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Different Conformers (different + conformer)
Selected AbstractsHydrogen bonding interaction between 1,4-dioxane and waterINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2010Ajay Chaudhari Abstract This work reports an interaction of 1,4-dioxane with one, two, and three water molecules using the density functional theory method at B3LYP/6-311++G* level. Different conformers were studied and the most stable conformer of 1,4-dioxane-(water)n (n = 1,3) complex has total energies ,384.1964038, ,460.6570694, and ,537.1032381 hartrees with one, two, and three water molecules, respectively. Corresponding binding energy (BE) for these three most stable structures is 6.23, 16.73, and 18.11 kcal/mol. The hydrogen bonding results in red shift in OO stretching and CC stretching modes of 1,4-dioxane for the most stable conformer of 1,4-dioxane with one, two, and three water molecules whereas there was a blue shift in CO symmetric stretching and CO asymmetric stretching modes of 1,4-dioxane. The hydrogen bonding results in large red shift in bending mode of water and large blue shift in symmetric stretching and asymmetric stretching mode of water. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Transition States of the Asymmetric Michael Reactions of Aldehydes Catalyzed by Trimethylsilyl-Protected DiphenylprolinolEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 16 2009Jian-Qiang Zhao Abstract The asymmetric Michael reactions of aldehydes and nitroalkenes catalyzed by trimethylsilyl-protected diphenylprolinol were investigated by using density functional theory calculations. As a result of the stereospecific blockade of the bulky diphenylsiloxymethyl group on the pyrrolidine ring, the Re face of the enamine double bond is effectively shielded. For acetaldehyde, there are two different conformers of the enamine intermediate. On the basis of the two conformers of the enamine intermediate, four different reaction pathways were considered and four different transition states were searched for the enantioselective asymmetric Michael reaction of acetaldehyde and nitroalkene. The lowest- and second-lowest-energy transition states are both formed via the same intermediate IM2. The enantiomeric excess, calculated to be 96,%,ee, is in good agreement with the experimental value. For propanal, on the basis of the four different conformers of the prolinol,enamine intermediate, eight different reaction pathways were considered and eight transition states were searched for the enantioselective asymmetric Michael reaction. The calculated ee value is 99.5,%, which is in good agreement with the experimental ee value of 99,%. The lowest- and second-lowest-energy transition states are formed via different enamine intermediates, which is different from the case of acetaldehyde. The calculations also reveal that the intermediates play an important role in the reactions.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] Formation of the B Ring in Steroids and Hopanoids from SqualeneEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 10 2004B. Andes Hess Jr. Abstract A theoretical conformational study based on density functional calculations provides evidence that the sterol and nonsterol cyclizations of squalene to triterpenes are controlled by conformational effects as has been previously suggested. It was found that different conformers of a model system of squalene give rise to the chair,boat conformation found in the steroids and the chair,chair conformation of the pentacyclic 3-deoxytriterpenes for their A and B rings. It is suggested that the enzymes play a key role in holding the substrate in the proper orientation for these cyclizations to occur. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Discrimination between diastereoisomeric dipeptides by IR,UV double resonance spectroscopy and ab initio calculationsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2005Ali G. Abo-Riziq Abstract We studied diastereoisomeric dipeptides, containing two chiral centers, by comparing ab initio calculations with laser desorption jet-cooling experiments. We studied the hetero-dipeptides LL,VF (L-Val-L-Phe) and DL,VF and the homo-dipeptides LL,FF (L-Phe-L-Phe) and LD,FF. Changing one of the chiral centers in each molecule leads to changes in the spectra that can be used to distinguish between diastereoisomeric pairs. We observed three different conformers for LL,VF, four for DL,VF, two for LL,FF, and one for LD,FF. By comparing the results from IR,UV double resonant spectroscopy with ab initio calculations, we can draw conclusions about the conformational structures. At the same time, the experimental data serve as a test for the computational results. We discuss the possibilities and limitations of the interplay between theory and experiment. