Molecular Sciences Software Institute

The simulation environment for atomistic and molecularmodeling(SEAMM) is an open-source software package written in Python thatprovides a graphical interface for setting up, executing, and analyzingmolecular and materials simulations. The graphical interface reducesthe entry barrier for the use of new simulation tools, facilitatingthe interoperability of a wide range of simulation tools availableto solve complex scientific and engineering problems in computationalmolecular science. Workflows are represented graphically by user-friendlyflowcharts, which are shareable and reproducible. When a flowchartis executed within the SEAMM environment, all results, as well asmetadata describing the workflow and codes used, are saved in a datastorethat can be viewed using a browser-based dashboard, which allows collaboratorsto view the results and use the flowcharts to extend the results.SEAMM is a powerful productivity and collaboration tool that enablesinteroperability between simulation codes and ensures reproducibilityand transparency in scientific research. We illustrate the flexibilityand productivity of SEAMM with three examples: a simple moleculardynamics calculation to provide an overview; exploring the rearrangementof methylisocyanide to acetonitrile using a wide range of quantumcodes and force fields; and using SEAMM for industrial research onbattery materials with simulations of the diffusivity and ionic conductivityof electrolytes and the density, thermal expansion, and thermal conductivityof cathode materials as a function of lithiation.

The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations. The graphical interface reduces the entry barrier for the use of new simulation tools, facilitating the interoperability of a wide range of simulation tools available to solve complex scientific and engineering problems in computational molecular science. Workflows are represented graphically by user-friendly flowcharts which are shareable and reproducible. When a flowchart is executed within the SEAMM environment, all results, as well as metadata describing the workflow and codes used, are saved in a datastore that can be viewed using a browser-based dashboard, which allows collaborators to view the results and use the flowcharts to extend the results. SEAMM is a powerful productivity and collaboration tool that enables interoperability between simulation codes and ensures reproducibility and transparency in scientific research.

A portable and performant graphics processing unit (GPU)-accelerated library for electron repulsion integral (ERI) evaluation, named LibERI, has been developed and implemented via directive-based (e.g., OpenMP and OpenACC) and standard language parallelism (e.g., Fortran DO CONCURRENT). Offloaded ERIs consist of integrals over low and high contraction s, p, and d functions using the rotated-axis and Rys quadrature methods. GPU codes are factorized based on previous developments [Pham et al., J. Chem. Theory Comput. 19(8), 2213-2221 (2023)] with two layers of integral screening and quartet presorting. In this work, the density screening is moved to the GPU to enhance the computational efficacy for large molecular systems. The L-shells in the Pople basis set are also separated into pure S and P shells to increase the ERI homogeneity and reduce atomic operations and the memory footprint. LibERI is compatible with any quantum chemistry drivers supporting the MolSSI Driver Interface. Benchmark calculations of LibERI interfaced with the GAMESS software package were carried out on various GPU architectures and molecular systems. The results show that the LibERI performance is comparable to other state-of-the-art GPU-accelerated codes (e.g., TeraChem and GMSHPC) and, in some cases, outperforms conventionally developed ERI CUDA kernels (e.g., QUICK) while fully maintaining portability.

Density functional calculations on atoms are often used for determining accurate initial guesses as well as generating various types of pseudopotential approximations and efficient atomic-orbital basis sets for polyatomic calculations. To reach the best accuracy for these purposes, the atomic calculations should employ the same density functional as the polyatomic calculation. Atomic density functional calculations are typically carried out employing spherically symmetric densities, corresponding to the use of fractional orbital occupations. We have described their implementation for density functional approximations (DFAs) belonging to the local density approximation (LDA) and generalized gradient approximation (GGA) levels of theory as well as Hartree-Fock (HF) and range-separated exact exchange [Lehtola, S. Phys. Rev. A 2020, 101, 012516]. In this work, we describe the extension to meta-GGA functionals using the generalized Kohn-Sham scheme, in which the energy is minimized with respect to the orbitals, which in turn are expanded in the finite element formalism with high-order numerical basis functions. Furnished with the new implementation, we continue our recent work on the numerical well-behavedness of recent meta-GGA functionals [Lehtola, S.; Marques, M. A. L. J. Chem. Phys. 2022, 157, 174114]. We pursue complete basis set (CBS) limit energies for recent density functionals and find many to be ill-behaved for the Li and Na atoms. We report basis set truncation errors (BSTEs) of some commonly used Gaussian basis sets for these density functionals and find the BSTEs to be strongly functional dependent. We also discuss the importance of density thresholding in DFAs and find that all of the functionals studied in this work yield total energies converged to 0.1 μEh when densities smaller than 10-11a0-3 are screened out.

