Structural,torsional, vibrational and response electric properties of 2,2′-bitellurophene rotamers. An ab initio and density functional theory investigation

The molecular structure, conformational behaviour, vibrational spectra and electronic (hyper)polarizabilities of tellurophene and 2,2′-bitellurophene rotamers were determined in gas by correlated ab initio and density functional theory calculations. The torsional potential for the rotation around the C²–C^2′ inter-ring bond shows two minima corresponding to anti-gauche and syn-gauche structures and three maxima to planar anti and syn forms and to perpendicular conformation. The potential energy curve is rather flat over the entire 0°–180° twisting range and free rotation cannot be excluded. The IR and Raman spectra of the gauche structures are rather similar to each other, vibrational transitions being scarcely helpful for an unambiguous identification of the rotamers. The dipole moment and the first-order hyperpolarizability increase on passing from the anti-gauche to the syn-gauche conformation by a factor of five and four, respectively. The second harmonic generation nonlinear optical process can be useful to identify the 2,2′-bitellurophene rotamers. On the other hand, the electronic polarizabilities of these structures are much more closer to each other, being predicted to be within 2–13 %.     

A suggested revised conformation of methylthionitrite as seen by its spectra and preliminary ab initio calculations

A proof has recently been given that gaseous methylthionitrite, CH₃SNO, occurs exclusively (or mainly) in its anti conformation [1]. The present paper claims that existing spectral evidence and ab initio calculations now performed suggest that gaseous methylthionitrite is mainly the syn conformer, the extra stability being of the order 1–2 kcal mol^?1. Methyl group rotation in the syn conformer is hindered by a three-fold barrier of height 689 cm^?1 while the methyl group rotation in the anti conformer is hardly hindered. The syn/anti energy difference and the barriers hindering methyl group rotation closely parallel the corresponding measured quantities in methylnitrite, CH₃ONO.     

Ab initio calculation of the potential functions for internal rotation around the CS bonds in simple ethene thiols

Ab initio calculations with complete geometry optimisation have been used to study internal rotation in compounds of the type XCH = CHSH, X = CN, H, CH₃ and F, with X located trans to the sulphur atom. Potential functions for the CS torsion have been obtained for each case and it has been established that the dominant framework changes accompanying internal rotation in these molecules involve the CCS angle and CS bond length. Furthermore, it has been shown that the nature of the substituent X significantly affects the molecular conformation of the SH group. The observed trends are discussed in terms of a simple model.     

Matrix-isolation infrared spectra of 2-, 3- and 4-pyridinecarboxaldehyde before and after UV irradiation

Three structural isomers of pyridinecarboxaldehydes (2-, 3- and 4-pyridinecarboxaldehyde) have been investigated in detail with matrix-isolation infrared spectroscopy in the 3000–600 cm⁻¹ region, combined with the UV photo-excitation and density-functional theory (DFT) calculations. Two rotamers (anti and syn) for 2- and 3-pyridinecarboxaldehyde (2- and 3-PCA, respectively) and one rotamer for 4-pyridinecarboxaldehyde (4-PCA) were identified upon photo-excitation. Most of the observed bands of each rotamer have been assigned. Both the infrared data and the results of the DFT calculations agree that the syn rotamer is a less stable isomer for 2- and 3-PCA. Formation of an intramolecular CH⋯N hydrogen bond in the anti rotamer of 2-PCA results in a shortening of the aldehyde CH bond length. The CO bond length is shortened in the syn rotamer due to the repulsion between the N and aldehyde O atoms. With 2-PCA, both photoinduced rotational isomerism and photolysis were observed upon UV irradiation.     

