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.     

Reduced odd–even effects in liquid crystalline carbonate dimers: molecular field analysis

Four liquid crystalline carbonate dimers DCn containing the dimethylbenzalazine mesogen, bis(oxycarbonyloxy)alkane flexible spacers with three to six methylene units and acetate terminal groups were synthesised and their mesogenic behaviour investigated. As compared with the corresponding ester dimers a strong reduction of odd–even fluctuations of nematic–isotropic (N–I) transition entropy is observed. A theoretical analysis of the dimers within the rotational isomeric states (RIS) mean-field approach is also reported. A satisfying agreement between calculated and observed thermodynamic properties is obtained. In fact, the theoretical analysis correctly predicts a significant reduction of the odd–even fluctuations for the core order parameter S as well as for the nematic to isotropic transition entropy △S_NI . The calculated distributions of conformers also show reduced differences between even and odd members. In particular, for even dimers the calculated fraction of linear extended conformers in the nematic phase at the N–I transition is around 27%, which is far below that of the corresponding ester dimers (46%).     

Association of symmetrical alkane diols with pyridine: DFT/GIAO calculation of 1H NMR chemical shifts

Proton nuclear magnetic resonance (NMR) shifts of the free diol and of its 1 : 1 and 1 : 2 hydrogen‐bonded complexes with pyridine have been computed for five symmetrical alkane diols on the basis of density functional theory, by applying the gauge‐including atomic orbital method to geometry‐optimized conformers. For certain conformers, intramolecular OH ···OH interactions, evidenced by high NMR OH proton shifts, are further enhanced on going from the free diol to the corresponding 1 : 1 diol/pyridine complex. This is confirmed by atoms‐in‐molecules and non‐covalent interaction plots. The computed OH and CH proton shifts for the diol and the two complexes correlate well with values obtained by analysing data from the NMR titration of the diols in benzene against pyridine. Shift values for the diols in neat pyridine are calculated by weighting the shifts of the various protons in the three forms (free diol, 1 : 1 and 1 : 2 diol/pyridine complexes) according to the experimentally determined association constants. The results are in good agreement with those observed, and after empirical scaling, the root mean square difference is 0.18 ppm. Copyright © 2016 John Wiley & Sons, Ltd.     

Vibrational spectroscopy of mechanically compressed monolayers

Sum-frequency spectroscopy has been used to investigate the behavior of self-assembled monolayers in a solid-solid contact. Various alkanethiol layers on gold were observed before, during, and after compression to 660 MPa against a sapphire counterface. Well-ordered layers that differ only in the length of their alkane tails (C(8) versus C(18)) behave similarly. In contrast, defective and partly melted monolayers are more sensitive to stress than are their well-ordered analogues, and they are more prone to irreversible changes. In all cases, the intensity of methyl C-H stretching modes decreases with applied pressure, indicating a loss of net orientational order among the terminal methyl groups. The magnitude of this effect in well-ordered layers can be compared with the theoretical sensitivity of the resonant sum-frequency signal to molecular orientation. On these grounds, an increased population of terminal gauche conformers is identified as the disordering mechanism under pressure.     

Theoretical calculation of the OH vibrational overtone spectra of 1-n alkane diols (n = 2-4): origin of disappearing hydrogen-bonded OH peak

In this theoretical study, we simulated the vibrational overtone spectrum of ethylene glycol (EG), 1-3 propanediol (PD), and 1-4 butanediol (BD). Using the local mode model along with the potential energy curve and dipole moment function calculated by B3LYP/6-31+G(d,p) and QCISD/6-311++G(3df,3pd), we obtained the theoretical peak position and integrated absorption coefficient. Furthermore, the vibrational spectra was simulated using a Voigt function using homogeneous and inhomogenous width obtained from quantum chemical calculation methods. Previously, Howard and Kjaergaard recorded the second and third overtone photoacoustic spectra of the three aforementioned alkane diols in the gas phase and observed that the intramolecular hydrogen bonded OH peak becomes difficult to observe as the intramolecular hydrogen bonding strength increased, that is, as the chain length was increased. In this paper we show that the disappearance of the hydrogen-bonded OH peak for the OH stretching overtone excitation for BD is partly due to the increase in homogeneous width due to the increase in the hydrogen bond strength and partly due to the decrease in the relative population of the intramolecular hydrogen-bonded conformers as the chain length is increased. This latter feature is a consequence of the unfavorable strained geometry needed to form the intramolecular hydrogen bond in longer alkane chains.     

