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Vibrational Circular Dichroism (vibrational + circular_dichroism)
Selected AbstractsDetermination of the Absolute Configurations of Natural Products via Density Functional Theory Calculations of Vibrational Circular Dichroism, Electronic Circular Dichroism, and Optical Rotation: The Iridoids Plumericin and Isoplumericin.CHEMINFORM, Issue 37 2007P. J. Stephens Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF. [source] Use of vibrational spectroscopy to study protein and DNA structure, hydration, and binding of biomolecules: A combined theoretical and experimental approachINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2006K. J. Jalkanen Abstract We report on our work with vibrational absorption, vibrational circular dichroism, Raman scattering, Raman optical activity, and surface-enhanced Raman spectroscopy to study protein and DNA structure, hydration, and the binding of ligands, drugs, pesticides, or herbicides via a combined theoretical and experimental approach. The systems we have studied systematically are the amino acids (L -alanine, L -tryptophan, and L -histidine), peptides (N -4271 acetyl L -alanine N,-methyl amide, N -acetyl L -tryptophan N,-methyl amide, N -acetyl L -histidine N,-methyl amide, L -alanyl L -alanine, tri- L -serine, N -acetyl L -alanine L -proline L -tyrosine N,-methyl amide, Leu-enkephalin, cyclo-(gly- L -pro)3, N -acetyl (L -alanine)nN,-methyl amide), 3-methyl indole, and a variety of small molecules (dichlobenil and 2,6-dochlorobenzamide) of relevance to the protein systems under study. We have used molecular mechanics, the SCC-DFTB, SCC-DFTB+disp, RHF, MP2, and DFT methodologies for the modeling studies with the goal of interpreting the experimentally measured vibrational spectra for these molecules to the greatest extent possible and to use this combined approach to understand the structure, function, and electronic properties of these molecules in their various environments. The application of these spectroscopies to biophysical and environmental assays is expanding, and therefore a thorough understanding of the phenomenon from a rigorous theoretical basis is required. In addition, we give some exciting and new preliminary results which allow us to extend our methods to even larger and more complex systems. The work presented here is the current state of the art to this ever and fast changing field of theoretical spectroscopic interpretation and use of VA, VCD, Raman, ROA, EA, and ECD spectroscopies. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Circular dichroism spectroscopic study of non-covalent interactions of poly- L -glutamic acid with a porphyrin derivative in aqueous solutionsJOURNAL OF PEPTIDE SCIENCE, Issue 9 2005Palivec Abstract The interactions of poly- L -glutamic acid and a cationic porphyrin derivative in aqueous solutions were studied by the combination of vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopies. It was found that non-covalent interactions between both agents influence the structure of the polymeric matrix and the guest porphyrins and vice versa, but the physico-chemical properties of the solutions, especially the pH and the relative permittivity of the solvent, play a key role in the structure of the polypeptide part of the formed complexes. It was shown that the interaction with porphyrins prevents the precipitation of poly- L -glutamic acid in aqueous solution at acidic pH. In special conditions, the porphyrins attached to the polypeptide probably possess face-to-face interaction as demonstrated by the enhancement of the characteristic ECD signal and the appearance of sidebands on its short and long wavelength sides. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd. [source] Renaissance in chiroptical spectroscopic methods for molecular structure determinationTHE CHEMICAL RECORD, Issue 2 2007Prasad L. Polavarapu Abstract Two of the chiroptical spectroscopic methods, namely optical rotatory dispersion (ORD) and electronic circular dichroism (ECD), have been around for several decades. But their use in determining the absolute configuration and predominant conformation is gaining renewed interest with the availability of quantum mechanical methods for predicting ORD and ECD. Two other methods, namely vibrational circular dichroism (VCD) and vibrational Raman optical activity (VROA), are relatively new and offer convenient approaches for deducing the structural information in chiral molecules. With the availability of quantum mechanical programs for predicting VCD and VROA, these methods have attracted numerous new researchers to this area. This review summarizes the latest developments in these four areas and provides examples where more than one method has been used to confirm the information obtained from individual methods. © 2007 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 7: 125,136; 2007: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20117 [source] Fourier transform vibrational circular dichroism as a decisive tool for conformational studies of peptides containing tyrosyl residuesBIOPOLYMERS, Issue 1 2003Attila Borics Abstract Previous UV,circular dichroism (UV,CD) and NMR studies showed that Ac-AAAAAAAEAAKA-NH2 has an ,-helical structure in 50% (v/v) aqueous trifluoroethanol. Replacement of Ala1 to Ala6 with Tyr results in spectra that