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.     

A matrix isolation study on Ac-l-Pro-NH2: a frequent structural element of β- and γ-turns of peptides and proteins

The fine tuned flexibility of peptides and proteins is one of their key features to achieve full bioactivity. Proline diamides are inherently the most rigid natural peptide models, but they still have a potential to adopt several backbone and side-chain conformers. It has been tried to spell out the residual conformational flexibility of Ac-l-Pro-NH₂ using matrix isolation IR and VCD spectroscopy in Ar and Kr matrices. Spectra were analyzed by the help of quantum chemical calculations. The spectra are dominated by the transitions of the tγ_L+ conformer, furthermore trace amounts of the cα_L+ conformer are also present. Another low-energy conformer, tγ_L−, cannot be identified in the spectra, which was interpreted as it converts to the lowest energy tγ_L+ form through a low-energy barrier during the deposition of the sample onto the cold window. Our results confirm that proline can act as a conformational lock, since the backbone predominantly adapts to the tγ_L structure.     

The hydrogen bonding and conformations of p-tert-butylcalix[4]arene as studied by IR spectroscopy and by DFT calculations

IR and far IR spectra of p-tert-butylcalix[4]arene were recorded at various temperatures between 16 and 180 degrees C and spectra of solutions and crystalline solids were obtained. Ab initio density functional calculations gave vibrational frequencies and infrared intensities for four conformers: cone, partial cone, 1,2- and 1,3-alternate. Complete assignments were made for experimental IR spectra of the cone conformer. The bands characteristic for each conformation were defined. It was revealed that O--H stretching low-frequency shift Deltanu in the cone conformation exceeds Deltanu shifts for other conformers. The effect was stipulated by a cooperative interaction of cyclic hydrogen bonds. The obtained spectra-structure correlation can be used for characteristic of calixarenes conformation.     

15N-1H and 15N-13C couplings in 15N-enriched dihydroxamic acids

(15)N-enriched dihydroxamic acids (HONHCO(CH(2))(n)CONHOH, n = 0, 1, and 2) were prepared and their spectra NMR ((1)H, (13)C, (15)N) recorded in dimethyl sulfoxide (DMSO) solutions with the aim of determining (15)N coupling constants ((15)N-(1)H and (15)N-(13)C). The results supplement chemical shifts published earlier and yield additional support to the structural conclusions derived from other NMR parameters. Notably, no trace of hydroximic structures could be found in the (15)N NMR spectra of these acids. The values of (15)N-(13)C coupling constants backed by theoretical calculations support the assignments made earlier for all of the major conformers and for the minor conformer of succinohydroxamic acid. The enrichment revealed that the minor component of malonodihydroxamic acid solution previously considered to be the ZE conformer is in fact the monohydroxamic acid (HOOC-CH(2)-CO-NH-OH).     

Chromatographic resolution, solution and crystal phase conformations, and absolute configuration of tert-butyl(dimethylamino)phenylphosphine-borane complex

The enantiomers of tert-butyl(dimethylamino)phenylphosphine-borane complex 2 have been separated by HPLC using cellulose tris-p-methylbenzoate as chiral stationary phase. The borane protection could be removed without racemization and the P-configuration of the free aminophosphine 1 has shown to be stable in solution. Infrared (IR) and vibrational circular dichroism (VCD) spectra have been measured in CD2Cl2 solution for both enantiomers. B3LYP/6-31+G(d) DFT calculations allowed a prediction that complex (S)-2 exists as three conformers in equilibrium and computed population-weighted IR and VCD spectra. Predicted and experimental IR and VCD spectra compared very well and indicate that enantiomer (+)-2 has the S absolute configuration. This assignment has been confirmed by an X-ray diffraction study on a single crystal of (+)-2. The crystal structure of enantiomerically pure 2 appears to be very close to the most stable computed conformer which proved to be predominant in solution.     

A combined theoretical and experimental study of the structure and vibrational absorption, vibrational circular dichroism, Raman and Raman optical activity spectra of the L-histidine zwitterion

A combined theoretical and experimental study of the vibrational absorption (VA)/IR, vibrational circular dichroism (VCD), Raman and Raman optical activity (ROA) spectra of l-histidine in aqueous solution has been undertaken to answer the questions (i) what are the species present and (ii) which conformers of the species are present under various experimental conditions. The VA spectra of l-histidine have been measured in aqueous solution and the spectral bands which can be used to identify both species (cation, zwitterion, anion) and conformer of the species have been identified and subsequently used to identify the species (zwitterion) and conformer (gauche minus minus, gauche minus plus for the side chain dihedral angles) present in solution at pH 7.6. The VCD spectral intensities have been used subsequently in combination with further theoretical studies to confirm the conclusions that have been arrived at by only analyzing the VA/IR spectra. Finally a comparison of measured Raman and ROA spectra of l-histidine with Raman and ROA spectral simulations for the conformers and species derived from the combined VA/IR and VCD experimental and theoretical work is presented as a validation of the conclusions arrived at from VA/IR and VCD spectroscopy. The combination of VA/IR and VCD with Raman and ROA is clearly superior and both sets of experiments should be performed.     

