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The transformative impact of modern computational paradigms and technologies, such as high-performance computing (HPC), quantum computing, and cloud computing, has opened up profound new opportunities for scientific simulations. Scalable computational chemistry is one beneficiary of this technological progress. The main focus of this paper is on the performance of various quantum chemical formulations, ranging from low-order methods to high-accuracy approaches, implemented in different computational chemistry packages and libraries, such as NWChem, NWChemEx, Scalable Predictive Methods for Excitations and Correlated Phenomena, ExaChem, and Fermi–Löwdin orbital self-interaction correction on Azure Quantum Elements, Microsoft's cloud services platform for scientific discovery. We pay particular attention to the intricate workflows for performing complex chemistry simulations, associated data curation, and mechanisms for accuracy assessment, which is demonstrated with the Arrows automated workflow for high throughput simulations. Finally, we provide a perspective on the role of cloud computing in supporting the mission of leadership computational facilities. [ABSTRACT FROM AUTHOR]

Many important chemical processes involve reactivity and dynamics in complex solutions. Gaining a fundamental understanding of these reaction mechanisms is a challenging goal that requires advanced computational and experimental approaches. However, important techniques such as molecular simulation have limitations in terms of scales of time, length, and system complexity. Furthermore, among the currently available solvation models, there are very few designed to describe the interaction between the molecular scale and the mesoscale. To help address this challenge, here, we establish a novel hybrid approach that couples first-principles plane-wave density functional theory with classical density functional theory (cDFT). In this approach, a region of interest described by ab initio molecular dynamics (AIMD) interacts with the surrounding medium described using cDFT to arrive at a self-consistent ground state. cDFT is a robust but efficient mesoscopic approach to accurate thermodynamics of bulk electrolyte solutions over a wide concentration range (up to 2M concentrations). Benchmarking against commonly used continuum models of solvation, such as SMD, as well as experiments, demonstrates that our hybrid AIMD–cDFT method is able to produce reasonable solvation energies for a variety of molecules and ions. With this model, we also examined the solvent effects on a prototype SN2 reaction of the nucleophilic attack of a chloride ion on methyl chloride in the solution. The resulting reaction pathway profile and the solution phase barrier agree well with experiment, showing that our AIMD/cDFT hybrid approach can provide insight into the specific role of the solvent on the reaction coordinate. [ABSTRACT FROM AUTHOR]

In this paper, we discuss the extension of the recently introduced subsystem embedding subalgebra coupled cluster (SES-CC) formalism to unitary CC formalisms. In analogy to the standard single-reference SES-CC formalism, its unitary CC extension allows one to include the dynamical (outside the active space) correlation effects in an SES induced complete active space (CAS) effective Hamiltonian. In contrast to the standard single-reference SES-CC theory, the unitary CC approach results in a Hermitian form of the effective Hamiltonian. Additionally, for the double unitary CC (DUCC) formalism, the corresponding CAS eigenvalue problem provides a rigorous separation of external cluster amplitudes that describe dynamical correlation effects—used to define the effective Hamiltonian—from those corresponding to the internal (inside the active space) excitations that define the components of eigenvectors associated with the energy of the entire system. The proposed formalism can be viewed as an efficient way of downfolding many-electron Hamiltonian to the low-energy model represented by a particular choice of CAS. In principle, this technique can be extended to any type of CAS representing an arbitrary energy window of a quantum system. The Hermitian character of low-dimensional effective Hamiltonians makes them an ideal target for several types of full configuration interaction type eigensolvers. As an example, we also discuss the algebraic form of the perturbative expansions of the effective DUCC Hamiltonians corresponding to composite unitary CC theories and discuss possible algorithms for hybrid classical and quantum computing. Given growing interest in quantum computing, we provide energies for H2 and Be systems obtained with the quantum phase estimator algorithm available in the Quantum Development Kit for the approximate DUCC Hamiltonians. [ABSTRACT FROM AUTHOR]

