2009. "Interactions of Cl- and OH Radical in Aqueous Solution." Journal of Physical Chemistry A 113(31):8823-8825. Abstract Fundamental understanding of ion-radical interactions in aqueous solutions is of significant relevance to many environmentally important applications. An important example can be found in the problem involving the excess production of molecular chlorine in marine layer, where interactions between OH radical and Cl- species have been implicated as the main reason for the unexpectedly high concentration of Cl2. Current understanding of this process is hindered due to uncertainty regarding the nature of the [OHCl]- complex in aqueous phase.
2009. "Excitons in Potassium Bromide: A Study using Embedded Time-dependent Density Functional Theory and Equation-of-Motion Coupled Cluster Methods." Chemical Physics Letters 470(4-6):353-357. doi:10.1016/j.cplett.2009.01.073 Abstract We present a study of the electronic excitations in insulating materials using an embedded- cluster method. The excited states of the embedded cluster are studied systematically using time-dependent density functional theory (TDDFT) and high-level equation-of-motion coupled cluster (EOMCC) methods. In particular, we have used EOMCC models with singles and doubles (EOMCCSD) and two approaches which account for the e®ect of triply excited con¯gurations in non-iterative and iterative fashions. We present calculations of the lowest surface excitations of the well-studied potassium bromide (KBr) system and compare our results with experiment. The bulk-surface exciton shift is also calculated at the TDDFT level and compared with experiment.
2009. "Excitation Energies of Zinc Porphyrin in Aqueous Solution Using Long-Range Corrected Time-Dependent Density Functional Theory." Journal of Physical Chemistry A 113(21):6041-6043. doi:10.1021/jp902118k Abstract We study the low-lying excited states of the zinc-porphyrin molecule in aqueous solution using long-range corrected TDDFT.We report results using the CAM-B3LYP and CAM-PBE0 functionals and compare them with previously reported excited states based on high-level coupled cluster (CC) methods. The aqueous environment is treated via a QM/MM approach.
2009. "A Dianionic Phosphorane Intermediate and Transition States in an Associative AN+DN Mechanism for the RibonucleaseA Hydrolysis Reaction." Journal of the American Chemical Society 131(11):3869-3871. doi:10.1021/ja807940y Abstract The ubiquitous presence of phosphoryl transfer as central step in many metabolic, signaling, energy storage, etc. enzymatic reactions requires that the details of the reaction mechanisms (e.g. reaction paths, transition state stabilization and structure, etc.) that leads to their remarkable rates in protein catalytic environments be understood1. It is expected that most of these reactions proceed through a pathway that includes a penta- coordinated phosphorane species. However, the nature of the bonding and the protonation of the structure in this region and the possibility of stable intermediates as the system passes along the reaction path through the transitions state (TS) are currently topics of considerable debate1a,b,c. Typically nucleophilic substitution reactions are classified in terms of extremes of two bonding situations along the reaction path: in a dissociative mechanism the substrate phosphate bridging bond is broken and the bond to the entering nucleophilic group is not yet formed leaving a metastable metaphosphate (PO3−) intermediate (a DN+AN reaction); in an associative mechanism in the extreme case a metastable pentacoordinated phosphorane species with nearly equivalent bonds is present in the TS, whose subsequent dissociation leads to the product state (an AN+DN reaction). Recently we published a computational study of the phosphoryl transfer step of a major class of enzymes, the serine kinases2a,b involved in signal transduction. These calculations2b support a dissociative mechanism (DNAN,) for this family of enzymes with unstable metaphosphate structure in loose transition state with total bond order of 22%.
2008. "Combined Quantum Mechanical and Molecular Mechanics Studies of the Electron-Transfer Reactions Involving Carbon Tetrachloride in Solution." Journal of Physical Chemistry A 112(12):2713-2720. doi:10.1021/jp7104709 Abstract The reductive dechlorination of carbon tetrachloride, CC₄, was investigated using combined high level quantum mechanical and molecular mechanics (QM/MM) approach. The first electron transfer process was assumed to proceed by a concerted electron transfer-bond breaking mechanism, and reaction barriers for the first electron reduction were estimated by using the crossing point of the free energy profiles of CCl₃-Cl and CCl₃-Cl•- as a function of the CCl₃-Cl distance. The results of these calculations showed that the activation barriers for this reaction are reachable under a wide range of reduction potentials. In the gas-phase, the barrier to reduction varied from 0.8 kcal/mol for reducing agent with a -5 kcal/mol work function to 24.7 kcal/mol for a reducing agent with a 40 kcal/mol work function at the CCSD(T)/aug-cc-pVDZ level. In the aqueous phase, QM/MM calculations at the CCSD(T)/aug-cc-pVDZ level predicted that the barrier to reduction varied from 0.7 kcal/mol to 35.2 kcal/mol for -2.32 V and 0.93 V reduction potentials respectively. COSMO continuum solvation calculations were also performed for comparison. For strong reducing agents (EH < -1.5V) very little difference was seen between the QM/MM and COSMO activation barriers. For weak reducing agents (EH > 0V) the activation barriers differed by as much as 6 kcal/mol between the QM/MM and COSMO calculations. These results demonstrate that ab initio electronic structure methods coupled with explicit molecular mechanics representation of the aqueous environment offer an efficient and accurate way to calculate the free energy reaction barriers for dissociative electron transfer reactions of organochlorine compounds to identify the potentially important environmental degradation processes.