Abstract Accurate small molecule force fields are crucial for predicting thermodynamic and kinetic properties of drug-like molecules in biomolecular systems. Torsion parameters, in particular, are essential for determining conformational distribution of molecules. However, they are usually fit to computationally expensive quantum chemical torsion scans and generalize poorly to different chemical environments. Torsion parameters should ideally capture local through-space non-bonded interactions such as 1-4 steric and electrostatics and non-local through-bond effects such as conjugation and hyperconjugation. Non-local through-bond effects are sensitive to remote substituents and are a contributing factor to torsion parameters poor transferability. Here we show that fractional bond orders such as the Wiberg Bond Order (WBO) are sensitive to remote substituents and correctly captures extent of conjugation and hyperconjugation. We show that the relationship between WBO and torsion barrier heights are linear and can therefore serve as a surrogate to QC torsion barriers, and to interpolate torsion force constants. Using this approach we can reduce the number of computationally expensive QC torsion scans needed while maintaining accurate torsion parameters. We demonstrate this approach to a set of substituted benzene rings.

Incorporating Necessary Skills for Research and Career Success. Programming and computational science is an essential part of chemistry, yet some curricula still do not prioritize its inclusion. This work contains a collection of strategies, activities, and resources available to incorporate programming into all levels of the chemistry curriculum, with a focus on how the programming learning objectives are integrated with chemistry learning objectives. Chapters highlight best practices in software development, emphasize their importance to the future of computational molecular sciences, and describe challenges instructors might face in implementing programming in their own curriculum.

We present a methodology for defining and optimizing a general force field for classical molecular simulations, and we describe its use to derive the Open Force Field 1.0.0 small molecule force field, code-named Parsley. Rather than traditional atom-typing, our approach builds on the SMIRKS-native Open Force Field (SMIRNOFF) parameter assignment formalism, which handles increases in the diversity and specificity of the force field definition without needlessly increasing the complexity of the specification. Parameters are optimized with the ForceBalance tool, based on reference quantum chemical data that include torsion potential energy profiles, optimized gas-phase structures, and vibrational frequencies. These quantum reference data are computed and are maintained with QCArchive, an open-source and freely available distributed computing and database software ecosystem. In this initial application of the method, we present essentially a full optimization of all valence parameters and report tests of the resulting force field against compounds and data types outside the training set. These tests show improvements in optimized geometries and conformational energetics and demonstrate that Parsley's accuracy for liquid properties is similar to that of other general force fields, as is accuracy on binding free energies. We find that this initial Parsley force field affords accuracy similar to that of other general force fields when used to calculate relative binding free energies spanning 199 protein-ligand systems. Additionally, the resulting infrastructure allows us to rapidly optimize an entire new force field with minimal human intervention.

Abstract The realization of fractional quantum chemistry is presented. Adopting the integro‐differential operators of the calculus of arbitrary‐order, we develop a general framework for the description of quantum nonlocal effects in the complex electronic environments. After a brief overview of the historical and fundamental aspects of the calculus of arbitrary‐order, various classes of fractional Schrödinger equations are discussed and pertinent controversies and open problems around their applications to model systems are detailed. We provide a unified approach toward fractional generalization of the quantum chemical models such as Hartree–Fock and Kohn–Sham density functional theory and develop fractional variants of the fundamental molecular integrals and correlation energy. Furthermore, we offer various strategies for modeling static‐ and dynamic‐order quantum nonlocal effects through constant‐ and variable‐order fractional operators, respectively. Possible directions for future developments of fractional quantum chemistry are also outlined.

The challenge of assigning the absolute stereochemical configuration to a chiral compound can be overcome via accurate ab initio predictions of optical rotation, a sensitive molecular property that is further complicated by solvent effects. The solvent's "chiral imprint"-the transfer of the chirality from the solute to the surrounding achiral solvent-is explored here using conformational averaging and time-dependent density-functional theory. These complex solvent effects are taken into account via simple averaging over a molecular dynamics trajectory together with the explicit quantum mechanical consideration of the solvent molecules within the solute's cybotactic region and implicit modeling of the bulk solvent. We consider several axes along which the system's optical rotation varies, including the sampling of the dynamical trajectory, the quality of the one-electron basis set, and the use of continuum solvent models to account for bulk effects.