Vibronically resolved electronic circular dichroism spectra of (R)-(+)-3-methylcyclopentanone: a theoretical study

The vibrationally resolved electronic circular dichroism (ECD) spectra of the two dominant conformers of (R)-(+)-3-methylcyclopentanone in gas phase are computed by density functional response theory, with a full account of Franck-Condon and Herzberg-Teller vibrational contributions at the harmonic level. Proper inclusion of the latter contributions was made possible by the recent implementation of effective-scaling computations of vibrational overlaps and of analytical gradients of time dependent DFT. The Coulomb-attenuated Becke three parameters Lee-Yang-Parr (CAM-B3LYP) functional reproduces both the position and the intensity of the experimental peaks, providing a remarkable improvement over the spectra obtained with the popular hybrid B3LYP functional, and allowing a confident assignment of the CD fine vibrational structure. Franck-Condon and Herzberg-Teller contributions are discussed in detail. The computed decrease of the CD intensity in the gas phase upon increase of the temperature of the sample follows the trend observed experimentally in different solvents.     

An ab initio study of pyruvic acid

The geometries and vibrational frequencies of two conformers of pyruvic acid have been obtained at the ab initio second order Möller-Plesset level of theory using the 6-311++G^** basis set. While the calculated geometries have been compared to the experimental microwave data, the vibrational frequencies have been assigned, using the experimental gas phase IR spectra of 13 isotopes of pyruvic acid by a recently developed scaling procedure (IRPROG). An attempt has been made to explain the stability of the eclipsed conformation over the staggered conformation of pyruvic acid by taking account of the molecular orbitals.     

Aziridinyl ketones and their heteroanalogs. 5. Synthesis and structures of 2-aryl-3-aroylaziridines

A number of trans- and cis-isomeric 1-R-2-aryl-3-aroylaziridines were synthesized, and their IR spectra were studied. Intramolecular hydrogen bonding is realized in the trans isomers when R = H, and they exist in the only possible conformation (intermediate between a gauche and a cisoid conformation). cis-Isomers II (R = alkyl) exist in solutions in the form of two conformers, viz., gauche and cisoid conformers, and the gauche conformer is thermodynamically preferable.See [1] for Communication A.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No, 11, pp. 1489–1494, November, 1980.     

Conformational analysis of quinine and its pseudo enantiomer quinidine: a combined jet-cooled spectroscopy and vibrational circular dichroism study

Laser-desorbed quinine and quinidine have been studied in the gas phase by combining supersonic expansion with laser spectroscopy, namely, laser-induced fluorescence (LIF), resonance-enhanced multiphoton ionization (REMPI), and IR-UV double resonance experiments. Density funtional theory (DFT) calculations have been done in conjunction with the experimental work. The first electronic transition of quinine and quinidine is of π-π* nature, and the studied molecules weakly fluoresce in the gas phase, in contrast to what was observed in solution (Qin, W. W.; et al. J. Phys. Chem. C2009, 113, 11790). The two pseudo enantiomers quinine and quinidine show limited differences in the gas phase; their main conformation is of open type as it is in solution. However, vibrational circular dichroism (VCD) experiments in solution show that additional conformers exist in condensed phase for quinidine, which are not observed for quinine. This difference in behavior between the two pseudo enantiomers is discussed.     

HF, MP2 and DFT calculations and spectroscopic study of the vibrational and conformational properties of N-diethylendiamine