2008. "A QM/MM Approach to Interpreting Zn-67 Solid-State NMR data in Zinc Proteins." Journal of the American Chemical Society 130(19):6224-6230. Abstract We present here a 67Zn solid-state NMR investigation of Zn2+ substituted rubredoxin. The sample has been prepared as both a dry powder and a frozen solution to determine the effects of static disorder on the NMR lineshape. Low temperature experiments have been performed at multiple fields to determine the relative contributions to the NMR lineshape from the electric field gradient and the anisotropic shielding tensors. Finally we present the theoretical interpretation of the experimental results utilizing a combined quantum mechanical molecular mechanics (QM/MM) approach. Theory predicts a sizable contribution from anisotropic shielding as compared with previously examined model systems. This is in good agreement with the experimental data.
2008. "The Application of High-Level Iterative Coupled-Cluster Methods to the Cytosine Molecule." Journal of Physical Chemistry A 112(24):5538-5541. Abstract The need for inclusion higher-order correlation effects for adequate description of the excitation energies of the DNA bases became clear in the last few years. In particular, we demonstrated that there is a sizable effect of triply excited configurations estimated in a non-iterative manner on the coupled-cluster excitation energies of the cytosine molecule in DNA environment. In this paper we discuss the accuracies of the non-iterative methods for biologically relevant systems in realistic environment in comparison with interative formulations that explicitly include the effect of triply excited clusters.
2008. "NonIterative Corrections to Equation-of-Motion Coupled-Cluster Excited State Energies Based on the Reduced Method of Moments of coupled cluster equation." International Journal of Quantum Chemistry 108(12):2178-2190. doi:10.1002/qua.21741 Abstract A new formalism closely related to the Method of Moment of Coupled-Cluster equations (MMCC) is obtained by embedding approximate coupled cluster (CC) or equation-of-motion CC (EOMCC) formalism into the formalism which uses cluster or excitation operators defined by excitation operators of higher rank with respect to a given approximation. Non-iterative corrections due to triples to the CC / EOMCC with singles and doubles (CCSD / EOMCCSD) reveal structural similarities to the CCSD(T) corrections for the ground state. Linked to our QM/MM module in NWChem this new algorithm is used to study the excited-state potential surfaces of C1₂O molecule in gas-phase and CC1₄ solution.
2008. "Fast Electron Correlation Methods for Molecular Clusters without Basis Set Superposition Errors ." Journal of Chemical Physics 128(7):Art. No. 074103. doi:10.1063/1.2828517 Abstract Two critical extensions to our fast, accurate, and easy-to-implement binary or ternary interaction method for weakly-interacting molecular clusters [Hirata et al. Mol. Phys. 103, 2255 (2005)] have been proposed, implemented, and applied to water hexamers, hydrogen fluoride chains and rings, and neutral and zwitterionic glycine–water clusters with an excellent result for an initial performance assessment. Our original method included up to two- or three-body Coulomb, exchange, and correlation energies exactly and higher-order Coulomb energies in the dipole–dipole approximation. In this work, the dipole moments are replaced by atom-centered point charges determined so that they reproduce the electrostatic potentials of the cluster subunits as closely as possible and also self-consistently with one another in the cluster environment. They have been shown to lead to dramatic improvement in the description of short-range electrostatic potentials not only of large, charge-separated subunits like zwitterionic glycine but also of small subunits. Furthermore, basis set superposition errors (BSSE) known to plague direct evaluation of weak interactions have been eliminated by com-bining the Valiron–Mayer function counterpoise (VMFC) correction with our binary or ternary interaction method in an economical fashion (quadratic scaling n2 with respect to the number of subunits n when n is small and linear scaling when n is large). A new variant of VMFC has also been proposed in which three-body and all higher-order Coulomb effects on BSSE are estimated approximately. The BSSE-corrected ternary interaction method with atom-centered point charges reproduces the VMFC-corrected results of conventional electron correlation calculations within 0.1 kcal/mol. The proposed method is significantly more accurate and also efficient than conventional correlation methods uncorrected of BSSE.
