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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.

Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have become an essential tool in computational chemistry, particularly for analyzing complex biological and condensed phase systems. Building on this foundation, our work presents a novel implementation of the Gaussian Electrostatic Model (GEM), a polarizable density-based force field, within the QM/MM framework. This advancement provides seamless integration, enabling efficient and optimized QM/GEM calculations in a single step using the LICHEM Code. We have successfully applied our implementation to water dimers and hexamers, demonstrating the ability to handle water systems with varying numbers of water molecules. Moreover, we have extended the application to describe the double proton transfer of the aspartic acid dimer in a box of water, which highlights the method's proficiency in investigating heterogeneous systems. Our implementation offers the flexibility to perform on-the-fly density fitting or to utilize pre-fitted coefficients to estimate exchange and Coulomb contributions. This flexibility enhances efficiency and accuracy in modeling molecular interactions, especially in systems where polarization effects are significant. [ABSTRACT FROM AUTHOR]

Many-Body eXpansion (MBX) is a C++ library that implements many-body potential energy functions (PEFs) within the "many-body energy" (MB-nrg) formalism. MB-nrg PEFs integrate an underlying polarizable model with explicit machine-learned representations of many-body interactions to achieve chemical accuracy from the gas to the condensed phases. MBX can be employed either as a stand-alone package or as an energy/force engine that can be integrated with generic software for molecular dynamics and Monte Carlo simulations. MBX is parallelized internally using Open Multi-Processing and can utilize Message Passing Interface when available in interfaced molecular simulation software. MBX enables classical and quantum molecular simulations with MB-nrg PEFs, as well as hybrid simulations that combine conventional force fields and MB-nrg PEFs, for diverse systems ranging from small gas-phase clusters to aqueous solutions and molecular fluids to biomolecular systems and metal-organic frameworks. [ABSTRACT FROM AUTHOR]

OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features automatically work on all supported hardware types (including both CPUs and GPUs) and perform well on all of them. In many cases they require minimal coding, just a mathematical description of the desired function. They also require no modification to OpenMM itself and can be distributed independently of OpenMM. This makes it an ideal tool for researchers developing new simulation methods, and also allows those new methods to be immediately available to the larger community.

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, density-fitted coupled cluster with frozen natural orbitals, orbital-optimized perturbation and coupled-cluster methods (e.g., OO-MP2 and OO-LCCD), density-fitted multiconfigurational self-consistent field, density cumulant functional theory, algebraic-diagrammatic construction excited states, improvements to the geometry optimizer, and the "X2C" approach to relativistic corrections, among many other improvements.

In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

The particle mesh Ewald (PME) method has become ubiquitous in the molecular simulation community due to its ability to deliver long range electrostatics accurately with O N ⁡ log (N) complexity. Despite this widespread use, spanning more than two decades, second derivatives (Hessians) have not been available. In this work, we describe the theory and implementation of PME Hessians, which have applications in normal mode analysis, characterization of stationary points, phonon dispersion curve calculation, crystal structure prediction, and efficient geometry optimization. We outline an exact strategy that requires O (1) effort for each Hessian element; after discussing the excessive memory requirements of such an approach, we develop an accurate, efficient approximation that is far more tractable on commodity hardware. [ABSTRACT FROM AUTHOR]

Particle Mesh Ewald (PME) has become a standard method for treating long-range electrostatics in molecular simulations. Although the method has inferior asymptotic computational complexity to its linear scaling competitors, it remains enormously popular due to its high efficiency, which stems from the use of fast Fourier transforms (FFTs). This use of FFTs provides great challenges for scaling the method up to massively parallel systems, in large part because of the need to transfer large amounts of data. In this work, we demonstrate that this data transfer volume can be greatly reduced as a natural consequence of the structure of the PME equations. We also suggest an alternative algorithm that supplants the FFT with a linear algebra approach, which further decreases communication costs at the expense of increased asymptotic computational complexity. This linear algebra based approach is demonstrated to have great potential for latency hiding by interleaving communication and computation steps of the short- and long-range electrostatic terms. [ABSTRACT FROM AUTHOR]

