Nonlinear time-resolved vibrational spectroscopy is used to compare spectral broadening of the amide I band of the small peptide trialanine with that of N-methylacetamide, a commonly used model system for the peptide bond. In contrast to N-methylacetamide, the amide I band of trialanine is significantly inhomogeneously broadened. Employing classical molecular-dynamics simulations combined with density-functional-theory calculations, the origin of the spectral inhomogeneity is investigated. While both systems exhibit similar hydrogen-bonding dynamics, it is found that the conformational dynamics of trialanine causes a significant additional spectral broadening. In particular, transitions between the poly͑Gly͒II and the ␣ R conformations are identified as the main source of the additional spectral inhomogeneity of trialanine. The experimental and computational results suggest that trialanine adopts essentially two conformations: poly͑Gly͒II ͑80%͒ and ␣ R ͑20%͒. The potential of the joint experimental and computational approach to explore conformational dynamics of peptides is discussed.

Driven by recent two-dimensional infrared experiments by Woutersen and Hamm, trialanine has emerged as a paradigm to study conformational dynamics of a small peptide in aqueous solution. Employing the exceptional amount of experimental and ab initio data, in this work, trialanine serves as a model problem to perform a comprehensive comparison of six popular force fields, including the recent versions of the AMBER, CHARMM, GROMOS, and OPLS models. For all force fields under consideration, 20 ns long molecular-dynamics simulations are performed, and the structure and conformational dynamics of the solvated peptide is studied in detail. Employing density-functional theory calculations at the B3LYP/6-31+G(d) level, a number of observable quantities are calculated directly from the molecular-dynamics data and compared to experiment. The comparison allows for a quite detailed interpretation of recent NMR and infrared experiments. The nowadays achievable reliability and accuracy of a molecular dynamics description of a highly flexible biomolecular system are discussed in some detail.

We investigate the origin of subthreshold K ϩ production in heavy ion collisions at intermediate energies. In particular we study the influence of the pion induced K ϩ creation processes. We find that this channel shows a strong dependence on the size of the system, i.e., the number of participating nucleons as well as on the incident energy of the reaction. In an energy region between 1 and 2 GeV/nucleon the pion induced processes essentially contribute to the total yield and can even become dominant in reactions with a large number of participating nucleons. Thus we are able to reproduce recent measurements of the KaoS Collaboration for 1 GeV/nucleon Au on Au reactions adopting a realistic momentum dependent nuclear mean field.

Various aspects of the ab initio-based parametrization of an exciton model of amide I vibrations in peptides are discussed. Adopting "glycine dipeptide" (Ac-Gly-NHCH3) as a simple building-block model that describes the vibrational interaction between two peptide units, we perform comprehensive quantum-chemical calculations to investigate the effect and importance of the level of theory, the choice of local coordinates, and the localization method. A solvent continuum model description turns out important to obtain planar CONH peptide units when a full geometry optimization (which is necessary to obtain the correct frequencies) is performed. To study the conformational dependence of the amide I vibrations, we calculate (phi,psi) maps of the local-mode frequencies and couplings. Performing conformational averages of the (phi,psi) maps with respect to the most important peptide conformational states in solution (alpha, beta, P(II), and C5), we discuss the relation between these measurable quantities and the corresponding conformation of the peptide. Finally, the transferability of these maps to dipeptides with hydrophilic and hydrophobic side chains as well as to tripeptides with charged end groups is investigated.

We discuss the use of super-fermion formalism to represent and solve quantum kinetic equations for the electron transport problem. Starting with the Lindblad master equation for the molecule connected to two metal electrodes, we convert the problem of finding the nonequilibrium steady state to the many-body problem with non-Hermitian Liouvillian in super-Fock space. We transform the Liouvillian to the normal ordered form, introduce nonequilibrium quasiparticles by a set of canonical nonunitary transformations and develop general many-body theory for the electron transport through the interacting region. The approach is applied to the electron transport through a single level. We consider a minimal basis hydrogen atom attached to two metal leads in Coulomb blockade regime (out of equilibrium Anderson model) within the nonequilibrium Hartree-Fock approximation as an example of the system with electron interaction. Our approach agrees with exact results given by the Landauer theory for the considered models.

An atom-atom partitioning of the electrostatic energy between unperturbed molecules is proposed on the basis of the topology of the electron density. Atom-atom contributions to the electrostatic energy are computed exactly, i.e., via a novel six-dimensional integration over two atomic basins, and by means of the spherical tensor multipole expansion, up to total interaction rank L ) l A + l B + 1 ) 6. The convergence behavior of the topological multipole expansion is compared with that using distributed multipole analysis (DMA) multipole moments for a set of van der Waals complexes at the B3LYP/6-311+G(2d,p) level. Within the context of the Buckingham-Fowler model it is shown that the topological and DMA multipole moments converge to a very similar interaction energy and geometry (average absolute discrepancy of 1.3 kJ/mol and 1.3°, respectively) and are both in good to excellent agreement with supermolecule calculations.

An atom–atom partitioning of the (super)molecular Coulomb energy is proposed on the basis of the topological partitioning of the electron density. Atom–atom contributions to the molecular intra- and intermolecular Coulomb energy are computed exactly, i.e., via a double integration over atomic basins, and by means of the spherical tensor multipole expansion, up to rank L=lA+lB+1=5. The convergence of the multipole expansion is able to reproduce the exact interaction energy with an accuracy of 0.1–2.3 kJ/mol at L=5 for atom pairs, each atom belonging to a different molecule constituting a van der Waals complex, and for nonbonded atom–atom interactions in single molecules. The atom–atom contributions do not show a significant basis set dependence (3%) provided electron correlation and polarization basis functions are included. The proposed atom–atom Coulomb interaction energy can be used both with post-Hartree–Fock wave functions and experimental charge densities in principle. The Coulomb interaction energy between two molecules in a van der Waals complex can be computed by summing the additive atom–atom contributions between the molecules. Our method is able to extract from the supermolecule wave function an estimate of the molecular interaction energy in a complex, without invoking the reference state of free noninteracting molecules. We provide computational details of this method and apply it to (C2H2)2; (HF)2; (H2O)2; butane; 1,3,5-hexatriene; acrolein and urocanic acid, thereby covering a cross section of hydrogen bonds, and covalent bonds with and without charge transfer.

SummaryWe performed density functional calculations to examine the effects of solvation, hydrogen bonding, backbone conformation, and the side chain on 15 N chemical shielding in proteins. We used Nmethylacetamide (NMA) and N-formyl-alanyl-X (with X being one of the 19 naturally occurring amino acids excluding proline) as model systems. In addition, calculations were performed for selected fragments from protein GB3. The conducting polarizable continuum model was employed to include the effect of solvent in the density functional calculations. Our calculations for NMA show that the augmentation of the polarizable continuum model with the explicit water molecules in the first solvation shell has a significant influence on isotropic 15 N chemical shift but not as much on the chemical shift anisotropy. The difference in the isotropic chemical shift between the standard β-sheet and α-helical conformations ranges from 0.8 ppm to 6.2 ppm depending on the residue type, with the mean of 2.7 ppm. This is in good agreement with the experimental chemical shifts averaged over a database of 36 proteins containing >6100 amino acid residues. The orientation of the 15 N chemical shielding tensor as well as its anisotropy and asymmetry are also in the range of values experimentally observed for peptides and proteins.