Stereoelectronic Aspects of the Anomeric Effect in Fluoromethylamine

High-level ab initio calculations have been made for fluoromethylamine to study structural and energetic effects of the relative orientation of the N lone pair to the C? F bond. The anti-conformer (N lone pair anti-planar to the C? F bond) corresponds to the global energy minimum. It has the longest C? F distance, the shortest C? N distance, and is 7.5 kcal·mol^?1 more stable than the related perpendicular conformation (lone pair perpendicular to the C? F bond). The syn-conformation also shows hallmarks of the anomeric effect: long C? F bond, short C? N bond, and energetic stability when allowance is made for the two pairs of eclipsed hydrogens. The transition state for N inversion is close to the syn-structure; rotation about the C? N bond is strongly coupled with this inversion process. Small bond distance changes of ca. 0.02 Å between parallel and perpendicular conformations are associated with dissociation energy differences of ca. 30 kcal·mol^?1. Various criteria for assessing the strength of the anomeric effect are discussed.     

Infrared spectra of p-, m- and o-fluorobenzaldehyde in low temperature argon matrices

Three structural isomers of fluorobenzaldehyde (p-, m- and o-forms) have been investigated in detail with matrix-isolation infrared spectroscopy, in the 700-3000 cm⁻¹ region, combined with the UV photoexcitation and the density functional calculations. Two rotamers (syn and anti) were identified for m- and o-fluorobenzaldehyde upon the photoexcitation and most of the bands of each rotamer were assigned. It is shown that the formation of the intramolecular C-H?F hydrogen bond for the anti rotamer of o-FB results in the shortening of the aldehyde C-H bond length and that the C-F and/or CO bond lengths are shortened for the syn rotamer of o-FB presumably due to the repulsion between the aldehyde O and F atoms.     

Microwave spectrum,conformational preference,intramolecular hydrogen bond,barrier to internal rotation,dipole moment,and centrifugal distortion of 1-fluoro-2-propanol

The microwave spectra of 1-fluoro-2-propanol, CH ₃CH(OH)CH ₂F, and one deuterated species, CH₃,CH(OD)CH₂F, have been investigated in the 18–30 GHz spectral region. Only one rotamer with an intramolecular hydrogen bond formed between the fluorine atom and the hydroxyl group was assigned. This conformation is also characterized by having the C-F bond approximately anti to the methyl group. The FCCO dihedral angle is 59 ± 2° and the HOCC dihedral angle is 58 ± 3°. Further conformations, if they exist, are at least 0.75 kcal mol^?1 less stable. Five vibrationally excited states belonging to four different normal modes were assigned and their fundamental frequencies determined. The barrier to internal rotation of the methyl group was found to be 2796 ± 50 cal mol^?1. The dipole moment is μ_a = 0.510 ± 0.009 D, μ_b = 1.496 t 0.026 D, μ_c = 0.298 ± 0.014 D, and μ_tot = 1.608 ± 0.030 D. Extensive centrifugal distortion analyses were carried out for the ground and the first excited state of the heavy-atom torsional mode and accurate values were determined for all quartic and two sextic coefficients.     

Structural relaxations and energy effects of intramolecular motions inN,N-dimethylnitramine: A theoretical study

The equilibrium geometry of theN,N-dimethylnitramine molecule and changes in the energy and structural parameters due to the internal rotation of the nitro group and the inversion of the N atom in the amino fragment were calculated by the restricted Hartree-Fock (RHF) method and at the second-order Møller-Plesset (MP2) level of perturbation theory with inclusion of electron correlation using the 6–31 G^* and 6–31 G^** basis sets. The one-dimensional potential functions of these motions calculated at the RHF/6–31 G^* level were approximated by a truncated Fourier and power series, respectively. The frequencies of torsional and inversion transitions were determined by solving direct vibrational problems for a non-rigid model,i.e., taking into account the molecular geometry relaxation. The equilibrium conformation of the molecular skeleton ofN,N-dimethylnitramine is nonplanar. Transition states of the internal rotation of the nitro group and inversion of the amine N atom are characterized by pronounced concerted changes in its bond angles and the length of the N?N bond. In the MP2/6–31 G^* approximation, the height of the barrier to internal rotation calculated taking into account the difference in the zero-point vibrational energies is equal to 9.7 kcal mol^?1. Inversion in the amino fragment is accompanied by a relatively small energy change at the barrier height of ?1.0 kcal mol^?1 calculated in the same approximation.     

