NWChem: Past, present, and future.

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

The role of ligand redox non-innocence in ring-opening polymerization reactions catalysed by bis(imino)pyridine iron alkoxide complexes.

The reactivity of iron-based ring opening polymerization catalysts is compared when the catalyst is in three different oxidation states. Formally iron(i) monoalkoxide complexes 3a (p-methoxyphenoxide) and 3b (neopentoxide) supported by bis(imino)pyridine ligands were synthesized and investigated as catalysts for the ring opening polymerization and copolymerization of various monomers. For most monomers, 3a and 3b were superior catalysts compared to analogous, formally iron(ii) and iron(iii) complexes (1a/1b and 2a/2b, respectively) for the ring opening polymerization of various cyclic ester and cyclic carbonate monomers. Experimental and computational investigation into the electronic structures of 3a and 3b revealed that they are most accurately described as containing a high spin iron(ii) center that is antiferromagnetically coupled to a singly reduced bis(imino)pyridine ligand. This electronic structure leads to increased electron density near the metal center without modulating the apparent metal oxidation state, which results in superior catalytic performance for the more highly reduced 3a and 3b compared to the increasingly more oxidized complexes (i.e.1a/1b and 2a/2b, respectively) in ring opening polymerization reactions. These findings have significant ramifications for the emerging field of redox-switchable polymerization catalysis.

Correction: Atomic layer deposition of Cu(i) oxide films using Cu(ii) bis(dimethylamino-2-propoxide) and water.

Correction for 'Atomic layer deposition of Cu(i) oxide films using Cu(ii) bis(dimethylamino-2-propoxide) and water' by J. R. Avila, et al., Dalton Trans., 2017, DOI: .

Atomic layer deposition of Cu(i) oxide films using Cu(ii) bis(dimethylamino-2-propoxide) and water.

To grow films of Cu2O, bis-(dimethylamino-2-propoxide)Cu(ii), or Cu(dmap), is used as an atomic layer deposition precursor using only water vapor as a co-reactant. Between 110 and 175 °C, a growth rate of 0.12 ± 0.02 Å per cycle was measured using an in situ quartz crystal microbalance (QCM). X-ray photoelectron spectroscopy (XPS) confirms the growth of metal-oxide films featuring Cu(i).

Optimization and prediction of the electron-nuclear dipolar and scalar interaction in 1H and 13C liquid state dynamic nuclear polarization.

During the last 10-15 years, dynamic nuclear polarization (DNP) has evolved as a powerful tool for hyperpolarization of NMR and MRI nuclides. However, it is not as well appreciated that solution-state dynamic nuclear polarization is a powerful approach to study intermolecular interactions in solution. For solutions and fluids, the 1H nuclide is usually dominated by an Overhauser dipolar enhancement and can be significantly increased by decreasing the correlation time (τc) of the substrate/nitroxide interaction by utilizing supercritical fluids (SF CO2). For molecules containing the ubiquitous 13C nuclide, the Overhauser enhancement is usually a profile of both scalar and dipolar interactions. For carbon atoms without an attached hydrogen, a dipolar enhancement usually dominates as we illustrate for sp2 hybridized carbons in the fullerenes, C60 and C70. However, the scalar interaction is dependent on a Fermi contact interaction which does not have the magnetic field dependence inherent in the dipolar interaction. For a comprehensive range of molecular systems we show that molecules that exhibit weakly acidic complexation interaction(s) with nitroxides provide corresponding large scalar enhancements. For the first time, we report that sp hybridized (H-C) alkyne systems, for example, the phenylacetylene-nitroxide system exhibit very large scalar dominated enhancements. Finally, we demonstrate for a wide range of molecular systems that the Fermi contact interaction can be computationally predicted via electron-nuclear hyperfine coupling and correlated with experimental 13C DNP enhancements.

Quantum chemical characterization of the reactions of guanine with the phenylnitrenium ion.

