Determining the absolute configuration of two marine compounds using vibrational chiroptical spectroscopy

Chiroptical techniques are increasingly employed for assigning the absolute configuration of chiral molecules through comparison of experimental spectra with theoretical predictions. For assignment of natural products, electronic chiroptical spectroscopies such as electronic circular dichroism (ECD) are routinely applied. However, the sensitivity of electronic spectral parameters to experimental conditions and the theoretical methods employed can lead to incorrect assignments. Vibrational chiroptical methods (vibrational circular dichroism, VCD, and Raman optical activity, ROA) provide more reliable assignments, although they, in particular ROA, have been little explored for assignments of natural products. In this study, the ECD, VCD, and ROA chiroptical spectroscopies are evaluated for the assignment of the absolute configuration of a highly flexible natural compound with two stereocenters and an asymmetrically substituted double bond, the marine antibiotic Synoxazolidinone A (SynOxA), recently isolated from the sub-Arctic ascidian Synoicum pulmonaria. Conformationally averaged nuclear magnetic resonance (NMR), ECD, Raman, ROA, infrared (IR) and VCD spectral parameters are computed for the eight possible stereoisomers of SynOxA and compared to experimental results. In contrast to previously reported results, the stereochemical assignment of SynOxA based on ECD spectral bands is found to be unreliable. On the other hand, ROA spectra allow for a reliable determination of the configuration at the double bond and the ring stereocenter. However, ROA is not able to resolve the chlorine-substituted stereogenic center on the guanidinium side chain of SynOxA. Application of the third chiroptical method, VCD, indicates unique spectral features for all eight SynOxA isomers in the theoretical spectra. Although the experimental VCD is weak and restricted by the limited amount of sample, it allows for a tentative assignment of the elusive chlorine-substituted stereocenter. VCD chiroptical analysis of a SynOxA derivative with three stereocenters, SynOxC, results in the same absolute configuration as for SynOxA. Despite the experimental challenges, the results convincingly prove that the assignment of absolute configuration based on vibrational chiroptical methods is more reliable than for ECD.     

A configurational and conformational study of aframodial and its diasteriomers via experimental and theoretical VA and VCD spectroscopies

In this work we present the experimental and theoretical vibrational absorption (VA) and the theoretical vibrational circular dichroism (VCD) spectra for aframodial. In addition, we present the theoretical VA and VCD spectra for the diasteriomers of aframodial. Aframodial has four chiral centers and hence has 2⁴ = 16 diasteriomers, which occur in eight pairs of enantiomers. In addition to the four chiral centers, there is an additional chirality due to the helicity of the entire molecule, which we show by presenting 12 configurations of the 5S,8S,9R,10S enantiomer of aframodial. The VCD spectra for the diasteriomers and the 12 configurations of one enantiomer are shown to be very sensitive not only to the local stereochemistry at each chiral center, but in addition, to the helicity of the entire molecule. Here one must be careful in analyzing the signs of the VCD bands due to the ‘non-chiral’ chromophores in the molecule, since one has two contributions; one due to the inherent chirality at the four chiral centers, and one due to the chirality of the side chain groups in specific conformers, that is, its helicity. Theoretical simulations for various levels of theory are compared to the experimental VA recorded to date. The VCD spectra simulations are presented, but no experimental VCD and Raman spectra have been reported to date, though some preliminary VCD measurements have been made in Stephens’ lab in Los Angeles. The flexible side chain is proposed to be responsible for the small size of the VCD spectra of this molecule, even though the chiral part of the molecule is very rigid and has four chiral centers. In addition to VCD and Raman measurements, Raman optical activity (ROA) measurements would be very enlightening, as in many cases bands which are weak in both the VA and VCD, may be large in the Raman and/or ROA spectra. The feasibility of using vibrational spectroscopy to monitor biological structure, function and activity is a worthy goal, but this work shows that a careful theoretical analysis is also required, if one is to fully utilize and understand the experimental results. The reliability, reproduceability and uniqueness of the vibrational spectroscopic experiments and the information which can be gained from them is discussed, as well as the details of the computation of VA, VCD and Raman (and ROA) spectroscopy for molecules of the complexity of aframodial, which have multiple chiral centers and flexible side chains. Festschrift in Honor of Philip J. Stephens’ 65th Birthday.     