Quantum algebraic–combinatoric study of the conformational properties of n‐alkanes. I

Based on quantum chemical calculation results, four rules were previously derived for the numbers and the sequences of the conformers of free alkane molecules. This paper builds up first an algebra to handle the conformational problem of alkanes. Partitioning the set of all sequences, the whole problem is then subdivided into three independent subcases. With the help of an equivalence relation, the sequences can be classified. According to the quantum chemical rules, certain equivalence classes do not represent conformers. A welldefined subcase of the whole problem is solved.     

Conformational aspects of caryophyllene. Population of stable conformers and ring inversion barrier of trans cyclononene ring portion

Cmr measurements of caryophyllene revealed two major conformers equilibrating in a ratio 76:24 at room temperature. The energy ordering of four possible conformers of caryophyllene predicted by molecular mechanics calculations agrees well with the experimental observation. The barrier of interconversion between the two conformers was determined as 16.25 kcal/mol.     

Chromatographic separation of conformers of substituted asymmetric nitrosamines.

The syn and anti conformers of N-nitrosoproline, N-nitrososarcosine and N-nitroso-2-(ethylamino)-ethanol, have been separated by liquid chromatography. These conformers result from hindered rotation about the N-N bond. Separation was achieved using adsorption, reversed-phase, and ion-exchange modes. For the nitroso-amino acids, a shift in the equilibrium conformer concentration was observed with changes in pH.     

Molecular properties from conformational ensembles. 1. Dipole moments of molecules with multiple internal rotations

We present a novel method for constructing the stable conformational space of small molecules with many rotatable bonds that uses our iterative stochastic elimination (ISE) algorithm, a robust stochastic search method capable of finding ensembles of best solutions for large combinatorial problems. To validate the method, we show that ISE reproduces the best conformers found in a fully exhaustive search, as well as compare computed dipole moments to experimental values, based on molecular ensembles and their Boltzmann distributions. Results were also compared to the alternative molecular dynamics and simulated annealing methods. Our results clarify that many low energy conformations may be required to reproduce molecular properties, while single low energy conformers or ensembles of low energy conformers cannot account for the experimental properties of flexible molecules. Whereas ISE well reproduces conformations that are not separated by very large energy barriers, it has not been successful in reproducing conformations of strained molecules.     

Wetting of surfactant solutions by alkanes.

Ellipsometry, surface tensiometry, and contact-angle measurement have been used to study the transition between partial wetting and pseudo-partial wetting of surfactant solutions by alkanes. In the partial wetting regime, the air-water surface tension is the same with and without alkane. In the pseudo-partial wetting regime, the air-water surface tension is lowered by the presence of alkane, showing that oil is solubilised into the surfactant monolayer. A discontinuous change in the coefficient of ellipticity with increasing surfactant concentration provides unequivocal evidence for the first-order nature of the wetting transitions. Ellipsometry has been used to explore the generality of wetting transitions of alkanes (dodecane, hexadecane, and squalane) on surfactant solutions [dodecyltrimethylammonium bromide, tetredecyltrimethylammonium bromide, dibucaine hydrochloride, and Aerosol OT (AOT)]. Of the systems studied, only hexadecane on AOT solutions did not show a wetting transition. Excess alkane remains as a lens on the surface of the surfactant solutions at all concentrations, but the contact angle is a minimum at the wetting transition. A semiquantitative model for the variation of the contact angle with surfactant concentration is provided.     

