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In this paper, the history, present status, and future of density-functional theory (DFT) is informally reviewed and discussed by 70 workers in the field, including molecular scientists, materials scientists, method developers and practitioners. The format of the paper is that of a roundtable discussion, in which the participants express and exchange views on DFT in the form of 300 individual contributions, formulated as responses to a preset list of 26 questions. Supported by a bibliography of 776 entries, the paper represents a broad snapshot of DFT, anno 2022.

Eight phloroglucinols from Garcinia dauphinensis were recently reported to have good to moderate antiplasmodial and anticancer activities, consistent with other phloroglucinol derivatives isolated from natural sources. Chiroptical properties were previously calculated and compared to experimental data for compound 2 as a means to deduce its absolute configuration. Tentative assignments for the remaining compounds were also reported based on these data. In order to arrive at stereochemical assignments for phloroglucinols 1 and 3-8, ECD spectra and specific rotations were computed for all stereoisomers of each compound. Molecular orbital analyses were also carried out for the most energetically favorable conformers of each compound. Absolute configurations are reported for all eight phloroglucinols for the first time.

The introduction of machine-learning (ML) algorithms to quantum mechanics enables rapid evaluation of otherwise intractable expressions at the cost of prior training on appropriate benchmarks. Many computational bottlenecks in the evaluation of accurate electronic structure theory could potentially benefit from the application of such models, from reducing the complexity of the underlying wave function parameter space to circumventing the complications of solving the electronic Schrödinger equation entirely. Applications of ML to electronic structure have thus far been focused on learning molecular properties (mainly the energy) from geometric representations. While this line of study has been quite successful, highly accurate models typically require a “big data” approach with thousands of train- ing data points. Herein, we propose a general, systematically improvable scheme for wave function-based ML of arbitrary molecular properties, inspired by the underlying equations that govern the canonical approach to computing the properties. To this end, we combine the established ML machinery of the t-amplitude tensor representation with a new reduced density matrix representation. The resulting model provides quantitative accuracy in both the electronic energy and dipoles of small molecules using only a few dozen training points per system.

We explore the framework of a real-time coupled cluster method with a focus on improving its computational efficiency. Propagation of the wave function via the time-dependent Schr\"odinger equation places high demands on computing resources, particularly for high level theories such as coupled cluster with polynomial scaling. Similar to earlier investigations of coupled cluster properties, we demonstrate that the use of single-precision arithmetic reduces both the storage and multiplicative costs of the real-time simulation by approximately a factor of two with no significant impact on the resulting UV/vis absorption spectrum computed via the Fourier transform of the time-dependent dipole moment. Additional speedups of up to a factor of 14 in test simulations of water clusters are obtained via a straightforward GPU-based implementation as compared to conventional CPU calculations. We also find that further performance optimization is accessible through sagacious selection of numerical integration algorithms, and the adaptive methods, such as the Cash-Karp integrator provide an effective balance between computing costs and numerical stability. Finally, we demonstrate that a simple mixed-step integrator based on the conventional fourth-order Runge-Kutta approach is capable of stable propagations even for strong external fields, provided the time step is appropriately adapted to the duration of the laser pulse with only minimal computational overhead., Comment: 36 pages, 6 figures

The An error in the conversion from LaTeX to XML has occurred here. MolSSI is a research and education center that supports software development in the An error in the conversion from LaTeX to XML has occurred here. CMS. One of An error in the conversion from LaTeX to XML has occurred here. MolSSI’s core objectives is to provide education and training for the next generation of computational researchers. An error in the conversion from LaTeX to XML has occurred here. MolSSI Education targets various career stages and skill levels through its live workshops, online resources, and software fellowship program. An error in the conversion from LaTeX to XML has occurred here. MolSSI Education focuses its efforts within four areas: programming and software development, An error in the conversion from LaTeX to XML has occurred here. HPC and An error in the conversion from LaTeX to XML has occurred here. AI, faculty and curriculum development, and the An error in the conversion from LaTeX to XML has occurred here. MolSSI software fellowship program. This article delineates educational efforts at the An error in the conversion from LaTeX to XML has occurred here. MolSSI, overall goals, and resources that can be useful to researchers in the computational molecular sciences.

