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Frequency Calculations (frequency + calculation)
Selected AbstractsNeural model of microwave cylindrical cavity loaded with arbitrary-raised dielectric slabINTERNATIONAL JOURNAL OF RF AND MICROWAVE COMPUTER-AIDED ENGINEERING, Issue 3 2009Stankovi, Zoran Abstract A combined knowledge-based neural-multilayer perceptron (KBN-MLP) model to account for a loading effect of arbitrary raised dielectric slab in a microwave cylindrical metallic cavity is presented. Existing partial knowledge about the resonant frequency behavior of loaded cavity is incorporated in the KBN part of suggested model. In comparison with the model based on classical MLP network, more accurate and efficient resonant frequencies calculation is achieved. © 2008 Wiley Periodicals, Inc. Int J RF and Microwave CAE, 2009. [source] Hydrogen bonding characterization of XH2NH2···HNO(X = B, Al, Ga) complexes: A theoretical investigationINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2008Ying Liu Abstract The complexes of XH2NH2···HNO(X = B, Al, Ga) are characterized as head to tail with hydrogen bonding interactions. The structural characteristics can be confirmed by atoms in molecules (AIM) analysis, which also provide comparisons of hydrogen bonds strengths. The calculated interaction energies at G2MP2 level show that stability of complexes decrease as BH2NH2···HNO > AlH2NH2···HNO > GaH2NH2···HNO. On the basis of the vibrational frequencies calculations, there are red-shifts for ,(X1H) and blue-shifts for ,(NH) in the complexes on dihydrogen bonding formations (X1H···HN). On hydrogen bonding formations (NH···O), there are red-shifts for ,(NH) compared to the monomers. Natural bond orbital (NBO) analysis is used to discuss the reasons for the ,(X1H) and ,(NH) stretching vibrational shifts by hyperconjugation, electron density redistribution, and rehybridization. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] [Fe-Fe]-hydrogenase reactivated by residue mutations as bridging carbonyl rearranges: A QM/MM studyINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 14 2010Stefan Motiu Abstract In this work, we found aqueous enzyme phase reaction pathways for the reactivation of the exogenously inhibited [Fe-Fe]-hydrogenases by O2, or OH,, which metabolizes to H2O (Dogaru et al., Int J Quantum Chem 2008, 108; Motiu et al., Int J Quantum Chem 2007, 107, 1248). We used the hybrid quantum mechanics/molecular mechanics (QM/MM) method to study the reactivation pathways of the exogenously inhibited enzyme matrix. The ONIOM calculations performed on the enzyme agree with experimental results (Liu et al., J Am Chem Soc 2002, 124, 5175), that is, wild-type [Fe-Fe]-hydrogenase H-cluster is inhibited by oxygen metabolites. An enzyme spherical region with a radius of 8 Å (from the distal iron, Fed) has been screened for residues that prevent H2O from leaving the catalytic site and reactivate the [Fe-Fe]-hydrogenase H-cluster. In the screening process, polar residues were removed, one at a time, and frequency calculations provided the change in the Gibbs' energy for the dissociation of water (due to their deletion). When residue deletion resulted in significant Gibbs' energy decrease, further residue substitutions have been carried out. Following each substitution, geometry optimization and frequency calculations have been performed to assess the change in the Gibbs' energy for the elimination of H2O. Favorable thermodynamic results have been obtained for both single residue removal (,G,Glu374 = ,1.6 kcal/mol), single substitution (,GGlu374His = ,3.1 kcal/mol), and combined residue substitutions (,GArg111Glu;Thr145Val;Glu374His;Tyr375Phe = ,7.5 kcal/mol). Because the wild-type enzyme has only an endergonic step to overcome, that is, for H2O removal, by eliminating several residues, one at a time, the endergonic step was made to proceed spontaneously. Thus, the most promising residue deletions which enhance H2O elimination are ,Arg111, ,Thr145, ,Ser177, ,Glu240, ,Glu374, and ,Tyr375. The thermodynamics and electronic structure analyses show that the bridging carbonyl (COb) of the H-cluster plays a concomitant role in the enzyme inhibition/reactivation. In gas phase, COb shifts towards Fed to compensate for the electron density donated to oxygen upon the elimination of H2O. However, this is not possible in the wild-type enzyme because the protein matrix hinders the displacement of COb towards Fed, which leads to enzyme inhibition. Nevertheless, enzyme reactivation can be achieved by means of appropriate amino acid substitutions. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Improvement of scale factors for harmonic vibrational frequency calculations using new polarization functionsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2008Anibal Sierraalta Abstract Density functional calculations were carried to improve the calculated CO vibrational frequencies for transition metal carbonyls. Two types of density functionals were studied, hybrid and generalized-gradient methods. Using the simplex optimization method, new polarization functions for C and O atoms were obtained. With these new optimized functions, new scaling factors were obtained. The results reveal that, with the new polarization functions, the agreement between the calculated and the experimental values improves considerably. In general, the new scaling factors are very close to unit, with standard uncertainties close to ±0.006 cm,1. The use of the new polarization functions allows more precise calculations of the transition metal carbonyl CO vibrational frequencies. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Influence of substituents on the infrared stretching frequencies of carbonyl group in esters of benzoic acidJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 10 2006Vilve Nummert Abstract Infrared spectra of 25 substituted phenyl esters of benzoic acid C6H5CO2C6H4 -X (XH, 3-Cl, 3-F, 3-CN, 3-NO2, 3-CH3, 3-OH, 3-NH2, 4-Cl, 4-F, 4-NO2, 4-CN, 4-OCH3, 4-CH3, 4-NH2, 2-Cl, 2-F, 2-I, 2-NO2, 2-CF3, 2-CN, 2-CH3, 2-OCH3, 2-N(CH3)2, 2-C(CH3)3), 8 alkyl benzoates C6H5CO2R (XCH3, CH2CH3, CH2Cl, CH2CN, CH2CCH, CH2CH2Cl, CH2CH2OCH3, CH2C6H5), and 22 phenyl esters of substituted benzoic acids X-C6H4CO2C6H5 (X3-Cl, 3-NO2, 3-CH3, 3-N(CH3)2, 4-F, 4-Cl, 4-Br, 4-NO2, 4-CH3, 4-C(CH3)3, 4-OCH3, 4-NH2, 2-Cl, 2-F, 2-Br, 2-I, 2-NO2, 2-CN, 2-CF3, 2-CH3, 2-OCH3, 2-NH2) were recorded in tetrachloromethane in the region of 400,4000,cm,1. Carbonyl stretching frequencies ,CO for meta - and para -substituted phenyl esters of benzoic acid and phenyl esters of meta -substituted benzoic acids were shown to correlate with the substituent constants ,o. The influence of the through resonance effect on ,CO was found to be important in the case of +Rpara substituents in the benzoyl part of phenyl benzoates as well. The carbonyl stretching frequencies of ortho derivatives in phenoxy part were shown to correlate with the inductive substituent constant ,I only. In the benzoyl part of the esters the carbonyl stretching frequencies of cis and trans conformers (relative to the carbonyl group) of ortho derivatives were nicely described by dual parameter equations: (,CO)cis,=,(,CO)o,+,c1,I,+,c3,and (,CO)trans,=,(,CO)o,+,c1,p+,+,c3, (R,=,0.99). The trans isomers of phenyl esters of ortho -substituted benzoic acids showed direct resonance similar to that for para derivatives. The positive steric term found for both the cis and trans conformers could be considered as measure of the steric inhibition of resonance between the phenyl ring and the carboxy-group caused by bulky ortho substituents. The existence of cis/trans conformations was supported by frequency calculations with Density Functional Theory (DFT) method at B3LYP/6-311+G** level for the ortho -substituted benzoates. In the case of alkyl benzoates good correlations of ,CO values were obtained when both the Taft ,* and the steric constants were used. For meta - and para -substituted phenyl benzoates s - trans conformation where the plane of the benzene ring in the benzoyl part of the ester is coplanar with the carbonyl bond plane and the plane of the benzene ring in the phenoxy part is twisted nearly perpendicular relative to the carbonyl bond plane was supported. Copyright © 2006 John Wiley & Sons, Ltd. [source] RelACCS-FP: A Structural Minimalist Approach to Fingerprint DesignCHEMICAL BIOLOGY & DRUG DESIGN, Issue 5 2008Ye Hu The design and evaluation of structural key-type fingerprints is reported that consist of only 10,30 substructures isolated from randomly generated fragment populations of different classes of active compounds. To identify minimal sets of fragments that carry substantial compound class-specific information, fragment frequency calculations are applied to guide fingerprint generation. These compound class-directed and extremely small structural fingerprints push the design of so-called mini-fingerprints to the limit and are the shortest bit string fingerprints reported to date. For the application of relative frequency-based activity class characteristic substructure fingerprints, a bit density-dependent similarity metric is introduced that makes it possible to adjust similarity coefficients for individual compound classes and balance the recall of active compounds with database selection size. In similarity search trials, these small compound class-directed fingerprints enrich active compounds in relatively small database selection sets and approach or exceed the performance of widely used structural fingerprints of much larger size and higher complexity. [source] | ||||||||||