The conformational stability and vibrational modes of the N-diethylendiamine organic cation (N-DD(2+)) were studied by experimental (Raman) spectroscopy combined with theoretical calculations. Various ab initio theories were used: Hartree-Fock (HF) theory, M?ller-Plesset second-order perturbation (MP2) theory and density functional theory (DFT). Three stable conformers of N-DD(2+), trans-trans, gauche-gauche and gauche-trans were calculated. A comparison between the computed structural parameters of the conformers at both levels of theory and the X-ray data was made. It is demonstrated that the N-DD(2+) cation adopts more probably the gauche-gauche conformation at room temperature. In order to make a more detailed interpretation of the low temperature phase transition of N-DDHP, the Raman spectra of N-DDHP were recorded at room and low temperature in the 200-3400 cm(-1) region. The vibrational frequencies of the different conformers of N-DD(2+) were also calculated using the DFT/B3LYP (6-31G(d)) level of theory. By comparison between the experimental and theoretical results, the conformational dynamic of the N-DD(2+) organic cation was confirmed. It is shown that the N-DD(2+) cation configuration changes from gauche-gauche conformer to gauche-trans conformer when decreasing the temperature.     

Calculation of relative energies of permethylated oligosilane conformers in vapor and in alkane solution

The geometries of 35 conformers of Me(SiMe2)nMe (n = 4, 1; n = 5, 2; n = 6, 3; n = 7, 4) were optimized at the MP2/VTDZ level, and CCSD(T) single-point calculations were done at three MP2/VTDZ conformer geometries of 1. The relative ground-state energies of the conformers of 1-4 in the gas phase were obtained from the MP2/VTDZ electronic energy, zero-point vibrational energy, and thermal corrections at 0, 77, and 298 K. Relative energies in an alkane solvent at 77 and 298 K were obtained by the addition of solvation energies, obtained from the SM5.42R model. The calculated energies of 26 of the conformers (n = 4-6) have been least-squares fitted to a set of 15 additive increments associated with each Si-Si bond conformation and each pair of adjacent bond conformations, with mean deviations of 0.06-0.20 kcal/mol. An even better fit for the energies of 24 conformers (mean deviations, 0.01-0.09 kcal/mol) has been obtained with a larger set of 19 increments, which also contained contributions from selected combinations of conformations of three adjacent bonds. The utility of the additive increments for the prediction of relative conformer energies in the gas phase and in solution has been tested on the remaining nine conformers (n = 6, 7). With the improved increment set, the average deviation from the SM5.42R//MP2 results for solvated conformers at 298 K was 0.18 kcal/mol, and the maximum error was 0.98 kcal/mol.     

n-pentanol at high pressures: rotational isomerism in the liquid phase and the liquid-solid phase transition

The vibrational spectrum of liquids constituted of chain molecules is difficult to analyze because it may have contributions of different rotational isomers. In turn, with a proper vibrational assignment, this feature allows us to extract information about the effect of temperature or pressure on the molecular conformations in the liquid state. In this regard, the information on the vibrational spectrum in the solid phase greatly simplifies the vibrational analysis of the different rotational conformers existing in the liquid, as the molecules usually present all-trans conformations in the crystalline state. Here we report room-temperature Raman experiments on n-pentanol performed in a sapphire-anvil cell up to 3 GPa. A detailed analysis of the liquid-solid phase transition occurring at 1.3 GPa is provided. The analysis of the Raman spectrum in the solid phase allows the identification of the bands due to the different rotational isomers present in the liquid. The analysis of the spectral region corresponding to skeletal vibrations of the carbon chain (800-1200 cm(-1)) indicates that gauche conformers are promoted by the application of pressure. The analysis of the intensity ratio of those bands assigned to trans and gauge conformations is used to calculate the change in molecular volume ascribed to the trans-gauge isomerization process. We find a value similar to that found in n-alkanes, i.e., -0.88 cm(3) mol(-1). In addition, we find indication that pressure varies the proportions of the different gauge conformers. Thus, it appears that the GTTt to TGTt transition in the carbon chain is favored at high pressures. As expected, a smaller change in the molecular volume accompanies this conformation change.     

Conformational identity change of 3-methylbutanone from gaseous phase to solutions: An IR vibrational spectroscopy study

Infrared vibrational spectroscopy of 3-methylbutanone [Me(CO)iPr] leads to two conclusions: (1) The conformational identity is different in the gas phase and in various solvents. (2) In the gas phase, type B rovibrational structures are observed. Thus, the molecular symmetry isC ₅. The following interpretation is based upon a model which implicitly takes the solvent into account in the framework of an empirical calculation. The solvent increases the interconversion barrier between two enantiomers. As a consequence, the molecule changes conformation, moving from the stable conformation with bisected carbonyl seen in the gas phase, to a conformation with an eclipsed carbonyl in solutions.     