Conformational dynamics of polypeptides and proteins in the dihedral angle space and in the cartesian coordinate space: Normal mode analysis of deca-alanine

Effects of different treatments of the degrees of freedom of bond length stretching and bond angle bending in computational analysis of conformational dynamics of proteins and polypeptides are assessed. More specifically, the normal mode analysis of conformational dynamics of α-helix of deca-alanine has been carried out both in the dihedral angle space (DAS) and in the Cartesian coordinate space (CCS). Almost perfect one-to-one correspondence has been found between normal modes in the CCS with frequencies less than 128 cm^?1 and those in the DAS with frequencies less than 164 cm^?1. Patterns of atomic displacements in the corresponding modes are very similar. This indicates that the effects of fixing degrees of freedom of bond length stretching and bond angle bending on the very-low-frequency normal modes in the CCS with frequencies less than 128 cm^?1 are almost solely to increase the frequencies by about 20%. The conclusion indicates that the different treatment of these degree does not lead to qualitatively different results as long as low-frequency motions are concerned. Based on the results of calculation, mechanical property of the α-helix of deca-alanine is discussed.     

Quantum Mechanical Study of the Syn and Anti Conformations of Solvated Cyclic GMP

Self-consistent Reaction Field (SCRF) computational methods have been applied to guanosine 3:5-cyclic monophosphate (cGMP) to determine the geometries and energetics of the syn and anti conformations of this cyclic nucleotide in aqueous solution. The syn conformation of cGMP has been predicted to be more stable in the gas phase due to an internal hydrogen bond. The syn conformation is observed in the crystal structure of the sodium tetrahydrate salt, although a bridging water molecule is present in lieu of the internal hydrogen bond. In the gas phase, we find from Hartree–Fock/6-31+G(d) optimizations that the syn conformation is more stable than the anti by about 4 kcal/mol. However, we report here that the anti conformation is more stable in aqueous solution, according to estimates based upon results from both the Onsager model and the Isodensity Polarized Continuum Method (IPCM). Our best estimate from single-point IPCM B3LYP/6-31+G(d) calculations has the anti conformation 19 kcal/mol lower in energy. For comparison purposes, we also present SCRF results for syn and anti adenosine 3:5-cyclic monophosphate (cAMP). For cAMP, we estimate the anti conformation to be more stable than the syn by about 6 kcal/mol. We suggest that the relative stability of the anti conformation of cGMP be considered in studies, such as, enzyme docking.     

Microwave spectrum,conformational preference,barrier to internal rotation,and centrifugal distortion of 1-amino-2-propanol

The microwave spectrum of CH₃CH(OH)CH₂NH₂ has been investigated in the 26.5–39.7 GHz region. One rotamer with an intramolecular hydrogen bond formed between hydroxyl and ammo groups was assigned. This conformation is also characterized by having the methyl group anti to the amino group. Other forms, if they exist, must be at least 1 kcal mole^?1 less stable. Four vibrationally excited states belonging to three different normal modes were assigned and the barrier to internal rotation of the methyl group was found to be 3173 ± 100 cal mole^?1.     

Vibrational spectra,methyl torsional potential functions,internal rotational potential functions,and conformational properties of ethyl vinyl ether

The vibrational spectra of ethyl vinyl ether in both the fluid and solid states have been recorded from 20 to 3500 cm^?1. The 33 fundamental modes of vibration have been assigned. Three rotational isomers have been observed and their structures have been determined. The most stable conformer, s-cis/s-trans, is planar and of C_s symmetry. The two less stable rotamers, skew/s-trans and skew/gauche, are non-planar and of C_i molecular symmetry. The barrier to internal rotation of the methyl rotor has been determined for each conformation; these barriers are 3.43 kcal mol^?1 (s-cis/s-trans), 3.35 kcal mol^?1 (skew/s-trans) and 3.19 kcal mol^?1 (skew/gauche). A potential function for each of the two asymmetric internal rotations has been calculated and barriers to conformer interconversion have been determined. From the asymmetric potential function calculations, ΔH, the enthalpy difference between the conformers, has been determined. The s-cis/s-trans conformer is 1.87 kcal mol^?1 more stable than the skew/s-trans conformer; the skew/s-trans conformer is more stable than the skew/gauche conformer by 1.10 kcal mol^?1. The energetics of conformer interconversion and methyl internal rotation have been described in terms of molecular geometry and non-bonded interactions. These results are compared to those found in other alkyl vinyl and dialkyl ethers.     