Density functional calculations at the B3LYP/6-311+G(2d,p)//pBP/DN level predict all cationic adducts combining guanine, at either its N2, O6, N7, or C8 positions, with phenylnitrenium ion, at either its N, 2, or 4 positions, to be lower in energy than the separated reactants. This relative stability of all adducts is preserved after addition of aqueous solvation free energies computed at the SM2 level, although some leveling of the adduct relative energies one to another is predicted. Cations having the lowest relative energies in solution correspond structurally to those adducts most commonly found when guanine reacts with larger, biologically relevant nitrenium ions in vitro and in vivo. One of these, the N-C8 adduct, is stabilized both by a rearomatized phenyl ring and by the operation of an anomeric effect not found in any of the others. On the basis of energetic analysis, direct conversion of an N-N7 cation to an N-C8 cation according to a previously proposed mechanism is unlikely; however, an alternative rearrangement converting a 2-N7 cation to an N-C8 cation via the intermediacy of a five-membered ring may be operative in nitrenium ions with aromatic frameworks better able than phenyl to stabilize endocyclic cationic charge.

Influence of hydroxyl substitution on benzyne properties. quantum chemical characterization of the didehydrophenols.

Geometries and singlet-triplet splittings for the 10 geometrical isomers of didehydrophenol are characterized at a variety of levels of electronic structure theory. The influence of the hydroxyl group is primarily to increase/decrease the weight of zwitterionic singlet mesomers that place positive/negative charge adjacent to oxygen in valence bond descriptions of the arynes. For some of the meta isomers, this interaction stabilizes distortion in the direction of a bicyclic geometry. The net effect, relative to the unsubstituted benzynes, is to increase the singlet-triplet splittings in 2,3-, 2,6-, and 3,5-didehydrophenol and to decrease that splitting in 2,4- and 2,5-didehydrophenol (3,4-didehydrophenol is essentially unaffected). As shown for other arynes, the singlet-triplet splittings can also be accurately estimated by correlation with proton hyperfine coupling constants in antecedent monoradicals, these values being accessible from very economical calculations.

Reductive dechlorination of hexachloroethane in the environment: mechanistic studies via computational electrochemistry.

Ab initio and density functional levels of electronic structure theory are applied to characterize alternative mechanisms for the reductive dechlorination of hexachloroethane (HCA) to perchloroethylene (PCE). Aqueous solvation effects are included using the SM5.42R continuum solvation model. After correction for a small systematic error in the electron affinity of the chlorine atom, theoretical predictions are accurate to within 23 mV for four aqueous reduction potentials relevant to HCA. A single pathway that proceeds via two successive single-electron transfer/barrierless chloride elimination steps, is predicted to be the dominant mechanism for reductive dechlorination. An alternative pathway predicted to be accessible involves trichloromethylchlorocarbene as a reactive intermediate. Bimolecular reactions of the carbene with other species at millimolar or higher concentrations are predicted to potentially be competitive with its unimolecular rearrangement to form PCE.

Biradical and zwitterionic cyclizations of oxy-substituted enyne-allenes.

[see reaction]. Oxyanion substitution of enyne-allenes causes both Myers-Saito and Schmittel cyclizations to switch their product formation preferences from diradicals to polar, closed-shell singlets. The oxyanion stabilization is larger for the Schmittel products than the Myers-Saito products because the latter must sacrifice aromaticity to maximize interaction. The changing character of the different reaction paths is reflected in their activation energies.

Constructing and evaluating energy surfaces of crystalline disaccharides.