The optical activity of carvone: a theoretical and experimental investigation

The optical rotatory dispersion (ORD) and circular dichroism of the conformationally flexible carvone molecule has been investigated in 17 solvents and compared with results from calculations for the "free" (gas phase) molecule. The G3 method was used to determine the relative energies of the six conformers. The optical rotation of (R)-(-)-carvone at 589 nm was calculated using coupled cluster and density functional methods, including temperature-dependent vibrational corrections. Vibrational corrections are significant and are primarily associated with normal modes involving the stereogenic carbon atom and the carbonyl group, whose n → π? excitation plays a significant role in the chiroptical response of carvone. Without the inclusion of vibrational corrections the optical rotation calculated with CCSD and DFT has the opposite sign of experimental data. Calculations of optical rotation performed in solution using the polarizable continuum model were also opposite in sign when compared to that of the experiment.     

Structural and vibrational characterisation of 3-amino-1-propanol a concerted SCF-MO ab initio, Raman and infrared (matrix isolation and liquid phase) spectroscopy study

Results obtained for the isolated and liquid 3-amino-1-propanol by a concerted molecular orbital and vibrational spectroscopic approach are reported. The relative energies and both structural and vibrational data of the different conformers of the studied compound were calculated using the extended 6-31G* basis set both at the HF-SCF and MP2 ab initio levels of theory and the theoretical results used to interpret Raman and infrared experimental data. In the gaseous phase and for the molecule isolated in an Argon matrix, monomeric 3-amino-1-propanol exists as a mixture of conformers, the first and second lowest energy forms corresponding to conformers which exhibit an intramolecular OH-N hydrogen bond (forms I and II). On the other hand, in the pure liquid, where intermolecular H-bonding occurs, the monomeric unit within the aggregates assumes a conformation similar to that of the third most stable form found for the isolated molecule situation (form III), which is characterised by having a weak intramolecular NH-O bond. The experimental data obtained for the pure liquid also reveals the presence of monomeric form I in this phase, a result that is in consonance with the strongly stabilizing OH-N intramolecular hydrogen bond that is present in this conformer.     

Conformations of cationized linear oligosaccharides revealed by FTMS combined with in‐ESI H/D exchange

Previously (Kostyukevich et al. Anal Chem 2014, 86, 2595), we have reported that oligosaccharides anions are produced in the electrospray in two different conformations, which differ by the rate of gas phase hydrogen/deuterium (H/D) exchange reaction. In the present paper, we apply the in‐electrospray ionization (ESI) source H/D exchange approach for the investigation of the oligosaccharides cations formed by attaching of metal ions (Na, K) to the molecule. It was observed that the formation of different conformers can be manipulated by varying the temperature of the desolvating capillary of the ESI interphase. Separation of the conformers was performed using gas phase H/D approach. Because the conformers have different rates of the H/D exchange reaction, the deuterium distribution spectrum becomes bimodal. It was found that the conformation corresponding to the slow H/D exchange rate dominates in the spectrum when the capillary temperature is low (~200 °C), and the conformation corresponding to the fast H/D exchange rate dominates at high (~400 °C) temperatures. In the intermediate temperature region, two conformers are present simultaneously. It was also observed that large oligosaccharide requires higher temperature for the formation of another conformer. It was found that the presence of the conformers considerably depends on the solvent used for ESI and the pH. We have compared these results with the previously performed in‐ESI source H/D exchange experiments with peptides and proteins. Copyright © 2015 John Wiley & Sons, Ltd.     