Role of hydration in determining the structure and vibrational spectra of L-alanine and N-acetyl L-alanine N′-methylamide in aqueous solution: a combined theoretical and experimental approach

In this work we have utilized recent density functional theory Born-Oppenheimer molecular dynamics simulations to determine the first principles locations of the water molecules in the first solvation shell which are responsible for stabilizing the zwitterionic structure of L-alanine. Previous works have used chemical intuition or classical molecular dynamics simulations to position the water molecules. In addition, a complete shell of water molecules was not previously used, only the water molecules which were thought to be strongly interacting (H-bonded) with the zwitterionic species. In a previous work by Tajkhorshid et al. (J Phys Chem B 102:5899) the L-alanine zwitterion was stabilized by 4 water molecules, and a subsequent work by Frimand et al. (Chem Phys 255:165) the number was increased to 9 water molecules. Here we found that 20 water molecules are necessary to fully encapsulate the zwitterionic species when the molecule is embedded within a droplet of water, while 11 water molecules are necessary to encapsulate the polar region with the methyl group exposed to the surface, where it migrates during the MD simulation. Here we present our vibrational absorption, vibrational circular dichroism and Raman and Raman optical activity simulations, which we compare to the previous simulations and experimental results. In addition, we report new VA, VCD, Raman and ROA measurements for L-alanine in aqueous solution with the latest commercially available FTIR VA/VCD instrument (Biotools, Jupiter, FL, USA) and Raman/ROA instrument (Biotools). The signal to noise of the spectra of L-alanine measured with these new instruments is significantly better than the previously reported spectra. Finally we reinvestigate the causes for the stability of the P_π structure of the alanine dipeptide, also called N-acetyl-L-alanine N′-methylamide, in aqueous solution. Previously we utilized the B3LYP/6-31G* + Onsager continuum level of theory to investigate the stability of the NALANMA4WC Han et al. (J Phys Chem B 102:2587) Here we use the B3PW91 and B3LYP hybrid exchange correlation functionals, the aug-cc-pVDZ basis set and the PCM and CPCM (COSMO) continuum solvent models, in addition to the Onsager and no continuum solvent model. Here by the comparison of the VA, VCD, Raman and ROA spectra we can confirm the stability of the NALANMA4WC due to the strong hydrogen bonding between the four water molecules and the peptide polar groups. Hence we advocate the use of explicit water molecules and continuum solvent treatment for all future spectral simulations of amino acids, peptides and proteins in aqueous solution, as even the structure (conformer) present cannot always be found without this level of theory. Festschift in Honor of Philip J. Stephens’ 65th Birthday. During the proof stage of this article a very relevant article has been published by M. Losada and Y. Xu titled “Chirality transfer through hydrogen-bonding: Experimental and ab initio analyses of vibrational circular dichroism spectra of methyl lactate in water” in Phys Chem Chem Phys 2007, 9: 3127–3135. In that work they confirm that the effects of water are seen in the VCD spectra and hence it is fundamental to include explicit water molecules in modeling studies of the vibrational spectra of biomolecules in aqueous solution.     

Spectra and structure of silicon containing compounds. XXXII. Raman and infrared spectra,conformational stability,vibrational assignment and ab initio calculations of n-propylsilane-d0 and Si-d3

