Marat Valiev

Fast electron correlation methods for molecular clusters in the ground and excited states

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 (and, if necessary, also three-body) Coulomb, exchange, and correlation energies exactly and higher-order Coulomb energies in the leading order of multipole expansion (hence the dipole polarization or induction effects). The latter makes the combination of this method with existing implementations of any electronic structure theory extremely easy. 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.

Fast electron correlation methods for molecular clusters without basis set superposition errors

Two critical extensions to our fast, accurate, and easy-to-implement binary or ternary interaction method for weakly interacting molecular clusters [S. 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 initial performance assessment result. 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 interaction 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 accurately and also self-consistently with one another in the cluster environment. They have been shown to lead to a dramatic improvement in the description of short-range electrostatic potentials not only of large, charge-separated subunits such as zwitterionic glycine but also of small subunits. Furthermore, basis set superposition errors (BSSEs) have been eliminated by combining the Valiron-Mayer function counterpoise (VMFC) correction with our binary or ternary interaction method. A new BSSE-correction scheme has been proposed on this basis, wherein three-body and all higher-order Coulomb effects on BSSE are also estimated. The BSSE-corrected ternary interaction method with atom-centered point charges reproduces the VMFC-corrected results within 0.1 kcal/mol. The proposed method is not only more efficient but also significantly more accurate than conventional correlation methods uncorrected of BSSE.

Hybrid approach for free energy calculations with high-level methods: Application to the SN2 reaction of CHCl3 and OH− in water

We present an approach to calculate the free energy profile along a condensed-phase reaction path based on high-level electronic structure methods for the reactive region. The bulk of statistical averaging is shifted toward less expensive descriptions by using a hierarchy of representations that includes molecular mechanics, density functional theory, and coupled cluster theories. As an application of this approach we study the reaction of CHCl3 with OH- in aqueous solution.

Excitation energies of zinc porphyrin in aqueous solution using long-range corrected time-dependent density functional theory.

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.

Hybrid coupled cluster and molecular dynamics approach: Application to the excitation spectrum of cytosine in the native DNA environment

Evolution of the excited state energies of cytosine base in the native DNA environment was investigated using a 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 the interaction of the quantum system with the surrounding environment.

Vertical ionization potentials of nucleobases in a fully solvated DNA environment.

Vertical ionization potentials (IPs) of nucleobases embedded in a fully solvated DNA fragment (12-mer B-DNA fragment + 22 sodium counterions + 5760 water molecules equilibrated to 298 K) have been calculated using a combined quantum mechanical molecular mechanics (QM/MM) approach. Calculations of the vertical IP of the anion Cl(-) are reported that support the accuracy of the application of a QM/MM method to this problem. It is shown that the pi nucleotide HOMO origin for the emitted electron is localized on the base by the hydration structure surrounding the DNA in a way similar to that recently observed for pyrimidine nucleotides in aqueous solutions (Slavicek, P.; et al. J. Am. Chem. Soc. 2009, 131, 6460). In a first step, a high level of theory, CCSD(T)/aug-cc-pVDZ, was used to calculate the vertical IP of each of the four single bases isolated in the QM region while the remaining DNA fragment, counterions, and water solvent molecules were included in the MM region. The calculated vertical IPs show a large positive shift of 3.2-3.3 eV compared to the corresponding gas-phase values. This shift is similar for all four DNA bases. The origin of the large increase in vertical IPs of nucleobases is found to be the long-range electrostatic interactions with the solvation structure outside the DNA helix. Thermal fluctuations in the fluid can result in IP changes of roughly 1 eV on a picosecond time scale. IPs of pi-stacked and H-bonded clusters of DNA bases were also calculated using the same QM/MM model but with a lower level of theory, B3LYP/6-31G(d=0.2). An IP shift of 4.02 eV relative to the gas phase is found for a four-base-pair B-DNA duplex configuration. The primary goal of this work was to estimate the influence of long-range solvation interactions on the ionization properties of DNA bases rather than provide highly precise IP evaluations. The QM/MM model presented in this work provides an attractive method to treat the difficult problem of incorporating a detailed long-range structural model of physiological conditions into investigations of the electronic processes in DNA.

