Theoretical and vibrational study of the conformation of 2-methoxy- 1,2-diphenylethanone.

The conformation and vibrational properties of 2-methoxy-1,2-diphenylethanone (MDPE) are investigated in the gas phase and in organic solvents. Ab initio calculations carried out at the B3LYP/6-31G(d) level demonstrate that three stable conformers having cisoid, skewed and transoid structures are present in the gas phase. In the gas phase, the conformers are separated by a low energy barrier and their relative energies do not differ by more than 7.2 kJ mol (-1) Like in crystalline MDPE 'Acta Crystallogr. Sect. C 44 (1988) 894', weak CH...O hydrogen bonds are present in the cisoid conformation. The IR and Raman spectra of solid MDPE are discussed. Several vibrational modes are split in organic solvents. A comparison between the theoretical data and the experimental dipole moments indicates that two conformers are present in solution, the population of the cisoid form increasing with the permittivity of the medium.     

Theoretical conformational analysis for neurotransmitters in the gas phase and in aqueous solution. Norepinephrine

The natural neurotransmitter (R)-norepinephrine takes the monocationic form in 93% abundance at the physiological tissue pH of 7.4. Ab initio and DFT/B3LYP calculations were performed for 12 protonated conformers of (R)-norepinephrine in the gas phase with geometry optimizations up to the MP2/6-311++G level, and with single-point calculations up to the QCISD(T) level at the HF/6-31G-optimized geometries. Four monohydrates were studied at the MP2/6-31G//HF/6-31G level. In the gas phase, the G1 conformer is the most stable with phenyl.NH(3)(+) gauche and HO(alc).NH(3)(+) gauche arrangements. A strained intramolecular hydrogen bond was found for conformers (G1 and T) with close NH(3)(+) and OH groups. Upon rotation of the NH(3)(+) group as a whole unit about the C(beta)-C(alpha) axis, a 3-fold potential was calculated with free energies for barriers of 3-12 kcal/mol at the HF/6-31G level. Only small deviations were found in MP2/6-311++G single-point calculations. A 2-fold potential was calculated for the phenyl rotation with free energies of 11-13 kcal/mol for the barriers at T = 310 K and p = 1 atm. A molecular mechanics docking study of (R)-norepinephrine in a model binding pocket of the beta-adrenergic receptor shows that the ligand takes a conformation close to the T(3) arrangement. The effect of aqueous solvation was considered by the free energy perturbation method implemented in Monte Carlo simulations. There are 4-5 strongly bound water molecules in hydrogen bonds to the conformers. Although hydration stabilizes mostly the G2 form with gauche phenyl.NH(3)(+) arrangement and a water-exposed NH(3)(+) group, the conformer population becomes T > G1 > G2, in agreement with the PMR spectroscopy measurements by Solmajer et al. (Z. Naturforsch. 1983, 38c, 758). Solvent effects reduce the free energies for barriers to 3-6 and 9-12 kcal/mol for rotations about the C(beta)-C(alpha) and the C(1)(ring)-C(beta) axes, respectively.     

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.     

Shape of 4S- and 4R-hydroxyproline in gas phase

The alpha-amino acids 4(S)-hydroxyproline and 4(R)-hydroxyproline have been studied under isolation conditions in gas phase using laser-ablation molecular-beam Fourier transform microwave spectroscopy. Two conformers of each molecule have been detected in the jet-cooled rotational spectrum. The most stable conformer in both molecules exhibits an intramolecular N...H-O hydrogen bond (configuration 1) between the hydrogen atom of the carboxylic group and the nitrogen atom. The second conformer is characterized by an intramolecular N-H...O=C hydrogen bond (configuration 2). The conformers of 4(R)-hydroxyproline adopt a C(gamma)-exo puckering, while those of 4(S)-hydroxyproline present a C(gamma)-endo ring conformation. These ring conformations, which show the same propensity observed in collagen-like peptides, are stabilized by additional intramolecular hydrogen bonds involving the 4-hydroxyl group, with the exception of the most stable form of 4(S)-hydroxyproline for which a n-pi interaction between the oxygen atom of the 4-hydroxyl group and the carboxyl group carbon seems to be established. A gauche effect could be also contributing to stabilize the observed conformers.     