The infrared (3100-40 cm(-1)) and Raman (3100-20 cm(-1)) spectra of gaseous and solid n-propylsilane, CH(3)CH(2)CH(2)SiH(3) and the Si-d(3) isotopomer, CH(3)CH(2)CH(2)SiD(3), have been recorded. Additionally, the Raman spectra of the liquids have been recorded and qualitative depolarization values obtained. Both the anti and gauche conformers have been identified in the fluid phases but only the anti conformer remains in the solid. Variable temperature (-105 to -150 degrees C) studies of the infrared spectra of n-propylsilane dissolved in liquid krypton have been recorded and the enthalpy difference has been determined to be 220+/-22 cm(-1) (2.63+/-0.26 kJ mol(-1)) with the anti conformer the more stable form. A similar value of 234+/-23 cm(-1) (2.80+/-0.28 kJ mol(-1)) was obtained for deltaH for the Si-d(3) isotopomer. At ambient temperature it is estimated that there is 30+/-2% of the gauche conformer present. The potential function governing the conformation interchange has been estimated from the far infrared spectral data, the enthalpy difference, and the dihedral angle of the gauche conformer, which is compared to the one predicted from ab initio MP2/6-31G(d) calculations. The barriers to conformational interchange are: 942, 970 and 716 cm(-1) for the anti to gauche, gauche to gauche, and gauche to anti conformers, respectively. Relatively complete vibrational assignments are proposed for both the n-propylsilane-d(0) and Si-d(3) molecules based on the relative infrared and Raman spectral intensities, infrared band contours, depolarization ratios, and normal coordinate calculations. The geometrical parameters, harmonic force constants, vibrational frequencies, infrared intensities, Raman activities and depolarization ratios, and energy differences have been obtained for the anti and gauche conformers from ab initio MP2/6-31G(d) calculations. Structural parameters and energy differences have also been obtained utilizing the larger 6-311 + G(d,p) and 6-311 + G(2d,2p) basis sets. From the isolated Si-H stretching frequency from the Si-d(2) isotopomer the r(0) distances of 1.484 and 1.485 A have been determined for the SiH(s) and SiH(a) bonds, respectively, for the anti conformer, and 1.486 A for the SiH bond for the gauche conformer. Utilizing previously reported microwave rotational constants for the anti conformer and the determined SiH distances along with ab initio predicted parameters 'adjusted r(0)' parameters have been obtained for the anti conformer. The results are discussed and compared to those obtained for some similar molecules.     

Spectra and structure of silicon containing compounds. XXXIX. Raman and infrared spectra,conformational stability,vibrational assignment and ab initio calculations of n-propyltrifluorosilane

The infrared (3100-40 cm(-1)) spectra of gaseous and solid and Raman (3200-20 cm(-1)) spectra of liquid with qualitative depolarization values and solid n-propyltrifluorosilane, CH(3)CH(2)CH(2)SiF(3), have been recorded. Additionally the infrared spectra of the sample in nitrogen and argon matrices have been recorded. Both the anti and gauche conformers have been identified in the fluid phases but only the anti conformer remains in the solid. Variable temperature (-105 to -150 degrees C) studies of the infrared spectra of the sample dissolved in liquid krypton have been recorded and the enthalpy difference has been determined to be 135+/-14 cm(-1) (1.62+/-0.17 kJ mol(-1)) with the anti conformer the more stable form. At ambient temperature it is estimated that there is 51+/-2% of the gauche conformer present. Also the enthalpy difference in the liquid was obtained from variable temperature studies of the Raman spectra and from three conformer pairs an average value of 179+/-18 cm(-1) (2.14+/-0.22 kJ mol(-1)) was obtained again with the anti form the more stable conformer. Relatively complete vibrational assignments are proposed for both conformers based on the relative infrared and Raman spectral intensities, infrared band contours, depolarization ratios which are supported by normal coordinate calculations. The geometrical parameters, harmonic force constants, vibrational frequencies, infrared intensities, Raman activities, depolarization ratios, and energy differences have been obtained for the anti and gauche conformers from ab initio MP2/6-31G(d) calculations. Structural parameters and energy differences have also been obtained utilizing the larger 6-311+G(d, p) and 6-311+G(2d, 2p) basis sets. By utilizing the previously reported microwave rotational constants for five isotopomers of CH(3)SiF(3) along with ab initio predicted structural values, r(0) parameters have been obtained for methyltrifluorosilane. Similarly, from the ab initio predicted parameters "adjusted r(0)" parameters have been estimated for both conformers of n-propyltrifluorosilane. The results are discussed and compared with those obtained for some similar molecules.     