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] When, in the context of drug design, can a fluorine atom successfully substitute a hydroxyl group?INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2002Marcin Hoffmann Abstract In this article, we deal with the question of whether a fluorine atom can substitute a hydroxyl group in such a way that will lead to a compound showing a desired biologic activity, that is, a potential new drug. It is obvious that a fluorine atom differs from a hydroxyl group, as it cannot donate hydrogen bonds. However, it can accept them. Moreover, both fluorine and oxygen are of similar size and are the most electronegative elements. Therefore, a fluorine atom is thought to be a good substitute for a hydroxyl group. However, it was shown that for conformationally labile aliphatic compounds a replacement of a hydroxyl by a fluorine increases conformational diversity, so the fluorine-containing aliphatic molecules are present in equilibrium at room temperature as a mixture of several different conformers. In contrast, for cyclic compounds the substitution of an OH group by an F atom does not much change shape and electrostatic potential around corresponding conformers. Moreover, these compounds are present in equilibrium at room temperature in aqueous solution as a mixture of the same most favored structures. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002 [source] Comparison of some representative density functional theory and wave function theory methods for the studies of amino acidsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2009Wenbo Yu Abstract Energies of different conformers of 22 amino acid molecules and their protonated and deprotonated species were calculated by some density functional theory (DFT; SVWN, B3LYP, B3PW91, MPWB1K, BHandHLYP) and wave function theory (WFT; HF, MP2) methods with the 6-311++G(d,p) basis set to obtain the relative conformer energies, vertical electron detachment energies, deprotonation energies, and proton affinities. Taking the CCSD/6-311++G(d,p) results as the references, the performances of the tested DFT and WFT methods for amino acids with various intramolecular hydrogen bonds were determined. The BHandHLYP method was the best overall performer among the tested DFT methods, and its accuracy was even better than that of the more expensive MP2 method. The computational dependencies of the five DFT methods and the HF and MP2 methods on the basis sets were further examined with the 6-31G(d,p), 6-311++G(d,p), aug-cc-pVDZ, 6-311++G(2df,p), and aug-cc-pVTZ basis sets. The differences between the small and large basis set results have decreased quickly for the hybrid generalized gradient approximation (GGA) methods. The basis set convergence of the MP2 results has been, however, very slow. Considering both the cost and the accuracy, the BHandHLYP functional with the 6-311++G(d,p) basis set is the best choice for the amino acid systems that are rich in hydrogen bonds. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 [source] Toward direct determination of conformations of protein building units from multidimensional NMR experiments VI.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2005Chemical shift analysis of his to gain 3D structure, protonation state information Abstract NMR,chemical shift structure correlations were investigated by using GIAO-RB3LYP/6-311++G(2d,2p) formalism. Geometries and chemical shifts (CSI values) of 103 different conformers of N,-formyl-L-histidinamide were determined including both neutral and charged protonation forms. Correlations between amino acid torsional angle values and chemical shifts were investigated for the first time for an aromatic and polar amino acid residue whose side chain may carry different charges. Linear correlation coefficients of a significant level were determined between chemical shifts and dihedral angles for CSI[1H,]/,, CSI[13C,]/,, and CSI[13C,]/,. Protonation of the imidazole ring induces the upfield shift of CSI[13C,] for positively charged histidines and an opposite effect for the negative residue. We investigated the correspondence of theoretical and experimental 13C,, 13C,, and 1H, chemical shifts and the nine basic conformational building units characteristic for proteins. These three chemical shift values allow the identification of conformational building units at 80% accuracy. These results enable the prediction of additional regular secondary structural elements (e.g., polyProlineII, inverse ,-turns) and loops beyond the assignment of chemical shifts to ,-helices and ,-pleated sheets. Moreover, the location of the His residue can be further specified in a ,-sheet. It is possible to determine whether the appropriate residue is located at the middle or in a first/last ,-strand within a ,-sheet based on calculated CSI values. Thus, the attractive idea of establishing local residue specific backbone folding parameters in peptides and proteins by employing chemical shift information (e.g., 1H, and 13C,) obtained from selected heteronuclear correlation NMR experiments (e.g., 2D-HSQC) is reinforced. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1307,1317, 2005 [source] Structural motifs in the maturation process of peptide hormones.JOURNAL OF PEPTIDE SCIENCE, Issue 2 2002The somatostatin precursor. Abstract Synthetic peptides reproducing both the native domain around the dibasic cleavage site of pro-somatostatin, and mutated sequences thereof, previously assayed in site-directed mutagenesis experiments, have been studied by CD in different solvent systems, such as water, TFE/H2O, MeCN/H2O and aqueous SDS, in order to ascertain the ability of each solvent to stabilize secondary structural motifs. A combination of deconvolution methods and empirical calculations, that allow subtraction of the contributions due to unordered structures from the spectra, suggests that mainly two distinct families of ordered conformers containing ,-helix and/or structurally different ,-turns are present in solution, the relative stability of the different conformers depending on the nature of the solvent. The presence of ,-turns is in line with a previous NMR study in DMSO and DMSO/H2O. Comparison of the CD spectra in aqueous SDS of peptides undergoing processing with a sequence not processed in vivo shows that only the latter possesses a stable and detectable ,-helix population. This observation suggests that the structuration involving ,-turns but no ,-helix, which was observed by CD both in SDS and organic solvent/H2O mixtures at high water contents, might be of biological significance. The similarity of this structuration to molecular models obtained from NMR data in DMSO and DMSO/H2O is discussed. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd. [source] Structural conformations and electronic interactions of the natural product, oroxylin: a vibrational spectroscopic studyJOURNAL OF RAMAN SPECTROSCOPY, Issue 12 2008Jose P. Abraham Abstract The oroxylin, 5,7-dihydroxy 6-methoxy flavone is a potent natural product extracted from ,Vitex peduncularis'. Density functional theory (DFT) at B3LYP/6-311G(d,p) level has been used to compute energies of different conformers of oroxylin to find out their stability, the optimized geometry of the most stable conformer and its vibrational spectrum. The conformer ORLN-1 with torsion angles 0, 180, 180 and 0 degrees, respectively, for H13O12C6C5, H14O10C4C5, H13O12C6C5 and H14O10C4C5 is found to be most stable. The optimized geometry reveals that the dihedral angle , between phenyl ring B and the chrome part of the molecule in , 19.21° is due to the repulsive force due to steric interaction between the ortho-hydrogen atom H29 of the B ring and H18 of the ring C (H29·H18 = 2.198 Å). A vibrational analysis based on the near-infrared Fourier transform(NIR-FT) Raman, Fourier transform-infrared (FT-IR) and the computed spectrum reveals that the methoxy group is influenced by the oxygen lone pair-aryl pz orbital by back donation. Hence the stretching and bending vibrational modes of the methoxy group possess the lowest wavenumber from the normal values of methyl group. The carbonyl stretching vibrations have been lowered due to conjugation and hydrogen bonding in the molecules. The intramolecular H-bonding and nonbonded intramolecular interactions shift the band position of O10H14 and O12H13 stretching modes, which is justified by DFT results. Copyright © 2008 John Wiley & Sons, Ltd. [source] The 293,K structure of tetradehydrohaliclonacyclamine AACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2010I. Wayan Mudianta The polycyclic title compound {systematic name: (1S,16S,17S,31S)-3,20-diazatetracyclo[15.15.01,17.13,31.116,20]tetratriaconta-6,8,23,25-tetraene}, C32H52N2, has recently been isolated and characterized structurally, in solution by NMR spectroscopy and in the solid state by X-ray crystallography. At 130,K the structure is monoclinic (P21, Z = 4) and comprises two molecules in the asymmetric unit with distinctly different conformations in the twelve-C-atom bridging chains. We report that, at 250,K, a phase change from monoclinic to orthorhombic (P22121, Z = 4) occurs. The higher-temperature phase is structurally characterized herein at 293,K. The two different conformers resolved in the monoclinic low-temperature form merge to give a single disordered molecule in the asymmetric unit of the high-temperature phase. [source] Complexes between Lithium Cation and Diphenylalkanes in the Gas Phase: The Pincer EffectCHEMISTRY - A EUROPEAN JOURNAL, Issue 29 2006Jean-François Gal Prof. Abstract The gas-phase lithium cation basicities (LCB values, Gibbs free energies of binding) of ,,,-diphenylalkanes Ph-(CH2)n -Ph (n=2, 3, or 7) and 1,1-diphenylethane Ph-CH(Me)-Ph were investigated by means of Fourier-transform ion cyclotron resonance (FTICR) mass spectrometry. Their structures, and those of