A procedure for defining virtual spaces, and the periodic one-electron and two-electron integrals, for plane-wave second quantized Hamiltonians has been developed, and it was validated using full configuration interaction (FCI) calculations, as well as executions of variational quantum eigensolver (VQE) circuits on Quantinuum's ion trap quantum computers accessed through Microsoft's Azure Quantum service. This work is an extension to periodic systems of a new class of algorithms in which the virtual spaces were generated by optimizing orbitals from small pairwise CI Hamiltonians, which we term as correlation optimized virtual orbitals with the abbreviation COVOs. In this extension, the integration of the first Brillouin zone is automatically incorporated into the two-electron integrals. With these procedures, we have been able to derive virtual spaces, containing only a few orbitals, that were able to capture a significant amount of correlation. The focus in this manuscript is on comparing the simulations of small molecules calculated with plane-wave basis sets with large periodic unit cells at the Γ -point, including images, to results for plane-wave basis sets with aperiodic unit cells. The results for this approach were promising, as we were able to obtain good agreement between periodic and aperiodic results for an LiH molecule. Calculations performed on the Quantinuum H1-1 quantum computer produced surprisingly good energies, in which the error mitigation played a small role in the quantum hardware calculations and the (noisy) quantum simulator results. Using a modest number of circuit runs (500 shots), we reproduced the FCI values for the 1 COVO Hamiltonian with an error of 11 milliHartree, which is expected to improve with a larger number of circuit runs. [ABSTRACT FROM AUTHOR]

Carbon dioxide (CO2) was used as a reaction gas to investigate the gas‐phase ion‐molecule interactions using the Agilent 8900 ICP‐MS/MS. A solution containing forty‐five elements representative of the periodic table was used to supply the ions to react with CO2 in the collision/reaction cell (CRC). The only significant product ions formed were monoxides. The general reactivity was shown to be consistent with density functional theory (DFT)‐predicted reaction enthalpies, such that all predicted exothermic reactions produced product ions at levels of at least 1% of the unreacted ion. Most endothermic reactions observed had sufficient kinetic energy in excess of the reaction enthalpies. Our results suggest that reaction enthalpy is a reasonable predictor of reactivity with CO2 on the timescales of the interactions in non‐thermal ICP‐MS/MS systems. The ease and rapidity of data collection with the ICP‐MS/MS and DFT calculations using the NWChem suite has value given the scarcity of thermochemical data of CO2 reactions in the literature. These studies are especially useful for the identification of targeted reaction chemistries to be leveraged for analytical method development, such as for the inline separation of isobaric interferences from analytes of interest. [ABSTRACT FROM AUTHOR]

An efficient and accurate approach for calculating exact exchange and other two-electron integrals has been developed for periodic electronic structure methods. Traditional approaches used for integrating over the Brillouin zone in band structure calculations, e.g. trapezoidal or Monkhorst-Pack, are not accurate enough for two-electron integrals. This is because their integrands contain multiple singularities over the double integration of the Brillouin zone, which with simple integration methods lead to very inaccurate results. A common approach to this problem has been to replace the Coulomb interaction with a screened Coulomb interaction that removes singularities from the integrands in the two-electron integrals, albeit at the inelegance of having to introduce a screening factor which must precomputed or guessed. Instead of introducing screened Coulomb interactions in an ad hoc way, the method developed in this work derives an effective screened potential using a Filon-like integration approach that is based only on the lattice parameters. This approach overcomes the limitations of traditionally defined screened Coulomb interactions for calculating two-electron integrals, and makes chemistry many-body calculations tractable in periodic boundary conditions. This method has been applied to several systems for which conventional DFT methods do not work well, including the reaction pathways for the addition of H2 to phenol and Au 20 − nanoparticle, and the electron transfer of a charge trapped state in the Fe(II) containing mica, annite. [ABSTRACT FROM AUTHOR]

The characteristic pathway for degradation of halogenated aliphatic compounds in groundwater or other environments with relatively anoxic and/or reducing conditions is reductive dechlorination. For 1,2-dihalocarbons, reductive dechlorination can include hydrogenolysis and dehydrohalogenation, the relative significance of which depends on various structural and energetic factors. To better understand how these factors influence the degradation rates and products of the lesser halogenated hydrocarbons (in contrast to the widely studied per-halogenated hydrocarbons, like trichloroethylene and carbon tetrachloride), density functional theory calculations were performed to compare all of the possible pathways for reduction and elimination of 1,2,3-trichloropropane (TCP). The results showed that free energies of each species and reaction step are similar for all levels of theory, although B3LYP differed from the others. In all cases, the reaction coordinate diagrams suggest that β-elimination of TCP to allyl chloride followed by hydrogenolysis to propene is the thermodynamically favored pathway. This result is consistent with experimental results obtained using TCP, 1,2-dichloropropane, and 1,3-dichloropropane in batch experiments with zerovalent zinc (Zn0, ZVI) as a reductant. [ABSTRACT FROM AUTHOR]