Infrared and Raman spectra, conformational stability, barriers to internal rotation, normal-coordinate calculations and vibrational assignments for vinyl silyl bromide

The infrared (3200-30 cm(-1) spectra of gaseous and solid, the Raman spectra (3200-30 cm(-1)) of the liquid and solid vinyl silyl bromide, CH2CHSiH2Br, have been recorded. Additionally, quantitative depolarization values have been obtained. Both the gauche and cis conformers have been identified in the fluid phases but only the gauche conformer remains in the solid. Variable temperature studies from 0 to -87 degrees C of the Raman spectrum of the liquid was carried out. From these data, the enthalpy difference has been determined to be 22 +/- 6 cm(-1) (0.26 +/- 0.08 kJ/mol), with the gauche conformer being the more stable form. The predictions from the ab initio calculations up to MP2/6-311 + + G(2d,2p) basis set favor the gauche as the more stable form. A complete vibrational assignment is proposed for both the gauche and cis conformers based on infrared band contours, relative intensities, depolarization values and group frequencies. The vibrational assignments are supported by normal coordinate calculations utilizing the force constants from ab initio MP2/6-31G(d) calculations and the potential energy terms for the conformer interconversion have been obtained from the same calculations. Complete equilibrium geometries have been determined for both rotamers by ab initio calculations employing a variety of basis sets up to 6-311 + + G(2d,2p) at levels of restricted Hartree-Fock (RHF) and/or Moller-Plesset (MP) to second order. The results are discussed and compared to those obtained for some similar molecules.     

Infrared and Raman spectra, conformational stability, ab initio calculations and vibrational assignment for 1,2-pentadiene (ethyl allene)

The infrared (3500-50 cm⁻¹) and Raman (3500-20 cm⁻¹) spectra of 1,2-pentadiene, H₂C=C=C(H)CH₂CH₃ (ethyl allene), have been recorded for both the gaseous and solid states. Additionally, the Raman spectrum of the liquid has been obtained with qualitative depolarization values. In the fluid phases both the cis and gauche conformers have been identified, with the gauche rotamer being the predominant form although it may not be the conformer of lowest energy. In the solid state only the cis conformer remains after repeated annealing of the crystal. The asymmetric torsion of the cis conformer is observed as a series of Q-branch transitions beginning at 103.4 cm⁻¹ and falling to lower frequency. An estimate of the potential function governing conformer interconversion is provided. A complete assignment of the normal modes for the cis conformer is given and several of the fundamentals are assigned for the gauche rotamer. Ab initio electronic structure calculations of energies, conformational geometries, vibrational frequencies, and potential energy functions have been made to complement and assist the interpretation of the infrared and Raman spectra. In particular, the transitions among torsional energy levels for both the symmetric (methyl) and asymmetric (ethyl) motions have been calculated. The results are compared to the corresponding quantities for some similar molecules.     

A matrix isolation study on Ac-Gly-NHMe and Ac-l-Ala-NHMe, the simplest chiral and achiral building blocks of peptides and proteins

The infrared absorption (IR) spectra of acetyl-N-methyl-glycine and acetyl-N-methyl-alanine have been recorded in dichloromethane and dimethyl sulfoxide-d(6) solution, as well as in Ar and Kr matrices. The spectra were assigned with the help of quantum chemical calculations. Based on the assignments of the matrix-isolation IR spectra, in line with theoretical predictions, two different hydrogen bonded conformers were identified, furthermore a third conformer is likely to be present, which cannot be unambiguously identified. In dichloromethane two conformers could be observed, while in dimethyl sulfoxide a single conformer could be identified. Vibrational circular dichroism (VCD) spectra of acetyl-N-methyl-l-alanine have also been recorded in solutions and matrices. These matrix-isolation VCD spectra not only support the assignments of the matrix-isolation IR spectra, but also demonstrate that these spectra can be interpreted much easier with the help of quantum chemical calculations than the VCD spectra recorded in solutions. It is also shown that the rotatory strength of some vibrational transitions changes rapidly as a function of the backbone torsional coordinates; hence the appearance of some regions in the VCD spectra is extremely dependent on any perturbations, e.g. weak intermolecular interactions.     