Molecular structure and conformational composition of 2-chloro-1-phenylethanone, ClH2C-C(=O)Ph, obtained using gas-phase electron-diffraction data and results from theoretical calculations

The structure and conformation of 2-chloro-1-phenylethanone, ClH(2)C-C(=O)Ph (phenacyl chloride), have been determined by gas-phase electron diffraction (GED), augmented by results from ab initio molecular orbital calculations, employing the second-order M?ller-Plesset (MP2) level of theory and the 6-311+G(d) basis set. The molecules may exist as a mixture of different conformers with the C-Cl bond either syn (torsion angle phi = 0 degrees ) or gauche to the carbonyl bond. At 179 degrees C, the majority of the molecules (90 +/- 11%) have the gauche conformation (phi = 112(3) degrees). Torsion is also possible about the C-Ph single bond. Both experimental and theoretical data indicated, however, that the phenyl ring is coplanar or nearly coplanar with the carbonyl group. The results for the principal distances (r(g)) and angles (angle(alpha)) for the gauche conformer from a combined GED/ab initio study (with estimated 2sigma uncertainties) are the following: r(C-C)(phenyl) = 1.394(2) (average value) A, r(C(phenyl)-C(carbonyl)) = 1.484(5) A, r(C(carbonyl)-C(alkyl)) = 1.513(5) A, r(C-Cl) = 1.790(5) A, r(C=O) = 1.218(6) A, r(C-H)(phenyl) = 1.087(9) (average value) A, r(C-H)(alkyl) = 1.090(9) A (average value), angle C(phenyl)-C=O = 119.5(9) degrees, angle C(phenyl)-C(carbonyl)-C(alkyl) = 119.2(10) degrees, angle C-C-Cl = 109.8(12) degrees, angle C(2)-C(1)-C(carbonyl) = 122.8(15) degrees, angle C-C(alkyl)-H = 111.2 degrees (ab initio value).     

Structure and conformation of heterocycles. 13. conformational analysis of 2,3-DI(R)OXY-1,4-dioxanes: anomeric and gauche effects

A series of $\text{trans}$- and $\text{cis}$-2,3-di R)oxy-1,4-dIoxanes (R = Me,Ph, Ac) and some 2,5-disubstituted analogis were prepared and analysed by various NMR techniques. The $\text{trans}$ isomers occur in more than 96% as diaxial conformers. Molecular mechanics calculations largely confirm these findings, which are interpreted -in terms of combined anomeric and gauche effects.     

The "azido gauche effect"-implications for the conformation of azidoprolines

The "azido gauche effect" was examined both experimentally and theoretically and was found to determine the conformation of, for example, (4R)- and (4S)-azidoproline (Azp) derivatives. For (4R)Azp derivatives, the azido gauche effect induces a preferred C(4)-exo conformation of the pyrrolidine ring, which leads to stabilization of the s-trans amide conformer of, e.g., Ac-(4R)Azp-OCH(3) (5R) via an n-->pi interaction between the nonbonding electrons of the oxygen of the acetyl group and the carbonyl group of the ester. For (4S)Azp derivatives, the azido gauche effect results in a C(4)-endo conformation of the pyrrolidine ring that does not allow for this stabilizing n-->pi interaction of the s-trans conformer. Consequently, a significantly higher s-trans:s-cis amide conformer ratio is observed for (4R)Azp compared to (4S)Azp derivatives (e.g., 6.1:1 versus 2.6:1 in D(2)O for Ac-(4R)Azp-OCH(3) (5R) compared to Ac-(4S)Azp-OCH(3) (5S)). These conformational preferences are reflected in the higher tendency of (4S)Azp-containing peptides to form cyclic peptides with all-cis amide bonds compared to (4R)Azp derivatives. Ab initio calculations demonstrate that the strength of the azido gauche effect is comparable to that of the well-known "fluorine gauche effect". For azidoethane derivatives N(3)-CH(2)CH(2)-X (X = N(3), NHCOH, NHAc, or N(CH(3))Ac), the ab initio calculations revealed energy differences of 5-13 kJ mol(-)(1) between the anti and gauche conformations in favor of the gauche conformer. Calculations were also performed for the (4R)Azp and (4S)Azp derivatives 5R and 5S, supporting the experimentally observed data.     

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.     

Conformation analysis of d‐glucaric acid in deuterium oxide by NMR based on its JHH and JCH coupling constants

d ‐Glucaric acid (GA) is an aldaric acid and consists of an asymmetric acyclic sugar backbone with a carboxyl group positioned at either end of its structure (i.e., the C1 and C6 positions). The purpose of this study was to conduct a conformation analysis of flexible GA as a solution in deuterium oxide by NMR spectroscopy, based on J‐resolved conformation analysis using proton–proton (³J_HH) and proton–carbon (²J_CH and ³J_CH) coupling constants, as well as nuclear overhauser effect spectroscopy (NOESY). The ²J_CH and ³J_CH coupling constants were measured using the J‐resolved heteronuclear multiple bond correlation (HMBC) NMR technique. NOESY correlation experiments indicated that H2 and H5 were in close proximity, despite the fact that these protons were separated by too large distance in the fully extended form of the chain structure to provide a NOESY correlation. The validities of the three possible conformers along the three different bonds (i.e., C2? C3, C3? C4, and C4? C5) were evaluated sequentially based on the J‐coupling values and the NOESY correlations. The results of these analyses suggested that there were three dominant conformers of GA, including conformer 1 , which was H2H3:gauche, H3H4:anti, and H4H5:gauche; conformer 2 , which was H2H3:gauche, H3H4:anti, and H4H5:anti; and conformer 3 , which was H2H3:gauche, H3H4: gauche, and H4H5:anti. These results also suggested that all three of these conformers exist in equilibrium with each other. Lastly, the results of the current study suggested that the conformational structures of GA in solution were ‘bent’ rather than being fully extended. Copyright © 2016 John Wiley & Sons, Ltd.     