In a previous work [Pan et al., Molecules 23, 2500 (2018)], a charge projection scheme was reported, where outer molecular mechanical (MM) charges [>10 Å from the quantum mechanical (QM) region] were projected onto the electrostatic potential (ESP) grid of the QM region to accurately and efficiently capture long-range electrostatics in ab initio QM/MM calculations. Here, a further simplification to the model is proposed, where the outer MM charges are projected onto inner MM atom positions (instead of ESP grid positions). This enables a representation of the long-range MM electrostatic potential via augmentary charges (AC) on inner MM atoms. Combined with the long-range electrostatic correction function from Cisneros et al. [J. Chem. Phys. 143, 044103 (2015)] to smoothly switch between inner and outer MM regions, this new QM/MM-AC electrostatic model yields accurate and continuous ab initio QM/MM electrostatic energies with a 10 Å cutoff between inner and outer MM regions. This model enables efficient QM/MM cluster calculations with a large number of MM atoms as well as QM/MM calculations with periodic boundary conditions. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Singlet carbenes exhibit a divalent carbon atom whose valence shell contains only six electrons, four involved in bonding to two other atoms and the remaining two forming a non-bonding electron [...]

The induced dipole and the classical Drude oscillator represent two major approaches for the explicit inclusion of electronic polarizability into force field-based molecular modeling and simulations. In this work, we explore the equivalency of these two models by comparing condensed phase properties computed using the Drude force field and a multipole and induced dipole (MPID) model. Presented is an approach to map the electrostatic model optimized in the context of the Drude force field onto the MPID model. Condensed phase simulations on water and 15 small model compounds show that without any reparametrization, the MPID model yields properties similar to the Drude force field with both models yielding satisfactory reproduction of a range of experimental values and quantum mechanical data. Our results illustrate that the Drude oscillator model and the point induced dipole model are different representations of essentially the same physical model. However, results indicate the presence of small differences between the use of atomic multipoles and off-center charge sites. Additionally, results on the use of dispersion particle mesh Ewald further support its utility for treating long-range Lennard Jones dispersion contributions in the context of polarizable force fields. The main motivation in demonstrating the transferability of parameters between the Drude and MPID models is that the more than 15 years of development of the Drude polarizable force field can now be used with MPID formalism without the need for dual-thermostat integrators nor selfconsistent iterations. This opens up a wide range of new methodological opportunities for polarizable models. [ABSTRACT FROM AUTHOR]

Many cutting edge force fields include polarization, to enhance their accuracy and range of applicability. In this work, we develop efficient strategies for the induced dipole polarization method. By fitting various orders of perturbation theory (PT) dipoles to a diverse training set, we arrive at a family of fully analytic methods -- whose nth order is referred to OPTn -- that span the full spectrum of polarization methods from the fast zeroth-order approach that neglects mutual dipole coupling, approaching the fully variational approach at high order. Our training set contains many difficult cases where the PT series diverges, and we demonstrate that our OPTn methods still deliver excellent results in these cases. Our tests show that the OPTn methods exhibit rapid convergence towards the exact answer with each increasing PT order. The fourth order OPT4 method, whose costs are commensurate with three iterations of the leading conjugate gradient method, is a particularly promising candidate to be used as a drop-in replacement for existing solvers without further parameterization. [ABSTRACT FROM AUTHOR]