The underlying reasons for the poor convergence of the venerated many-body expansion (MBE) for higher-order response properties are investigated, with a particular focus on the impact of basis set superposition errors. Interaction energies, dipole moments, dynamic polarizabilities, and specific rotations are computed for three chiral solutes in explicit water cages of varying sizes using the MBE including corrections based on the site-site function counterpoise (or "full-cluster" basis) approach. In addition, we consider other possible causes for the observed oscillatory behavior of the MBE, including numerical precision, basis set size, choice of density functional, and snapshot geometry. Our results indicate that counterpoise corrections are necessary for damping oscillations and achieving reasonable convergence of the MBE for higher order properties. However, oscillations in the expansion cannot be completely eliminated for chiroptical properties such as specific rotations due to their inherently nonadditive nature, thus limiting the efficacy of the MBE for studying solvated chiral compounds.

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.

We present a detailed discussion of our novel diagrammatic coupled cluster Monte Carlo (diagCCMC) [Scott et al. J. Phys. Chem. Lett. 10, 925 (2019)]. The diagCCMC algorithm performs an imaginary-time propagation of the similarity-transformed coupled cluster Schrodinger equation. Imaginary-time updates are computed by the stochastic sampling of the coupled cluster vector function: each term is evaluated as a randomly realized diagram in the connected expansion of the similarity-transformed Hamiltonian. We highlight similarities and differences between deterministic and stochastic linked coupled cluster theory when the latter is re-expressed as a sampling of the diagrammatic expansion and discuss details of our implementation that allow for a walker-less realization of the stochastic sampling. Finally, we demonstrate that in the presence of locality, our algorithm can obtain a fixed errorbar per electron while only requiring an asymptotic computational effort that scales quartically with system size, independent of the truncation level in coupled cluster theory. The algorithm only requires an asymptotic memory cost scaling linearly, as demonstrated previously. These scaling reductions require no ad hoc modifications to the approach.

The Molecular Sciences Software Institute's (MolSSI) Quantum Chemistry Archive (QCArchive) project is an umbrella name that covers both a central server hosted by MolSSI for community data and the Python-based software infrastructure that powers automated computation and storage of quantum chemistry results.The MolSSI-hosted central server provides the computational molecular sciences community a location to freely access tens of millions of quantum chemistry computations for machine learning, methodology assessment, force-field fitting, and more through a Python interface.Facile, user-friendly mining of the centrally archived quantum chemical data also can be achieved through web applications found at https://qcarchive.molssi.org.The software infrastructure can be used as a standalone platform to compute, structure, and distribute hundreds of millions of quantum chemistry computations for individuals or groups of researchers at any scale.The QCArchive Infrastructure is open-source (BSD-3C), code repositories can be found at https://github.com/MolSSI, and releases can be downloaded via PyPI and Conda.

We propose a modified coupled cluster Monte Carlo algorithm that stochastically samples connected terms within the truncated Baker--Campbell--Hausdorff expansion of the similarity transformed Hamiltonian by construction of coupled cluster diagrams on the fly. Our new approach -- diagCCMC -- allows propagation to be performed using only the connected components of the similarity-transformed Hamiltonian, greatly reducing the memory cost associated with the stochastic solution of the coupled cluster equations. We show that for perfectly local, noninteracting systems, diagCCMC is able to represent the coupled cluster wavefunction with a memory cost that scales linearly with system size. The favorable memory cost is observed with the only assumption of fixed stochastic granularity and is valid for arbitrary levels of coupled cluster theory. Significant reduction in memory cost is also shown to smoothly appear with dissociation of a finite chain of helium atoms. This approach is also shown not to break down in the presence of strong correlation through the example of a stretched nitrogen molecule. Our novel methodology moves the theoretical basis of coupled cluster Monte Carlo closer to deterministic approaches., Comment: 31 pages, 6 figures

Psi4 is a free and open-source ab initio electronic structure program providing 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 functionality 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, make 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.