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.     

Vibrational spectroscopic studies, conformations and ab initio calculations of 3,3,3-trifluoropropyltrichlorosilane

Infrared spectra of 3,3,3-trifluoropropyltrichlorosilane (CF3CH2CH2SiCl3) were obtained in the vapour, amorphous and crystalline solid phases in the range 4000-50 cm-1. Additional spectra in argon matrices at 5.0 K were recorded before and after annealing to 20-36 K. Raman spectra of the compound as a liquid were recorded at various temperatures between 298 and 210 K and spectra of the amorphous and crystalline solids were obtained. The spectra suggested the existence of two conformers (anti and gauche) in the fluid phases and in the matrix. When the vapour was shock-frozen on a cold finger at 80 K and subsequently annealed to 120-150 K, six weak or very weak Raman bands vanished in the crystal. Similar variations were observed in the corresponding infrared spectra after annealing and four very weak IR bands disappeared after crystallization. From intensity variations between 298 and 210 K of three Raman band pairs an average value Delta(conf)H degrees (gauche-anti)=6.1+/-0.5 kJmol-1 was obtained in the liquid. Annealing experiments indicate that the anti conformer also has a lower energy in the argon matrices. The conformational equilibrium is highly shifted towards anti in the liquid, and the low energy conformer also forms the crystal. The spectra of the abundant anti conformer and the few bands ascribed to the gauche conformer have been interpreted. Ab initio calculations at the HF/6-311G(**) and B3LYP/6-311G(**) gave optimized geometries, infrared and Raman intensities and vibrational frequencies for the anti and gauche conformers. The conformational energy differences derived were 11.8 and 9.2 kJmol-1 from the HF and the B3LYP calculations, respectively.     

FT-IR, FT-Raman spectra, density functional computations of the vibrational spectra and molecular conformational analysis of 2,5-di-tert-butyl-hydroquinone

The purpose of finding conformer among six different possible conformers of 2,5-di-tert-butyl-hydroquinone (DTBHQ), its equilibrium geometry and harmonic wavenumbers were calculated by the B3LYP/6-31G(d,p) method. The infrared and Raman spectra of DTBHQ were recorded in the region 400-4000 cm(-1) and 50-3500 cm(-1), respectively. In addition, the IR spectra in CCl(4) at various concentrations of DTBHQ are also recorded. The computed vibrational wavenumbers were compared with the IR and Raman experimental data. Computational calculations at B3LYP level with two different basis sets 6-31G(d,p) and 6-311++G(d,p) are also employed in the study of the possible conformer of DTBHQ. The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes, calculated using VEDA 4 program. The general agreement between the observed and calculated frequencies was established.     

High Susceptibility of Histidine to Charge Solvation Revealed by Cold Ion Spectroscopy

Histidine remained the last aromatic amino acid for which the intrinsic spectroscopic properties and structures were obscure. We measured the UV and IR spectra of protonated histidine, isolated in the gas phase, using photofragmentation cold ion spectroscopy. Unexpectedly, the UV absorption appears strongly redshifted relative to that of the cation in aqueous solutions. In investigating this phenomenon, we solved the geometries of all abundant conformers using IR conformer‐selective spectroscopy and ab initio quantum chemical calculations. In all of the structures, the proton resides on the imidazole ring. The measured UV spectra of protonated methylimidazole, histamine and histidine, together with calculations of the electronic spectra for the latter, suggest that, in comparison with other aromatic amino acids, such location of proton makes UV absorption of histidine highly sensitive to the local environment of its side chain.     