Raman optical activity spectra and conformational elucidation of chiral drugs. The case of the antiangiogenic aeroplysinin-1

We present the determination of the conformational properties of aeroplysinin-1 in aqueous solution by means of a combined experimental and theoretical Raman optical activity (ROA) and vibrational circular dichroism (VCD) study. Aeroplysinin-1 is an antiangiogenic drug extracted from the sponge Aplysina cavernicola which has been proved to be a valuable candidate for the treatment of cancer and other antiangiogenic diseases. Our study shows that this molecule possesses the 1S,6R absolute configuration in aqueous solution, where only two conformers are present to a significant level. We discuss in detail the relationships between the chiro-optical ROA and VCD features, and the structural properties of various energy accessible conformers are described. The present work is one of the first studies in which both ROA and VCD have been used as complementary tools for the determination of absolute configuration and dominant solution-state conformations of an unknown therapeutically significant molecule.     

Infrared and Raman spectra, conformational stability and vibrational assignment of 1-chloro-1-silacyclopentane

Infrared and Raman spectra (3500-60 cm⁻¹) of gas and/or liquid and solid 1-chloro-1-silacyclopentane (c-C₄H₈SiClH) have been recorded and the vibrational data indicate the presence of a single conformer with no symmetry which is consistent with the twisted form. Ab initio calculations with a variety of basis sets up to MP2(full)/aug-cc-pVTZ predict the envelope-axial and envelope-equatorial conformers are saddle points with nearly the same energies but much lower in energy than the planar conformer. Density functional theory calculations by the B3LYP method predicts slightly lower energies for the two envelope forms and considerably lower for the planar form. By utilizing the MP2(full)/6-31G(d) calculations the force constants, frequencies, infrared intensities, band contours, Raman activities, and depolarization values have been obtained to support the vibrational assignment. Estimated r₀ structural parameters have been obtained from adjusted MP2(full)/6-311 + G(d, p) calculations. These experimental and theoretical results are compared to the corresponding quantities of some other five-membered rings.     

Conformational study of (R)-(+)-limonene in the liquid phase using vibrational spectroscopy (IR,Raman, and VCD) and DFT calculations

A conformational study in the liquid phase of the terpene (R)-(+)-limonene has been carried out, revealing the presence of three conformers. For this task, experimental vibrational techniques, such as IR, Raman, and VCD spectroscopies, together with quantum chemical calculations, have been used. Our study reveals that a previous vibrational analysis is desirable to achieve a thorough analysis of the VCD spectrum as well as that these three experimental techniques are complementary to characterize flexible systems, which present several conformers.     

Spectra and structure of silicon-containing compounds. Part XXXVIII: Infrared and Raman spectra,vibrational assignment,conformational stability,and ab initio calculations of vinyldifluorosilane

Infrared spectra (3500-50 cm(-1)) of gaseous and solid, and Raman spectrum (3500-30 cm(-1)) of liquid vinyldifluorosilane, CH(2)z.dbnd6;CHSiF(2)H, are reported. Both the cis and gauche rotamers have been identified in the fluid phases. From temperature-dependent FT-infrared spectra of krypton solutions, it is shown that the cis conformer is more stable than the gauche form by 119+/-12 cm(-1) (1.42+/-0.14 kJ mol(-1)). At ambient temperature there is 53+/-2% of the gauche conformer present. Complete vibrational assignments are provided for the cis conformer and several modes are identified for the gauche form. Harmonic force constants, fundamental frequencies, infrared intensities, and Raman activities have been obtained from MP2/6-31G(d) calculations with full electron correlation. The optimized geometries and conformational stabilities have also been obtained from ab initio MP2/6-31G(d), MP2/6-311+G(d,p), and MP2/6-311+G(2d,2p) calculations with full electron correlation as well as from density functional theory calculations (DFT) by the B3LYP method. The SiH bond distances (r(0)) of 1.472 and 1.471 A have been obtained for the cis and gauche conformers, respectively, from the silicon-hydrogen stretching frequencies. These results are compared to the corresponding quantities of the corresponding carbon analogue as well as with some similar molecules.     