Full MP2 study of solvent implicit and explicit effect on tautomers of Dithio-Biuret

Dithio biuret conformers were optimised and frequency calculations were performed at MP2/6–311++G(d,p) level of theory. Classification of conformers was done to five different tautomers and the most stable conformer of each tautomer was selected. Tautomer 3 having trans conformation of amino and thiocarbonyl functional group was the most stable tautomer in the gas phase. Optimisation and frequency calculations were also done in four different solvents as follows: benzene, acetonitrile, DMSO and water. Stability of tautomers were compared in these solvents to explore effect of polarity on stabilisation of tautomers. Inter-conversion of selected tautomers was investigated both in the gas phase and in four different media. Results showed that when solvent is used as an implicit media, it has negligible effect on proton transfer. Water-explicit effect was also investigated and the results exhibited high dependency of proton transfer mechanism on water molecules when they participate in breaking and formation of bonds.     

<Emphasis Type="Italic">Ab initio</Emphasis> prediction of plausible conformers of a flexible N-(3-chloro-4-fluorophenyl)thiourea (CFT) molecule: A validation study

The current aim of the ab initio crystal structure prediction is to find the possible conformers of the flexible N-(3-chloro-4-fluorophenyl)thiourea (CFT) molecule using gas phase optimization with an MP2/6-31G(d,p) basis set, and the lattice energy minimization in the presence of a repulsion-dispersion electrostatic potential. If the molecule deviates from the gas phase conformation, suitable intermolecular interactions are added, and the molecule favours stable packing. The crystal structure is said to be feasible if the intermolecular lattice energy compensates the intermolecular energy penalty associated with the suboptimal gas phase conformers. The idea of the current research is to find the least energy hydrogen bonded crystal structure from a set of rigid conformers in a conformation region, with a significant similarity of packing, which may lead to the prediction of polymorphs associated with the considered CFT molecule.     

Gas Phase Conformations of Tetrapeptide Glycine-Phenylalanine-Glycine-Glycine

Systematic search of the potential energy surface of tetrapeptide glycine-phenylalanine-glycine-glycine (GFGG) in gas phase is conducted by a combination of PM3, HF and BHandHLYP methods. The conformational search method is described in detail. The rela-tive electronic energies, zero point vibrational energies, dipole moments, rotational constants, vertical ionization energies and the temperature dependent conformational distributions for a number of important conformers are obtained. The structural characteristics of these conformers are analyzed and it is found that the entropic effect is a dominating factor in determining the relative stabilities of the conformers. The measurements of dipole moments and some characteristic IR mode are shown to be effective approaches to verify the theoreti-cal prediction. The structures of the low energy GFGG conformers are also analyzed in their connection with the secondary structures of proteins. Similarity between the local structures of low energy GFGG conformers and the α-helix is discussed and many β- and γ-turn local structures in GFGG conformers are found.     

Theoretical studies on hydrogen bonding, NMR chemical shifts and electron density topography in alpha, beta and gamma-cyclodextrin conformers

Hydrogen-bonded interactions in alpha-, beta-, and gamma-CD conformers are investigated from the molecular electron density topography and chemical shift in the nuclear magnetic resonance (NMR) spectra calculated by using the Gauge Invariant Atomic Orbital (GIAO) method within the framework of density functional theory. For the lowest-energy CD conformers in the gas phase, the O3-H...O2' hydrogen-bonding interactions are present. Calculated 1H NMR chemical shifts (delta H) correlate well with the hydrogen-bond distance as well as electron density at the bond critical point in the molecular electron density (MED) topography. The conformers of beta- and gamma-CD comprised of relatively strong secondary hydroxyl interactions are stabilized by solvation from polar solvents.     

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.     