Chiral terpenes in different phases: <Emphasis Type="Italic">R</Emphasis>-(−)-camphorquinone studied by IR–Raman–VCD spectroscopies and theoretical calculations

R-(−)-camphorquinone is a bicyclical terpenoid with many usages and application in different fields. Different experimental and theoretical works reveal that there is only one stable conformer of this chiral chemical species in agreement to the sterical restriction that the bicycle introduces. In the current work, from a complete assignment of the vibrational IR and Raman spectra, we are able to explain the VCD spectrum of the title compound. The recorded spectra of R-(−)-camphorquinone in different phases have been analyzed and compared: the first one in CCl₄ solution, the second one using Nujol and Fluorolube suspensions and the third one using thin films. Finally, to study the coupling between the two C=O stretching normal modes, a NBO analysis is performed. The present work reveals that IR, Raman and VCD, combined with quantum chemical calculations, are helpful complementary techniques to characterize chiral systems, as terpenes, in different phases.     

A single chiroptical spectroscopic method may not be able to establish the absolute configurations of diastereomers: dimethylesters of hibiscus and garcinia acids

Electronic circular dichroism (ECD), optical rotatory dispersion (ORD), and vibrational circular dichroism (VCD) spectra of hibiscus acid dimethyl ester have been measured and analyzed in combination with quantum chemical calculations of corresponding spectra. These results, along with those reported previously for garcinia acid dimethyl ester, reveal that none of these three (ECD, ORD, or VCD) spectroscopic methods, in isolation, can unequivocally establish the absolute configurations of diastereomers. This deficiency is eliminated when a combined spectral analysis of either ECD and VCD or ORD and VCD methods is used. It is also found that the ambiguities in the assignment of absolute configurations of diastereomers may also be overcome when unpolarized vibrational absorption is included in the spectral analysis.     

Conformational stability from variable temperature infrared spectra of krypton solutions, ab initio calculations, vibrational assignment, and r0 structural parameters of 1,3-difluoropropane

The infrared spectra (3200-400 cm(-1)) of krypton solutions of 1,3-difluoropropane, FCH2CH2CH2F, at variable temperatures (-105 to -150 degrees C) have been recorded. Additionally, the infrared spectra (3200-50 cm(-1)) of the gas and solid have been recorded as well as the Raman spectrum of the liquid. From a comparison of the spectra of the fluid phases with that in the solid, all of the fundamental vibrations of the C2 conformer (gauche-gauche) where the first gauche indicates the form for one of the CH2F groups and the second gauche the other CH2F, and many of those for the C1 form (trans-gauche) have been identified. Tentative assignments have been made for a few of the fundamentals of the other two conformers, i.e. C2v (trans-trans) and Cs (gauche-gauche'). By utilizing six pairs of fundamentals for these two conformers in the krypton solutions, an enthalpy difference of 277 +/- 28 cm(-1) (3.31 +/- 0.33 kJ mol(-1)) has been obtained for the C2 versus C1 conformer with the C2 conformer the more stable form. For the C2v conformer, the enthalpy difference has been determined to be 716 +/- 72 cm(-1) (8.57 +/- 0.86 kJ mol(-1)) and for the Cs form 971 +/- 115 cm(-1) (11.6 +/- 1.4 kJ mol(-1)). It is estimated that there is 64 +/- 3% of the C2 form, 34 +/-3% of the C1 form, 1% of the C2v form and 0.6% of the Cs conformer present at ambient temperature. Equilibrium geometries and total energies of the four stable conformers have been determined from ab initio calculations with full electron correlation by the perturbation method to second order as well as by hybrid density functional theory calculations with the B3LYP method using a number of basis sets. The MP2 calculations predict the C1 conformer stability to be slightly higher than the experimentally determined value whereas for the C2v and Cs conformers the predicted energy difference is much larger than the experimental value. The B3LYP calculations predict a better energy difference for both the C1 and C2v as well as for the Cs conformers than the MP2 values. A complete vibrational assignment is proposed for the C2 conformer and many of the fundamentals have been identified for the C1 form based on the force constants, relative intensities and rotational-vibrational band contours obtained from the predicted equilibrium geometry parameters. By combining previously reported rotational constants for the C2 and C1 conformers with ab initio MP2/6-311 + G(d, p) predicted parameters, adjusted r0 parameters have been obtained for both conformers. Comparisons are made with the parameters obtained for some other molecules containing the FCH2 group. The spectroscopic and theoretical results are compared to the corresponding properties for some similar molecules.     

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.     

Conformational and vibrational analysis of butyronitrile

IR and Raman spectra have been obtained for butyronitrile and are interpreted with the aid of normal coordinate calculations. This compound exists as trans and gauche conformers in the liquid and amorphous solid states, but only the gauche conformer is present in the crystalline solid. Simultaneous calculations for propionitrile and the two conformers of butyronitrile result in an average error of 4.7 cm⁻¹, or 0.42%. Vibrational assignments are made for all three molecules in terms of ordinary symmetry coordinates.     