This paper focuses on the methods used to construct Ramachandran plots for disaccharides. Our recent work based on a hybrid of molecular mechanics and quantum mechanics energies pointed to the need to take extra care when making these maps. Care is also important in the quantitative validation of these energy surfaces with linkage conformations that were determined by crystallography. To successfully predict conformations that have been observed experimentally, the calculation of the energy should include stereoelectronic effects and correctly weight the hydrogen bonding. Technical concerns include the method used to scan the range of conformations, starting geometries, and finding the zero of relative potential energy on a surface where the values were collected at regular intervals. The distributions of observed conformations on energy maps of sucrose, maltose, and laminarabiose at dielectric constants of 1.5 and 7.5 illustrate the effects of an elevated dielectric constant for the MM3 component of the hybrid energy calculations. At dielectric constants of 3.5 and 7.5, the overall average energies of observed conformations of sucrose and seven disaccharides of glucose were less than 1.0 kcal mol-1. The distribution of corresponding energies of the various crystalline conformations conformed well to a Boltzmann-like equation.

A QM/MM analysis of the conformations of crystalline sucrose moieties.

Both ab initio quantum mechanics (QM) and molecular mechanics (MM) were used to produce a hybrid energy surface for sucrose that simultaneously provides low energies for conformations that are observed in crystal structures and high energies for most unobserved structures. HF/6-31G* QM energies were calculated for an analogue based on tetrahydropyran (THP) and tetrahydrofuran (THF). Remaining contributions to the potential energy of sucrose were calculated with MM. To do this, the MM surface for the analogue was subtracted from the MM surface for the disaccharide, and the QM surface for the analogue was added. Prediction of the distribution of observable geometries was enhanced by reducing the strength of the hydrogen bonding. Reduced hydrogen-bonding strength is probably useful because many crystalline sucrose moieties do not have intramolecular hydrogen bonds between the fructose and glucose residues. Therefore, hydrogen bonding does not play a large role in determining the molecular conformation. On the hybrid energy surface that was constructed with a dielectric constant of 3.5, the average potential energy of 23 sucrose moieties from crystal structures is 1.16 kcal/mol, and the population of observed structures drops off exponentially as the energy increases.

Importance of discriminator base stacking interactions: molecular dynamics analysis of A73 microhelix(Ala) variants.

Transfer of alanine from Escherichia coli alanyl-tRNA synthetase (AlaRS) to RNA minihelices that mimic the amino acid acceptor stem of tRNA(Ala) has been shown, by analysis of variant minihelix aminoacylation activities, to involve a transition state sensitive to changes in the 'discriminator' base at position 73. Solution NMR has indicated that this single-stranded nucleotide is predominantly stacked onto G1 of the first base pair of the alanine acceptor stem helix. We report the activity of a new variant with the adenine at position 73 substituted by its non-polar isostere 4-methylindole (M). Despite lacking N7, this analog is well tolerated by AlaRS. Molecular dynamics (MD) simulations show that the M substitution improves position 73 base stacking over G1, as measured by a stacking lifetime analysis. Additional MD simulations of wild-type microhelix(Ala) and six variants reveal a positive correlation between N73 base stacking propensity over G1 and aminoacylation activity. For the two DeltaN7 variants simulated we found that the propensity to stack over G1 was similar to the analogous variants that contain N7 and we conclude that the decrease in aminoacylation efficiency observed upon deletion of N7 is likely due to loss of a direct stabilizing interaction with the synthetase.

Application of a universal solvation model to nucleic acid bases: comparison of semiempirical molecular orbital theory, ab initio Hartree-Fock theory, and density functional theory.

The free energies of solvation of six nucleic acid bases (adenine, cytosine, hypoxanthine, guanine, thymine, and uracil) in water and chloroform are calculated using CM2 class IV charges and SM5.42R atomic surface tensions. Using any of three approximations to the electronic wave function (AM1, Hartree-Fock, or DFT), we obtain good agreement with experiment for five cases where the experimental results are known for the partition coefficients between the two solvents. Decomposition of the solvation effects into bulk electrostatic contributions and first-solvation-shell effects shows that the partitioning is dominated by the former, and this illustrates the importance of using accurate partial atomic charges for modeling these molecules in aqueous solution.

Understanding and estimating membrane/water partition coefficients: approaches to derive quantitative structure property relationships.

