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Proton Acceptor (proton + acceptor)
Selected AbstractsHydrogen bond of radicals: Interaction of HNO with HCO, HNO, and HOOINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2010Yong Yang Abstract Ab initio quantum mechanics methods are employed to investigate hydrogen bonding interactions between HNO and HCO, HOO radicals, and closed-shell HNO. The systems were calculated at MP2/6-311++G (2d, 2p) level and G2MP2 level. The topological and NBO analysis were investigated the origin of hydrogen bonds red- or blue-shifts. In addition, the comparisons were performed between HNO-opened-shell radical (HCO, HOO) complexes and HNO-corresponding closed-shell molecule (H2CO, HOOH) complexes. It is found that the stabilities of complexes increase from HNO-HCO to HNO-HOO. There are blue-shifts of NH, CH stretching vibrational frequencies and a red-shift of OH stretching vibrational frequency in the complexes. Rehybridization and electron density redistribution contribute to the blue-shifts of CH and NH stretching vibrational frequencies. Compared with the closed-shell H2CO, HCO is weaker proton donor and weaker proton acceptor. For the HOO, it is stronger proton donor and weaker proton acceptor than the HOOH is. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Crystal structure of the yeast His6 enzyme suggests a reaction mechanismPROTEIN SCIENCE, Issue 6 2006Sophie Quevillon-Cheruel Abstract The Saccharomycescerevisiae His6 gene codes for the enzyme phosphoribosyl-5-amino-1-phosphoribosyl-4-imidazolecarboxamide isomerase, catalyzing the fourth step in histidine biosynthesis. To get an insight into the structure and function of this enzyme, we determined its X-ray structure at a resolution of 1.30 Å using the anomalous diffraction signal of the protein's sulphur atoms at 1.77 Å wavelength. His6 folds in an (,/,)8 barrel similar to HisA, which performs the same function in bacteria and archaea. We found a citrate molecule from the buffer bound in a pocket near the expected position of the active site and used it to model the open form of the substrate (phosphoribulosyl moiety), which is a reaction intermediate. This model enables us to identify catalytic residues and to propose a reaction mechanism where two aspartates act as acid/base catalysts: Asp134 as a proton donor for ring opening, and Asp9 as a proton acceptor and donor during enolization of the aminoaldose. Asp9 is conserved in yeast His6 and bacterial or archaeal HisA sequences, and Asp134 has equivalents in both HisA and TrpF, but they occur at a different position in the protein sequence. [source] Critical catalytic functional groups in the mechanism of aspartate-,-semialdehyde dehydrogenaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2004Julio Blanco Aspartate-,-semialdehyde dehydrogenase (ASADH) catalyzes the reductive dephosphorylation of ,-aspartyl phosphate to l -aspartate-,-semialdehyde in the aspartate biosynthetic pathway. This pathway is not found in humans or other eukaryotic organisms, yet is required for the production of threonine, isoleucine, methionine and lysine in most microorganisms. The mechanism of this enzyme has been examined through the structures of two active-site mutants of ASADH from Haemophilus influenzae. Replacement of the enzyme active-site cysteine with serine (C136S) leads to a dramatic loss of catalytic activity caused by the expected decrease in nucleophilicity, but also by a change in the orientation of the serine hydroxyl group relative to the cysteine thiolate. In contrast, in the H277N active-site mutant the introduced amide is oriented in virtually the same position as that of the histidine imidazole ring. However, a shift in the position of the bound reaction intermediate to accommodate this shorter asparagine side chain, coupled with the inability of this introduced amide to serve as a proton acceptor, results in a 100-fold decrease in the catalytic efficiency of H277N relative to the native enzyme. These mutant enzymes have the same overall fold and high structural identity to native ASADH. However, small perturbations in the positioning of essential catalytic groups or reactive intermediates have dramatic effects on catalytic efficiency. [source] On Differences between Hydrogen Bonding and Improper Blue-Shifting Hydrogen BondingCHEMPHYSCHEM, Issue 4 2005Wiktor Zierkiewicz Dr. Abstract Twenty two hydrogen-bonded and improper blue-shifting hydrogen-bonded complexes were studied by means of the HF, MP2 and B3LYP methods using the 6-31G(d,p) and 6,311++G(d,p) basis sets. In contrast to the standard H bonding, the origin of the improper blue-shifting H bonding is still not fully understood. Contrary to a frequently presented idea, the electric field of the proton acceptor cannot solely explain the different behavior of the H-bonded and improper blue-shifting H-bonded complexes. Compression of the hydrogen bond due to different attractive forces,dispersion or electrostatics,makes an important contribution as well. The symmetry-adapted perturbation theory (SAPT) has been utilized to decompose the total interaction energy into physically meaningful contributions. In the red-shifting complexes, the induction energy is mostly larger than the dispersion energy while, in the case of blue-shifting complexes, the situation is opposite. Dispersion as an attractive force increases the blue shift in the blue-shifting complexes as it compresses the H bond and, therefore, it increases the Pauli repulsion. On the other hand, dispersion in the red-shifting complexes increases their red shift. [source] A new method for the determination of cooperative hydrogen bonding enthalpy of proton acceptors with associated species of alcoholsJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 4 2006Boris N. Solomonov Abstract A calorimetric method for the determination of cooperative hydrogen bonding (HB) enthalpy of protonacceptors (B) with associated species of alcohols is proposed. The average enthalpy of cooperative HB ofpyridine with associated species of alcohols was found to be ,19.8,±,0.6,kJ,mol,1 for all alcohols investigated. Thisvalue exceeds the enthalpy of HB in the complex ROH,,,NC5H5 (the average for all alcohols is ,15.8,± 0.2,kJ,mol,1) by 20,30%. Cooperativity factors (Ab, AOx) of hydrogen bonds for (ROH)2,,,NC5H5 complexes were determined using the IR-spectroscopic method. The average values for the alcohols under consideration were found to be Ab,=,1.41,±,0.04 and AOx,=,1.54,±,0.05. On the basis of IR-spectroscopic and calorimetric data, the enthalpy of cooperative interactions of pyridine with the dimer (ROH)2 was estimated. This value for all the alcohols studied is, on average, ,20.9,±,0.1,kJ,mol,1. Copyright © 2006 John Wiley & Sons, Ltd. [source] | ||||||||||