Comparison of experimental and density functional study on the molecular structure, infrared and Raman spectra and vibrational assignments of 6-chloronicotinic acid

The experimental and theoretical study on the structures and vibrations of 6-chloronicotinic acid (6-CNA, C(6)H(4)ClNO(2)) are presented. The Fourier transform infrared spectra (4,000-50 cm(-1)) and the Fourier transform Raman spectra (3,500-50 cm(-1)) of the title molecule in solid phase have been recorded, for the first time. The geometrical parameters and energies have been obtained for all four conformers from DFT (B3LYP) with different basis sets calculations. There are four conformers, C1, C2, C3, and C4 for this molecule. The computational results diagnose the most stable conformer of 6-CNA as the C1 form. The vibrations of the two stable and two unstable conformers of 6-CNA are researched with the aid of quantum chemical calculations. The molecular structure, vibrational frequencies, infrared intensities and Raman scattering activities and theoretical vibrational spectra were calculated a pair of molecules linked by the intermolecular OH...O hydrogen bond. The spectroscopic and theoretical results are compared to the corresponding properties for 6-CNA stable monomers and dimer of C1 conformer.     

Conformational stability and vibrations of aminopropylsilanol molecule

Density functional theory (DFT), using the B3-LYP/6-31G(d,p) method have been used to investigate the conformation and vibrational spectra of aminopropylsilanetriol (APST) NH2CH2CH2CH2Si(OH)3. The potential function for CCCSi torsion gives rise to two distinct conformers trans and gauche. The predicted energy of the more stable trans conformer is 337 cm-1 less than the energy of gauche conformer. The calculated barriers to the conformation interchange are: 1095, 2845 and 438 cm-1 for the trans to gauche, gauche to gauche and gauche to trans conformers, respectively. For the trans conformer the potential energy curve for the Si(OH)3 groups torsion in APST has been calculated changing the HOSiC dihedral angle. The barrier for the internal rotation of 3065 cm-1 has been obtained. The optimized molecular structure of APST dimer calculated for trans conformer has a SiOSi angle of 143.2 degrees, and a SiOSi bond length of 0.164 nm. A complete vibrational assignment for both conformers as well as for trans-dimer is supported by the normal coordinate analysis, calculated IR intensities as well as Raman activities. On the basis of the results, the vibrational spectra of APST aqueous solution and APST polymer have been analyzed. The average error between the observed and calculated frequencies is 14 cm-1.     

Spectra and structure of silicon-containing compounds. XXX. Raman and infrared spectra,conformational stability,vibrational assignment of chloromethyl silyl dichloride

The Raman spectra (3200-30 cm(-1)) of liquid and solid, and infrared spectra of gaseous and solid chloromethyl silyl dichloride, ClCH2SiHCl2, have been recorded. Variable temperature (-105 to -150 degrees C) studies of the infrared spectra of the sample dissolved in liquid krypton have been carried out. From these data, the enthalpy difference was determined to be 363 +/- 40 cm(-1) (4.34 +/- 0.48 kJ mol(-1)), with the more stable form being the gauche conformer, which is consistent with the prediction from ab initio calculations at both the Hartree-Fock level and with full electron correlation by the perturbation method to second order. It is estimated that 92% of the sample is in the gauche form at ambient temperature. A complete vibrational assignment is proposed for the gauche conformer and several of fundamentals of the trans conformer based on infrared band contours, relative intensities, depolarization values, and group frequencies, which is supported by normal coordinate calculations utilizing the force constants from the ab initio MP2/6-31G(d) calculations. The r0 SiH bond distances of 1.476 and 1.472 A have been obtained for the trans and gauche conformers, respectively, from the silicon-hydrogen stretching frequencies. The optimized geometries have also been obtained from ab initio calculations utilizing several different basis sets with full electron correlation by the perturbation method up to MP2/6-311 + G(2d,2p). The results are discussed and compared to some corresponding results for several related molecules.     