the corresponding Li+ complexes were optimized at the B3LYP/6-31G(d) level and their relative stabilities calculated at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d) level. Whereas the most stable conformers of the free diphenylalkanes were found to adopt a completely stretched aliphatic chain connecting the two benzene rings, the most stable Li+ complexes correspond to conformers in which the alkali metal cation interacts simultaneously with both benzene rings through the folding of the aliphatic chain ("pincer effect"). This chelation brings about a significant enhancement of the Li+ binding enthalpies (LBE values), which were calculated to be approximately 75 kJ,mol,1 higher than those evaluated for conventional (singly coordinated) , complexes in which the metal cation interacts with only one of the benzene rings. The increase of the corresponding lithium cation basicities, however, (Gibbs free energies of Li+ binding, LCB values) was calculated to be smaller by approximately 15 kJ,mol,1 as the pincer effect is entropically disfavored. The good agreement between the calculated LCB values, assuming a statistical distribution of the different conformers present in the gas phase, and the experimental LCB values measured by means of FTICR mass spectrometry are considered indirect evidence of the existence of the pincer effect. [source] Insights into the Role of the Liquid,Liquid Interface in Biphasic Reactions: The Reaction of Vitamin B12s(aq) with Vicinal Dibromides(oil)CHEMPHYSCHEM, Issue 12 2005Trevor J. Davies Dr. Abstract Electrocatalytic processes can take place either homogeneously in a single liquid phase or heterogeneously at the liquid,liquid interface formed in emulsions. This Article addresses the question as to whether a change in rate and/or mechanism can occur between the two possibilities. Specifically, cyclic voltammetry and electrosynthetic experiments are used to demonstrate that for the vitamin B12 mediated reduction of vicinal dibromides producing olefins, electric field effects likely operate at the liquid,liquid interface which can change the populations of different conformers relative to the single homogeneous-phase experiment, leading to significant changes in rate. [source] The Excited-State Chemistry of Phycocyanobilin: A Semiempirical StudyCHEMPHYSCHEM, Issue 7 2005Andreas H. Göller Dr. Abstract Based on previous time-resolved absorption studies, phycocyanobilin undergoes a photoreaction from an A - into a B - and C -form, with the latter two photoproducts showing absorption spectra red-shifted from A. To identify the molecular mechanism involved in the excited-state reactions, the structural origin of the red shift in the absorption spectra is investigated. Using semiempirical AM1 calculations that include configuration interaction by pair doubles excitation configuration interaction, the absorption spectra of different conformers as well as different protonation states were calculated. The results clearly indicate a pronounced red shift in the spectra of structures either protonated or deprotonated at the basic/acidic centres of the tetrapyrrole chromophore whereas, in contrast, conformational changes alone result in a blue shift. Furthermore, it is shown by quantum chemical calculations that the basicity of phycocyanobilin is much higher in the excited than in the ground state, with a decrease in the excited-state pKB* of ,9.5 units. The acidity is only slightly enhanced with a drop in pKA* of only ,1.6 units. From these findings, a reaction model for the excited-state processes in phycocyanobilin is proposed. According to this model, photoexcitation of phycocyanobilin triggers an excited-state proton transfer giving rise to the formation of a protonated species. In parallel, the local increase in the medium pH associated with protonation then forwards a deprotonation at an acidic NH-group so that in effect both protonated and deprotonated phycocyanobilin would arise from the initial photoreaction and account for the observed red shift in the spectra of the B - and C -forms. [source] Comparison of Properties of Aib-Rich Peptides in Crystal and Solution: A Molecular Dynamics StudyCHEMPHYSCHEM, Issue 5 2004Haibo Yu Abstract In order to study the differences of the structural properties of Aib-rich peptides in solution and in the crystalline state, molecular dynamics (MD) simulations of the Aib-containing peptide II (pBrBz-(Aib)5 -Leu-(Aib)2 -OMe) were performed in the crystalline state, starting from two different conformers obtained experimentally by X-ray diffraction. The structural properties as derived from X-ray crystallography (e.g., torsional angles and hydrogen bonds) are well-reproduced in both constant-volume and constant-pressure simulations, although the force-field parameters used result in a too-high density of the crystals. Through comparison with the results from previous MD and nuclear magnetic