Conformational space of the Pseudosaccharin allyl ether 3-(allyloxy)-1,2-benzisothiazole 1,1-dioxide in gas phase and in rare gas matrices

In this work, the conformational space of the pseudosaccharyl ether 3-(allyloxy)-1,2-benzisothiazole 1,1-dioxide (ABID) has been studied by means of infrared spectroscopy and density functional theory (DFT) calculations. Five different low energy conformers (TSk, TC, GSk, GSk' and GC, with relative energies of 0.00, 1.97, 2.00, 3.82 and 6.02 kJ mol(-1), respectively) were found on the DFT(B3LYP)/6-311++G(3df,3pd) potential energy surface of the molecule, all of them differing in the conformation of the allyl substituent. According to the calculations, in the gaseous phase all conformers are significantly populated (TSk:TC:GSk:GSk':GC = 47%:16%:18%:12%:7%, at 350 K). In the cryogenic matrices, however, only the TSk and TC conformers exist due to isomerization from the higher energy gauche forms to the most stable trans isomers during deposition of the matrix (conformational cooling). The observed conformational cooling is in consonance with the low calculated energy barriers for the GSk --> TSk, GSk' --> TSk and GC --> TC isomerization processes. Results from annealing experiments in krypton matrix doubtlessly show that in this matrix the order of stability of the TSk and TC conformers is reversed, with the more planar TC form becoming the most stable conformer.     

Conformational Study of 8—C—glucosyl—prunetin by Dynamic NMR Spectroscopy

By means of variable temperature NMR spectra,conformation of 8-C-glucosyl prunetin, isolated from the leaves of Dalbergia hainanensis (Leguminosae), was studied. The restricted rotation around the C(sp^3)-C(sp^2) bond in the C-glucosides isoflavonoid results in two main conformers (syn and anti). With the help of MM calculation, the preferred conformation A has H-1″ gauche to the 7-OCH3. The barrier to rotation was 18.1 kcal/mol. This result agrees with the calculated value 16.2 kcal/mol of free energy of activation for the interconversion between the conformers.     

Resonant two-photon ionization and ab initio conformational analysis of haloethyl benzenes (PhCH(2)CH(2)X,X=Cl,F)

The S(1) <-- S(0) transitions of the gaseous (2-fluoroethyl)-benzene (FEB) and (2-chloroethyl)-benzene (CEB) have been investigated using a combination of two-color resonant two-photon ionization and UV-UV hole burning spectroscopy. Both anti and gauche conformers have been identified on the basis of rotational band contour analysis supported by ab initio calculations on the ground and electronically excited states. The gauche origin band of FEB at 37,673 cm(-1) is redshifted 50 cm(-1) relative to the corresponding anti origin, while CEB origin bands overlap at 37,646 cm(-1). Relative conformational stability and populations in the jet have been estimated for both molecules, based on the intensity ratio of S(1) <-- S(0) band origin transitions. These are compared with a range of related molecules with the structural motif PhCH(2)CH(2)X (X=CH(3),CH(2)CH(3),NH(2),OH,COOH,CCH,CN). Theory and experimental results for FEB and CEB show repulsive interactions between the halogen substituents and the pi cloud of the phenyl rings destabilizing the gauche conformers, but the preference for the anti conformers is relatively modest. The gauche conformer origins show very different hybrid character: FEB is largely b type, while CEB is an ac hybrid in keeping with theoretically computed TM "rotations" (theta(elec)) of -7 degrees and -56 degrees , respectively. This difference is attributed largely to rotation of the side chain in opposite directions about the C(1)C(alpha) bond. Spectra of FEB(H(2)O) and CEB(H(2)O) single water clusters show evidence of an anti conformation in the host molecule.     

Pressure-induced structural transition in n-pentane: a Raman study

Pressure-induced Raman spectroscopy studies on n-pentane have been carried out up to 17 GPa at ambient temperature. n-Pentane undergoes a liquid-solid transition around 3.0 GPa and a solid-solid transition around 12.3 GPa. The intensity ratio of the Raman modes related to all-trans conformation (1130 cm-1 and 2850 cm-1) to that of gauche conformation (1090 cm-1 and 2922 cm-1) suggests an increase in the gauche population conformers above 12.3 GPa. This is accompanied with broadening of Raman modes above 12.3 GPa. The high-pressure phase of n-pentane above 12.3 GPa is a disordered phase where the carbon chains are kinked. The pressure-induced order-disorder phase transition is different from the behavior of higher hydrocarbon like n-heptane.     