Spectra and structure of silicon containing compounds. XXVII. Raman and infrared spectra, conformational stability, vibrational assignment and ab initio calculations of vinyldichlorosilane

The infrared (3200-30 cm(-1) spectra of gaseous and solid and the Raman spectra of liquid (3200-30 cm(-1), with quantitative depolarization values, and solid vinyldichlorosilane, CH2=CHSiHCl2, have been recorded. Both the gauche and the cis conformers have been identified in the fluid phases. Variable temperature (105-150 degrees C) studies of the infrared spectra of the sample dissolved in liquid krypton have been carried out. From these data the enthalpy difference has been determined to be 20 +/- 5 cm(-1) (235 +/- 59 J mol(-1) with the gauche conformer the more stable rotamer. It was not possible to obtain a single conformer in the solid even with repeated annealing of the sample. The experimental enthalpy difference is in agreement with the prediction from MP2/6-311 + G(2d,2p) ab initio calculations with full electron correlation. However, when smaller basis sets, i.e. 6-31G(d) and 6-311 + G(d,p) were utilized the cis conformer was predicted to be the more stable form. Complete vibrational assignments are proposed for both conformers based on infrared contours, relative infrared and Raman intensities, depolarization values and group frequencies, which are supported by normal coordinate calculations utilizing the force constants from ab initio MP2/6-31G(d) calculations. From the frequencies of the Si-H stretches, the Si-H bond distance of 1.474 A has been determined for both the gauche and the cis conformers. Complete equilibrium geometries have been determined for both rotamers by ab initio calculations employing the 6-31G(d), 6-311 + G(d,p) and 6-311 + (2d,2p) basis sets at level of Hartree-Fock (RHF) and/or Moller Plesset to the second order (MP2) with full electron correlation. The potential energy terms for the conformer interconversion have been obtained from the MP2/6-31G(d) calculations. The results are discussed and compared with those obtained for some similar molecules.     

Infrared and Raman spectra, conformational stability, ab initio calculations of structure, and vibrational assignment of ethynylmethyl cyclobutane.

The infrared spectra (3200-300 cm(-1)) of the gas and solid and the Raman spectra (3200-30 cm(-1) of the liquid with quantitative depolarization values and the solid have been recorded of ethynylmethyl cyclobutane (cyclobutylmethyl acetylene), c-C4H7CH2C[ triple bond]CH. Both the equatorial and the axial conformers have been identified in the fluid phases and both the gauche and trans conformations of the methyl acetylenic group have been identified for each ring conformer. Variable temperature (-105 to -150 degrees C) studies of the infrared spectra of the sample dissolved in liquid krypton have been carried out. From these data the enthalpy differences have been determined to the 112 +/- 11 cm(-1) (1.34 +/- 0.13 kJ mol) between the most stable equatorial-trans (Et) conformer and the equatorial-gauche (Eg) conformer which is the second most stable conformer and 327 +/- 35 cm(-1) (3.91 + 0.42 kJ/mol) with the axial-gauche (Ag) conformer which is the least stable conformer. The enthalpy difference between the axial-trans (At) and the equatorial-gauche(Eg) is 56 +/- 6 cm(-1). At ambient temperature there is approximately 33% of the Et conformer, 38% of the Eg form, 15% of the At and 14% of the Ag conformer. For the polycrystalline solid the Eg conformer is the only form present which probably results form the packing in the crystal. A complete vibrational assignment is proposed for both equatorial conformers and additionally a few of the fundamentals of the At and Ag conformers have been assigned. The vibrational assignments are supported by normal coordinate calculations utilizing the force constants from ab initio MP2/6-31G(d) calculations. Complete equilibrium geometries have been determined for all four possible rotamers by ab initio calculations employing the 6-31G(d) and 6-311 + + G(d,p) basis sets at levels of restricted Hartree-Fock (RHF) and /or Moller-Plesset (MP2) with full electron correlation by the perturbation method to second order. The results are discussed and compared to those obtained for some similar molecules.     