Most existing treatments of induced dipoles in polarizable molecular mechanics force field calculations use either the self-consistent variational method, which is solved iteratively, or the "direct" approximation that is non-iterative as a result of neglecting coupling between induced dipoles. The variational method is usually implemented using assumptions that are only strictly valid under tight convergence of the induced dipoles, which can be computationally demanding to enforce. In this work, we discuss the nature of the errors that result from insufficient convergence and suggest a strategy that avoids such problems. Using perturbation theory to reintroduce the mutual coupling into the direct algorithm, we present a computationally efficient method that combines the precision of the direct approach with the accuracy of the variational approach. By analyzing the convergence of this perturbation series, we derive a simple extrapolation formula that delivers a very accurate approximation to the infinite order solution at the cost of only a few iterations. We refer to the new method as extrapolated perturbation theory. Finally, we draw connections to our previously published permanent multipole algorithm to develop an efficient implementation of the electric field and Thole terms and also derive some necessary, but not sufficient, criteria that force field parameters must obey. [ABSTRACT FROM AUTHOR]

Next-generation molecular force fields deliver accurate descriptions of non-covalent interactions by employing more elaborate functional forms than their predecessors. Much work has been dedicated to improving the description of the electrostatic potential (ESP) generated by these force fields. A common approach to improving the ESP is by augmenting the point charges on each center with higher-order multipole moments. The resulting anisotropy greatly improves the directionality of the non-covalent bonding, with a concomitant increase in computational cost. In this work, we develop an efficient strategy for enumerating multipole interactions, by casting an efficient spherical harmonic based approach within a particle mesh Ewald (PME) framework. Although the derivation involves lengthy algebra, the final expressions are relatively compact, yielding an approach that can efficiently handle both finite and periodic systems without imposing any approximations beyond PME. Forces and torques are readily obtained, making our method well suited to modern molecular dynamics simulations. [ABSTRACT FROM AUTHOR]

Density cumulant functional theory (DCFT) is one of a number of nascent electron correlation methods that are derived from reduced density matrices and cumulants thereof, instead of the wavefunction. Deriving properties from the density cumulant naturally yields methods that are size extensive and size consistent. In this work, we derive expressions for the analytic gradient, with respect to an external perturbation, for the DCFT-06 variant of density cumulant functional theory. Despite the fact that the DCFT-06 energy functional is stationary with respect to the density cumulant, the analytic gradients of the energy require the solution of perturbation-independent equations for both orbital and cumulant response. These two sets of linear response equations are coupled in nature and are solved iteratively with the solution of orbital and cumulant response equations each macroiteration, exhibiting rapid convergence. The gradients are implemented and benchmarked against coupled cluster theory with single and double excitations (CCSD) and CCSD with perturbative triple excitations [CCSD(T)], as well as accurate empirically corrected experimental data, for a test set comprising 15 small molecules. For most of the test cases, results from DCFT-06 are closer to CCSD(T) and empirical data than those from CCSD. Although the total energy and analytic gradient have the same asymptotic scaling, the present experience shows that the computational cost of the gradient is significantly lower. [ABSTRACT FROM AUTHOR]

The structure and energetics of Be4 are investigated using state-of-the-art coupled-cluster methods. We compute the optimized bond length, dissociation energy, and anharmonic vibrational frequencies. A composite approach is employed, starting from coupled-cluster theory with single, double, and perturbative triple excitations extrapolated to the complete basis set (CBS) limit using Dunning's correlation consistent cc-pCVQZ and cc-pCV5Z basis sets. A correction for full triple and connected quadruple excitations in the smaller cc-pCVDZ basis set is then added, yielding an approximation to CCSDT(Q)/CBS denoted c∼CCSDT(Q). Corrections are included for relativistic and non-Born-Oppenheimer effects. We obtain De = 89.7 kcal mol-1, D0 = 84.9 kcal mol-1, and re = 2.043 Å. Second-order vibrational perturbation theory (VPT2) is applied to a full quartic force field computed at the c∼CCSDT(Q) level of theory, yielding Be = 0.448 cm-1 and fundamental frequencies of 666 (a1), 468 (e), and 571 (t2) cm-1. Computations on the spectroscopically characterized Be2 molecule are reported for the purpose of benchmarking our methods. Perturbative estimates of the effect of quadruple excitations are found to be essential to computing accurate parameters for Be2; however, they seem to exert a much smaller influence on the structure and energetics of Be4. Our extensive characterization of the Be4 bonding potential energy surface should aid in the experimental identification of this thermodynamically viable but elusive molecule. [ABSTRACT FROM AUTHOR]

