Axial Chair Conformers Research Articles

Conformational Analysis of 5-Methyl-1,3-oxathiane

Computer simulation of conformational transformations of 5-methyl-1,3-oxathiane at the DFT PBE/3ζ, RI-MP2/λ2, and HF/6-31++G(d,p) levels of theory has shown that the interconversion between the equatorial (global minimum) and axial chair conformers occurs along several independent pathways through five flexible forms. Nine transition states corresponding to different half-chair forms, as well as symmetrical and unsymmetrical boat conformers, have been localized on the potential energy surface. The free conformational energy of the methyl group has been estimated at 0.9–1.0 kcal/mol by comparison of the calculated and experimental vicinal coupling constants in the 1H NMR spectra.

Conformational Effects in the Transport of Glucose through a Cyclic Peptide Nanotube: A Molecular Dynamics Simulation Study.

The transport behavior of glucose through a cyclic peptide nanotube (CPN), composed of 8 × cyclo[-(Trp-d-Leu)4-Gln-d-Leu-] rings embedded in DMPC lipid bilayers was examined using all-atom molecular dynamics (AAMD) simulations. Two conformational isomers of β-d-glucose, equatorial (4C1) and axial (1C4) chair conformers, were used to examine conformational effects on the hydrogen bond network, energetics, and diffusivity of glucose transport through the CPN. Calculations of the number of hydrogen bonds of the two glucose conformers with water molecules and with the CPN illustrate that the total number of hydrogen bonds of the conformers decreases inside the channel compared to bulk water due to the confinement characteristics of the interior of the CPNs although new hydrogen bonds between the hydroxyl and hydroxymethyl hydrogens of glucose and the carbonyl oxygens in the CPN backbone are formed. Despite the decrease of the number of hydrogen bonds inside the CPN, intramolecular hydrogen bonds of 1C4 are maintained during permeation of 1C4 through the CPN. The retention of intramolecular hydrogen bonds and the spherical shape of 1C4 give rise to considerably weaker orientational preferences and higher diffusion coefficients for 1C4 than those of 4C1 inside and outside the CPN. Due to larger dipole moments induced by the alignment of hydroxyl and hydroxymethyl groups, 1C4 has more favorable interactions with the CPN backbone at the channel entrances and inside the channel than 4C1. In the middle of the CPN channel, entropic gains originating from higher orientational and translational degrees of freedom of 1C4 than those of 4C1 also contribute to lower free energy wells for 1C4 inside the CPN. This work reveals that the conformational variation and intramolecular hydrogen bond formation of β-d-glucose can have important effects on the energetics and dynamics of glucose transport through CPNs, providing insight into the translocation mechanism of d-glucose into the cell through glucose transporters (GLUTs) and the dynamics of glucose confined in silica nanochannels. It is also demonstrated that CPNs can indeed facilitate the permeation of small hydrophilic molecules such as glucose and can be utilized as a novel carrier system for hydrophilic drug compounds into the cell.

Conformational preference of perhydro-1,3,2-dioxazine inside nanotubes

Conformational changes of perhydro-1,3,2-dioxazine in open single-walled carbon nanotubes have been studied by hybrid DFT PBE/3z method. It was established that relative stability of equatorial and axial chair conformers of encapsulated molecule has been inverted, the latter form becoming favorable. In this case the barrier of pyramidal inversion of nitrogen atom has been slightly de

Conformational analysis of 2,2-dimethyl-5-alkyl-1,3-dioxa-2-silacyclohexanes

Study of conformational isomerization of 2,2-dimethyl-5-alkyl-1,3-dioxa-2-silacyclohexanes using quantum-chemical HF/6-31G(d) and PBE/3z approximations showed that its route involves an equilibrium between the chair conformers with different orientation of substituent at C5 ring atom and proceeds through a transition state corresponding to the 2,5-twist conformation. Molecular dynamics method showed that at room temperature this conformation transforms into the equatorial or axial chair conformers through 1,4-twist or sofa forms. Based on the experimental and theoretical values of vicinal 1H NMR coupling constants we determined quantitative conformational composition of the molecules of these compounds and the values of ΔG0 of the conformational equilibrium.

Conformational analysis of 5-methyl- and 2,2,5-trimethyl-1,3-dithianes

Conformational isomerization of 5-methyl- and 2,2,5-trimethyl-1,3-dithianes was studied using quantum-chemical HF/6-31G(d), HF/pVDZ, and PBE/3z approximations. The potential energy surface of molecules of both compounds is shown to contain the main minimum corresponding to the equatorial chair conformer C-5e. The calculated potential barriers of the conformational isomerization were found. Based on the experimental (1H NMR) and theoretical vicinal coupling constants the ΔG 0 values were determined of the methyl group at the ring C5 atom. The reasons for the distinctions between the values of this parameter from the ΔG 0, obtained by energy minimizations of the equatorial and axial chair conformers are discussed.

