Efficient model chemistries for peptides. I. Split-valence Gaussian basis sets and the heterolevel approximation in RHF and MP2

We present an exhaustive study of more than 250 ab initio potential energy surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The model chemistries (MCs) used are constructed as homo- and heterolevels involving possibly different RHF and MP2 calculations for the geometry and the energy. The basis sets used belong to a sample of 39 selected representants from Pople's split-valence families, ranging from the small 3-21G to the large 6-311++G(2df,2pd). The reference PES to which the rest are compared is the MP2/6-311++G(2df,2pd) homolevel, which, as far as we are aware, is the more accurate PES of a dipeptide in the literature. The aim of the study presented is twofold: On the one hand, the evaluation of the influence of polarization and diffuse functions in the basis set, distinguishing between those placed at 1st-row atoms and those placed at hydrogens, as well as the effect of different contraction and valence splitting schemes. On the other hand, the investigation of the heterolevel assumption, which is defined here to be that which states that heterolevel MCs are more efficient than homolevel MCs. The heterolevel approximation is very commonly used in the literature, but it is seldom checked. As far as we know, the only tests for peptides or related systems, have been performed using a small number of conformers, and this is the first time that this potentially very economical approximation is tested in full PESs. In order to achieve these goals, all data sets have been compared and analyzed in a way which captures the nearness concept in the space of MCs.Comment: 54 pages, 16 figures, LaTeX, AMSTeX, Submitted to J. Comp. Che

Effects of constraints in general branched molecules: A quantitative ab initio study in HCO-L-Ala-NH2

A general approach to the design of accurate classical potentials for protein folding is described. It includes the introduction of a meaningful statistical measure of the differences between approximations of the same potential energy, the definition of a set of Systematic and Approximately Separable and Modular Internal Coordinates (SASMIC), much convenient for the simulation of general branched molecules, and the imposition of constraints on the most rapidly oscillating degrees of freedom. All these tools are used to study the effects of constraints in the Conformational Equilibrium Distribution (CED) of the model dipeptide HCO-L-Ala-NH2. We use ab initio Quantum Mechanics calculations including electron correlation at the MP2 level to describe the system, and we measure the conformational dependence of the correcting terms to the naive CED based in the Potential Energy Surface (PES) without any simplifying assumption. These terms are related to mass-metric tensors determinants and also occur in the Fixman's compensating potential. We show that some of the corrections are non-negligible if one is interested in the whole Ramachandran space. On the other hand, if only the energetically lower region, containing the principal secondary structure elements, is assumed to be relevant, then, all correcting terms may be neglected up to peptides of considerable length. This is the first time, as far as we know, that the analysis of the conformational dependence of these correcting terms is performed in a relevant biomolecule with a realistic potential energy function.Comment: 8 pages, 1 figure, LaTeX, aipproc style (included

Self-energy and lifetime of Shockley and image states on Cu(100) and Cu(111): Beyond the GW approximation of many-body theory

We report many-body calculations of the self-energy and lifetime of Shockley and image states on the (100) and (111) surfaces of Cu that go beyond the $GW$ approximation of many-body theory. The self-energy is computed in the framework of the GW\Gamma approximation by including short-range exchange-correlation (XC) effects both in the screened interaction W (beyond the random-phase approximation) and in the expansion of the self-energy in terms of W (beyond the GW approximation). Exchange-correlation effects are described within time-dependent density-functional theory from the knowledge of an adiabatic nonlocal XC kernel that goes beyond the local-density approximation.Comment: 8 pages, 5 figures, to appear in Phys. Rev.

The role of surface plasmons in the decay of image-potential states on silver surfaces

The combined effect of single-particle and collective surface excitations in the decay of image-potential states on Ag surfaces is investigated, and the origin of the long-standing discrepancy between experimental measurements and previous theoretical predictions for the lifetime of these states is elucidated. Although surface-plasmon excitation had been expected to reduce the image-state lifetime, we demonstrate that the subtle combination of the spatial variation of s-d polarization in Ag and the characteristic non-locality of many-electron interactions near the surface yields surprisingly long image-state lifetimes, in agreement with experiment.Comment: 4 pages, 2 figures, to appear in Phys. Rev. Let

Comment on "Correlated electron-nuclear dynamics: Exact factorization of the molecular wavefunction" [J. Chem. Phys. 137, 22A530 (2012)]

In spite of the relevance of the proposal introduced in the recent work A. Abedi, N. T. Maitra and E. K. U. Gross, J. Chem. Phys. 137, 22A530, 2012, there is an important ingredient which is missing. Namely, the proof that the norms of the electronic and nuclear wavefunctions which are the solutions to the nonlinear equations of motion are preserved by the evolution. To prove the conservation of these norms is precisely the objective of this Comment.Comment: 2 pages, published versio

One-dimensional potential for image-potential states on graphene

In the framework of dielectric theory the static non-local self-energy of an electron near an ultra-thin polarizable layer has been calculated and applied to study binding energies of image-states near free-standing graphene. The corresponding series of eigenvalues and eigenfunctions have been obtained by solving numerically the one-dimensional Schr{\"o}dinger equation. Image-potential-state wave functions accumulate most of their probability outside the slab. We find that a Random Phase Approximation (RPA) for the non-local dielectric function yields a superior description for the potential inside the slab, but a simple Fermi-Thomas theory can be used to get a reasonable quasi-analytical approximation to the full RPA result that can be computed very economically. Binding energies of the image-potential states follow a pattern close to the Rydberg series for a perfect metal with the addition of intermediate states due to the added symmetry of the potential. The formalism only requires a minimal set of free parameters; the slab width and the electronic density. The theoretical calculations are compared to experimental results for work function and image-potential states obtained by two-photon photoemission.Comment: 24 pages; 10 figures. arXiv admin note: text overlap with arXiv:1301.448

An exact expression to calculate the derivatives of position-dependent observables in molecular simulations with flexible constraints

In this work, we introduce an algorithm to compute the derivatives of physical observables along the constrained subspace when flexible constraints are imposed on the system (i.e., constraints in which the hard coordinates are fixed to configuration-dependent values). The presented scheme is exact, it does not contain any tunable parameter, and it only requires the calculation and inversion of a sub-block of the Hessian matrix of second derivatives of the function through which the constraints are defined. We also present a practical application to the case in which the sought observables are the Euclidean coordinates of complex molecular systems, and the function whose minimization defines the constraints is the potential energy. Finally, and in order to validate the method, which, as far as we are aware, is the first of its kind in the literature, we compare it to the natural and straightforward finite-differences approach in three molecules of biological relevance: methanol, N-methyl-acetamide and a tri-glycine peptideComment: 13 pages, 8 figures, published versio