Influence of the Counterpoise Correction on the Optimized Relativi Degrees of Freedom in the H-Bonded Complex Water-Formamide

peer reviewedThe correction of the basis set superposition error by the counterpoise method has been investigated at the SCF level for the weak H-bonded water-formamide complex and the results have been compared with the uncorrected results at the SCF, post SCF and semi-empirical AM1 and MNDO levels. Our particular concern has been the determination of the three optimized relative degrees of freedom and the relative stability of three C(s) geometrical conformations. The conclusions are that the counterpoise correction weakly conditions the variation in the degrees of freedom and the relative stabilities of the three conformers. The correction is obviously inadequate to describe intramolecular deformation

Qualitative Comparison between the Quantum Calculations and Electrospray Mass Spectra of Complexes of Polyammonium Macrotricyclic Ligands with Dicarboxylic Acids

The host-guest interactions play a very important role in chemical and biological processes. It is therefore important to be able to characterize these complexes. Electrospray mass spectrometry can be used to characterize the complex formation. It provides information on the mass and the charge of these ionic complexes. In this article, we show that the use of ab initio and semiempirical calculations, in addition to the results obtained by electrospray mass spectrometry, reveal to be a promising tool for the study of these noncovalent complexes. In this article, host-guest complexes formed by macropolycyclic polyammonium host molecules and dicarboxylic acids are studied

NMR structure of Citrobacter freundii AmpD, comparison with bacteriophage T7 lysozyme and homology with PGRP domains.

AmpD is a bacterial amidase involved in the recycling of cell-wall fragments in Gram-negative bacteria. Inactivation of AmpD leads to derepression of beta-lactamase expression, presenting a major pathway for the acquisition of constitutive antibiotic resistance. Here, we report the NMR structure of AmpD from Citrobacter freundii (PDB accession code 1J3G). A deep substrate-binding pocket explains the observed specificity for low molecular mass substrates. The fold is related to that of bacteriophage T7 lysozyme. Both proteins bind zinc at a conserved site and require zinc for amidase activity, although the enzymatic mechanism seems to differ in detail. The structure-based sequence alignment identifies conserved features that are also conserved in the eukaryotic peptidoglycan recognition protein (PGRP) domains, including the zinc-coordination site in several of them. PGRP domains thus belong to the same fold family and, where zinc-binding residues are conserved, may have amidase activity. This hypothesis is supported by the observation that human serum N-acetylmuramyl-L-alanine amidase seems to be identical with a soluble form of human PGRP-L

Numerical computation of the electrostatic interaction energy between methanol and the dyad water-imidazole

peer reviewedThe electrostatic interaction energy between methanol and the dyad water-imidazole has been computed numerically at three levels of approximation from 3D grids of the charge density of one partner and the electrostatic potential of the other. The minimum positions and energy values thus obtained compare well with those calculated analytically. The numerical procedure is especially interesting for the prediction of the stable conformers

Structure-activity relationships on adrenoceptors and imidazoline-preferring binding sites (I(1,2)-PBSs). Part 1: Weak intramolecular H-bond and conformational flexibility in a new I1-PBS-selective imidazoline analogue, trans1-(4',5'-dihydro-1'H-imidazol-2'-yl)methyl-2-hydroxyindane (PMS 952).

The highly selective I1-PBS imidazoline analogue PMS 952 has been selected to study the incidence of intramolecular hydrogen bond and molecular flexibility on its biological activity. On one hand, the weak energy difference between three calculated conformers does not support the stabilization of one conformer by an internal hydrogen bond. The 3-D electrostatic map confirms this feature and the solvent effect does not significantly modify the relative energy of these conformers. On the other hand, the conformational spaces of the neutral and ionized forms present a great number of equilibrium structures, in a short energetic range (20 Kcal). The results are representative of an exceptional conformational flexibility due to a cooperative effect between several parts of the molecule

SEMICLASSICAL WAVE PACKET DYNAMICS IN NONADIABATIC PROCESSES - THE CONICAL INTERSECTION BETWEEN THE X AND A STATES OF C2H4+

Autocorrelation and probablitity functions are calculated by semiclassical wave packet dynamics for the nuclear evolution of C2H4+ in its A state, connected with the X state via a conical intersection. Three distinct choices of potential energy surfaces were made: the canonic diabatic surface H22, as defined by Köppel, the adiabatic surface E2 and the Nikitin diabatic one. The wave packet is expanded in a Gaussian basis set restricted to 40 functions. The influence of the initial Gaussian width as well as the influence of freezing this width or not is studied. Taking into account the fact that this basis set is very small, one can conclude that the results are in qualitative agreement with those obtained by Köppel. The apparent discrepancy between the canonic diabatic autocorrelation function and the exact one could be explained by the existence of a dynamical condition for the choice of the diabatic potential energy surface. In the case of C2H4+(A), the behavior during the relaxation cannot be considered as essentially diabatic or adiabatic: it is intermediate

Catalytic reaction pathways approached by quantum chemistry: a challenge

This review explores the potential of quantum chemistry to help understand complex biochemical reactions such as enzyme catalysis. Starting from a historical background, the article introduces the reader to the great diversity of problems than can be dealt with in the framework of quantum chemistry

The Threshold Photoelectron Spectrum of Geminal Chloro-Fluoro-ethene (1,1-C2H2FCl) isomer. Experiment and Theory.

The threshold photoelectron spectrum (TPES) of 1,1-C2H2FCl has been measured for the first time using synchrotron radiation. It has been compared to the HeI photoelectron spectrum (PES) obtained earlier [Tornow G. et al., Chem.Phys. 146 115 (1990)]. Eight photoelectron bands have been observed at 10.22 eV, 12.45 eV, 13.28 eV, 14.29 eV, 14.99 eV, 17.12 eV, 17.67 eV, and at 20.23 eV successively. Only the first three bands exhibit a rich and extensive vibrational structure. Their adiabatic ionization energies are measured and a detailed vibrational analysis is presented. The assignments of the electronic bands and of the vibrational wavenumbers were made by using ab initio quantum chemical calculations. These allowed us to provide the MO description of the eight electronic states in terms of ionization and double excitation. The good correlation between predicted vibrational wavenumbers and the experimental values provides a strong basis for the assignment of all the vibrational structures.TMR (EU-HPRI-1999CT-00028) and I3 (R II 3 CT-2004-506008