1H NMR spectra of alkane‐1,3‐diols in benzene: GIAO/DFT shift calculations

The proton nuclear magnetic resonance (NMR) spectra of propane‐1,3‐diol, 2‐methylpropane‐1,3‐diol, 2,2‐dimethylpropane‐1,3‐diol, butane‐1,3‐diol, 3‐methylbutane‐1,3‐diol, pentane‐2,4‐diols (dl and meso), 2‐methylpentane‐2,4‐diol and cyclohexane‐1,3‐diols (cis and trans) in benzene have been analysed. The conformer distribution and the NMR shifts of these diols have been computed on the basis of density functional theory, the solvent being included by means of the integral equation formalism phase continuum model (IEFPCM) implemented in Gaussian 09. Relative Gibbs energies of all conformers are calculated at the Perdew, Burke and Ernzerhof (PBE)0/6‐311 + G(d,p) level, and NMR shifts by the gauge‐including atomic orbital method with the PBE0/6‐311 + G(d,p) geometry and the cc‐pVTZ basis set. Vicinal coupling constants for 1,2‐ and 1,3‐diols are rationalised in terms of relative conformer populations and geometries. The NMR shifts of hydrogen‐bonded protons in individual conformers of alkane‐1,n‐diols show a very rough correlation with the OH?OH distances. The computed overall NMR shifts for CH protons in 1,2‐ and 1,3‐diols are systematically high but correlate very well with the experimental values, with a gradient of 1.07 ± 0.01. Some values for nonequivalent methylene protons in 1,3‐diols are reversed, calculation giving enhanced values for the proton anti to the C? OH bonds. Errors in the NMR shifts computed for the OH protons of nonsymmetrical diols appear to be related to relative populations of conformers where one or other of the OH groups is the donor. Some results based on the second‐order Møller–Plesset approach, the Becke three‐parameter Lee‐Yang‐Parr method and on the IEFPCM solvation model implemented in Gaussian 03 are included. Copyright © 2013 John Wiley & Sons, Ltd.     

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

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

Remote substituent effects on the oxymercuration of 2-substituted norbornenes: an experimental and theoretical study.

The effect of a remote substituent on regioselectivity in the oxymercuration of 2-substituted norbornenes has been investigated experimentally and theoretically using density functional theory (DFT). Regioselectivities of 1:1 to 14:1 were observed with various 2-substituted norbornenes. Exo-2-substituted norbornenes always gave greater regioselectivities compared to the corresponding endo-2-substituted norbornenes. The effects of solvents on the regioselectivity have also been examined, and ethereal solvents were found to be the best choice giving the optimal yield and regioselectivity. The relative rate of oxymercuration was estimated by competition experiments. The least reactive substrate (X = OAc) gave the highest regioselectivity. According to DFT predictions, the increased difference between the reaction barriers that results in the greater regioselectivity is correlated directly with the larger polarity of the C=C double bond, which is attacked by the mercury and oxygen. A number of stable exo and endo conformers were predicted. All exo conformers show the same polarity of the double bond, while some endo conformers have a reversal of this polarity. All the conformers except those with the OAc substituent are very close in energy and thus should react. The existence of a mixture of endo conformers with the C=C double bond of opposite polarity clearly explains a decrease in regioselectivity for the endo species. The origin of the greatest regioselectivity for the OAc-2-norbornenes lies in the fact that the conformer with the largest polarity is notably lower in energy than others due to an internal C-H-O hydrogen bond.     

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.     

