Conformational stability and vibrations of aminopropylsilanol molecule

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

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

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

Monte Carlo study of the aqueous hydration of dimethylphosphate conformations

Monte Carlo computer simulations were performed on dilute aqueous solutions of the dimethylphosphate anion and the sodium dimethylphosphate ion pair, with the two phosphodiester torsional angles in the gauche–gauche, gauche–trans, and trans–trans conformations. The structural and energetic aspects of the aqueous hydration of each molecule were analyzed in terms of quasi component distribution functions based on the proximity criterion and partitioned into ionic, hydrophilic, and hydrophobic contributions to facilitate an understanding of the hydration pattern and conformational trends in these multifunctional solutes. Special attention was also paid to methodological issues affecting hydration, such as statistical uncertainty in the determined hydration indices, choice of partial atomic charges for the solute atoms, and solute–water interaction potentials adopted in the simulations. The results showed that gauche–trans and gauche–gauche forms are equally favorable for the dimethylphosphate anion with the trans extended form destabilized by hydration. The sodium dimethylphosphate ion pair hydration energetically favors the trans–trans conformation.     

Gas-phase Raman spectra and the potential energy function for the internal rotation of 1,3-butadiene and its isotopologues

The gas-phase Raman spectra of 1,3-butadiene and its 2,3-d(2), 1,1,4,4-d(4), and -d(6) isotopologues have been recorded with high sensitivity in the region below 350 cm(-1) in order to investigate the internal rotation (torsional) vibration. Based on more accurate structural information, the internal rotor constants F(n) were calculated as a function of rotation angle (?). The data for all the isotopologues were then fit using a one-dimensional potential energy function of the form V = (1)/(2)∑V(n)(1 - cos ?). Initial V(n) values were based on those generated from theoretical calculations. The agreement between observed and calculated frequencies is very good, although bands not taken into account were present in the spectra. The energy difference between the trans and gauche forms was determined to be about 1030 cm(-1) (2.94 kcal/mol), and the barrier between the two equivalent gauche forms was determined to be about 180 cm(-1) (0.51 kcal/mol), which agrees well with high-level ab initio calculations. An alternative set of assignments also fits the data quite well for all of the isotopologues. For this model, the energy difference between the trans and gauche forms is about 1080 cm(-1) (3.09 kcal/mol), and the barrier between gauche forms is about 405 cm(-1) (1.16 kcal/mol).     

NMR Studies of Solvent Effect on Internal Rotation in Some Non-Symmetrical 1,2-Disubstituted Ethanes

The A₂B₂ system of PMR spectra of 3-bromopropionic acid, 3-chloropropionic acid, 3-bromopropionitrile, and 3-chloropropionitrile exhibit appreciable solvent effect at room temperature. NMR spectroscopic parameters of A₂B₂ spectrum as well as physical parameters related to internal rotation, i. e. the highest energy barrier and the energy difference between rotamers, were determined for these compounds in the medium of various solvents. It was found that in the case of 3-bromopropionic acid, the trans rotamer is more stable than the gauche rotamers, and the energy difference decreases with increasing dielectric constant of solvent. While in the case of 3-bromopropionitrile, the gauche rotamers were found to be more stable than the trans rotamer and the energy difference increases with increasing dielectric constant of solvent. In the remaining two compounds, 3-chloropropionic acid and 3-chloropropionitrile, both trans and gauche rotamers are equally stable in a solvent of low dielectric constant, however in a solvent of higher dielectric constant, the gauche rotamers become more stable than the trans rotamer and the energy difference becomes more pronounced with increasing dielectric constant of solvent.     

The preference for anti over Gauche migration in the Baeyer-Villiger reaction

Explanations for stereoselectivity in the Baeyer-Villiger reaction have relied on the assumption that the antiperiplanar (app) group migrates. However, the magnitude of the preference for app-migration over gauche migration is unknown. To investigate this, the energy differences between the two were estimated from ab initio calculations. App-migration was found to be the preferred pathway since no transition structure could be located for gauche migration. Barriers for gauche migration were estimated by performing constrained optimizations. App-migration was found to be strongly favored with a barrier that is at least 3.8 kcal/mol and as much as 58.0 kcal/mol lower in energy than the gauche migration barrier.     