Conformational analysis of 2-substituted 5,5-bis(chloromethyl)-1,3-dioxanes

Quantum-chemical study on stationary points on the potential energy surfaces of 2-alkyl-, 2-phenyl-, and 2-methyl-2-phenyl-5,5-bis(chloromethyl)-1,3-dioxanes in terms of HF/6-31G(d), B3PW91/6-31G(d,p), and B3PW91/LanL2Dz nonempirical approximations revealed only one pathway for conformational isomerization of the equatorial and axial chair conformers through intermediate energy minimum corresponding to the 2,5-twist conformer.

Conformational analysis of 5-substituted 1,3-dioxanes

Quantum-chemical study on the potential energy surface of 5-alkyl- and 5-phenyl-1,3-dioxanes at the RHF/6-31G(d) level of theory revealed two pathways for conformational isomerizations of the equatorial and axial chair conformers. Potential barriers to this process were estimated. The Gibbs conformational energies ΔG° of substituents at C5 in the 1,3-dioxane ring were determined on the basis of experimental (1H NMR) and theoretical vicinal coupling constants, which turned out to be consistent with published data.

Adsorption changes of cyclohexyl isothiocyanate on gold surfaces

The adsorption and structure of cyclohexyl isothiocyanate (CHIT) on gold surfaces has been investigated by surface-enhanced Raman scattering (SERS) and scanning tunneling microscopy (STM). Depending on the concentration, the spectral changes of the NCS stretching vibration on gold nanoparticles appeared to be more conspicuous than those of cyclohexyl ring modes. Both equatorial and axial chair conformers of CHIT were found to exist at low bulk concentrations near the monolayer coverage limit, whereas the equatorial chair conformer appeared to be dominant at high bulk concentrations. It was also observed that the ring conversion of equatorial to axial conformers can easily occur at higher temperatures, and the mole fraction of the axial form is assumed to increase with increasing temperature from 30 to 60 °C. Alternatively, STM imaging revealed that the adsorption of CHIT molecules on Au(1 1 1) leads to the formation of disordered SAMs with a few vacancy islands, as opposed to the formation of well-ordered self-assembled monolayers (SAMs) by cyclohexanethiols.

Nonempirical study on the potential energy surface of 5-methyl-1,3-dioxane

Quantum-chemical study on the potential energy surface of 5-methyl-1,3-dioxane at the nonempirical RHF//STO-3G, RHF//3-21G, RHF//6-31G(d), RHF//6-31G(d,p), and MP2//6-31G(d,p) levels of theory revealed two energy-equivalent paths of conformational transformation of the equatorial and axial chair conformers. Potential barriers to these processes were estimated. The δG° value for the methyl substituent on C5 in 1,3-dioxane ring, determined on the basis of the experimental (NMR) and calculated vicinal 1H-1H coupling constants, was very consistent with published data

Concentration‐ and temperature‐dependent conformation change of cyclohexyl isocyanide on gold nanoparticle surfaces

AbstractThe conformational changes of cyclohexyl isocyanide (CHNC) on gold nanoparticle surfaces were investigated by means of concentration‐ and temperature‐dependent surface‐enhanced Raman scattering (SERS). The equatorial chair conformer appeared to be dominant at high‐bulk concentrations or low temperatures, whereas both the equatorial and axial chair conformers of CHNC were found to exist at low‐bulk concentrations or high temperatures as in the previous reports of cyclohexanethiol (CHT). Depending on concentrations and temperatures, the spectral changes of the NC stretching vibration on gold nanoparticles appeared to be more conspicuous than those of the cyclohexyl ring modes. A density functional theory (DFT) calculation was performed at the level of B3LYP/6‐31G + + (d,p) to compare the energetic stability of the various conformers of CHT and CHNC. The energy differences between the equatorial and axial chair conformers were predicted to be smaller for CHNC than for CHT by ∼3 kJ mol−1 from the DFT calculation. Copyright © 2008 John Wiley & Sons, Ltd.

Conformational changes of cyclohexanethiol adsorbed on gold surfaces

The conformational changes of cyclohexanethiol (CHT) on gold nanoparticles and gold plate surfaces were investigated by means of surface-enhanced Raman scattering. The equatorial chair conformer appeared to be dominant at high bulk concentrations, whereas, both the equatorial and axial chair conformers of CHT were found to exist at low bulk concentrations corresponding to a near monolayer coverage limit. Molecular-scale scanning tunneling microscopy imaging revealed the existence of two axial and equatorial conformers in the CHT monolayer on an Au(1 1 1) surface as well as the existence of the meta-stable conformer, which may be due to dynamic conformational changes of the cyclic ring. It was also found that the peaks corresponding to the axial bands disappeared below room temperature, indicating the equatorial conformer is dominant at low temperatures. From this result, we found that the conformation of CHT on an Au surface was easily changed by surface temperature.