Microwave spectrum,conformation, dipole moment and centrifugal distortion of glyoxylic acid

Microwave spectra of CHO-COOH and CHO-COOD are reported. The molecule has a planar equilibrium conformation with the two carbonyl groups trans to each other. A weak five-member intramolecular hydrogen bond is formed between the hydroxyl proton of the carboxyl group and the oxygen atom of the carbonyl group thus stabilizing the trans planar form. Other conformations having a statistical weight of 1 (cis and trans) are at least 1.3 kcal mol^?1 less stable, and rotamers with a statistical weight of 2 (e.g., gauche and skew) have at least 1.7 kcal mol^?1 higher energy. Four vibrationally excited states of CHO-COOH have been analyzed and relative intensity measurements yielded 167 ± 12 cm^?1 for the C-C torsional mode and 288 ± 26 cm^?1 for the lowest in-plane bending mode. The dipole moment was determined to be μ_a = 1.85 ± 0.03 D, μ_b = 0.20 ± 0.10 D, and μ_tot = 1.86 ± 0.04 D. A seven-parameter centrifugal distortion analysis has been carried out for the ground vibrational state of CHO-COOD and for the ground and three vibrationally excited states of CHO-COOH.     

The synthesis and conformational behaviour of 2,11-dithia[3,3]metacyclophanes with internal phenyl substituents.

The synthesis of syn- and anti-9-methyl-18-phenyl- and anti-9, 18-diphenyl 2, 11 dithia[3,3]metacyclophanes is described, together with their variable temperature ¹Hmr spectra. Only partial rotation of the phenyl substituents (gD^≠_c ?50 kJ. mol^?1) is believed to occur.     

Spectra and structure of organophosphorus compounds: XVII. Infrared and Raman spectra. vibrational assignment and barriers to internal rotation for t-butylphosphine

The infrared spectra of gaseous and solid tertiary-butylphosphine, [(CH₃)₃CPH₂], have been recorded from 50 cm^?1 to 3500 cm^?1. The Raman spectra of gaseous, liquid and solid (CH₃)₃CPH₂ have been recorded from 10 to 3500 cm^?1. A vibrational assignment of the 42 normal modes has been made. A harmonic approximation of the methyl torsional barrier from observed transitions in the solid state gave a result of 4.22 kcal mol^?1 and 3.81 kcal mol^?1 in the gaseous state. Hot band transitions for the phosphino torsional mode have been observed. The potential function for internal rotation about the C-P bond has been calculated. The two potential constants were determined to be: V₃ = 2.79 ± 0.01 kcal mol^?1 and V₆ = 0.07 ± 0.01 kcal mol^?1.     

Microwave spectrum of propionyl chloride

The microwave spectrum of propionyl chloride has been investigated in the region 18.0–40.0 GHz, and transitions due to a cis conformer have been assigned. This form has a heavy atom planar configuration and the methyl group and the carbonyl oxygen atom are cis to each other. Using the substitution structures of propionic acid and acetyl chloride as molecular models for the propionyl chloride molecule, good agreement is found between observed and calculateò effective rotational constants. For the ³⁵Cl species satellite spectra assigned to the first four excited states of the C-C torsional mode have been observed together with the first excited state of the methyl torsional mode. The ground state spectrum has also been assigned for the ³⁷Cl species. Relative intensity measurements yielded the lowest C-C torsional vibration frequency of 86 ± 10 cm^?1. The CH₃ internal rotation frequency was found to be 197 cm^?1. Nuclear quadrupole coupling constants were determined for the ground state of the ³⁵Cl and ³⁷Cl species. From observed A-E splittings of ^bQ-branch transitions of the first excited state of the methyl torsional mode a barrier to internal rotation was estimated to be V₃ = 2480 ± 40 cal mol^?1 (867 ± 14 cm^?1).     