Density cumulant functional theory [W. Kutzelnigg, J. Chem. Phys. 125, 171101 (2006)] is implemented for the first time. Benchmark results are provided for atoms and diatomic molecules, demonstrating the performance of DCFT-06 for both nonbonded and bonded interactions. The results show that DCFT-06 appears to perform similarly to coupled cluster theory with single and double excitations (CCSD) in describing dispersion. For covalently bound systems, the physical properties predicted by DCFT-06 appear to be at least of CCSD quality around equilibrium geometries. The computational scaling of both DCFT-06 and CCSD is O(N6), but the former has reduced nonlinearities among the variables and a Hermitian energy functional, making it an attractive alternative. [ABSTRACT FROM AUTHOR]

The enthalpy of formation of diacetylene (C4H2) is pinpointed using state-of-the-art theoretical methods, accounting for high-order electron correlation, relativistic effects, non-Born–Oppenheimer corrections, and vibrational anharmonicity. Molecular energies are determined from coupled cluster theory with single and double excitations (CCSD), perturbative triples [CCSD(T)], full triples (CCSDT), and perturbative quadruples [CCSDT(Q)], in concert with correlation-consistent basis sets (cc-pVXZ, X=D, T, Q, 5, 6) that facilitate extrapolations to the complete basis set limit. The first full quartic force field of diacetylene is determined at the highly accurate all-electron CCSD(T) level with a cc-pCVQZ basis, which includes tight functions for core correlation. Application of second-order vibrational perturbation theory to our anharmonic force field yields fundamental frequencies with a mean absolute difference of only 3.9 cm-1 relative to the experimental band origins, without the use of any empirical scale factors. By a focal point approach, we converge on an enthalpy change for the isogyric reaction 2 H–C≡C–H→H–C≡C–C≡C–H+H2 of (+0.03, +0.81) kcal mol-1 at (0, 298.15) K. With the precisely established ΔfH° of acetylene, we thus obtain ΔfH°(C4H2)=(109.4,109.7)±0.3 kcal mol-1 at (0, 298.15) K. Previous estimates of the diacetylene enthalpy of formation range from 102 to 120 kcal mol-1. [ABSTRACT FROM AUTHOR]

We report the first implementation with correct scaling of the Mukherjee multireference coupled cluster method with singles, doubles, and approximate iterative triples (Mk-MRCCSDT-n, n=1a,1b,2,3) as well as full triples (Mk-MRCCSDT). These methods were applied to the classic H4, P4, BeH2, and H8 model systems to assess the ability of the Mk-MRCCSDT-n schemes to accurately account for triple excitations. In all model systems the inclusion of triples via the various Mk-MRCCSDT-n approaches greatly reduces the nonparallelism error (NPE) and the mean nonparallelism derivative diagnostics for the potential energy curves, recovering between 59% and 73% of the full triples effect on average. The most complete triples approximation, Mk-MRCCSDT-3, exhibits the best average performance, reducing the mean NPE to below 0.6 mEh, compared to 1.4 mEh for Mk-MRCCSD. Both linear and quadratic truncations of the Mk-MRCC triples coupling terms are viable simplifications producing no significant errors. If the off-diagonal parts of the occupied-occupied and virtual-virtual blocks of the Fock matrices are ignored, the storage of the triples amplitudes is no longer required for the Mk-MRCCSDT-n methods introduced here. This proves to be an effective approximation that gives results almost indistinguishable from those derived from full consideration of the Fock matrices. [ABSTRACT FROM AUTHOR]