Garcinia dauphinensis is a previously uninvestigated endemic plant species of Madagascar. The new phloroglucinols dauphinols A-F and 3'-methylhyperjovoinol B (1-7) and six known phloroglucinols (8-13) together with tocotrienol 14 and three triterpenoids 15-17 were isolated from an ethanolic extract of G. dauphinensis roots using various chromatographic techniques. The structures of the isolated compounds were elucidated by NMR, MS, optical rotation, and ECD data. Theoretical ECD spectra and specific rotations for 2 were calculated and compared to experimental data in order to assign its absolute configuration. Among the compounds tested, 1 showed the most promising growth inhibitory activity against A2870 ovarian cancer cells, with IC(50) = 4.5 ± 0.9 μM, while 2 had good antiplasmodial activity against the Dd2 drug-resistant strain of Plasmodium falciparum, with IC(50) = 0.8 ± 0.1 μM.

The National Strategic Computing Initiative (NSCI) creates a framework for partnerships among government, industry, and academia to advance the use of high-performance computing. The National Science Foundations Office of Advanced Cyberinfrastructure furthers this mission through the instantiation of two new software institutes. Although the program predates NSCI, The Science Gateways Community Institute and the Molecular Sciences Software Institute advance NSCIs objectives by acting as hubs of excellence, serving broad communities and creating software and workforce ecosystems.

The effectiveness of the optical rotation prediction (ORP) basis set for computing specific rotations at the coupled cluster (CC) level has been evaluated for a test set of 14 chiral compounds. For this purpose, the ORP basis set has been developed for the second-row atoms present in the investigated systems (that is, for sulfur, phosphorus, and chlorine). The quality of the resulting set was preliminarily evaluated for seven molecules using time-dependent density-functional theory (TD-DFT). Rotations were calculated with the coupled cluster singles and doubles method (CCSD) as well as the second-order approximate coupled cluster singles and doubles method (CC2) with the correlation-consistent aug-cc-pVDZ and aug-cc-pVTZ basis sets and extrapolated to estimate the complete basis-set (CBS) limit for comparison with the ORP basis set. In the compounds examined here, the ORP calculations on molecules containing only first-row atoms compare favorably with results from the larger aug-cc-pVTZ basis set, in some cases lying closer to the estimated CBS limit, while results for molecules containing second-row atoms indicate that larger correlation-consistent basis sets are necessary to obtain reliable estimates of the CBS limit.

Psi4 is an ab initio electronic structure program providing methods such as Hartree-Fock, density functional theory, configuration interaction, and coupled-cluster theory. The 1.1 release represents a major update meant to automate complex tasks, such as geometry optimization using complete-basis-set extrapolation or focal-point methods. Conversion of the top-level code to a Python module means that Psi4 can now be used in complex workflows alongside other Python tools. Several new features have been added with the aid of libraries providing easy access to techniques such as density fitting, Cholesky decomposition, and Laplace denominators. The build system has been completely rewritten to simplify interoperability with independent, reusable software components for quantum chemistry. Finally, a wide range of new theoretical methods and analyses have been added to the code base, including functional-group and open-shell symmetry adapted perturbation theory (F-SAPT and O-SAPT), density-fitted coupled cluster with frozen natural orbitals [DF-FNO-CCSD(T)], orbital-optimized perturbation and coupled-cluster methods (e.g., OO-MP2 and OO-CCSD), density-fitted multiconfigurational self-consistent field (DF-MCSCF), density cumulant functional theory (DCT), algebraic-diagrammatic construction [ADC(2)] excited states, improvements to the geometry optimizer, and the “X2C” approach to relativistic corrections, among many other improvements.