show an apparent loss of helicity in the same solvent. This apparent loss of helicity could be attributed to the coupling of the tyrosyl side chain chromophore with the backbone amide. However, such electronic coupling does not affect the vibrational CD (VCD) spectra. The VCD spectra of the peptides with tyrosyl residues were identical to that of the peptide containing no Tyr, which shows the same ,-helical structure. Because it is now clear that Tyr replacement does not change the backbone conformation of peptides, UV,CD measurements should be complemented by VCD to determine the secondary structure when electronic effects can disturb the UV,CD spectrum of the inherent structure. © 2002 Wiley Periodicals, Inc. Biopolymers (Biospectroscopy) 72: 21,24, 2003 [source] Circular Dichroism of Designed Peptide Helices and ,-Hairpins: Analysis of Trp- and Tyr-Rich PeptidesCHEMBIOCHEM, Issue 12 2005Radhakrishnan Mahalakshmi VCD versus ECD spectroscopy. Peptides rich in aromatic residues yield anomalous far-UV electronic circular dichroism (ECD) spectra that preclude secondary structure assignment. The utility of vibrational circular dichroism (VCD) in conformation analysis is demonstrated by using a set of well-defined peptide helices and hairpins containing proximal aromatic residues. [source] Characterization of folded conformations in a tetrapeptide containing two tryptophan residues by vibrational circular dichroism,CHIRALITY, Issue 1E 2009Ana G. Petrovic Abstract The intramolecularly hydrogen bonded conformations of the tetrapeptide Boc-Trp-Aib-Gly-Trp-OMe (WUGW) are investigated using experimental and quantum chemical predictions of vibrational circular dichroism (VCD) in the 1800,1550 cm,1 region. The predicted VCD spectrum, for a conformation (conformer A) obtained from optimization of crystal structure, reproduced the dominant negative VCD band observed experimentally in CH3OH and CHCl3 solvents. However, the predicted VCD spectrum of Conformation A also has an extra positive band which is not seen in the experimental spectra. This mismatch appears to be due to the lack of solvent influence in the quantum chemical geometry optimizations. However, Conformations I and II, obtained, respectively, from constrained optimization of crystal and NMR structures, mimic the solvent stabilized structures and are predicted to have dominant negative VCD band as found in the experimental spectra. It is noted that, for the peptide investigated here, unconstrained quantum chemical geometry optimizations in vacuum converged to structures that are not the realistic models of conformations found in solution. It is also noted that undertaking quantum chemical vibrational property calculations directly using geometries obtained from crystal data or NMR data resulted in unrealistic vibrational frequencies and descriptions. However, constraining the backbone dihedral angles to those found in condensed medium, and optimizing the remaining geometrical parameters resulted in a better reproduction of the observed VCD in condensed medium. The vibrational origins of bands in all of the predicted VCD spectra for the WUGW-tetrapeptide have also been presented. Chirality 21:E76,E85, 2009. © 2009 Wiley-Liss, Inc. [source] Diastereoisomeric assignment in a pacifenol derivative using vibrational circular dichroism,CHIRALITY, Issue 1E 2009Marcelo A. Muñoz Abstract The configuration of a chiral center in semisynthetic (,)-(2R,5R,5aR,8,,9aS)- 2,8-dibromo-2,5,9,9a-tetrahydro-5-hydroxy-5,8,10,10-tetramethyl-6H -2,5a-methano-1-benzoxepin-7(8H)-one (3 or 4), prepared in two steps from (,)-(2R,5R,5aR,7S,8S,9aS)-2, 7-dibromo-8-chloro-2,5,7,8,9,9a-hexahydro-5,8,10,10-tetramethyl-6H -2,5a-methano-1-benzoxepin-5-ol, known as pacifenol 1, has been determined using vibrational circular dichroism (VCD) measurements. The vibrational spectra (IR and VCD) of diastereoisomers 3 and 4 were calculated using density functional theory (DFT) at the B3LYP/DGDZVP level of theory for the two conformers that in each case account for the total energetic distribution found in the first 10 kcal/mol range. The DFT conformational optimization of the 8R diastereoisomer 3 indicates the cyclohexanone exists almost exclusively in a boat conformation with a ,-equatorial bromine atom and an ,-axial methyl group at the chiral center alpha to the carbonyl group, while for the 8S diastereoisomer 4 a 5:1 conformational distribution in favor of a chair conformation with an ,-axial bromine atom and a ,-equatorial methyl group is calculated, suggesting due to well-known chair versus boat relative stabilities that the plausible diastereoisomer would be the 8S molecule. A comparison of the IR spectrum of the reaction product with the calculated spectra of 3 and 4 provided no means for the diastereoisomeric assignment, while from comparison of the VCD spectra it became immediately evident that the rearranged molecule possesses the 8R absolute configuration as shown in 3, in concordance with a single crystal X-ray diffraction study that could be refined to an R -factor of 2.9%. Chirality 21:E208,E214, 2009. © 2009 Wiley-Liss, Inc. [source] A VCD robust mode analysis of induced chirality: The case of pulegone in chloroform,CHIRALITY, Issue 1E 2009Valentin Paul Nicu Abstract Vibrational modes in an achiral molecule may acquire rotational strength by complexation to a chiral molecule, as