Pyrrolizidine alkaloids necine bases: II. Conformational analysis of free bases

Molecular mechanics calculations were applied to the conformational analysis of two diasteroisomers, the pyrrolizidine alkaloids (PAs) retronecine and heliotridine. The application of reoptimized parameters for H bonding corrected the tendency of MM3(92) calculations to give unrealistic H(DOTTED BOND)O distances for intramolecular OH interactions occurring in both diasterisomers. Inversions in the H-bond direction of exo-retronecine and in the relative stability of heliotridine endo–exo conformers were also observed with the application of the new parameters. A set of probable conformers was obtained for each diasterisomer, based on conformational and Boltzmann population analysis. Only exo-puckered conformers were found in the retronecine set, whereas both exo- and endo-puckered conformers were obtained for heliotridine. Transition state conformations supplied arguments supporting the design of models for H-bond interconversion in the case of exo-retronecine and for the exo–endo interconversion of heliotridine. Reactivity behaviors and ¹H-NMR data of both diasterisomers were elucidated in light of the theoretical results. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1853–1861, 1998     

Tautomerism of anthraquinones: XI. 1-amino-4-hydroxyanthraquinone

The disperse dye red 2C regarded as 1-amino-4-hydroxy-9,10-anthraquinone is not a 9,10-anthraquinone derivative. It is characterized by a keto-enol and amino-imine tautomerism, and it consists of equilibrium mixtures of tautomers and conformers containing 4-amino-9-hydroxy-1,10-, 9 amino-4-hydroxy-1,10-, 9 amino-10-hydroxy-1,4-anthraquinones, 9 hydroxy-1,10-anthraquinone 10-imine, and also their conformers with a single intramolecular hydrogen bond. The significant differences in the absorption spectra known for this dye originate from the dissimilar isomeric composition of the samples of this dye prepared or purified by various procedures     

Crystallization of alkane melts induced by carbon nanotubes and graphene nanosheets: a molecular dynamics simulation study

The crystallization of alkane melts on carbon nanotubes (CNT) and the surface of graphene nanosheets (GNS) is investigated using molecular dynamics (MD) simulations. The crystallization process of the alkane melts is analyzed in terms of the bond-orientational order parameter, atomic radial distribution for the CNT/alkane, atomic longitudinal distribution for the GNS/alkane, and diffusion properties. The dimensional effects of the different carbon-based nanostructures on the crystallization of alkane melts are shown. It is found that one-dimensional CNT has a stronger ability to induce the crystallization of the polymer than that of two-dimensional GNS, which provides a support at molecular level for the experimental observation [Li et al., J. Am. Chem. Soc., 2006, 128, 1692 and Xu et al., Macromolecules, 2010, 43, 5000]. From the MD simulations, we also find that the crystallization of alkane molecules has been completed with the highly cooperative processes of adsorption and orientation.     

Pair-wise interactions by gas chromatography. VII. Interaction free enthalpies of solutes with secondary alcohol groups

A polar type liquid having a secondary alcohol substituent on a branched alkane skeleton, SOH, was used as stationary phase. The molecules of this stationary phase are nearly isomorphous and isochor with those of the branched alkane, C78, elected as standard, i.e., the molecules of both solvents have nearly the same form and the same size. Partition properties of 158 chosen molecular probes were measured by gas chromatography on SOH and on an SOH-C78 mixture having a volume fraction of thetaOH = 0.5. Based on the resulting data an interaction free enthalpy could be calculated, i.e., the additional effect of the secondary alcohol to partition. Comparison with data determined earlier on another member of this solvent family, POH, having a primary alcohol as interacting group gives information about the effect of steric hindrance on polar type solute-solvent interaction free energies.     

Transition metal-alkane σ-complexes with oxygen donor co-ligands

A new family of long-lived alkane σ-complexes of the type (L(OEt))Re(CO)(2)(alkane) [alkane = cyclopentane, cyclohexane, pentane; L(OEt) = cyclopentadienyltris(diethylphosphito)cobaltate(III)] has been observed using both IR and NMR spectroscopies and computationally interrogated with DFT methods. The oxygen-rich coordination spheres makes these complexes perhaps more relevant as models for intermediates in metal oxide mediated hydrocarbon transformations than other known alkane σ-complexes.