Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs.

Community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.

CLIFF: A component-based, machine-learned, intermolecular force field.

Computation of intermolecular interactions is a challenge in drug discovery because accurate ab initio techniques are too computationally expensive to be routinely applied to drug-protein models. Classical force fields are more computationally feasible, and force fields designed to match symmetry adapted perturbation theory (SAPT) interaction energies can remain accurate in this context. Unfortunately, the application of such force fields is complicated by the laborious parameterization required for computations on new molecules. Here, we introduce the component-based machine-learned intermolecular force field (CLIFF), which combines accurate, physics-based equations for intermolecular interaction energies with machine-learning models to enable automatic parameterization. The CLIFF uses functional forms corresponding to electrostatic, exchange-repulsion, induction/polarization, and London dispersion components in SAPT. Molecule-independent parameters are fit with respect to SAPT2+(3)δMP2/aug-cc-pVTZ, and molecule-dependent atomic parameters (atomic widths, atomic multipoles, and Hirshfeld ratios) are obtained from machine learning models developed for C, N, O, H, S, F, Cl, and Br. The CLIFF achieves mean absolute errors (MAEs) no worse than 0.70 kcal mol-1 in both total and component energies across a diverse dimer test set. For the side chain-side chain interaction database derived from protein fragments, the CLIFF produces total interaction energies with an MAE of 0.27 kcal mol-1 with respect to reference data, outperforming similar and even more expensive methods. In applications to a set of model drug-protein interactions, the CLIFF is able to accurately rank-order ligand binding strengths and achieves less than 10% error with respect to SAPT reference values for most complexes.

Optimized damping parameters for empirical dispersion corrections to symmetry-adapted perturbation theory.

Symmetry-adapted perturbation theory (SAPT) has become an invaluable tool for studying the fundamental nature of non-covalent interactions by directly computing the electrostatics, exchange (steric) repulsion, induction (polarization), and London dispersion contributions to the interaction energy using quantum mechanics. Further application of SAPT is primarily limited by its computational expense, where even its most affordable variant (SAPT0) scales as the fifth power of system size [O(N5)] due to the dispersion terms. The algorithmic scaling of SAPT0 is reduced from O(N5)→O(N4) by replacing these terms with the empirical D3 dispersion correction of Grimme and co-workers, forming a method that may be termed SAPT0-D3. Here, we optimize the damping parameters for the -D3 terms in SAPT0-D3 using a much larger training set than has previously been considered, namely, 8299 interaction energies computed at the complete-basis-set limit of coupled cluster through perturbative triples [CCSD(T)/CBS]. Perhaps surprisingly, with only three fitted parameters, SAPT0-D3 improves on the accuracy of SAPT0, reducing mean absolute errors from 0.61 to 0.49 kcal mol-1 over the full set of complexes. Additionally, SAPT0-D3 exhibits a nearly 2.5× speedup over conventional SAPT0 for systems with ∼300 atoms and is applied here to systems with up to 459 atoms. Finally, we have also implemented a functional group partitioning of the approach (F-SAPT0-D3) and applied it to determine important contacts in the binding of salbutamol to G-protein coupled ß1-adrenergic receptor in both active and inactive forms. SAPT0-D3 capabilities have been added to the open-source Psi4 software.

Psi4 1.4: Open-source software for high-throughput quantum chemistry.

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.

Time dependent adaptive configuration interaction applied to attosecond charge migration.

In this work, we present a time-dependent (TD) selected configuration interaction method based on our recently introduced adaptive configuration interaction (ACI). We show that ACI, in either its ground or excited state formalisms, is capable of building a compact basis for use in real-time propagation of wave functions for computing electron dynamics. TD-ACI uses an iteratively selected basis of determinants in real-time propagation capable of capturing strong correlation effects in both ground and excited states, all with an accuracy-and associated cost-tunable by the user. We apply TD-ACI to study attosecond-scale migration of charge following ionization in small molecules. We first compute attosecond charge dynamics in a benzene model to benchmark and understand the utility of TD-ACI with respect to an exact solution. Finally, we use TD-ACI to reproduce experimentally determined ultrafast charge migration dynamics in iodoacetylene. TD-ACI is shown to be a valuable benchmark theory for electron dynamics, and it represents an important step toward accurate and affordable TD multireference methods.

A Combined Selected Configuration Interaction and Many-Body Treatment of Static and Dynamical Correlation in Oligoacenes.

We have combined our adaptive configuration interaction (ACI) [J. B. Schriber and F. A. Evangelista, J. Chem. Phys. 2016, 144, 161106] with a density-fitted implementation of the second-order perturbative multireference-driven similarity renormalization group (DSRG-MRPT2) [K. P. Hannon, C. Li, and F. A. Evangelista, J. Chem. Phys. 2016, 144, 204111]. We use ACI reference wave functions to recover static correlation for active spaces larger than the conventional limit of 18 orbitals. The dynamical correlation is computed using the DSRG-MRPT2 method to yield a complete treatment of electron correlation. We apply the resulting method, ACI-DSRG-MRPT2, to predict singlet-triplet gaps, metrics of open-shell character, and spin-spin correlation functions for the oligoacene series (2-7 rings). Our computations employ active spaces with as many as 30 electrons in 30 orbitals and up to 1350 basis functions, yielding gaps that are in good agreement with available experimental results. Large bases and reference relaxation lead to a significant reduction in the estimated radical character of the oligoacenes, with respect to previous valence-only treatments of correlation effects.

Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development.

Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory. Furthermore, several reference codes have been integrated into Jupyter notebooks, allowing background, underlying theory, and formula information to be associated with the implementation. Psi4NumPy tools and associated reference implementations can lower the barrier for future development of quantum chemistry methods. These implementations also demonstrate the power of the hybrid C++/Python programming approach employed by the Psi4 program.

Adaptive Configuration Interaction for Computing Challenging Electronic Excited States with Tunable Accuracy.

We introduce and analyze various approaches for computing excited electronic states using our recently developed adaptive configuration interaction (ACI) method [ Schriber , J. B. and Evangelista , F. A. J. Chem. Phys. 2016 , 144 , 161106 ]. These ACI methods aim to describe multiple electronic states with equal accuracy, including challenging cases like multielectron, charge-transfer, and near-degenerate states. We develop both state-averaged and state-specific approaches to compute excited states whose absolute energy error can be tuned by a user-specified energy error threshold, σ. State-averaged schemes are found to be more efficient in that they obtain all of the states simultaneously in one computation, but they lose some degree of statewise tunability. State-specific algorithms allow for direct control of the error of each state, though the states must be computed sequentially. We compare each method using methylene, LiF, and all-trans polyene benchmark data.

Communication: An adaptive configuration interaction approach for strongly correlated electrons with tunable accuracy.

We introduce a new procedure for iterative selection of determinant spaces capable of describing highly correlated systems. This adaptive configuration interaction (ACI) determines an optimal basis by an iterative procedure in which the determinant space is expanded and coarse grained until self-consistency. Two importance criteria control the selection process and tune the ACI to a user-defined level of accuracy. The ACI is shown to yield potential energy curves of N2 with nearly constant errors, and it predicts singlet-triplet splittings of acenes up to decacene that are in good agreement with the density matrix renormalization group.