采用动态NMR对8-C-glucosyl-prunetin构象研究

采用动态NMR方法,对从海南黄檀中分得的8-C-glucosyl-prunetin及其它7位 上羟基烷基化了的8－C苷异黄酮的构象进行了研究。结果表明,在8－C苷异黄酮中 ,当7位上羟基烷基化了时,由于1"-C(sp~3)-8C(sp~2)单键旋转受阻,产生两种构 象异构体。同时,借助分子力场（MM）计算方法,确定了8-C-glucosyl-prunetin 两种构象异构栓中的优势构象,即为1"-H与7－OCH_3位于同侧。由低能量构象转化 为高能量构象所需活化能为75.66 kJ/mol。这一结果与动态NMR实验计算的71. 48kJ/mol活化自由能数值相符。     

Conformational study of tyramine and its water clusters by laser spectroscopy

Tyramine and its monohydrated clusters have been investigated by several laser spectroscopic methods in a pulsed molecular beam. The conformational structures and their effects on hydration have been revealed by resonant two-photon ionization (R2PI), UV-UV ion-dip, and ab initio calculations. UV rotational band contour spectra of the S1 <-- S0 origin bands enabled determination of ethylamine side chain conformations for all seven stable conformers of tyramine. When coexpanding tyramine with a mixture of Ar and water vapor, we have found two kinds of conformational effects on hydration. One is sensitive to conformation of the ethylamine chain and the other to the orientation of the OH group, particularly in the most stable pair of conformers. UV-UV ion-dip spectra detected seven stable conformers of the monohydrated clusters, of which hydrogen-bonding structures, spectral shifts, and origin band intensity distributions are well explained by considering tyramine as a hybrid of phenylethylamine (PEA) and phenol. Monohydration of the most stable gauche conformer pair (cis and trans) of tyramine leads to more detailed conformational assignments regarding the orientation of the phenolic OH group. Cyclic hydrogen-bonding linkage formed in the monohydrated cluster pair is found to be sensitive to the orientation of the phenolic OH group. One of the cluster pair, in which tyramine has the gauche-cis conformation, is more stabilized by the cyclic hydrogen bonding and its origin band intensity becomes stronger than that of the other.     

Theoretical study and X-ray determination of bianthronyl [corrected] : long C-C bond length and preferred gauche conformation

Five X-ray crystallographic structures of bianthronyl (1, 2b-5b) revealed the presence of long central C(sp3)-C(sp3) bonds (> or =1.60 A) and mostly gauche conformation. DFT calculations were carried out to study the structural features of bianthronyl and related model molecules [corrected]. Our B3LYP/6-31G gas-phase calculation results suggest that steric effect plays a role in causing the long C-C sigma bond length (>1.60 A), nonplanarity of the anthracenone moiety (>20 degrees ), and preferred gauche conformation. However, when the gauche preference is weak, environmental effects such as solvation and packing forces can reverse it. As the degree of nonplanarity of the anthracenone moiety is consistently larger in the anti conformation than in the gauche and the ease of achieving nonplanarity is determined by flexibility of the central six-membered rings directly connected to the C(sp3)-C(sp3) bond, one way to control the structure and anti-gauche energy difference of closely related compounds is by changing the clamping group (Z) in the central six-membered ring.     

Conformational analysis of dimethylmethylphosphonate

The results of a CNDO/2 conformation analysis on dimethylmethylphosphonate are reported. Six stable conformers were found; their relative stabilities can be understood in terms of steric hindrance and gauche effect. Calculated barriers to internal rotation around P—O and O—C bonds are tabulated.     

Ab initio studies on polymers. VI. Torsional potential in regular polyethylene chains

Ab initio crystal orbital calculations have been performed on regular polyethylene chains applying basis sets of minimal and double-zeta quality. Relative stabilities of periodic all-trans, all-gauche, and alternating trans–gauche conformers have been evaluated, including extensive geometry optimization. Potential curves for a simultaneous rotation around C? C single bonds from the all-trans to the all-gauche conformation have been computed applying the rigid-rotor approximation, the flexible-rotor approximation, and an additional reoptimization of C? C distances. A rigid-rotor potential curve from the all-trans to the alternating trans-gauche conformation has been computed as well. Results obtained are compared with ab initio calculations on butane and pentane and with semiempirical and empirical force-field studies on polyethylene.     

Investigation of the conformation of epoxychalcones by IR spectroscopy

Molecules of ketone oxides in the solid phase exist exclusively in the gauche form, whereas compounds of the open type form a mixture of cis and gauche conformers in solution. The effect of temperature on the conformational equilibrium was investigated.     

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.