In the current study we describe three approaches to derive quantitative structure property relationships (QSPRs) that give insight in the interactions that are important in membrane/water partitioning. In the first model only semiempirically (AM1) calculated descriptors are used to model membrane/water partition coefficients. Additionally, differences between the n-octanol/water and membrane/water partition coefficients are explored using a small selection of calculated descriptors. The results from both these models show that besides the partitioning between an organic phase and water, additional hydrogen-bonding parameters (epsilonLUMO, Q-, and Q+) should be taken into account. Finally, using structural fragment values, a QSPR was derived to correct the n-octanol/water partition coefficient to obtain membrane/water partition coefficients, in case that obtaining AM1 descriptors is not feasible. The QSPRs that are presented here include only alcohols, benzenes, anilines, phenols, nitrobenzenes, quinoline, esters, and amines. Due to the data limitation, the models should be regarded preliminary for other structures, and caution is necessary when modeling charged species.

Class IV charge models: a new semiempirical approach in quantum chemistry.

We propose a new criterion for defining partial charges on atoms in molecules, namely that physical observables calculated from those partial charges should be as accurate as possible. We also propose a method to obtain such charges based on a mapping from approximate electronic wave functions. The method is illustrated by parameterizing two new charge models called AM1-CM1A and PM3-CM1P, based on experimental dipole moments and, respectively, on AM1 and PM3 semiempirical electronic wave functions. These charge models yield rms errors of 0.30 and 0.26 D, respectively, in the dipole moments of a set of 195 neutral molecules consisting of 103 molecules containing H, C, N and O, covering variations of multiple common organic functional groups, 68 fluorides, chlorides, bromides and iodides, 15 compounds containing H, C, Si or S, and 9 compounds containing C-S-O or C-N-O linkages. In addition, partial charges computed with this method agree extremely well with high-level ab initio calculations for both neutral compounds and ions. The CM1 charge models provide a more accurate point charge representation of the dipole moment than provided by most previously available partial charges, and they are far less expensive to compute.

AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution.

Two new continuum solvation models have been presented recently, and in this paper they are explained and reviewed in detail with further examples. Solvation Model 2 (AM1-SM2) is based on the Austin Model 1 and Solvation Model 3 (PM3-SM3) on the Parameterized Model 3 semiempirical Hamiltonian. In addition to the incorporation of phosphorus parameters, both of these new models address specific deficiencies in the original Solvation Model 1 (AM1-SM1), viz., (1) more accurate account is taken of the hydrophobic effect of hydrocarbons, (2) assignment of heavy-atom surface tensions is based on the presence or absence of bonded hydrogen atoms, and (3) the treatment of specific hydration-shell water molecules is more consistent. The new models offer considerably improved performance compared to AM1-SM1 for neutral molecules and essentially equivalent performance for ions. The solute charges within the Parameterized Model 3 Hamiltonian limit the utility of PM3-SM3 for compounds containing nitrogen and possibly phosphorus. For other systems both AM1-SM2 and PM3-SM3 give realistic results, but AM1-SM2 in general outperforms PM3-SM3. Key features of the models are discussed with respect to alternative approaches.

An SCF Solvation Model for the Hydrophobic Effect and Absolute Free Energies of Aqueous Solvation.

A model for absolute free energies of solvation of organic, small inorganic, and biological molecules in aqueous solution is described. This model has the following features: (i) the solute charge distribution is described by distributed monopoles, and solute screening of dielectric polarization is treated with no restrictions on solute shape; (ii) the energetic effects of cavity formation, dispersion interactions, and solute-induced restructuring of water are included by a semiempirical cavity surface tension; and (iii) both of these effects are included in the solute Hamiltonian operator for self-consistent field (SCF) calculations to allow solvent-induced electronic and geometric distortion of the solute. The model is parameterized for solutes composed of H, C, N, O, F, P, S, Cl, Br, and I against experimental data for 150 neutral solutes and 28 ions, with mean absolute errors of 0.7 and 2.6 kilocalories per mole, respectively.