Advances in methods and algorithms in a modern quantum chemistry program package

Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.     

TensorView: A software tool for displaying NMR tensors

The representation of nuclear magnetic resonance (NMR) tensors as surfaces on three-dimensional molecular models is an information-rich presentation that highlights the geometric relationship between tensor principal components and the underlying molecular and electronic structure. Here, we describe a new computational tool, TensorView, for depicting NMR tensors on the molecular framework. This package makes use of the graphical interface and built-in molecular display functionality present within the Mathematica programming environment and is robust for displaying tensor properties from a broad range of commercial and user-specific computational chemistry packages. Two mathematical forms for representing tensor interaction surfaces are presented, the popular ellipsoidal construct and the more technically correct “ovaloid” form. Examples are provided for chemical shielding and shift tensors, dipole–dipole and quadrupolar couplings, and atomic anisotropic displacement parameters (thermal ellipsoids) derived from NMR crystallography.     

An extensible interface for QM/MM molecular dynamics simulations with AMBER

We present an extensible interface between the AMBER molecular dynamics (MD) software package and electronic structure software packages for quantum mechanical (QM) and mixed QM and classical molecular mechanical (MM) MD simulations within both mechanical and electronic embedding schemes. With this interface, ab initio wave function theory and density functional theory methods, as available in the supported electronic structure software packages, become available for QM/MM MD simulations with AMBER. The interface has been written in a modular fashion that allows straight forward extensions to support additional QM software packages and can easily be ported to other MD software. Data exchange between the MD and QM software is implemented by means of files and system calls or the message passing interface standard. Based on extensive tests, default settings for the supported QM packages are provided such that energy is conserved for typical QM/MM MD simulations in the microcanonical ensemble. Results for the free energy of binding of calcium ions to aspartate in aqueous solution comparing semiempirical and density functional Hamiltonians are shown to demonstrate features of this interface. © 2013 Wiley Periodicals, Inc.     

Ab initio calculation of anisotropic magnetic properties of complexes. I. Unique definition of pseudospin Hamiltonians and their derivation

A methodology for the rigorous nonperturbative derivation of magnetic pseudospin Hamiltonians of mononuclear complexes and fragments based on ab initio calculations of their electronic structure is described. It is supposed that the spin-orbit coupling and other relativistic effects are already taken fully into account at the stage of quantum chemistry calculations of complexes. The methodology is based on the establishment of the correspondence between the ab initio wave functions of the chosen manifold of multielectronic states and the pseudospin eigenfunctions, which allows to define the pseudospin Hamiltonians in the unique way. Working expressions are derived for the pseudospin Zeeman and zero-field splitting Hamiltonian corresponding to arbitrary pseudospins. The proposed calculation methodology, already implemented in the SINGLE_ANISO module of the MOLCAS-7.6 quantum chemistry package, is applied for a first-principles evaluation of pseudospin Hamiltonians of several complexes exhibiting weak, moderate, and very strong spin-orbit coupling effects.     

A new algorithm to handle finite nuclear mass effects in electronic calculations: the ISOTOPE program

We report the development of a simple algorithm to modify quantum chemistry codes based on the LCAO procedure, to account for the isotope problem in electronic structure calculations. No extra computations are required compared to standard Born-Oppenheimer calculations. An upgrade of the Gamess package called ISOTOPE is presented, and its applicability is demonstrated in some examples.     

Gabedit—A graphical user interface for computational chemistry softwares

Gabedit is a freeware graphical user interface, offering preprocessing and postprocessing adapted (to date) to nine computational chemistry software packages. It includes tools for editing, displaying, analyzing, converting, and animating molecular systems. A conformational search tool is implemented using a molecular mechanics or a semiempirical potential. Input files can be generated for the computational chemistry software supported by Gabedit. Some molecular properties of interest are processed directly from the output of the computational chemistry programs; others are calculated by Gabedit before display. Molecular orbitals, electron density, electrostatic potential, nuclear magnetic resonance shielding density, and any other volumetric data properties can be displayed. It can display electronic circular dichroism, UV–visible, infrared, and Raman‐computed spectra after a convolution. Gabedit can generate a Povray file for geometry, surfaces, contours, and color‐coded planes. Output can be exported to a selection of popular image and vector graphics file formats; the program can also generate a series of pictures for animation. Quantum mechanical electrostatic potentials can be calculated using the partial charges on atoms, or by solving the Poisson equation using the multigrid method. The atoms in molecule charges can also be calculated. Gabedit is platform independent. The code is distributed under free open source X11 style license and is available at http://gabedit.sourceforge.net/ . © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Evaluation of the Coulomb energy in relativistic self-consistent-field theory