Results of ab initio molecular dynamics (AIMD) simulations (density functional theory+PBE96) of the dynamics of waters in the hydration shells surrounding the Zn2+ ion (T≈300 K, ρ≈1 gm/cm3) are compared to simulations using a combined quantum and classical molecular dynamics [AIMD/molecular mechanical (MM)] approach. Both classes of simulations were performed with 64 solvating water molecules (∼15 ps) and used the same methods in the electronic structure calculation (plane-wave basis set, time steps, effective mass, etc.). In the AIMD/MM calculation, only six waters of hydration were included in the quantum mechanical (QM) region. The remaining 58 waters were treated with a published flexible water-water interaction potential. No reparametrization of the water-water potential was attempted. Additional AIMD/MM simulations were performed with 256 water molecules. The hydration structures predicted from the AIMD and AIMD/MM simulations are found to agree in detail with each other and with the structural results from x-ray data despite the very limited QM region in the AIMD/MM simulation. To further evaluate the agreement of these parameter-free simulations, predicted extended x-ray absorption fine structure (EXAFS) spectra were compared directly to the recently obtained EXAFS data and they agree in remarkable detail with the experimental observations. The first hydration shell contains six water molecules in a highly symmetric octahedral structure is (maximally located at 2.13–2.15 Å versus 2.072 Å EXAFS experiment). The widths of the peak of the simulated EXAFS spectra agree well with the data (8.4 Å2 versus 8.9 Å2 in experiment). Analysis of the H-bond structure of the hydration region shows that the second hydration shell is trigonally bound to the first shell water with a high degree of agreement between the AIMD and AIMD/MM calculations. Beyond the second shell, the bonding pattern returns to the tetrahedral structure of bulk water. The AIMD/MM results emphasize the importance of a quantum description of the first hydration shell to correctly describe the hydration region. In these calculations the full d10 electronic structure of the valence shell of the Zn2+ ion is retained. The simulations show substantial and complex charge relocation on both the Zn2+ ion and the first hydration shell. The dipole moment of the waters in the first hydration shell is 3.4 D (3.3 D AIMD/MM) versus 2.73 D bulk. Little polarization is found for the waters in the second hydration shell (2.8 D). No exchanges were seen between the first and the second hydrations shells; however, many water transfers between the second hydration shell and the bulk were observed. For 64 waters, the AIMD and AIMD/MM simulations give nearly identical results for exchange dynamics. However, in the larger particle simulations (256 waters) there is a significant reduction in the second shell to bulk exchanges. [ABSTRACT FROM AUTHOR]

First principles molecular dynamics simulations of the hydration shells surrounding UO22+ ions are reported for temperatures near 300 K. Most of the simulations were done with 64 solvating water molecules (22 ps). Simulations with 122 water molecules (9 ps) were also carried out. The hydration structure predicted from the simulations was found to agree with very well-known results from x-ray data. The average U==O bond length was found to be 1.77 Å. The first hydration shell contained five trigonally coordinated water molecules that were equatorially oriented about the O–U–O axis with the hydrogen atoms oriented away from the uranium atom. The five waters in the first shell were located at an average distance of 2.44 Å (2.46 Å, 122 water simulation). The second hydration shell was composed of distinct equatorial and apical regions resulting in a peak in the U–O radial distribution function at 4.59 Å. The equatorial second shell contained ten water molecules hydrogen bonded to the five first shell molecules. Above and below the UO22+ ion, the water molecules were found to be significantly less structured. In these apical regions, water molecules were found to sporadically hydrogen bond to the oxygen atoms of the UO22+, oriented in such a way as to have their protons pointed toward the cation. While the number of apical waters varied greatly, an average of five to six waters was found in this region. Many water transfers into and out of the equatorial and apical second solvation shells were observed to occur on a picosecond time scale via dissociative mechanisms. Beyond these shells, the bonding pattern substantially returned to the tetrahedral structure of bulk water. [ABSTRACT FROM AUTHOR]

First principles simulations of the hydration shells surrounding Al3+ ions are reported for temperatures near 300 °C. The predicted six water molecules in the octahedral first hydration shell were found to be trigonally coordinated via hydrogen bonds to 12 s shell water molecules in agreement with the putative structure used to analyze the x-ray data, but in disagreement with the results reported from conventional molecular dynamics using two-and three-body potentials. Bond lengths and angles of the water molecules in the first and second hydration shells and the average radii of these shells also agreed very well with the results of the x-ray analysis. Water transfers into and out of the second solvation shell were observed to occur on a picosecond time scale via a dissociative mechanism. Beyond the second shell the bonding pattern substantially returned to the tetrahedral structure of bulk water. Most of the simulations were done with 64 solvating water molecules (20 ps). Limited simulations with 128 water molecules (7 ps) were also carried out. Results agreed as to the general structure of the solvation region and were essentially the same for the first and second shell. However, there were differences in hydrogen bonding and Al–O radial distribution function in the region just beyond the second shell. At the end of the second shell a nearly zero minimum in the Al–O radial distribution was found for the 128 water system. This minimum is less pronounced minimum found for the 64 water system, which may indicate that sizes larger than 64 may be required to reliably predict behavior in this region. [ABSTRACT FROM AUTHOR]