happens for achiral solvent molecules complexed to a chiral solute. We investigate this transfer of chirality in vibrational circular dichroism for the pulegone molecule in CDCl3 solvent from the point of view of the robustness concept introduced recently. It turns out that the transfer of chirality yields nonrobust modes, which means that, although they are observed in vibrational circular dichroism (VCD) experiments, the sign of these modes cannot be predicted reliably with standard (Density Functional Theory) VCD calculations. This limits the usefulness of the induced chirality phenomenon for obtaining information on the intermolecular interactions that give rise to it. Chirality 21:E287,E297, 2009. © 2010 Wiley-Liss, Inc. [source] Structural transition during thermal denaturation of collagen in the solution and film states,CHIRALITY, Issue 1 2009Ganesh Shanmugam Abstract Temperature dependent vibrational circular dichroism (VCD) spectra of type I collagen, in solution and film states, have been measured. These spectra obtained for solution sample suggest that the thermal denaturation of collagen results in transition from poly- L -proline II (PPII) to unordered structure. The PPII structure of collagen is identified by the presence of negative VCD couplet in the amide I region, while the formation of unordered structure is indicated by the disappearance of VCD in the amide I region. The temperature dependent spectra obtained for the supported collagen film indicated a biphasic transition, which is believed to be the first vibrational spectroscopic report to support a biphasic transition during thermal denaturation of collagen film. The temperature dependent spectra of collagen films suggest that the thermal stability of collagen structure depends on its state and decreases in the order: supported film > free standing film > solution state. These observations are believed to be significant in the VCD spectroscopic analysis of secondary structures of proteins and peptides. Chirality, 2009. © 2008 Wiley-Liss, Inc. [source] C3 -symmetrical self-assembled structures investigated by vibrational circular dichroism,CHIRALITY, Issue 9 2008Maarten M. J. Smulders Abstract We demonstrate by using vibrational circular dichroism (VCD) spectroscopy that it is possible to investigate the chirality of a supramolecular polymeric system in relatively dilute solutions. Chiral C3 -symmetrical discotic molecules, based on a trialkylbenzene-1,3,5-carboxamide, form supramolecular columnar stacks with a right-handed helical structure in solution due to intermolecular hydrogen bonds. The handedness of the supramolecular chirality is determined using electronic spectroscopy measurements. Under dilute conditions (at 10,3 M concentrations), it was also possible to probe the hydrogen bonding moieties with IR and VCD spectroscopy on these self-assembled structures. In combination with density functional theory (DFT) calculations, we could verify the preference for a right-handed chirality in the helical stacks and the nonplanar orientation of the carbonyl groups present in the molecule. This chiral arrangement is in agreement with the structure determined for a related benzene-1,3,5-tricarboxamide by X-ray diffraction. Chirality, 2008. © 2008 Wiley-Liss, Inc. [source] Determination of absolute configurations by X-ray crystallography and 1H NMR anisotropyCHIRALITY, Issue 5 2008Nobuyuki Harada Abstract To determine the absolute configurations of chiral compounds, many spectroscopic and diffraction methods have been developed. Among them, X-ray crystallographic Bijvoet method, CD exciton chirality method, and the combination of vibrational circular dichroism and quantum mechanical calculations are of nonempirical nature. On the other hand, X-ray crystallography using a chiral internal reference, and 1H NMR spectroscopy using chiral anisotropy reagents are relative and/or empirical methods. In addition to absolute configurational determinations, preparations of enantiopure compounds are strongly desired. As chiral reagents useful for both the preparation of enantiopure compounds by HPLC separation and the simultaneous determination of their absolute configurations, we have developed camphorsultam dichlorophthalic acid (CSDP acid) for X-ray crystallography and 2-methoxy-2-(1-naphthyl)propionic acid (M,NP acid) for 1H NMR spectroscopy. In this review, the principles and applications of these X-ray and NMR methods are explained using mostly our own data. Chirality, 2008. © 2007 Wiley-Liss, Inc. [source] Observation and characterization of a specific vibrational circular dichroism band in phenyl glycosides,CHIRALITY, Issue 3-4 2008Tohru Taniguchi Abstract Application of vibrational circular dichroism (VCD) spectroscopy to structural analysis of carbohydrates has recently progressed. However, few studies on glycoconjugates VCD have thus far been reported, despite the fact that naturally occurring carbohydrates exist as various glycoconjugates. To further explore the application of the VCD technique, we have measured a series of aromatic glycosides and found that axial aromatic glycosides exhibited a negative band at around 1230 cm,1 while equatorial ones showed flat features in this region. This is the first structure,spectra relationship on glycoconjugate VCD that distinguishes the stereochemistry of the sugar anomers. Several model