Authors:Konrad Patkowski Pages: 3 - 91 Abstract: Publication date: 2017 Source:Annual Reports in Computational Chemistry, Volume 13 Author(s): Konrad Patkowski Theoretical and computational chemistry is constantly striving for a more accurate, more efficient, and more robust description of noncovalent interactions. In this quest, a very important factor has been the development of benchmark databases of accurate interaction energies for model complexes. In this review, we first establish the coupled-cluster approach with single, double, and perturbative triple excitations (CCSD(T)) at the complete basis set (CBS) limit as the method of choice for generating accurate benchmark interaction energies and illustrate the options and challenges to obtaining a precise CCSD(T)/CBS estimate. We then discuss the effects beyond the frozen-core CCSD(T) level that need to be included to further improve the accuracy. Moving on from single-system interaction energies to complete databases, we discuss the issues of geometrical and system type diversity that need to be considered for the transferability of the conclusions reached for a particular dataset. We then review the most popular existing databases of noncovalently interacting dimers and clusters, paying special attention to the newest and largest “third-generation” benchmark sets exhibiting the highest diversity. While benchmark noncovalent databases have been utilized for a broad range of purposes, we focus our attention on their use in the assessment and refinement of various efficient approximations to CCSD(T)/CBS, including density functional, wavefunction, semiempirical, and force field approaches.

Authors:Eric J. Bylaska Pages: 185 - 228 Abstract: Publication date: 2017 Source:Annual Reports in Computational Chemistry, Volume 13 Author(s): Eric J. Bylaska A detailed description of modern plane-wave density functional theory (DFT) methods and software (contained in the NWChem package) is described that allows for both geometry optimization and ab initio molecular dynamics simulations. Significant emphasis is placed on aspects of these methods that are of interest to computational chemists and useful for simulating chemistry, including techniques for calculating charged systems, exact exchange (i.e., hybrid DFT methods), and highly efficient AIMD/MM methods. Sample applications on the structure of the goethite + water interface and the hydrolysis of nitroaromatic molecules are described.

Authors:Yinglong Miao; J. Andrew McCammon Pages: 231 - 278 Abstract: Publication date: 2017 Source:Annual Reports in Computational Chemistry, Volume 13 Author(s): Yinglong Miao, J. Andrew McCammon A novel Gaussian Accelerated Molecular Dynamics (GaMD) method has been developed for simultaneous unconstrained enhanced sampling and free energy calculation of biomolecules. Without the need to set predefined reaction coordinates, GaMD enables unconstrained enhanced sampling of the biomolecules. Furthermore, by constructing a boost potential that follows a Gaussian distribution, accurate reweighting of GaMD simulations is achieved via cumulant expansion to the second order. The free energy profiles obtained from GaMD simulations allow us to identify distinct low energy states of the biomolecules and characterize biomolecular structural dynamics quantitatively. In this chapter, we present the theory of GaMD, its implementation in the widely used molecular dynamics software packages (AMBER and NAMD), and applications to the alanine dipeptide biomolecular model system, protein folding, biomolecular large-scale conformational transitions, and biomolecular recognition.

Authors:Roberto Cammi Abstract: Publication date: Available online 1 August 2017 Source:Annual Reports in Computational Chemistry Author(s): Roberto Cammi A new quantum chemical method, XP-PCM, for studying reactive systems at extreme high pressures (p > 1 GPa) is reviewed. The method is an extension of the standard polarizable continuum model, that is, usually used for the description of a molecular solute at a standard condition of pressure and temperature. It introduces the effects of the pressure by means of the increase of the Pauli repulsion interaction between the solute and the environment, which is the dominant component of the intermolecular interactions in dense system at extreme high pressure. The XP-PCM method allows one to build an effective potential energy surface from which the effect of the pressure on the activation energy and the reaction energy can be determined. From this information, the activation and reaction volumes can be estimated. The Diels–Alder dimerization of cyclopentadiene under extremely high pressure is presented as working case.

Authors:Joseph V. Ortiz Abstract: Publication date: Available online 1 August 2017 Source:Annual Reports in Computational Chemistry Author(s): Joseph V. Ortiz Electron propagator theory provides a strategy with computational and interpretive advantages for the prediction of electron attachment and detachment energies and other properties of molecules and molecular ions. Although the effects of electron correlation may be systematically included up to the exact limit, transparent generalizations of one-electron concepts also are procured by the electron propagator approach to molecular electronic structure. Generalized molecular-orbital concepts emerge from the Dyson quasiparticle equation, including correlated electron binding energies and their Dyson orbitals. This information suffices to predict transition probabilities which are probed in various kinds of spectroscopic and scattering experiments. Relationships between correlated transition and reference-state properties are discussed. Approximations in the self-energy operator, wherein relaxation and correlation effects on electron binding energies reside, are described. Emphasis is placed on approaches that employ a separation between occupied and virtual spin-orbitals such as the renormalized partial third order, the nondiagonal renormalized second order, the second-order transition operator and the Brueckner-doubles, triple-index ionization operator methods. Computational characteristics of these methods are compared with those of older precedents, including the second order, outer valence green function, and GW self-energies. Results of numerical tests on molecules of general interest and improved strategies for treating basis-set effects are reviewed. Recent and noteworthy applications to molecular wires, solvated molecules and ions, gas-phase anions, super-halogens, positron–molecule complexes, anionic resonances, and photoionization cross sections are summarized.

Authors:Gregory S. Tschumper; Thomas L. Ellington; Sarah N. Johnson Abstract: Publication date: Available online 1 August 2017 Source:Annual Reports in Computational Chemistry Author(s): Gregory S. Tschumper, Thomas L. Ellington, Sarah N. Johnson Certain processes, such as proton transfer or dissociation, can introduce inconsistencies into computational techniques based on the many-body expansion if the identities of the fragments that define the expansion change. This report uses simple binary acid/base clusters to illustrate this potential problem and to quantify the effects of these inconsistencies on the total and relative electronic energies of the clusters. The 2-body:Many-body CCSD(T):MP2 approach developed in our lab typically deviates from CCSD(T) reference values by only a few hundredths of a kcal mol−1 for clusters in which monomer-based fragment definitions are entirely consistent. These deviations generally grow to at least several tenths of a kcal mol−1 for clusters where inconsistencies are introduced by such simple fragment definitions. In fact, the magnitude of the discrepancies can actually exceed 1kcal mol−1 (or 25%) for the relative electronic energies.