NMR investigations of the static and dynamic structures of bisphosphonates on human bone: a molecular model

We report the results of an investigation of the binding of a series of bisphosphonate drugs to human bone using 2H, 13C, 15N, and 31P nuclear magnetic resonance spectroscopy. The 31P NMR results show that the bisphosphonate groups bind irrotationally to bone, displacing orthophosphate from the bone mineral matrix. Binding of pamidronate is well described by a Langmuir-like isotherm, from which we deduce an approximately 30-38 A2 surface area per pamidronate molecule and a deltaG = -4.3 kcal mol(-1). TEDOR of [13C3, 15N] pamidronate on bone shows that the bisphosphonate binds in a gauche [N-C(1)] conformation. The results of 31P as well as 15N shift and cross-polarization measurements indicate that risedronate binds weakly, since it has a primarily neutral pyridine side chain, whereas zoledronate (with an imidazole ring) binds more strongly, since the ring is partially protonated. The results of 2H NMR measurements of side-chain 2H-labeled pamidronate, alendronate, zoledronate, and risedronate on bone show that all side chains undergo fast but restricted motions. In pamidronate, the motion is well simulated by a gauche+/gauche- hopping motion of the terminal -CH2-NH3(+) group, due to jumps from one anionic surface group to another. The results of double-cross polarization experiments indicate that the NH3(+)-terminus of pamidronate is close to the bone mineral surface, and a detailed model is proposed in which the gauche side-chain hops between two bone PO4(3-) sites.     

Determination of the most stable conformers of branched alkanes by 13C-NMR spectroscopy at very low temperatures

¹³C-NMR measurements at 90,51 MHz at 85- 94 K lead to the conclusion, that for 2,3-dimethylbutane, 2,3-dimethylpentane as well as for meso- and DL- 3,4- dimethylhexane gauche is the minimum energy conformation     

Adjacent gauche stabilization in linear alkanes: implications for polymer models and conformational analysis

High-level ab initio quantum mechanical calculations are used to study various gauche conformational energies of n-pentane to n-decane. The destabilizing "pentane effect" (adjacent gauche states of opposite sign) for alkanes is confirmed, but the energies were found to depend slightly on chain length. In contrast, introducing an adjacent gauche of the same sign requires only 0.22-0.37 kcal/mol, approximately half of the single gauche state energy. This adjacent gauche stabilization should be taken into account when formulating or analyzing rotational isomeric models, carrying out conformational analysis, and developing force fields for alkanes, lipids, and related polymers.     

Conformation of drawn poly(trimethylene terephthalate) studied by solid-state 13C NMR

The change in the conformation of the flexible O-CH2-CH2-CH2-O segment of poly(trimethylene terephthalate) (PTT) monofilament caused by drawing was investigated by means of the gamma-gauche effect on the 13C solid-state NMR chemical shift of the internal methylene carbon, combined with the NMR relaxations. The conformation around the O-CH2 and CH2-O bonds for as-spun fiber was trans/trans. On drawing, followed by heat treatment, the conformation changed to gauche/gauche. The ratio of gauche/gauche to trans/trans for the drawn PTT fiber was determined quantitatively.     

Rotation about the C?N bond in 2-aza-1,3-butadiene and the N?N bond in 2,3-diaza-1,3 butadiene: A molecular orbital study

The geometry and energy of 2-aza-1,3-butadiene and 2,3-diaza-1,3-butadiene have been calculated using the 6-31G* basis set as a function of the CNCC and CNNC dihedral angles, respectively. With the 2-aza derivative potential minima are located at 0° (trans) and at about 130° for a gauche structure approximately 9.5 kJ mol^?1 less stable than the trans. Potential maxima are at about 75° giving a gauche barrier height of approximately 19 kJ mol^?1 relative to the trans structure, and at 180° (cis) giving a barrier height of approximately 14.5 kJ mol^?1 relative to the 130° gauche structure. With the 2,3-diaza derivative the gauche barrier has disappeared and there are a series of gauche structures in the region 70°–100° of almost equal energy 12.5-15 kJ mol^?1 less stable than the trans. In addition the cis barrier is much greater, nearly 70 kJ mol^?1 relative to the trans structure. Inclusion of electron correlation, accounting for about 50% of the correlation energy, produces no significant changes in the shape of the potential energy curves. There are systematic and progressive changes in almost all the geometrical parameters as the ?CH? groups in butadiene are replaced by ?N? . The outward tilt and compression within the methylene groups show adverse steric interactions to be operative in the cis structures. The values of V_nn indicate that gauche structures of both the 2-aza and the 2,3-diaza derivatives near the cis structure are more compact (as with butadiene), and gauche structures of the 2-aza derivative near the trans structure are less compact (as with butadiene). Originating in the changes in bond lengths and bond angles, rotation-independent nuclear–nuclear interactions again play an important role.     

