods. PS-HF was between 9 and 26 times faster than conventional integral technology, and PS-DFT (Becke three-parameter Lee–Yang–Parr) was between 6 and 21 times faster. [ABSTRACT FROM AUTHOR]

We have developed algorithms based on pseudospectral (PS) ab initio electronic structure methods for solving the first- and second-order Hartree–Fock/Kohn–Sham equations and evaluating molecular polarizabilities and first- and second-order hyperpolarizabilities in the spin-restricted and spin-unrestricted formalisms at the Hartree–Fock (HF) and density functional theory (DFT) levels. We carry out calculations on 50 small molecules to test the accuracy of the PS approach. Our results demonstrate that the molecular polarizability α computed by the PS method is essentially identical to the value obtained from conventional methods for both HF and DFT calculations, while the first-order hyperpolarizability β and second-order hyperpolarizability γ have mean unsigned percentage differences of 1.26% and 0.62% (HF) and 0.78% and 0.65% (DFT), respectively. We also present CPU timing comparisons between the PS and conventional methods at the 6-31 G** level for 14 molecules having 185 to 1185 basis functions. The timing results show that the PS method is 25 (PS-HF) and 13 (PS-DFT) times faster than the conventional method for a system with 500 basis functions. The PS methods are found scale as N2.70 (PS-HF) and N2.40 (PS-DFT), while the conventional methods scale as N2.93 (PRISM-HF) and N2.87 (PRISM-DFT), where N is the number of basis functions. [ABSTRACT FROM AUTHOR]

Issues concerning the examination of intermediates in the catalytic cycle of soluble methane monooxygenase hydroxylase (MMOH) using ab initio density functional theory are discussed. A comparison made between these quantum chemical models and the X-ray crystal structure of MMOH has revealed a water molecule within the structure, which is important for catalytic activity.

Density functional theory (DFT) and localized orbital methods for performing correlated ab initio electronic structure calculations for large molecules are analyzed. It is shown that DFT methods are the most accurate and easy to use for a variety of applications. However, localized orbital methods are the most practical alternatives in cases where DFT methods are unapplicable. Comparisons between DFT and localized orbital methods are discussed.

A polarizable force field, and associated continuum solvation model, have been developed for the explicit purpose of computing and studying the energetics and structural features of protein binding to the wide range of ligands with potential for medicinal applications. Parameters for the polarizable force field (PFF) are derived from gas-phase ab initio calculations and then utilized for applications in which the protein binding to ligands occurs in aqueous solvents, wherein the charge distributions of proteins and ligands can be dramatically altered. The continuum solvation model is based on a self-consistent reaction field description of solvation, incorporating an analytical gradient, that allows energy minimizations (and, potentially, molecular dynamics simulations) of protein/ligand systems in continuum solvent. This technology includes a nonpolar model describing the cost of cavity formation, and van der Waals interactions, between the continuum solvent and protein/ligand solutes. Tests of the structural accuracy and computational stability of the methodology, and timings for energy minimizations of proteins and protein/ligand systems in the condensed phase, are reported. In addition, the derivation of polarizability, electrostatic, exchange repulsion, and torsion parameters from ab initio data is described, along with the use of experimental solvation energies for determining parameters for the solvation model.