Combined Quantum Mechanical and Molecular Mechanics Studies of the Electron-Transfer Reactions Involving Carbon Tetrachloride in Solution

The reductive dechlorination of carbon tetrachloride, CCl4, by a concerted electron transfer-bond breaking mechanism was studied using combined high level quantum mechanical and molecular mechanics (QM/MM) approach. The free energy activation barriers for the first electron-transfer step were determined from the dissociation profiles of CCl4 and *CCl4(-) complexes in aqueous phase using hybrid-free energy QM/MM methodologies. Both density functional and coupled cluster perturbative triples (CCSD(T)) versions of QM/MM methods were investigated. The impact of the implicit solvent description based on continuum (COSMO) solvent models was also analyzed. QM/MM calculations at the CCSD(T)/aug-cc-pVDZ/SPCE level of theory predict that the activation barriers vary from 0.7 to 35.2 kcal/mol for -2.32 and 0.93 V reduction potentials respectively. Good agreement with experimental data for oxide-free iron electrodes (-0.6 to -1.2 V reduction potentials) is observed indicating that the measured activation barriers are consistent with the concerted electron transfer-bond-breaking mechanism.

Simulating Ru L3-Edge X-ray Absorption Spectroscopy with Time-Dependent Density Functional Theory: Model Complexes and Electron Localization in Mixed-Valence Metal Dimers

Ruthenium L3-edge X-ray absorption (XA) spectroscopy probes unoccupied 4d orbitals of the metal atom and is increasingly being used to investigate the local electronic structure in ground and excited electronic states of Ru complexes. The simultaneous development of computational tools for simulating Ru L3-edge spectra is crucial for interpreting the spectral features at a molecular level. This study demonstrates that time-dependent density functional theory (TDDFT) is a viable and predictive tool for simulating ruthenium L3-edge XA spectroscopy. We systematically investigate the effects of exchange correlation functional and implicit and explicit solvent interactions on a series of Ru(II) and Ru(III) complexes in their ground and electronic excited states. The TDDFT simulations reproduce all of the experimentally observed features in Ru L3-edge XA spectra within the experimental resolution (0.4 eV). Our simulations identify ligand-specific charge transfer features in complicated Ru L3-edge spectra of [Ru(CN)6](4-) and Ru(II) polypyridyl complexes illustrating the advantage of using TDDFT in complex systems. We conclude that the B3LYP functional most accurately predicts the transition energies of charge transfer features in these systems. We use our TDDFT approach to simulate experimental Ru L3-edge XA spectra of transition metal mixed-valence dimers of the form [(NC)5M(II)-CN-Ru(III)(NH3)5](-) (where M = Fe or Ru) dissolved in water. Our study determines the spectral signatures of electron delocalization in Ru L3-edge XA spectra. We find that the inclusion of explicit solvent molecules is necessary for reproducing the spectral features and the experimentally determined valencies in these mixed-valence complexes. This study validates the use of TDDFT for simulating Ru 2p excitations using popular quantum chemistry codes and providing a powerful interpretive tool for equilibrium and ultrafast Ru L3-edge XA spectroscopy.

Calculations of the electronic structure of 3d transition metal dimers with projector augmented plane wave method

The projected augmented plane wave method provides an all-electron solution to the Kohn–Sham local density approximation to the electronic Schrodinger equation. By projecting the fast-varying parts of the single-particle orbitals onto a local basis it allows accurate calculations for molecules and solids throughout the periodic table using a plane wave basis without the introduction of pseudopotentials. The method, thereby, preserves the efficiency required for applications to first-principles molecular dynamics simulations, while still allowing an unambiguous solution for systems containing strong scattering atoms such as transition metals. In this work, we made a comprehensive comparison of the structural and energetic properties of homonuclear 3d transition metal diatomic molecules as predicted by projector augmented plane wave and by various local basis methods. These molecules are particularly difficult to treat with plane-wave pseudopotential methods. The bond energies, bond lengths, and vibrational...

Structure and dynamics of the hydration shells of the Al3+ ion

First principles simulations of the hydration shells surrounding Al3+ ions are reported for temperatures near 300 degrees 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.