Conformational flexibility of L-alanine zwitterion determines shapes of Raman and Raman optical activity spectral bands

Detailed analysis of Raman and Raman optical activity (ROA) of L-alanine zwitterion (ALAZW) revealed that shapes of the spectral bands are to a large extent determined by the rotation of the NH(3)(+), CO(2)(-), and CH(3) groups. Aqueous solution ALAZW spectra were measured down to 100 cm(-1) and compared to complex simulations based on ab initio (B3LYP/CPCM/6-31++G**) computations of molecular energies and spectral parameters. The bands exhibit different sensitivities to the motion of the rotating group; typically, for more susceptible bands the Raman signal becomes broader and the ROA intensity decreases. When these dynamical factors are taken into account in Boltzmann averaging of conformer contributions, simulated spectra not only better agree with the experiment, but shapes of the rotational potentials can be estimated. Effects of the molecular flexibility could be also demonstrated on differences in Raman spectra of the solution, crystalline, and glass (gellike) solid states of ALAZW. Experimental Raman and ROA spectra of four model dipeptides of different rigidities (Ala-Pro, Pro-Ala, Pro-Gly, and Gly-Pro) indicate that the broadening of spectral lines can be used as a general site-specific indicator of molecular rigidity or flexibility.     

Absolute configuration and conformation analysis of 1-phenylethanol by matrix-isolation infrared and vibrational circular dichroism spectroscopy combined with density functional theory calculation

The absolute configuration and conformation of 1-phenylethanol (1-PhEtOH) have been determined by matrix-isolation infrared (IR) and vibrational circular dichroism (VCD) spectroscopy combined with quantum chemical calculations. Quantum chemical calculations have identified that there are three conformers, namely, I, II, and III, in which characteristic intramolecular interactions are found. The IR spectrum-conformation correlation for 1-PhEtOH has been developed by the Ar matrix-isolation IR measurement and used for the assignments of the observed IR bands. In a dilute CCl(4) solution, 1-PhEtOH exists predominantly as conformer I along with a trace amount of conformer II. By considering conformations and intermolecular hydrogen-bonding in the spectral simulation for (S)-1-PhEtOH, we have successfully reproduced the VCD spectrum of (-)-1-PhEtOH observed in a dilute CS(2) solution. Thus, (-)-1-PhEtOH is of S-configuration and conformer I in the dilute solution. The same method has been applied to analyze the VCD spectra measured in the liquid state of (-)-1-PhEtOH. The absolute configuration of 1-PhEtOH in the condensed phase is enabled by identifying VCD bands that are insensitive to conformational changes and intermolecular interactions. The present work provides a combinatorial procedure for determination of both the absolute configuration and the conformation of chiral molecules in a dilute solution and condensed phase.     

Conformational landscape and hydrogen bonding in (S)-(−)-perillyc acid: experimental VCD,IR, Raman,and theoretical DFT studies

(S)-(?)-Perillyc acid (4-isopropenylcyclohexene-1-carboxylic acid) is an intermediate in the limonene and pinene pathway degradation and its measurement in urine is used to monitor cancer patients receiving oral limonene. For the first time, a theoretical study of the conformational preference in the monomer and H-bonded dimers complemented with a theoretical and experimental analysis of the infrared, raman, and vibrational vircular dichroism spectra of (S)-(?)-perillyc acid in solution and solid phases is presented. With regard to the monomer, theoretical calculations revealed the existence of two conformers depending on the position of the isopropenyl group (axial and equatorial) and 24 rotamers (12 equatorials and 12 axials). The study of the H-bonded dimers revealed great complexity in the conformational landscape with a total of 36 structures studied. Herein, from a reliable assignment of the IR and Raman spectra and with help from the study of the VCD spectrum of the title compound, the most stable rotamers of the H-bonded complexes have been detected experimentally in the liquid and solid phases. Additionally, natural bond orbitals (NBO) analysis indicates an electronic delocalization between the two subunits in the dimer. The IR, Raman, and VCD are helpful and complementary techniques to characterize flexible systems, such as terpenes, which present several conformers and H-bonded aggregates.