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Hydrogen Bond Donor (hydrogen + bond_donor)
Selected AbstractsOxidation of substituted benzaldehydes by quinolinium chlorochromate: A structure and solvent dependent kinetic studyINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 4 2003G. Fatima Jeyanthi The kinetics of oxidation of several para-substituted benzaldehydes by quinolinium chlorochromate was studied under pseudo-first-order conditions in different (hydrogen bond donor and hydrogen bond acceptor) neat organic solvents. The operation of nonspecific and specific solvent,solvent,solute interactions was explored by correlating the rate data with solvent parameters through correlation analysis. Both electron-releasing and electron-withdrawing substituents enhanced the rate and the Hammett plot showed a break in the reactivity order indicating applicability of dual mechanism. An explanation in conformity with structure and solvent effects on reactivity has been proposed. © 2003 Wiley Periodicals, Inc. Int J Chem Kinet 35: 154,158, 2003 [source] Non-aqueous reverse micelles media for the SNAr reaction between 1-fluoro-2,4-dinitrobenzene and piperidine,JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 12 2006N. Mariano Correa Abstract The kinetics of the nucleophilic aromatic substitution (SNAr) reaction between 1-fluoro-2,4- dinitrobenzene (FDNB) and piperidine (PIP) in ethylene glycol (EG)/ sodium bis (2-ethyl-1-hexyl) sulfosuccinate (AOT)/n -heptane and dimethylformamide (DMF)/AOT/n -heptane non-aqueous reverse micelle systems is reported. EG and DMF were used as models for hydrogen bond donor (HBD) and non-hydrogen bond donor (non-HBD) polar solvents, respectively. The reaction was found not to be base catalyzed in these media. A mechanism to rationalize the kinetic results is proposed in which both reactants may be distributed between the two environments. The distribution constants of FDNB between the organic and each micellar pseudophases were determined by an independent fluorescence method. These results were used to evaluate the amine distribution constant and the intrinsic second-order rate coefficient of the SNAr reaction in the interface. The reaction was also studied in the pure solvents EG and DMF for comparison. The results in EG/AOT/n -heptane at Ws,=,2 give similar kinetic profiles than in water/AOT/n -hexane at W,=,10. With these HBD solvents, the interface saturation by the substrate is reached at around the same value of [AOT] and the intrinsic second-order rate coefficient in the interface, k,b, has comparable values. On the other hand, when DMF is used as a polar non-HBD solvent, the intrinsic second-order rate constant increases by a factor of about 200 as compared to the values obtained using HBD solvents as a polar core. It is concluded that higher catalytic power is obtained when non-HBD solvents are used as polar solvent in the micelle interior. Copyright © 2006 John Wiley & Sons, Ltd. [source] Generation of Selective TACE Inhibitors: Ligand and Structure Based Molecular Modeling, Virtual Screening, Counter Pharmacophore Screening to Get Selective MoleculesMOLECULAR INFORMATICS, Issue 11-12 2009Malkeet, Singh Bahia Abstract This study describes the ligand based as well as structure based molecular modeling and virtual screening of selective tumor necrosis factor-, converting enzyme (TACE) inhibitors. In ligand based molecular modeling, two statistically reliable pharmacophore models HypoA1 and HypoB1 were generated using a same training set of 22,molecules. HypoA1,consists of two hydrogen bond acceptor and three hydrophobic groups whereas HypoB1 consists of one hydrogen bond donor, one ring aromatic and three hydrophobic groups. Virtual screening was performed with both models in in-house database of 1.2,million molecules. To remove non selective hits from screened molecules, a counter pharmacophore was generated using inhibitors of MMP-1, an important enzyme involved in musculoskeletal degradation. In structure based molecular modeling, docking analysis was performed to explore the important interactions between ligands and protein. On comparison, HypoA1 and HypoB1 were found to be complementing with results of docking analysis suggesting high reliability of both models for their use in virtual screening/designing of new molecules. [source] The solution structure of the methylated form of the N-terminal 16-kDa domain of Escherichia coli Ada proteinPROTEIN SCIENCE, Issue 3 2006Hiroto Takinowaki N-Ada16k, the N-terminal 16-kDa domain of the Ada protein; meC38 N-Ada16k, the Cys38 methylated form of N-Ada16k; MTase, methyltransferase; HTH, helix-turn-helix; NMR, nuclear magnetic resonance; MALDI-TOF MS, matrix assisted laser desorption/ionization time of flight mass spectrometry; MNU, methylnitrosourea Abstract The N-terminal 16-kDa domain of Escherichia coli Ada protein (N-Ada16k) repairs DNA methyl phosphotriester lesions by an irreversible methyl transfer to its cysteine residue. Upon the methylation, the sequence-specific DNA binding affinity for the promoter region of the alkylation resistance genes is enhanced by 103 -fold. Then, it acts as a transcriptional regulator for the methylation damage. In this paper, we identified the methyl acceptor residue of N-Ada16k and determined the solution structure of the methylated form of N-Ada16k by using NMR and mass spectrometry. The results of a 13C-filtered 1H- 13C HMBC experiment and MALDI-TOF MS and MS/MS experiments clearly showed that the methyl acceptor residue is Cys38. The solution structure revealed that it has two distinct subdomains connected by a flexible linker loop: the methyltransferase (MTase) subdomain with the zinc,thiolate center, and the helical subdomain with a helix-turn-helix motif. Interestingly, there is no potential hydrogen bond donor around Cys38, whereas the other three cysteine residues coordinated to a zinc ion have potential donors. Hence, Cys38 could retain its inherent nucleophilicity and react with a methyl phosphotriester. Furthermore, the structure comparison shows that there is no indication of a remarkable conformational change occurring upon the methylation. This implies that the electrostatic repulsion between the negatively charged DNA and the zinc,thiolate center may avoid the contact between the MTase subdomain and the DNA in the nonmethylated form. Thus, after the Cys38 methylation, the MTase subdomain can bind the cognate DNA because the negative charge of the zinc,thiolate center is reduced. [source] Insight into the Bioactivity and Metabolism of Human Glucagon Receptor Antagonists from 3D-QSAR AnalysesMOLECULAR INFORMATICS, Issue 8 2004HaiFeng Chen Abstract Descriptors, such as logP, the number of hydrogen bond donors, the number of hydrogen bond acceptors, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) combined with fields of CoMFA and CoMSIA to construct models for hyperglycemia decrease activity and metabolism of human glucagon receptor antagonists. The results reveal that including logP, HOMO and LUMO energies is meaningful for QSAR/QSMR model. The models were validated by using a test set of structural diverse compounds that had not been included in the CoMFA and CoMSIA models. Support Vector Machines (SVM) have been used to select the suitable additional descriptors to construct 3D-QSAR/QSMR models. A key factor to mention is that activity and metabolism models simultaneously. These in silico ADME models are helpful in making quantitative prediction of inhibitory activities and rates of metabolism before resorting in vitro and in vivo experimentation. [source] | ||||||||||