Previous experimental assignments of the fundamental vibrational frequencies of NCCO have been brought into question by subsequent unsuccessful attempts to observe IR signatures of this radical at these frequencies. Here we compute the fundamental vibrational frequencies by applying second-order vibrational perturbation theory to the complete quartic force field computed at the all-electron (AE) coupled cluster singles, doubles, and perturbative triples level [CCSD(T)] with the correlation-consistent, polarized core-valence quadruple-zeta (cc-pCVQZ) basis set, which has tight functions to correctly describe core correlation. The AE-CCSD(T)/cc-pCVQZ geometric parameters are re(N–C)=1.1623 Å, re(C–C)=1.4370 Å, re(C–O)=1.1758 Å, θe(N–C–C)=168.55°, and θe(C–C–O)=132.22°. Our CCSD(T)/cc-pCVQZ values of the characteristic stretching frequencies ν1 and ν2 are 2171 and 1898 cm-1, respectively, in stark contrast to the experimentally derived values of 2093 and 1774 cm-1. Finally, focal-point extrapolations using correlation-consistent basis sets cc-pVXZ (X=D,T,Q,5,6) and electron correlation treatments as extensive as full coupled cluster singles, doubles, and triples (CCSDT) with perturbative accounting of quadruple excitations [CCSDT(Q)] determine the vibrationless barrier to linearity of NCCO and the dissociation energy (D0) of NCCO→NC+CO to be 8.4 and 26.5 kcal mol-1, respectively. Using our precisely determined dissociation energy, we recommend a new 0 K enthalpy of formation for NCCO of 50.9±0.3 kcal mol-1. [ABSTRACT FROM AUTHOR]

The ortho-benzyne diradical, o-C6H4 has been produced with a supersonic nozzle and its subsequent thermal decomposition has been studied. As the temperature of the nozzle is increased, the benzyne molecule fragments: o-C6H4+Δ→ products. The thermal dissociation products were identified by three experimental methods: (i) time-of-flight photoionization mass spectrometry, (ii) matrix-isolation Fourier transform infrared absorption spectroscopy, and (iii) chemical ionization mass spectrometry. At the threshold dissociation temperature, o-benzyne cleanly decomposes into acetylene and diacetylene via an apparent retro-Diels-Alder process: o-C6H4+Δ→HC=CH+HC=C–C=CH. The experimental ΔrxnH298(o-C6H4→HC=CH+HC=C–C=CH) is found to be 57±3 kcal mol-1. Further experiments with the substituted benzyne, 3,6-(CH3)2-o-C6H2, are consistent with a retro-Diels-Alder fragmentation. But at higher nozzle temperatures, the cracking pattern becomes more complicated. To interpret these experiments, the retro-Diels-Alder fragmentation of o-benzyne has been investigated by rigorous ab initio electronic structure computations. These calculations used basis sets as large as [C(7s6p5d4f3g2h1i)/H(6s5p4d3f2g1h)] (cc-pV6Z) and electron correlation treatments as extensive as full coupled cluster through triple excitations (CCSDT), in cases with a perturbative term for connected quadruples [CCSDT(Q)]. Focal point extrapolations of the computational data yield a 0 K barrier for the concerted, C2v-symmetric decomposition of o-benzyne, Eb(o-C6H4→HC=CH+HC=C–C=CH)=88.0±0.5 kcal mol-1. A barrier of this magnitude is consistent with the experimental results. A careful assessment of the thermochemistry for the high temperature fragmentation of benzene is presented: C6H6→H+[C6H5]→H+[o-C6H4]→HC=CH+HC=C–C=CH. Benzyne may be an important intermediate in the thermal decomposition of many alkylbenzenes (arenes). High engine temperatures above 1500 K may crack these alkylbenzenes to a mixture of alkyl radicals and phenyl radicals. The phenyl radicals will then dissociate first to benzyne and then to acetylene and diacetylene. [ABSTRACT FROM AUTHOR]

Molecular structures, energetics, vibrational frequencies and electron affinities of phenylethynyl radical and its isomers are described. The bond dissociation energies of the aromatic and ethynyl C-H bonds and the proton affinities of the phenylethynyl and ethynylphenyl anions are examined.