Modelling conformations and IR spectra of p-tert-butylthiacalix[4]arene tetraester using DFT method

The infrared spectra of the cone, partial cone and 1,3-alternate conformers of p-tert-butyltetrakis(ethoxycarbonyl)methoxytetrathiacalix[4]arene (TEMT) have been recorded. The structural optimization and normal mode analysis were performed for this molecule on the basis of the density functional theory. These calculations gave the frequencies of vibrations and infrared intensities for the cone, partial cone (paco) and 1,3-alternate (1,3-alt) conformers. The energy difference between the paco and 1,3-alt conformers is 3.1 kcal/mol. The cone conformer is likely to be less stable compared to the paco and 1,3-alt conformers. The calculated in gas phase dipole moments 5.65, 3.33, and 0.02 D for the cone, paco and 1,3-alt conformers of the TEMT are in good accordance with theoretical values for the thiacalix[4]arene. Complete assignments were made for the experimental IR spectra of all conformers. The softness of sulphur atoms to nucleophilic and electrophilic attack is higher than softness of oxygen atoms of ester groups in the lower rim. The bands characteristic for each conformation were defined. IR spectroscopy combined with DFT computation provides unique detailed information about the structure of the technologically relevant materials, which could not be obtained before with any other technique.     

Vibrational spectra, conformations, ab initio calculations and vibrational assignments of 3-pentyn-2-ol

The infrared spectra of 3-pentyn-2-ol, CH₃CCCH(OH)CH₃, have been recorded as a vapour and liquid at ambient temperature, as a solid at 78 K in the 4000–50 cm⁻¹ range and isolated in an argon matrix at ca. 5 K. Infrared spectra of the solid phase at 78 K were obtained before and after annealing to temperatures of 120 and 130 K. The IR spectra of the solid were quite similar to that of the liquid.

Raman spectra of the liquid were recorded at room temperature and at various temperatures between 295 and 153 K. Spectra of an amorphous and annealed solid were recorded at 78 K. In the variable temperature Raman spectra, some bands changed in relative intensity and were interpreted in terms of conformational equilibria between the three possible conformers. Complete assignments were made for all the bands of the most stable conformer in which OH is oriented anti to C₁(a_Me). From various bands assigned to a second conformer in which OH is oriented anti to H_gem(a_H), the conformational enthalpy differences was found to be between 0.4 and 0.8 kJ mol⁻¹. The highest energy conformer with OH anti to C₃(a_C) was not detected.

Quantum-chemical calculations have been carried out at the MP2 and B3LYP levels with a variety of basis sets. Except for small basis set calculations for which the a_H conformer had slightly lower energy, all the calculations revealed that a_Me was the low energy conformer. The B3LYP/cc-pVTZ calculations suggested the a_Me conformer as more stable by 0.8 and 8.3 kJ mol⁻¹ relative to a_H an a_C, respectively. Vibrational wavenumbers and infrared and Raman band intensities for two of the three conformers are reported from B3LYP/cc-pVTZ calculations.     

Conformation and vibrational spectra of 1-bromo-1,5-hexadiyne (bromobipropargyl)

The IR spectra of 1-bromo-1,5-hexadiyne (bromobipropargyl) as a vapour, liquid and crystalline solid and in several solvents have been recorded. Raman spectra were obtained for the liquid (including polarization measurements) and the crystal.The data were interpreted in terms of two conformers, trans and gauche, in the vapour and liquid states and one, trans, in the crystal. The conclusion that the trans conformer was the one present in the crystal was based on several independent pieces of evidence. Vibrational assignments were made, supported by normal coordinate calculations.     

FTIR spectra of HSCH2CH2SH,CH3SCH2SH,and CH3SSCH3 in argon and nitrogen matrices

Matrix-isolated IR spectra of 1,2-ethanedithiol, (methylthio)methanethiol, and dimethyldisulfide were recorded from 400 to 4000 cm⁻¹ in argon and nitrogen matrices at 12 K. The appearances of new bands around the vibrations of the monomers provide evidence for the presence of dimer and multimers of 1,2-ethanedithiol and (methythio)methanethiol in argon and nitrogen matrices. The co-existence of two different dimers of (methylthio)methanethiol in nitrogen matrices is considered on the basis of the experimental data. The spectroscopic data confirm the presence of one gauche and one trans conformer for 1,2-ethanedithiol and at least three conformers for (methylthio)methanethiol, but only one gauche form for dimethyl disulfide in the matrices.