2008. "Large-Scale Parallel Calculations with Combined Coupled Cluster and Molecular Mechanics Formalism: Excitation Energies of Zinc-porphyrin in Aqueous Solution." Chemical Physics Letters 458(1-3):205-209. Abstract The vertical excitation energies of low-lying excited states of the zinc-porphyrin molecule in aqueous solution are characterized using a combination of coupled cluster and molecular mechanics descriptions. Coupled cluster description of excited states is based on equation-of-motion approach with singles and doubles (EOMCCSD) as well as its non-iterative extension for triply excited configurations. These results are compared with those obtained with time-dependent density functional theory (TD-DFT), which experiences severe problems with adequate description of low-lying states of chargetransfer character.
2008. "On the Electronically Excited States of Uracil." Journal of Physical Chemistry A 112(40):9983-9992. doi:10.1021/jp803758q Abstract Vertical excitation energies in uracil in the gas phase and in water solution are investigated by the equation-of-motion coupled-cluster and multi-reference configuration interaction methods. Basis set effects are found to be important for converged results. The analysis of electronic wave functions reveals that the lowest singlet states are predominantly of a singly excited character and are therefore well described by single-reference equation-of-motion methods augmented by a perturbative triples correction to account for dynamical correlation. Our best estimates for the vertical excitation energies for the lowest singlet n and are 5.0±0.1 eV and 5.3±0.1 eV, respectively. The solvent effects for these states are estimated to be +0.5 eV and ±0.1 eV, respectively. We attribute the difference between the computed vertical excitations and the maximum of the experimental absorption to strong vibronic interaction between the lowest A00 and A0 states leading to intensity borrowing by the forbidden transition.
2007. "Phosphorylation Reaction in cAPK Protein Kinase - Free Energy Quantum Mechanic/Molecular Mechanics Simulations." Journal of Physical Chemistry B 111(47):13455-13464. doi:10.1021/jp074853q Abstract Protein kinases catalyze the transfer of the γ-phosphoryl group from ATP, a key regulatory process governing signalling pathways in eukaryotic cells. The structure of the active site in these enzymes is highly conserved implying common catalytic mechanism. In this work we investigate the reaction process in cAPK protein kinase (PKA) using a combined quantum mechanics and molecular mechanics approach. The novel computational features of our work include reaction pathway determination with nudged elastic band methodology and calculation of free energy profiles of the reaction process taking into account finite temperature fluctuations of the protein environment. We find that the transfer of the γ-phosphoryl group in the protein environment is an exothermic reaction with the reaction barrier of 15 kcal/mol.
2007. "Hybrid Approach for Free Energy Calculations with High-Level Methods: Application to the S(N)2 Reaction of CHCl3 and OH- in Water." Journal of Chemical Physics 127(5):51102 (1-4). Abstract We present an approach for potential of mean force calculations within quantum mechanical molecular mechanics framework using hierarchy of approximations involving density functional and high level coupled cluster theories. As an example application we study the reaction process of CHC1₃ with OH¯ in aqueous solution.
2007. "Signature OH Absorption Spectrum from cluster Models of Solvation: a solvent-to-solute charge transfer state." Journal of Physical Chemistry A 111(42):10478-10482. doi:10.1021/jp074617f Abstract ab initio electronic structure theories applied to cluster models support the characterization of the signature of the OH absorption spectrum to be a solvent-to-solute charge transfer state affected by the hydrogen bonding environment in the region of 250 nm (calculated). The vertical excited states were calculated at the TDDFT level of theory with using OH(H2O)n clusters (n = 0-7, 16) with companion calculations at the EOM-CCSD level of theory for n ≤ 7. An intense solvent-to-solute charge transfer transition was calculated for n = 16 cluster where the donor and acceptor molecular orbitals are in favorable alignment. In the other smaller clusters the transitions in this region were found to be weak. The present findings are consistent with the experimental absorption at 230 nm suggested to be a solvent-to-solute charge transfer and provide insight into the electronic states and orbitals that give rise to the intensity of the band. This work was supported by the U.S. Department of Energy's (DOE) Office of Basic Energy Sciences, Chemical Sciences program, and was performed in part using the Molecular Science Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences Laboratory, a DOE national scientific user facility located at the Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for DOE.