closo-Borate anions [closo-BnXn]2− are part of the most famous textbook examples of polyhedral compounds. Substantial differences in their reactivity and interactions with other compounds depending on the substituent X and cluster size n have been recognized, which favor specific closo-borates for different applications in cancer treatment, chemical synthesis, and materials science. Surprisingly, a fundamental understanding of the molecular properties underlying these differences is lacking. Here, we report our study comparing the electronic structure and reactivity of closo-borate anions [closo-BnXn]2− (X = Cl, Br, I, n = 10, 11, 12 in all combinations) in the gas phase and in solution. We investigated the free dianions and the ion pairs [nBu4N]+[closo-BnXn]2− by gas phase anion photoelectron spectroscopy accompanied by theoretical investigations. Strong similarities in electronic structures for n = 10 and 11 were observed, while n = 12 clusters were different. A systematic picture of the development in electronic stability along the dimension X is derived. Collision induced dissociation shows that fragmentation of the free dianions is mainly dependent on the substituent X and gives access to a large variety of boron-rich molecular ions. Fragmentation of the ion pair depends strongly on n. The results reflect the high chemical stability of clusters with n = 10 and 12, while those with n = 11 are much more prone to dissociation. We bridge our study to the condensed phase by performing comparative electrochemistry and reactivity studies on closo-borates in solution. The trends found at the molecular level are also reflected in the condensed-phase properties. We discuss how the gas phase values allow evaluation of the influence of the condensed phase on the electronic stability of closo-borates. A synthetic method via an oxidation/chlorination reaction yielding [closo-B10Cl10]2− from highly chlorinated {closo-B11} clusters is introduced, which underlines the intrinsically high reactivity of the {closo-B11} cage. [ABSTRACT FROM AUTHOR]

Quantitative structure–activity relationships (QSARs) have long been used in the environmental sciences. More recently, molecular modeling and chemoinformatic methods have become widespread. These methods have the potential to expand and accelerate advances in environmental chemistry because they complement observational and experimental data with “in silico” results and analysis. The opportunities and challenges that arise at the intersection between statistical and theoretical in silico methods are most apparent in the context of properties that determine the environmental fate and effects of chemical contaminants (degradation rate constants, partition coefficients, toxicities, etc.). The main example of this is the calibration of QSARs using descriptor variable data calculated from molecular modeling, which can make QSARs more useful for predicting property data that are unavailable, but also can make them more powerful tools for diagnosis of fate determining pathways and mechanisms. Emerging opportunities for “in silico environmental chemical science” are to move beyond the calculation of specific chemical properties using statistical models and toward more fully in silico models, prediction of transformation pathways and products, incorporation of environmental factors into model predictions, integration of databases and predictive models into more comprehensive and efficient tools for exposure assessment, and extending the applicability of all the above from chemicals to biologicals and materials. [ABSTRACT FROM AUTHOR]

Phenols and anilines have been studied extensively as reductants of environmental oxidants (such as manganese dioxide) and as reductates (e.g., model contaminants) that are transformed by environmental oxidants (ozone, triple organic matter, etc.). The thermodynamics and kinetics of these reactions have been interpreted using oxidation potentials for substituted phenols and anilines, often using a legacy experimental dataset that is of uncertain quality. Although there are many alternative oxidation potential data, there has been little systematic analysis of the relevance, reliability, and consistency of the data obtained by different methods. We have done this through an extensive correlation analysis of kinetic data for phenol or aniline oxidation by manganese oxide―compiled from multiple sources―and oxidation potentials obtained from (i) electrochemical measurements using cyclic and square wave voltammetry and (ii) theoretical calculations using density functional theory. Measured peak potentials (Ep) from different sources and experimental conditions correlate very strongly, with minimal root mean squared error (RMSE), slopes ≈ 1, and intercepts indicative of consistent absolute differences of 50–150 mV; whereas, one-electron oxidation potentials (E1) from different sources and theoretical conditions exhibit large RMSE, slopes, and intercepts vs. measured oxidation potentials. Calibration of calculated E1 data vs. measured Ep data gave corrected values of E1 with improved accuracy. For oxidation by manganese dioxide, normalization of rate constants (to the 4-chloro congener) allowed correlation of phenol and aniline data from multiple sources to give one, unified quantitative structure–activity relationship (QSAR). Comparison among these QSARs illustrates the principle of matching the observational vs. mechanistic character of the response and descriptor variables. [ABSTRACT FROM AUTHOR]