Vibrational spectra and conformations of chloromethyldimethyl- and tris(chloromethyl)phosphine oxides

A study was carried out on the IR spectra of (CH₃)₂P(O)CH₂Cl and (CH₂Cl)₂PO. The frequencies and forms of the normal modes were calculated. The molecular mechanics method was used to calculate the energy of the various conformations of these molecules. (CH₃)₂P(O)CH₂Cl in the liquid and solution is a mixture of trans and gauche conformations, while (CH₂Cl)₃PO is a mixture of trans,gauche,gauche, trans,gauche,gauche, and gauche,gauche,gauche conformations.S. M. Kirov Kazan Chemical Engineering Institute and A. E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Branch, Academy of Sciences of the USSR. Translated from Zhurnal Strukturnoi Khimii, Vol. 30, No. 6, pp. 38–46, November–December, 1989.     

Is there a general rule for the gauche effect in the conformational isomerism of 1,2-disubstituted ethanes?

The stabilities of the gauche and anti conformations of butane, 1,2-dicyanoethane (DCE), and 1,2-dinitroethane (DNE) have been investigated through theoretical calculations. The gauche effect-the tendency of keeping close vicinal electronegative substituents (thetaX-C-C-X approximately 60 degrees ) in an ethane fragment-is expected to drive the conformational equilibrium of DCE and DNE toward the gauche conformation. It was found that, for butane, where the gauche effect is supposed to be poor/null, the hyperconjugation effect contributes mostly to the anti stabilization in opposition to the traditional sense that the methyl groups repel each other, and this should govern its conformational equilibrium. For DCE the equilibrium was shifted to the anti conformer, essentially due to a gauche repulsion, while for DNE, despite the higher electronic delocalization energies, a predominance of the gauche conformer was obtained, and this was attributed mainly to the attractive dipolar interaction between the two nitro groups. A full orbital energy analysis was performed using the natural bond orbital approach, which showed that bond bending and anti-C-H/C-X* hyperconjugation models, usually applied to explain the origin of the gauche effect in fluorinated derivatives, are not adequate to completely explain the conformational behavior of the titled compounds.     

Structural and conformational changes during thermally‐induced crystallization of poly(trimethylene terephthalate) by infrared spectroscopy

Conformational changes occurring during thermally‐induced crystallization of poly(trimethylene terephthalate) (PTT) by annealing have been studied using density measurement, differential scanning calorimetry (DSC), and mid‐infrared spectroscopy (MIR). Infrared spectra of amorphous and semicrystalline PTT were obtained, and digital subtraction of the amorphous contribution from the semicrystalline PTT spectra provided characteristic MIR spectra of amorphous and crystalline PTT. The normalized absorbance of 1577, 1173, and 976 cm^?1 were plotted against the crystallinity showing that these bands can be used unambiguously to represent the trans conformation while the band at 1358 cm^?1 can be used to represent gauche conformation of methylene segment. The presence of a weak band at 1358 cm^?1 in the amorphous spectrum suggested that a small amount of gauche conformation is present in the amorphous phase. Infrared spectroscopy has been used for the first time as a means to estimate the trans and gauche conformations of methylene segments in PTT as a function of T_a. The amount of gauche conformation was plotted against the crystalline fraction and the extrapolation of this plot to zero crystalline fraction provided a value of 0.07, suggested that the pure amorphous phase consist of ～ 7% gauche conformation. It was found that the amorphous and crystalline gauche conformation increases at the expense of amorphous trans conformation during thermally induced crystallization of PTT. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1497–1504, 2008     

Conformational preferences and orbital interactions for methyl haloacetates

Conformational preferences and orbital interactions of methyl chloroacetate (1), methyl bromoacetate (2) and methyl iodo-acetate (3) were analyzed using experimental infra-red data, theoretical calculations and NBO analyses. The conformational equilibria of compounds 1-3 can be represented by their cis and gauche rotamers. The gauche form of 1 is stable in the vapour phase and in a non-polar solvent, but the cis is predominant in a polar solvent. For 2 the gauche form is more stable than the cis, in both the vapour and liquid phases, but for compound 3 only the gauche form was observed both in vapour phase as in solution. These conformational preferences were attributed to the orbital interaction between two antibonding orbitals pi(C=O)(*)-->sigma(C-X)(*). This unexpected interaction was possibly due to the high (0.2) electron density on pi(C=O)(*), which results from the interaction between ether oxygen lone pair and pi(C=O)(*).     