2007. "Molecular Computational Investigation of Electron Transfer Kinetics across Cytochrome-Iron Oxide Interfaces." Journal of Physical Chemistry C 111(30):11363-11375. Abstract The interface between electron transfer proteins such as cytochromes and solid phase mineral oxides is central to the activity of dissimilatory-metal reducing bacteria. A combination of potential-based molecular dynamics simulations and ab initio electronic structure calculations are used in the framework of Marcus’ electron transfer theory to compute elementary electron transfer rates from a well-defined cytochrome model, namely the small tetraheme cytochrome (STC) from Shewanella oneidensis, to surfaces of the iron oxide mineral hematite (α-Fe2O3). Room temperature molecular dynamics simulations show that an isolated STC molecule favors surface attachment via direct contact of hemes I and IV at the poles of the elongated axis, with electron transfer distances as small as 9 Å. The cytochrome remains attached to the mineral surface in the presence of water and shows limited surface diffusion at the interface. Ab initio electronic coupling matrix element (VAB) calculations of configurations excised from the molecular dynamics simulations reveal VAB values ranging from 1 to 20 cm-1, consistent with nonadiabaticity. Using these results, together with experimental data on the redox potential of hematite and hemes in relevant cytochromes and calculations of the reorganization energy from cluster models, we estimate the rate of electron transfer across this model interface to range from 1 to 1000 s-1 for the most exothermic driving force considered in this work, and from 0.01 to 20 s-1 for the most endothermic. This fairly large range of electron transfer rates highlights the sensitivity of the rate upon the electronic coupling matrix element, which is in turn dependent on the fluctuations of the heme configuration at the interface. We characterize this dependence using an idealized bis-imidazole heme to compute from first principles the VAB variation due to porphyrin ring orientation, electron transfer distance, and mineral surface termination. The electronic matrix element and consequently the rate of electron transfer are found to be sensitive to all parameters considered. This work indicates that biomolecularly similar solvent-exposed bis-histidine hemes in outer-membrane cytochromes such as MtrC or OmcA are likely to have an affinity for the oxide surface in water governing the approach and interfacial conformation and, if allowed sufficient conformational freedom, will achieve distances and configurations required for direct interfacial electron transfer.
2007. "Calculations of Molecular Properties in Hybrid Coupled-Cluster and Molecular Mechanics Approach." Journal of Physical Chemistry A 111(25):5492-5498. doi:10.1021/jp070553x Abstract The ability to describe properties of molecular system in realistic environment is important for many applications. To address this issue we recently combined [M. Valiev, K. Kowalski, J. Chem. Phys. 2006, 125, 211101] classical molecular mechanics (MM) and ab initio coupled-cluster (CC) modules of NWChem. This paper reports the results of calculations of dipole moments and static polarizabilities for the C1₂0 system in the CC1₄ solution using the CCSD (CC with singles and doubles) linear response approach. We also discuss the application of the asymptotic extrapolation scheme (AES) [K. Kowalski, M. Valiev, J. Phys. Chem. A 2006, 110, 13106] in reducing the numerical cost of ab initio methods in the quantum region.
2007. "Structure and Dynamics of the Hydration Shells of the Al3+ Ion ." Journal of Chemical Physics 126(10):Art.no.104505. Abstract First principles simulations of the hydration shells surrounding Al3+ ions are reported for temperatures near 300oC. The predicted six waters in the octahedral first hydration shell were found to be trigonally coordinated via hydrogen-bonds to 12 second shell waters in agreement with the putative structure used to analyze the X-ray data, but in disagreement with 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 shell 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 2nd solvation shell were observed to occur on a picosecond (ps) 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 waters (20 ps). Limited simulations with 128 waters (5 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 was found for the 64 water system, which may indicate that sizes larger than 64 may be required to reliably predict behavior in this region,
2006. "Hybrid Coupled Cluster and Molecular Dynamics Approach: Application to the Excitation Spectrum of Cytosine in the Native DNA Environment." Journal of Chemical Physics 125(21):Art. No. 211101. doi:10.1063/1.2403847 Abstract Evolution of the excited state energies of cytosine base in the native DNA environment was investigated using hybrid coupled cluster and classical molecular dynamics approach. The time averaged excitation energies obtained with the variant of the completely renormalized equation-of-motion with singles, doubles, and non-iterative triples approach that includes a bulk of the correlation effects for excited states, are compared with the analogous calculations in the gas phase. Significant blue shifts for the two lowest singlet excitation energies can be observed as a result of interaction of the quantum system with surrounding environment.