 Computational schemes are presented with which to evaluate the electrostatic Coulomb energy in relativistic molecular electronic structure calculations using a basis of four-component Dirac spinor amplitudes. We demonstrate that algorithms may be constructed and implemented which differ only in minor details from those in common use in nonrelativistic quantum chemistry, and that the four-component formalism is neither as complicated nor as expensive as has been suggested recently in the literature. Spherically symmetrical atomic basis sets are presented which indicate that accurate representations of the Coulomb energy may be obtained using modest expansions of the electronic density in a scalar auxiliary basis set of spherical harmonic Gaussian-type functions. Received: 15 April 2002 / Accepted: 15 May 2002 / Published online: 29 July 2002     

Heuristic approaches to the optimization of acceptor systems in bulk heterojunction cells: a computational study

A computational protocol combining a heuristic search based on genetic algorithms (GAs) and quantum chemistry methods is implemented and applied to a family of acceptor compounds based on the 9,9′-bifluorenylidene backbone, to be coupled with the poly-3(hexylthiophene) polymer (donor) in a bulk heterojunction solar cell. Highly performing candidates are generated via GA from an initial generation, after a number of iterations (i.e., new generations), under the selective pressure of electronic constrains calculated at density functional theory level. The combination of heuristic search techniques and advanced electronic structure methodologies for characterization seems to be amenable to further applications in the field of molecular design.     

Computational Characterization of Nanosystems

Nanosystems play an important role in many applications. Due to their complexity, it is challenging to accurately characterize their structure and properties. An important means to reach such a goal is computational simulation, which is grounded on ab initio electronic structure calculations. Low scaling and accurate electronic-structure algorithms have been developed in recent years. Especially, the efficiency of hybrid density functional calculations for periodic systems has been significantly improved. With electronic structure information, simulation methods can be developed to directly obtain experimentally comparable data. For example, scanning tunneling microscopy images can be effectively simulated with advanced algorithms. When the system we are interested in is strongly coupled to environment, such as the Kondo effect, solving the hierarchical equations of motion turns out to be an effective way of computational characterization. Furthermore, the first principles simulation on the excited state dynamics rapidly emerges in recent years, and nonadiabatic molecular dynamics method plays an important role. For nanosystem involved chemical processes, such as graphene growth, multiscale simulation methods should be developed to characterize their atomic details. In this review, we review some recent progresses in methodology development for computational characterization of nanosystems. Advanced algorithms and software are essential for us to better understand of the nanoworld.     

Registering the Amica electronic structure code in the extensible computational chemistry environment

We describe the integration and use of the Amica software package ("Atoms & Molecules In Chemical Accuracy") within the Extensible Computational Chemistry Environment (Ecce). Amica is capable of accurately solving the electronic Schrodinger equation of small atoms and molecules using terms that are linear in the interelectronic distances, r(12), on multireference level of theory, but it requires expert knowledge to configure and execute its algorithms. Ecce is a comprehensive suite of tools that support the computational chemistry research processes of computation setup, execution, and analysis through a convenient graphical user interface. Additionally, Ecce was architected with mechanisms to integrate alternative electronic structure codes. The successful integration of Amica within Ecce validates the architecture of the latter and brings the high-accuracy capabilities of Amica to a wider audience.     

A quasi-Newton algorithm for first-order saddle-point location

Summary A new algorithm for the location of a transition-state structure on an energy hypersurface is proposed. The method is compared to three other quasi-Newton step calculations available in literature. Numerical results derived from several examples are compared to those obtained by the two algorithms implemented in the Gaussian package.     

New algorithms for iterative matrix‐free eigensolvers in quantum chemistry

New algorithms for iterative diagonalization procedures that solve for a small set of eigen‐states of a large matrix are described. The performance of the algorithms is illustrated by calculations of low and high‐lying ionized and electronically excited states using equation‐of‐motion coupled‐cluster methods with single and double substitutions (EOM‐IP‐CCSD and EOM‐EE‐CCSD). We present two algorithms suitable for calculating excited states that are close to a specified energy shift (interior eigenvalues). One solver is based on the Davidson algorithm, a diagonalization procedure commonly used in quantum‐chemical calculations. The second is a recently developed solver, called the “Generalized Preconditioned Locally Harmonic Residual (GPLHR) method.” We also present a modification of the Davidson procedure that allows one to solve for a specific transition. The details of the algorithms, their computational scaling, and memory requirements are described. The new algorithms are implemented within the EOM‐CC suite of methods in the Q‐Chem electronic structure program. © 2014 Wiley Periodicals, Inc.     