resonance (NMR) studies of the very similar peptide I (Z-(Aib)5 -Leu-(Aib)2 -OMe) in dimethylsulfoxide (DMSO) solution, it is found that, in the crystal simulation, the conformational distribution of peptide II is much narrower than that in the solution simulation of peptide I. This leads to a significant difference in 3J(HN, HC,) coupling constant values, in agreement with experimental data, whereas the NOE intensities or proton,proton distance bounds appear insensitive to the difference in conformational distribution. For small peptides the differences between their conformational distribution in the crystalline form and in solution may be much larger than for proteins, a fact which should be kept in mind when interpretating molecular properties in the solution state by using X-ray crystallographic data. [source] DFT Studies of the Molecular Structures and Conformational Processes of 1,2-, 1,3- and 1,4-DithiepaneCHINESE JOURNAL OF CHEMISTRY, Issue 3 2008Mina HAGHDADI Abstract In this study density functional theory (DFT) calculations at B3LYP/6-31G(d), B3LYP/6-31+G(d) and B3LYP/6-311+G(2df,2p) levels for geometry optimization and total energy calculation were applied for investigation of the important energy-minimum conformations and transition-state of 1,2-, 1,3-, and 1,4-dithiepanes. Moreover, ab initio calculations at HF/6-31G(d) level of theory for geometry optimization and MP2/6-311G(d)//HF/ 6-31G(d) level for a single-point total energy calculation were reported for different conformers. The obtained results reveal that, the twist-chair conformer is a global minimum for all of these compounds. Also, two local minimum were found in each case, which are twisted-chair and twisted-boat conformers. The boat and chair geometries are transition states. The minimum energy conformation of 1,2-dithiepane is more stable than the lowest energy forms of 1,3-dithiepane and 1,4-dithiepane. Furthermore, the anomeric effect was investigated for 1,3-dithiepane by the natural bond orbital method. The computational results of this study shows that all conformers of 1,3-dithiepane have a hypercojugation system. Finally, the 13C NMR chemical shifts for the conformers of 1,4-dithiepane were calculated, which have good correlation with their experimental values. [source] Absolute configurations of chiral herbicides determined from vibrational circular dichroismCHIRALITY, Issue S1 2005Jiangtao He Abstract Enantiopure herbicides (+)-2-(4-chloro-2-methylphenoxy) propanoic acid, (+)- 1 and (+)-2-(2,4-dichlorophenoxy) propanoic acid, (+)- 2 were investigated using vibrational circular dichroism (VCD). Experimental absorption and VCD spectra of (+)- 1 and (+)- 2 in CDCl3 solution in the 2000,900 cm,1 region were compared with the ab initio predictions of absorption and VCD spectra obtained with density functional theory using the B3LYP/6-31G* basis set for different conformers of (R)- 1 and (R)- 2. Due to the intermolecular hydrogen bonding, this comparison did not provide unambiguous conclusions. To eliminate intermolecular hydrogen bonding influence, the two acids 1 and 2 were converted to the corresponding methyl esters, namely, (+)-methyl 2-(4-chloro-2-methylphenoxy) propanoate, (+)- 3 and (+)-methyl 2-(2,4-dichlorophenoxy) propanoate, (+)- 4. The experimental VCD spectra were measured for these esters and ab initio calculations for different conformers of (R)- 3 and (R)- 4 were carried out. The experimental VCD spectra and corresponding population-weighted theoretical VCD spectra were found to be in excellent agreement, which allowed unambiguous determination of absolute configuration of 3 and 4 as (+)-(R). Since esterification does not invert the configuration, the absolute configuration of the parent acids 1 and 2 is the same as that of corresponding methyl esters. Chirality 17:S1,S8, 2005. © 2004 Wiley-Liss, Inc. [source] Absolute configuration and conformational analysis of a degradation product of inhalation anesthetic Sevoflurane: A vibrational circular dichroism studyCHIRALITY, Issue 8 2002Feng Wang Abstract 1,1,1,3,3-pentafluoro-2-(fluoromethoxy)-3-methoxypropane, compound B, is a product obtained in the degradation of the anesthetic Sevoflurane. Enantiopure (+)- B was investigated using vibrational circular dichroism (VCD). Experimental absorption and VCD spectra of (+)- B in CDCl3 solution in the 2,000,900 cm,1 region are compared with the ab initio predictions of absorption and VCD spectra obtained from density functional theory using B3LYP/6-31G* basis set for different conformers of (S)-1,1,1,3,3-pentafluoro-2-(fluoromethoxy)-3-methoxypropane. This comparison indicates that (+)- B is of the (S)-configuration in CDCl3 solution, in agreement with previous literature results. Our results also indicate that this compound adopts six predominant conformations in CDCl3 solution. Chirality 14:618,624, 2002. © 2002 Wiley-Liss, Inc. [source] | ||||||||||||||||||||||