Semi-local functionals commonly used in density functional theory (DFT) studies of solids usually fail to reproduce localized states such as trapped holes, polarons, excitons, and solitons. This failure is ascribed to self-interaction which creates a Coulomb barrier to localization. Pragmatic approaches in which the exchange correlation functionals are augmented with small amount of exact exchange (hybrid-DFT, e.g., B3LYP and PBE0) have shown to promise in rectifying this type of failure, as well as producing more accurate band gaps and reaction barriers. The evaluation of exact exchange is challenging for large, solid state systems with periodic boundary conditions, especially when plane-wave basis sets are used. We have developed parallel algorithms for implementing exact exchange into pseudopotential plane-wave DFT program and we have implemented them in the NWChem program package. The technique developed can readily be employed in Γ-point plane-wave DFT programs. Furthermore, atomic forces and stresses are straightforward to implement, making it applicable to both confined and extended systems, as well as to Car-Parrinello ab initio molecular dynamic simulations. This method has been applied to several systems for which conventional DFT methods do not work well, including calculations for band gaps in oxides and the electronic structure of a charge trapped state in the Fe(II) containing mica, annite. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [ABSTRACT FROM AUTHOR]

Many different degradation reactions of chlorinated hydrocarbons are possible in natural groundwaters. In order to identify which degradation reactions are important, a large number of possible reaction pathways must be sorted out. Recent advances in ab initio electronic structure methods have the potential to help identify relevant environmental degradation reactions by characterizing the thermodynamic properties of all relevant contaminant species and intermediates for which experimental data are usually not available, as well as provide activation energies for relevant pathways. In this paper, strategies based on ab initio electronic structure methods for estimating thermochemical and kinetic properties of reactions with chlorinated hydrocarbons are presented. Particular emphasis is placed on strategies that are computationally fast and can be used for large organochlorine compounds such as 4,4′-DDT [ABSTRACT FROM AUTHOR]

Presents information on a study which investigated the structures of five NaOH hydrate phases through optimization of lattice parameters and atomic coordinates. Computational approach; Results; Discussion.

The atom-centered density-matrix propagation method is used to illustrate how time-dependent conformational changes affect the electronic structure and derived spectroscopic properties of a prototypical finite metal cluster-bound π-conjugated organic complex, Ag7-benzenethiol. We establish that there is considerable conformational flexibility to the model structure, even at relatively low temperatures, which influences the predicted spectroscopic properties. Namely, the computed electron densities, dipoles, and polarizabilities are all dictated by torsional motion which controls the coupling between the π-framework of the chemisorbed molecular system and the cluster. [ABSTRACT FROM AUTHOR]

Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0...tM can be transformed into a root finding problem, F(X) = [xi - f(x(i - 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H2O AIMD simulation at the MP2 level. The maximum speedup (serial execution timeparallel execution time) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step. [ABSTRACT FROM AUTHOR]

Results of local density approximation (LDA) and Hartree-Fock (HF) calculations for even numbered monocyclic rings are reported. Small C[sub n] rings satisfying n=4N+2 show aromatic stability with equal bond-length structures, whereas rings of size n=4N show antiaromatic destabilization with bond-length alternation. For large rings a transition, the Peierls transition, from aromatic and antiaromatic to nonaromatic behavior, takes place. Above the Peierls transition, both n=4N and n=4N+2 rings show bond-length alternation and no differences in stability. The critical size for the transition to nonaromatic behavior depends on the electron-phonon coupling strength and therefore depends on the choice of ab initio method. HF predicts nonaromatic behavior for ring sizes n=14 and above. Fully optimized LDA results are presented up to n=42, which still has a cumulenic structure. Calculations based on periodic infinite ring systems show that within LDA the onset of nonaromatic behavior does not occur until n=82. Experimental results suggest that aromatic behavior exists in these ring systems to at least n=22. The force constant for in-plane angle bending may also be estimated from these calculations and was found to be 0.022 kcal mol-1 deg-2 per atom, not a strong function of size beyond n=22, and in good agreement with experimental estimates. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]