Valence : A Massively Parallel Implementation of the Variational Subspace Valence Bond Method

This work describes the software package, Valence , for the calculation of molecular energies using the variational subspace valence bond (VSVB) method. VSVB is an ab initio electronic structure method based on nonorthogonal orbitals. Important features of practical value include high parallel scalability, wave functions that can be constructed automatically by combining orbitals from previous calculations, and ground and excited states that can be modeled with a single configuration or determinant. The open-source software package includes tools to generate wave functions, a database of generic orbitals, example input files, and a library build intended for integration with other packages. We also describe the interface to an external software package, enabling the computation of optimized molecular geometries and vibrational frequencies. © 2019 Wiley Periodicals, Inc.     

Implementation of solvent reaction fields for electronic structure

 Methods are described to incorporate solvent reaction field effects into solute electronic structure calculations. Included are several old and new approaches based on approximate solutions of Poisson's equation through boundary element methods, wherein the solutions are represented in terms of certain apparent surface charge or apparent surface dipole distributions. Practical algorithms to set up and solve the requisite equations are described and implemented in a new general reaction field computer program. Illustrative computational results are presented to show the performance of the program. Received: 2 July 2001 / Accepted: 11 September 2001 / Published online: 19 December 2001     

Optimal peeling order for pedigrees with incomplete genotypic information

The likelihood approach is common in linkage analysis of large extended pedigrees. Various peeling procedures, based on the conditional independence of separate parts of a pedigree, are typically used for likelihood calculations. A peeling order may significantly affect the complexity of such calculations, particularly for pedigrees with loops or when many pedigrees members have unknown genotypes. Several algorithms have been proposed to address this problem for pedigrees with loops. However, the problem has not been solved for pedigrees without loops until now. In this paper, we suggest a new graph theoretic algorithm for optimal selection of peeling order in zero-loop pedigrees with incomplete genotypic information. It is especially useful when multiple likelihood calculation is needed, for example, when genetic parameters are estimated or linkage with multiple marker loci is tested. The algorithm can be easily introduced into the existing software packages for linkage analysis based on the Elston-Stewart algorithm for likelihood calculation. The algorithm was implemented in a software package PedPeel, which is freely available at http://mga.bionet.nsc.ru/nlru/.     

Use of GAMESS/COSMO program in support of COSMO-SAC model applications in phase equilibrium prediction calculations

Thermodynamic models based on conductor-like screening models (COSMO) offer viable alternatives to existing group-contribution methods for the prediction of phase equilibria. Normally a COSMO-based model requires input of the distribution of screening charges on the molecular surface, aka. the sigma profile, determined from a specific quantum chemistry program and settings. For example, the COSMO-SAC model requires input of DMol³ generated sigma profiles. In this paper, we investigate the proper settings for an open-source quantum chemistry package GAMESS in order to generate sigma profiles to be used directly in the COSMO-SAC model. The phase behaviors (VLE and VLLE) of 45 binary mixtures from 10 commonly used solvents and the solubilities of 4 complex drug compounds in these solvents calculated from DMol³ and GAMESS generated sigma profiles are compared. While noticeable fine structure differences are observed in the individual sigma profiles for the same chemical compound generated from the two packages, it is found that the accuracy in the VLE/VLLE and solubility predictions from the two packages are comparable. Based on the systems we studied here, the open-source GAMESS/COSMO program with proper program settings could be used as an alternative sigma profile generation source in support of COSMO-SAC model applications in phase equilibrium prediction calculations.     

Computer-aided drug design platform using PyMOL

The understanding and optimization of protein-ligand interactions are instrumental to medicinal chemists investigating potential drug candidates. Over the past couple of decades, many powerful standalone tools for computer-aided drug discovery have been developed in academia providing insight into protein-ligand interactions. As programs are developed by various research groups, a consistent user-friendly graphical working environment combining computational techniques such as docking, scoring, molecular dynamics simulations, and free energy calculations is needed. Utilizing PyMOL we have developed such a graphical user interface incorporating individual academic packages designed for protein preparation (AMBER package and Reduce), molecular mechanics applications (AMBER package), and docking and scoring (AutoDock Vina and SLIDE). In addition to amassing several computational tools under one interface, the computational platform also provides a user-friendly combination of different programs. For example, utilizing a molecular dynamics (MD) simulation performed with AMBER as input for ensemble docking with AutoDock Vina. The overarching goal of this work was to provide a computational platform that facilitates medicinal chemists, many who are not experts in computational methodologies, to utilize several common computational techniques germane to drug discovery. Furthermore, our software is open source and is aimed to initiate collaborative efforts among computational researchers to combine other open source computational methods under a single, easily understandable graphical user interface.