Proton Transfer Chemistry in the Gas Phase. Is a Spontaneous \u27Neutralization\u27 Reaction a Myth or a Reality?

Relying on physicochemical knowledge, the proton cannot be spontaneously transferred from a gaseous mineral acid (HF, HCl, HBr, HI, HNO3, H2SO4, or HClO4) to a gaseous nitrogen base (NH3, alkylamine, aniline, pyridine, amidine, or guanidine). For example, the full proton-transfer from HCl to NH3, followed by the separation of Cl- and NH4+ requires more than 500 kJ mol-1. The same is true for a spontaneous intramolecular proton-transfer for gaseous amino acids, aminophenols and other amphiprotic compounds. From the gas-phase acidity parameter of COOH and the gas-phase basicity parameter of NH2 (or other more basic group in the side chain), it appears that proton transfer is endothermic or endergonic. For arginine, an amino acid with a highly basic guanidine function, this difference is still larger than about 300 kJ mol-1. Only solvation of the acid-base system by neutral species (e.g., one or more water molecules), complexation by ions (e.g., ionic acids or bases, metal cations) or even electrons may reduce the energetic barrier and facilitate the proton-transfer. Recent extension of the gas-phase acidity-basicity scale toward superacids and superbases, and recent development of spectroscopic techniques adapted to the gas phase for less volatile organic compounds give some perspectives for observing the full intermolecular proton-transfer between a molecular Brønsted-Lowry superacid and a molecular Brønsted-Lowry superbase

Proton Transfer Chemistry in the Gas Phase. Is a Spontaneous \u27Neutralization\u27 Reaction a Myth or a Reality?

Relying on physicochemical knowledge, the proton cannot be spontaneously transferred from a gaseous mineral acid (HF, HCl, HBr, HI, HNO3, H2SO4, or HClO4) to a gaseous nitrogen base (NH3, alkylamine, aniline, pyridine, amidine, or guanidine). For example, the full proton-transfer from HCl to NH3, followed by the separation of Cl- and NH4+ requires more than 500 kJ mol-1. The same is true for a spontaneous intramolecular proton-transfer for gaseous amino acids, aminophenols and other amphiprotic compounds. From the gas-phase acidity parameter of COOH and the gas-phase basicity parameter of NH2 (or other more basic group in the side chain), it appears that proton transfer is endothermic or endergonic. For arginine, an amino acid with a highly basic guanidine function, this difference is still larger than about 300 kJ mol-1. Only solvation of the acid-base system by neutral species (e.g., one or more water molecules), complexation by ions (e.g., ionic acids or bases, metal cations) or even electrons may reduce the energetic barrier and facilitate the proton-transfer. Recent extension of the gas-phase acidity-basicity scale toward superacids and superbases, and recent development of spectroscopic techniques adapted to the gas phase for less volatile organic compounds give some perspectives for observing the full intermolecular proton-transfer between a molecular Brønsted-Lowry superacid and a molecular Brønsted-Lowry superbase

Effect of metal Ions (Ni2+, Cu2+ and Zn2+) and water coordination on the structure of L-phenylalanine, L-tyrosine, L-tryptophan and their zwitterionic forms

Methods of quantum chemistry have been applied to double-charged complexes involving the transition metals Ni2+, Cu2+ and Zn2+ with the aromatic amino acids (AAA) phenylalanine, tyrosine and tryptophan. The effect of hydration on the relative stability and geometry of the individual species studied has been evaluated within the supermolecule approach. The interaction enthalpies, entropies and Gibbs energies of nine complexes Phe•M, Tyr•M, Trp•M, (M = Ni2+, Cu2+ and Zn2+) were determined at the Becke3LYP density functional level of theory. Of the transition metals studied the bivalent copper cation forms the strongest complexes with AAAs. For Ni2+and Cu2+ the most stable species are the NO coordinated cations in the AAA metal complexes, Zn2+cation prefers a binding to the aromatic part of the AAA (complex II). Some complexes energetically unfavored in the gas-phase are stabilized upon microsolvation