compounds were prepared and their vibrational properties calculated by using the density functional theory (DFT) method, which assigned the vibrational mode of this band based on the stretching motion of the glycosidic oxygen and aromatic carbon. This concept that aglycan parts can reflect stereochemical information of sugar moieties may encourage further VCD studies on glycoconjugates to realize practical structural analysis of carbohydrates. Chirality, 2008. © 2007 Wiley-Liss, Inc. [source] Spectroscopic rationalization of the separation abilities of decaproline chiral selector in dichloromethane,isopropanol solvent mixtureCHIRALITY, Issue 2 2007Peng Zhang Abstract A chiral column, with decaproline as the chiral selector, has broad chiral selectivity. To understand the separation mechanism of this chiral column, multiple spectroscopic techniques, including optical rotation, electronic circular dichroism, infrared absorption and vibrational circular dichroism, have been used here to study the conformation of the decaproline oligomer in isopropanol(IPA)/dichloromethane(DCM) mixtures. These studies indicate that decaproline oligomer adopts polyproline II conformation in IPA/DCM solvent system (0% IPA , 100% IPA). Hydrogen bonding interactions between CO groups of decaproline and IPA molecules increase as the content of IPA in the solvent mixture increases up to 60% and become less significant from then onwards. These spectroscopic observations are found to have a good correlation with the enantiomeric separation of racemic 2,2,2-trifluoro-1-[10-(2,2,2-trifluoro-1-hydroxy-ethyl-anthracen-9-yl]-ethanol by the decaproline column. Chirality 2006. © 2006 Wiley-Liss, Inc. [source] Chirality of camphor derivatives by density functional theory,CHIRALITY, Issue 10 2006Hayato E. Morita Abstract Infrared (IR) and vibrational circular dichroism (VCD) spectra of chiral camphor, camphorquinone and camphor-10-sulfonic acid (CSA), known as standard compounds for electronic circular dichroism (ECD) spectroscopy, are measured and their vibrational frequencies, infrared intensities, and rotational strengths are calculated using density functional theory (DFT). The observed IR and VCD spectra of chiral camphor and camphorquinone in carbon tetrachloride solution are reproduced by the DFT calculations, but those of CSA are not. DFT calculations of hydration models, where an anionic CSA specifically binds a few water molecules, are carried out. The average of the simulated VCD spectra in the hydration models is more consistent with the observed spectra. In addition, the wavelengths and dipole and rotational strengths for chiral camphor, camphorquinone, anionic CSA, and the hydration models were calculated by time-dependent DFT. In the region of 280,300 nm, the calculated wavelengths of the ECD bands for chiral camphor and camphorquinone coincide with the observed wavelengths that have been reported, and the calculated wavelengths for the hydration models are closer to the observed wavelengths reported than are those calculated for chiral anionic CSA. Consequently, the analysis combined with VCD and ECD spectroscopy using DFT calculations can elucidate the chirality of optically active molecules, even in an aqueous solution. Chirality, 2006. © 2006 Wiley-Liss, Inc. [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] Determination of the absolute configuration and solution conformation of the antifungal agents ketoconazole, itraconazole, and miconazole with vibrational circular dichroismCHIRALITY, Issue S1 2005David Dunmire Abstract The absolute configuration assignments of three antifungal agents, (+)-(2R,4S)-ketoconazole, (+)-(2R,4S)-itraconazole (with (S)-configuration at the sec -butyl group) and (+)-(S)-miconazole nitrate have been confirmed by using vibrational circular dichroism (VCD). For these three antifungal drugs, this study also provides evidence for the most abundant conformations of miconazole and for the relative conformations of the azole, dichlorophenyl, and methoxyphenyl groups in ketoconazole and itraconazole, in chloroform solution. Chirality 17:S101,S108, 2005. © 2005 Wiley-Liss, Inc. [source] Absolute configuration determination of chiral molecules in the solution state using vibrational circular dichroismCHIRALITY, Issue 9 2003Teresa B. Freedman Abstract Advances in the measurement, calculation, and application of vibrational circular dichroism (VCD) for the determination of absolute configuration are described. The purpose of the review is to provide an up-to-date perspective on the capability of VCD to solve problems of absolute stereochemistry for chiral molecules primarily in the solution state. The scope of the article covers the experimental methods needed for the accurate measurement of VCD spectra and the theoretical steps required to systematically deduce absolute configuration. Determination of absolute configuration of a molecule by VCD requires knowledge of its conformation or conformational distribution, and hence VCD analysis necessarily provides solution-state conformation information, in many cases available by no other method, as an additional benefit. Comparisons of the advantages and limitations of VCD relative to other available chiroptical methods of analysis are also presented. Chirality 15:743,758, 2003. © 2003 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] | ||||||||||