Effect of ionization on infrared and electronic absorption spectra of methyl and ethyl formate in the gas phase and in astrophysical H2O ice: a computational study

This work reports infrared and electronic absorption spectra of trans and gauche conformers of neutral ethyl formate, trans and cis conformers of neutral methyl formate, their ions in the gas phase, and neutral ethyl and methyl formate in astrophysical H(2)O ice. The second-order M?ller-Plesset perturbation (MP2) method with TZVP basis set has been used to obtain ground-state geometries. An influence of ice on vibrational frequencies of neutral ethyl and methyl formate was obtained using integral equation formalism polarizable continnum model (IEFPCM). Significant shift in vibrational frequencies for neutral methyl and ethyl formate when studied in H(2)O ice and upon ionization is observed. Rotational and distortion constants for neutral ethyl and methyl formate from this work are in excellent agreement with the available experimental values. Electronic absorption spectra of conformers of ethyl and methyl formate and their ions are obtained using time-dependent density functional method (TDDFT). The nature of electronic transitions is also identified. We suggested lines especially good to detect these molecules in interstellar medium. Using these lines, we can identify the conformers of ethyl and methyl formate in gas phase and H(2)O ice in interstellar medium. This comparative study should provide useful guidelines to detect conformers of ethyl and methyl formate and their ions in gas phase and neutral molecules in H(2)O ice in different astronomical environment.     

A semi-empirical and ab initio combined approach for the full conformational searches of gaseous lysine and lysine–H2O complex

A full structural search of the canonical, zwitterionic, protonated and deprotonated lysine conformers in gas phase is presented. A total of 17,496 canonical, 972 zwitterionic, 11,664 protonated and 1458 trial deprotonated structures were generated by allowing for all combinations of internal single-bond rotamers. All the trial structures were initially optimized at the AM1 level, and the resulting structures were determined at the B3LYP/6-311G^* level. A total of 927 canonical, 730 protonated and 193 deprotonated conformers were found, but there were no stable zwitterionic structures in the gas phase. The most stable conformers of the canonical, protonated and deprotonated lysine were further optimized at the B3LYP/6-311++G^** level. The energies of the most stable structures were determined at the MP2/6-311G(2df,p) level and the vibrational frequencies were calculated at the B3LYP/6-311++G^** level. The rotational constants, dipole moments, zero-point vibrational energies, harmonic frequencies, vertical ionization energies, enthalpies, Gibbs free energies and conformational distributions of gaseous lysine were presented. Numerous new structures are found and the lowest-energy lysine conformer is more stable than the existing one by 1.1 kcal/mol. Hydrogen bonds are classified and may cause significant red-shifts to the associated vibrational frequencies. The calculated proton affinity/dissociation energy and gas-phase basicity/acidity are in good agreement with the experiments. Calculations are also presented for the canonical lysine–H₂O and zwitterionic lysine–H₂O clusters. Interaction between lysine and H₂O significantly affects the relative conformational stabilities. Only one water molecule is sufficient to produce the stable zwitterionic structures in gas phase. The lowest-energy structure is found to be zwitterions when applying the conductor-like polarized continuum solvent model (CPCM) to the lysine–H₂O complexes.     

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.     

Spectroscopic and theoretical investigation of (R)-3-methylcyclopentanone. The effect of solvent and temperature on the distribution of conformers

Temperature-dependent electronic circular dichroism (CD) spectra are reported for (R)-(+)-3-methylcyclopentanone (R3MCP) in 34 solvents. Analysis of these data yielded the enthalpy and entropy differences between axial methyl and equatorial methyl conformers, the dominant conformers for R3MCP. The weakly absorbing n-->pi* transition exhibited a decrease in lambdamax as the solvent polarity increased. Vibrational CD fine structure of the n-->pi* transition was observed in the gas phase in addition to several of the solvents. Vapor-phase CD spectra were compared to both the solution-phase spectra and theoretical calculations of the axial and equatorial methyl conformers. Optical rotation (OR) measurements for R3MCP in cyclohexane solution in the visible region showed excellent agreement with OR DFT calculations of the equatorial and axial methyl conformers. Density functional calculations with B3LYP and the 6-13G* and aug-cc-pVDZ basis sets, which incorporate the solvent dielectric constant, yielded trends in thermodynamic quantities as a function of polarity and solvent dipole moments that are only weakly or not observed in experiments.