Relative energies of conformations and sulfinyl oxygen‐induced pentacoordination at silicon in 4‐bromo‐ and 4,4‐dibromo‐4‐silathiacyclohexane 1‐oxide: A computational study

AbstractThe equilibrium geometries and relative energies of the chair, twist, and boat conformations of cis‐ and trans‐4‐bromo‐4‐silathiacyclohexane 1‐oxide and 4,4‐dibromo‐4‐silathiacyclohexane 1‐oxide have been calculated at the B3LYP/6‐311G(d,p) and MP2/6‐311+G(d,p) theoretical levels. The axial (SO) chair conformers of the sulfoxides are of lower energy than the chair conformers of the corresponding equatorial (SO) sulfoxides. The chair conformer of the axial (SO) trans‐4‐bromo‐4‐silathiacyclohexane 1‐oxide is only 0.10 kcal/mol more stable than the corresponding 1,4‐boat conformer which is stabilized by a transannular coordination of the sulfinyl oxygen with silicon that results in trigonal bipyramidal geometry at silicon. The 1,4‐boat structure of equatorial (SO) trans‐4‐bromo‐4‐silathiacyclohexane 1‐oxide is a transition state and is 5.77 kcal/mol higher in energy than the respective chair conformer. The 1,4‐boat conformer of axial (SO) 4,4‐dibromo‐4‐silathiacyclohexane 1‐oxide is also stabilized by transannular coordination of the sulfinyl oxygen and silicon, but it is 4.31 kcal/mol higher in energy than the corresponding chair conformer. The relatively lower stability of the 1,4‐boat conformer of 4,4‐dibromo‐4‐silathiacyclohexane 1‐oxide may be due to repulsive interactions of the axial halogen and sulfinyl oxygen atom. The relative energies of the conformers and transition states are discussed in terms of hyperconjugative interactions, orbital interactions, nonbonded interactions, and transannular sulfinyl oxygen‐silicon coordination. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

Thermodynamic properties of crystalline and liquid chlorocyclohexane and inversion of ring

Heat capacity of crystalline and liquid chlorocyclohexane ( c-C 6H 11Cl) at T = 5 K to 304 K was measured by vacuum adiabatic calorimetry. Two solid-to-solid transformations were found: at T = 120 K with Δ trs H m = (50.5 ± 0.5) J·mol -1 and at T = 220.4 K with Δ trs H m = (8010.7 ± 2.9) J·mol -1. Melting temperature of c -C 6H 11Cl is 229.34 K, and Δ fus H m = (2042.8 ± 4.4) J·mol -1. The enthalpy of vaporization was directly determined with a heat-conduction differential microcalorimeter: Δ vap H o m(298.15 K) = (42.92 ± 0.62) kJ·mol -1. Values Δ T o S m(1, 298.15 K) = (242.2 ± 1.0) J·K -1·mol -1, Φ m(1, 298.15) = (111.4 ± 0.5) J·K -1·mol -1, and Δ T o S o m(g, 298.15 K) = (348.0 ± 2.3) J·K -1·mol -1 were calculated on the base of these. The temperature dependence of Δ vap H o m in the temperature range from T = 296 K to 320 K was studied, and Δ C o p(1 to g) was estimated. By low-temperature i.r. spectroscopy it was established that the liquid and the crystal I consist of a mixture of the equatorial and axial-chair conformers, but crystals II and III (at T < 220.4 K) consist of only e-conformer. The conformational analysis of chlorocyclohexane was made by the molecular-mechanics method. Statistical calculations of standard thermodynamic properties of c -C 6H 11Cl in the gaseous state were carried out for T = 100 K to 1000 K, taking into account conformation composition. Calculated and experimental values of C o p,m and S o m(g) at T = 298.15 K, and S o m (g) at T = 353.15 K are in satisfactory agreement. The following thermodynamic functions of chlorocyclohexane were obtained: Δ f H o m(g, 298.15 K) = -(164.2 ± 2.0) kJ·mol -1; Δ f H o m(1, 298.15 K) = -(206.9 ± 2.1) kJ·mol -1; Δ f G o m(g, 298.15 K) = -(9.9 ± 2.5) kJ·mol -1; Δ f G o m(l, 298.15 K) = -(21.3 ± 2.6) kJ·mol -1.

Raman spectroscopy of cyclohexanethiol adsorbed on a silver surface

AbstractThe surface‐enhanced Raman scattering of cyclohexanethiol was investigated in a silver sol. Cyclohexanethiol was found to adsorb dissociatively after losing its thiol proton and adsorption was found to occur via its sulphur atom. Both the equatorial and axial chair conformers were found to exist on the surface at low surface coverage. However, at full monolayer coverage, the equatorial chair was the sole conformation of the adsorbed thiolate. An improved vibrational assignment for the molecule has been made.