Panel at PEARC19

The calculation of specific rotation of molecules in solution is probed at the coupled cluster (CC) level utilizing a continuum dielectric model based on a definition of the dielectric permittivity as a smooth function of electron density. Solvation effects are captured through polarization of Hartree-Fock (HF) molecular orbitals before subsequent calculations with the coupled cluster singles and doubles (CCSD) method. For the challenging ( S)-methyloxirane molecule, CCSD specific rotations yield an incorrect sign for the rotation in water, and the continuum model is unable to predict the wide variations in the optical rotatory dispersion (ORD) curves seen for nonpolar solvents of similar dielectric constant. In two molecules, (1 S,4 S)-norbornenone and ( S)-2-chloropropionitrile, specific rotations computed with CCSD in conjunction with implicit solvent fail to provide solvent shifts of the correct order of magnitude, indicating that the solvent response is a major contribution to the overall solvation effect.

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.

We have investigated the performance of the reduced-scaling coupled cluster method based on projected atomic orbitals (PAOs), pair natural orbitals (PNOs), and orbital specific virtuals (OSVs) for the prediction of linear response properties. These methods introduce different degrees of controllable sparsity in the ground-state and perturbed coupled cluster wave functions, leading to localization errors in properties such as dynamic polarizabilities and specific optical rotations. Using a series of chiral test compounds, we find that the inherent costs associated with computing response properties are significantly greater than those for determining the ground-state energy. As the dimensionality of the molecular system increases-from (pseudo)linear structures, such as fluoroalkanes, to cagelike structures, such as β-pinene-the crossover point between canonical-orbital and localized-orbital algorithms increases substantially. Furthermore, both the OSV and PNO methods provide greater reduction in cost (as measured by the size of the double-excitation space) than do PAOs, and PNOs provide the greatest level of sparsity for the systems examined here. Single-excitation truncation induces much larger errors than corresponding doubles truncation due to the fact that the first-order contribution to the one-electron perturbed wave function appears in the singles amplitudes. Both the PNO and OSV methods perform reasonably well for frequency-dependent polarizabilities provided appropriate thresholds are used for the occupation-number and weak-pair cutoffs on which each method depends. Specific rotations, however, are very sensitive to wave function truncation, to the extent that aggressive thresholds can yield the incorrect sign of the rotation, due to the delicate balance of positive and negative wave function contributions to the mixed electric-/magnetic-field response.

The efficacy of the frozen density embedding (FDE) approach to the simulation of solvent effects is examined for two key chiroptical properties-specific rotation and circular dichroism spectra. In particular, we have investigated the performance of a wave function-theory-in-density-functional-theory (WFT-in-DFT) FDE approach for computing such properties for the small, rigid chiral compound (P)-dimethylallene interacting with up to three water molecules. Although the solvent potential is obtained through DFT, the optical response is computed using coupled cluster linear response theory for mixed electric and magnetic field perturbations. We find that the FDE potential generally yields too small a shift from the isolated molecule as compared to that introduced by the explicit solvent. In one case, the FDE potential fails to reproduce a change in sign of the ORD in which the solute interacts with two solvent molecules. The source of these errors is due primarily to the lack of solvent response to the external field and is analyzed in terms of solvent-solute charge transfer excitations.

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. Further, several reference codes have been integrated into Jupyter notebooks, allowing background and explanatory information to be associated with the imple- mentation. 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.

In this work we present the first implementation of the incremental scheme for coupled cluster linear-response frequency-dependent dipole polarizabilities. The implementation is fully automated and makes use of the domain-specific basis set approach. The accuracy of the approach is determined on the basis of a test suite of 47 molecules and small clusters. The local approximation in the coupled cluster singles and doubles polarizability exhibits a mean error of 0.02% and a standard deviation of 0.32% when using a third-order incremental expansion. With the proposed approach, it is possible to compute polarizabilities with larger basis sets compared to the canonical implementation and thus it is possible to obtain higher total accuracy. The incremental scheme yields the smallest errors for weakly-bound and quasi-linear systems, while two- and three-dimensional (cage-like) structures exhibit somewhat larger errors as compared to the full test set. Dieser Beitrag ist aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