Spectroscopic studies of 1,4-dibromobutyne-2

Infrared spectra of 1,4-dibromobutyne-2 have been recorded over the 4000-200 cm^?1 region in the vapour, liquid, amorphous and crystalline states Raman spectra were extended to ca. 20 cm^?1 in the same states of aggregation, except for the non-recorded vapour phase spectrum. The temperature was varied between ?190 and 160 °C, and the pressure up to 10 kbar.A high proportion of the molecules exhibited free, internal rotation in the vapour and liquid phases, but to a smaller extent in the amorphous state at ?190 °C. For those molecules not being excited beyond the potential barrier, an unsymmetric conformation was preferred, whereas in the crystalline state the molecules possessed the anti conformation (C_2h) both at low temperature and at high pressure at ambient temperature.A vibrational analysis based upon force field calculations was carried out and the mean amplitudes of vibration computed. The data have been related to preliminary results from dipole moment and electron diffraction investigations.     

A conformational analysis of the six isomers of bipyridinium dication

The conformational analysis of the bipyridinium dications have been investigated using ab initio STO-3G calculations in which the inter-ring bond length was optimized at each torsional angle. The variation of the inter-ring separation has been rationalized using a heuristic valence bond model (which is electrostatic in nature) and which was suggested by the molecular orbital calculations. Furthermore, all six isomers show a double potential minima at the optimium torsional angles of ～ 50° and ～ 130° respectively. Moreover, all barrier heights are calculated to be less than 8 kJ mol^?1, thereby suggesting that the barrier heights are not large enough to prevent rapid interconversion between different rotamers.     

Change of the molecular surface and volume during internal rotation and its effect on conformational equilibrium in solution

Conformational dependence of the molecular surface S and molecular volume V for hexane and 1,1,2-trichloroethane during rotation around a central bond in the molecules have been calculated. A model of overlapping spheres is used, the size of the spheres being determined by Van der Waals radii of individual atoms. Plots of S and V against torsional angle φ are compared with the potential of internal rotation of both molecules E(φ). The calculated molecular surfaces and volumes of the two molecules for the most stable conformers mutually differ by several percent as experimental results also indicate. We also show that the differences in S and V between individual conformers always affect conformational equilibrium in solution even if solvent-solute interaction energies are not explicitly considered. As a consequence of the mentioned volume changes during internal rotation in a molecule, the conformational energies for hydrocarbons in the condensed and gaseous phases can differ by as much as several kJ mol^?1.     

A microwave and quantum chemical study of allyltrifluorosilane

The structural and conformational properties of allytrifluorsilane, H₂CCH-CH₂-SiF₃, have been explored by microwave (MW) spectroscopy and high-level ab initio and density functional theory quantum chemical calculations. The microwave spectrum was investigated in the 18-62 GHz spectral regions. The a-type R-branch transitions of one conformer were assigned for the ground as well as for 10 vibrationally excited states. The CC-C-Si chain of atoms in this rotamer takes an anti-clinal (‘skew’) conformation, with a dihedral angle calculated to be 111.6° from the syn-periplanar (0°) conformation. The question whether a CC-C-Si syn-periplanar conformer exists as a high-energy form in the gas phase remains open. In most of the quantum chemical calculations this conformation is predicted to be a transition state. However, in the most advanced calculations (B3LYP/aug-cc-pVTZ level of theory) the syn-periplanar conformer is predicted to be a stable rotamer that is calculated to be 6.5 kJ/mol higher in energy than the anti-clinal form. Since there is no indication in the MW spectrum for the presence of high-energy form(s), it is concluded that the anti-clinal conformer is at least 4 kJ/mol more stable than any other hypothetical rotamer.