Atoms in molecules interpretation of the anomeric effect in the O--C--O unit

The conformational preferences of two model compounds for the O--CH2--O anomeric unit: methanediol and dimethoxymethane analyzed within the framework of the QTAIM theory provide a new interpretation of the anomeric effect. The characteristic stabilization of the gauche conformers of these compounds is accompanied by a progressive reduction of the electron population of the hydrogens of the central methylene as the number of their gauche interactions to lone pairs rises. The electron population removed from these atoms during the conformational change is gained in the gauche conformers by atoms of larger atomic number, which results in a more negative molecular energy. Also, the variations displayed by atomic populations and the QTAIM delocalization indexes are not keeping in line with the hyperconjugative model of the anomeric effect.     

Structural relaxation in amorphous 1,2-dichloroethane studied by transformation between conformation isomers

Structural relaxation in amorphous 1,2-dichloroethane (DCE) samples prepared by vapor deposition on cold substrates were studied by Raman scattering. The gauche and trans molecules of DCE were found to coexist in amorphous states immediately after the deposition, and structural relaxation occurred with temperature elevation before crystallization. Mole fraction of the gauche isomer increased during this relaxation process, although trans is the stable isomer in gaseous and crystalline states. At the final amorphous stage immediately before crystallization, the gauche mole fraction was close to the mole fraction of the supercooled liquid state. It was also found that trans molecules located at positions with lower density were more easily transformed into the gauche conformation, while the distribution of the local structure around the resultant gauche molecules remained almost unchanged during the structural relaxation. Such behaviors of amorphous DCE are discussed from the viewpoint of the characteristic molecular structure of DCE.     

Conformational equilibrium of 1,2-dichloroethane in water: comparison of PCM and RISM-SCF methods

The RISM-SCF and polarizable continuum model (PCM) approaches have been applied to study the conformational equilibrium of 1,2-dichloroethane (DCE) in water. Both the electron correlation effect and basis sets play an important role in the relative energies of the gauche and trans conformers in gas and solution phases. Both PCM and RISM-MP2 methods resulted in a consistent trend with the previous experimental and theoretical studies that the population of the gauche conformer increases in going from the gas phase to the aqueous solution. However, the PCM treatment could not describe the solvent effect completely in that the sign of the relative free energy of the gauche and trans forms is opposite to the most recent experimental and theoretical data, while the RISM-MP2 gives the right sign in the free energy difference. We found that the larger excess chemical potential gain (by ca. -4.1 kcal/mol) for the gauche conformer is large enough to result in the gauche preference of DCE in water, though it has to compensate for more solute reorganization energy (approximately 1.6 kcal/mol) and overcome the energy difference (approximately 1.6 kcal/mol) in the gas phase. The radial distribution functions between DCE and the nearest water shows that the electrostatic repulsion between chlorine and oxygen atoms is higher in the trans conformer than in the gauche one, while the attractive interaction between chlorine and hydrogen of water is higher in the gauche conformer.     

The observation of a large gauche preference when 2-fluoroethylamine and 2-fluoroethanol become protonated

The energies of the gauche and anti conformers of 2-fluoroethylamine, 2-fluoroethanol and their protonated analogues are calculated using density functional theory. Unlike the non protonated systems, the protonated systems show a strong gauche effect where the C-F and the C-(+)NH(3) or C-F and C-(+)OH(2) bonds are gauche rather than anti to each other. Single crystal X-ray diffraction studies of 2-fluoroethylammonium compounds identify the same conformational preference.     

Enantioselective synthesis of an all-syn four vicinal fluorine motif

Alkanes bearing multiple vicinal fluorine atoms at adjacent stereocenters may be considered intermediate between alkanes and perfluoroalkanes, and as a class, their chemistry and behavior remain to be explored. We report here a stereoselective synthesis of an all-syn four vicinal fluorine motif as a single enantiomer. The four vicinal fluorine compound was amenable to single-crystal X-ray analysis, and the resulting structure displays gauche relationships between all four fluorines, consistent with the fluorine gauche effect, and CF...HC hydrogen bonding between adjacent fluoroalkyl chains.