A first principles study of proton transport through model helical pores

Proton transport (PT) across cell membranes is a fundamental process and a key step in many biological functions, including cell signalling and enzymatic reactions. All biochemical reactions that convert energy from one form to another are mediated by PT, which also serves as a vital route to achieve cell pH stabilisation. The coding for membrane -bound proteins constitutes 25 -30% of all genes, and they are implicated in many diseases such as diabetes and Parkinson's. Consequently, they are the subject of major drug target studies (in fact the drug targets for all neurological diseases are membrane -bound proteins). Whilst PT is known to occur via transient water molecules across the cell membrane itself, it is more often the case that the mechanism involves proteins that span the membrane surface and act as proton- specific ion channels. PT has been widely studied in protein systems such as gramicidin A, cytochrome C oxidase, the M2 channel protein in the influenza A virus and bacteriorhodopsin. Evidence for the relay of H+ by buried water molecules ('water wires') mediated by the side -chains of alpha -helices have been substantiated in these and other proteins, but finding direct experimental evidence for the reaction pathway is extremely challenging work.When experiment can provide only partial answers, it is the role of computational modelling to complete the picture. Modelling these trans -membrane proteins at the full atomistic quantum mechanical level, however, lies beyond the capabilities of current computational techniques, necessitating the use of simplified models. To this end, work undertaken in this thesis has derived and tested a simplified model that is large enough to maintain the essential tertiary structures of transmembrane proteins, but small enough to permit full ab initio MD simulations over long time periods to be performed. The model is based on a single helix scaffold placed under periodic boundary conditions to create a cavity that supports a water wire. The simulations then focus on monitoring the behaviour of a proton as it 'hops' along this wire in a manner akin to the classical Grotthuss mechanism.Mechanistic studies have taken place using poly-glycine, poly-glycine-serine and poly-glycine-aspartic models, and show that the mechanism of PT in channel environments shares some features with the simulations reported for bulk water, with, e.g., the hydrogen bond distance shortening in the time period leading up to successful proton transfer. There are, however, also some important differences, such as the observation of a heightened number of proton rattling events. The channel environment also removes the need for the loss of a water molecule from the inner coordination sphere of the receiving water molecule as the constriction in space only allows a coordination sphere of three molecules, as opposed to four for bulk water.The effect of varying the density of water molecules in the channel has also been investigated. A range of cationic states have been identified, with widely varying lifetimes and compared across all models. We also observe that the helix plays an important role in directing the behaviour of the water wire: the most active proton transport regions of the water -wire are found in areas where the helix is most tightly coiled. Finally, we report on the effects of different DFT functionals to model a water - wire using the simplest poly -glycine model, and on the importance of including dispersion corrections to stabilize the helical structure.Finally, using the poly -glycine- aspartic acid model, a study was undertaken that focused on the direction of proton transport through the channel when the side chains of the aspartic acid residues interacted directly with the water wire. In this model there were two different pathways for the excess proton to pass along: a long hydrogen - bonded network of water molecules and amino acid residues, or a short [H30]+ diffusion pathway. It was found that the proton- hopping route over multiple water molecules and amino acid residues was preferred over the diffusion route, even though this pathway was substantially longer

A computational investigation of the interaction of the collagen molecule with hydroxyapatite

This thesis presents the results of computer simulation studies of the interaction of the predominant molecules in the collagen protein with the hydroxyapatite mineral. Using a combination of computational techniques, quantum-mechanical methods based on the density functional theory (DFT) and molecular dynamics simulations based on interatomic potentials, we have investigated the interface between the collagen protein and the apatite mineral. First we have employed electronic structure techniques (DFT) to study a range of different binding modes of the amino acids glycine, proline and hydroxyproline, which are major constituents of the collagen I protein, at two important hydroxyapatite surfaces, (0001) and (0110) . We have performed full geometry optimizations of the hydroxyapatite surface with adsorbed amino acid molecules to obtain the optimum substrate/adsorbate structures and interaction energies. We have also used DFT to investigate the binding of a series of representative peptides containing hydrophobic side groups (proline), uncharged polar side groups (glycine and hydroxyproline), and charged polar side groups (lysine and hydroxylysine) to the hydroxyapatite (0001) and (0110) surfaces. This selection of adsorbates has given us the opportunity to study separately the interactions of the carboxylic acid and amine functional groups, as well as the effect of hydroxylation and the charges of the side group, on the strength of interaction with the surfaces. We have also investigated the same systems in an aqueous environment using classical molecular dynamics simulation, where we have calculated the energies and geometries of adsorption of the peptide at the surfaces of hydroxyapatite in competition with pre-adsorbed water. Finally, we have studied the onset of nucleation of the hydroxyapatite mineral at an entire collagen molecule in aqueous solution

Proceedings of the Thirteenth International Conference on Time-Resolved Vibrational Spectroscopy

The thirteenth meeting in a long-standing series of “Time-Resolved Vibrational Spectroscopy” (TRVS) conferences was held May 19th to 25th at the Kardinal Döpfner Haus in Freising, Germany, organized by the two Munich Universities - Ludwig-Maximilians-Universität and Technische Universität München. This international conference continues the illustrious tradition of the original in 1982, which took place in Lake Placid, NY. The series of meetings was initiated by leading, world-renowned experts in the field of ultrafast laser spectroscopy, and is still guided by its founder, Prof. George Atkinson (University of Arizona and Science and Technology Advisor to the Secretary of State). In its current format, the conference contributes to traditional areas of time resolved vibrational spectroscopies including infrared, Raman and related laser methods. It combines them with the most recent developments to gain new information for research and novel technical applications. The scientific program addressed basic science, applied research and advancing novel commercial applications. The thirteenth conference on Time Resolved Vibrational Spectroscopy promoted science in the areas of physics, chemistry and biology with a strong focus on biochemistry and material science. Vibrational spectra are molecule- and bond-specific. Thus, time-resolved vibrational studies provide detailed structural and kinetic information about primary dynamical processes on the picometer length scale. From this perspective, the goal of achieving a complete understanding of complex chemical and physical processes on the molecular level is well pursued by the recent progress in experimental and theoretical vibrational studies. These proceedings collect research papers presented at the TRVS XIII in Freising, German