2006. "Electronic Coupling between Heme Electron-Transfer Centers and Its Decay with Distance Depends Strongly on Relative Orientation." Journal of Physical Chemistry B 110(31):15582-15588. doi:10.1021/jp057068r Abstract A method for calculating the electron-transfer matrix element VRP using density functional theory Kohn-Sham orbitals is presented and applied to heme dimers of varying relative orientation. The electronic coupling decays with increased iron separation according to VRP ) V0RP exp(-βr/2) with a distance dependence parameter β ≈ 2 Å-1 for hemes with parallel porphyrins and either 1.1 or 4.0 Å-1 when the porphyrin planes are perpendicular, depending on the alignment of the iron dл orbital. These findings are used to interpret the observed orientation of the hemes in tetraheme redox proteins such as Flavocytochrome c3 fumarate reductase (Ifc3, PDB code 1QJD) of Shewanella frigidimarina, another flavocytochrome from the same bacterium (Fcc3, 1E39) and a small tetraheme cytochrome of Shewanella oneidensis strain MR1 (1M1P). Our results show that shifting and rotating the hemes controls the adiabaticity of the three electron hopping steps.
2006. "Asymptotic Extrapolation Scheme for Large-Scale Calculations with Hybrid Coupled Cluster and Molecular Dynamic Simulations." Journal of Physical Chemistry A 110(48):13106-13111. Abstract In this paper we discuss a simple extrapolation scheme based on the asymptotic behavior of the electronic energies considered as functions of cut-off factor for orbital energies corresponding to virtual orbitals. The performance of this approach is illustrated in the context of large-scale dynamical simulations for excitation energies of the cytosine molecule in its native DNA environment. We demonstrate that the extrapolation errors are significantly smaller that the excitation-energy fluctuations due to the fluctuating environment.
2005. "Fast Electron Correlation Methods for Molecular Clusters in the Ground and Excited States." Molecular Physics 103(15-16):2255-2265. Abstract An efficient and accurate electronic structure method for clusters of weakly interacting molecules has been proposed, on the basis of the pair-interaction method of Kitaura et al., and combined with density functional, many-body perturbation, coupled-cluster, equation-of-motion coupled-cluster, configuration-interaction singles, and time-dependent density functional theories. The method retains the one- and two-body Coulomb, exchange, and correlation energies exactly and higher-order Coulomb energies in the leading order of multipole expansion (hence the dipole polarisation effects). It typically recovers the total energies within 0.001 %, binding energies within a few kilocalories per mole, and excitation energies within a few hundredths of an electron volt of the conventional implementations. The size dependence of the computational cost of the method is asymptotically linear for total energies and constant for excitation energies. The method has been applied to the total energies of water clusters, to the total energies of zwitterionic and neutral glycine–water clusters, and to the excitation energies of formaldehyde–water clusters. The largest calculation was performed at an equation-of-motion coupled-cluster singles and doubles level for a formaldehyde–(H2O)81 cluster containing 247 atoms that predicted the solvatochromic shift of 1360 cm–1 in the lowest transition energy of formaldehyde in water.
2003. "Calculations of the Electronic Structure of 3d Transition Metal Dimers with Projector Augmented Plane Wave Method." Journal of Chemical Physics 119(12):5955-5964. Abstract The projected augmented plane wave (PAW) method provides an all-electron implementation of plane wave basis set in density-functional calculations. It allows an accurate treatment of systems throughout the periodic table while preserving the efficiency required for applications to first principles molecular dynamics simulations. In this article we report a comprehensive comparison of structural and energetic properties of 3d transition metal dimmers predicted by PAW and various local basis set methods. The bond energies, distances, and vibrational frequencies for the lowest lying multiplet states are calculated with both PAW as well local basis method using NWChem. Our results demonstrate that PAW calculations deliver the same level of accuracy as local basis set methods.
2002. "Parallel Implementation of the Projector Augmented Plane Wave Method for Charged Systems." Computer Physics Communications 143(1):11-28. Abstract The parallel implementation of the projector augmented plane wave (PAW) method with the applications to several transition metal complexes is presented. A unique aspect of our PAW code is that it can treat both charged and neutral cluster systems. We discuss how this can be achieved via accurate numerical treatment of the Coulomb Greens function with free space boundary conditions. The strategy for parallelizing of the PAW code is based on distributing the plane wave basis across processors. This is a most versatile approach and is easily implemented using a parallel three-dimensional Fast Fourier Trasformation (FFT). We report parallel performance analysis of our program as well as three-dimensional FFT's and discuss large-scale parallelization issues of the PAW code. Using a series of transition metal monoxides and dioxides, as well as two iron aqueous complexes, it is shown that a free space PAW code can give structural parameters and energies in good agreement with more traditional Gaussian based methods. PACS-1996 number(s): 71.15.a, 71.15.H, 71.15.p, 41.20.C