We present a method for computing excitation energies for molecules in solvent, based on the combination of a minimal parameter implicit solvent model and the equation-of-motion coupled-cluster singles and doubles method (EOM-CCSD). In this method, the solvent medium is represented by a smoothly varying dielectric function, constructed directly from the quantum mechanical electronic density using only two tunable parameters. The solvent–solute electrostatic interactions are computed by numerical solution of the nonhomogeneous Poisson equation and incorporated at the Hartree–Fock stage of the EOM-CCSD calculation by modification of the electrostatic potential. We demonstrate the method by computing excited state transition energies and solvent shifts for several small molecules in water. Results are presented for solvated H2O, formaldehyde, acetone, and trans-acrolein, which have low-lying n → π* transitions and associated blue shifts in aqueous solution. Comparisons are made with experimental data and other theoretical approaches, including popular implicit solvation models and QM/MM methods. We find that our approach provides surprisingly good agreement with both experiment and the other models, despite its comparative simplicity. This approach only requires modification of the Fock operator and total energy expressions at the Hartree–Fock level—solvation effects enter into the EOM-CCSD calculation only through the Hartree–Fock orbitals. Our model provides a theoretically and computationally simple route for accurate simulations of excited state spectra of molecules in solution, paving the way for studies of larger and more complex molecules.

We review the current state and future prospects of coupled cluster response theory for modeling chiroptical properties in both gas-phase and solvated systems. We first provide an overview of ground-state coupled cluster theory and the analytic derivative approach to computing time-independent properties, and then extend this to time-dependent perturbations. Through the well-established “quasi-energy” approach, we demonstrate the connection between the analytic derivative and response approaches, emphasizing the usefulness of the latter for frequency-dependent chiroptical properties. In addition, we review successes of response theory in the prediction of gas-phase specific rotations and electronic circular dichroism spectra for small molecules and the physical requirements of a robust computational model of such properties. We also discuss the many challenges of extending this reliability to solvated systems through several key examples for which theory and experiment diverge significantly.

A dichloromethane extract of Trichospira verticillata from the Natural Products Discovery Institute was discovered to have good antiplasmodial activity (IC50 ∼5 μg/mL). After purification by liquid–liquid partition and C18 reversed-phase HPLC, four new germacranolide-type sesquiterpenoid lactones named trichospirolides A–D (1–4) were isolated. The structures of the new compounds were elucidated by analysis of their 1D and 2D NMR and MS data. The relative and absolute configurations were assigned based on a comparison of calculated and experimental ECD and UV spectra, specific rotations, internuclear distances, and coupling constants for all possible diastereomers for each compound. Among these four compounds, the conjugated dienone 1 displayed the most potent antiplasmodial activity, with an IC50 value of 1.5 μM.

The frozen-virtual natural-orbital (NO) approach, whereby the unoccupied-orbital space is constructed using a correlated density such as that from many-body perturbation theory, has proven to yield compact wave functions for determining ground-state correlation energies and associated properties, with corresponding occupation numbers providing a guide to the truncation of the virtual space. In this work this approach is tested for the first time for the calculation of higher-order response properties, particularly frequency-dependent dipole polarizabilities using coupled-cluster theory. We find that such properties are much more sensitive to the truncation of virtual space in the NO basis than in the original canonical molecular orbital (CMO) basis, with truncation errors increasing linearly with respect to the number of frozen virtual NOs. The reasons behind this poor performance include the more diffuse nature of NOs with low occupation numbers as well as the reduction in sparsity of the perturbed singles amplitudes in the NO basis and the neglect of orbital response. We tested a number of approaches to improve the performance of the NO space, including the use of a field-perturbed density to define the virtual orbitals and various external-space corrections. The truncation of the CMO space, on the other hand, yields errors in coupled-cluster dipole polarizabilities of less than 2% even after removing as much as 50% of the full virtual space. We find that this positive performance of the CMO space results from a cancellation of errors due to the truncation of the unperturbed and perturbed amplitudes, as well as sparsity of the singles amplitudes. We introduce a simple criterion called a dipole amplitude to use as a threshold for truncating the CMO basis for such property calculations.