Chlorine K X-ray absorption-edge structures of CIS-[Pt(NH3)2Cl2], trans-[Pt(NH3)2Cl2], trans-[Pd(NH3)2Cl2] and (NH4)2PdCl4

The K absorption-edge spectra of the ligand chlorine ion in square-planar complex compounds cis- and trans-[Pt(NH₃)₂Cl₂], trans-[Pd(NH₃)₂Cl₂], and (NH₄)₂PdCl₄ are reported and discussed in connection with the chlorine K absorption spectra of K₂PtCl₄ and K₂PdCl₄, reported previously. The observed chemical shift of a white line at the absorption threshold is interpreted in terms of the difference of the ligand-field splitting of electronic states for metal ions. The white line is attributed to the electronic transition from the Cl^? ls level to the lowest unoccupied antibonding molecular orbital (MO), which is specified by a $\text{MO}\text{b}{}_{\mathrm{1g}}\text{(σ}{}^1\text{)}$ in the square-planar complex with D_4h symmetry. The other absorption structures are regarded as continuum “shape resonances” of the outgoing electron trapped by the cage of the surrounding atoms. The effect of geometrical isomerism is found in the chlorine K absorption spectra of cis- and trans-[Pt(NH₃)₂Cl₂].     

Conformational analysis of 3‐methyl‐3‐silathiane and 3‐fluoro‐3‐methyl‐3‐silathiane

The conformational equilibria of 3‐methyl‐3‐silathiane 5 , 3‐fluoro‐3‐methyl‐3‐silathiane 6 and 1‐fluoro‐1‐methyl‐1‐silacyclohexane 7 have been studied using low temperature ¹³C NMR spectroscopy and theoretical calculations. The conformer ratio at 103 K was measured to be about 5 _ax: 5 _eq = 15:85, 6 _ax: 6 _eq = 50:50 and 7 _ax: 7 _eq = 25:75. The equatorial preference of the methyl group in 5 (0.35 kcal mol^?1) is much less than in 3‐methylthiane 9 (1.40 kcal mol^?1) but somewhat greater than in 1‐methyl‐1‐silacyclohexane 1 (0.23 kcal mol^?1). Compounds 5–7 have low barriers to ring inversion: 5.65 (ax → eq) and 6.0 (eq → ax) kcal mol^?1 ( 5 ), 4.6 ( 6 ), 5.1 (Me_ax → Me_eq) and 5.4 (Me_eq → Me_ax) kcal mol^?1 ( 7 ). Steric effects cannot explain the observed conformational preferences, like equal population of the two conformers of 6 , or different conformer ratio for 5 and 7 . Actually, by employing the NBO analysis, in particular, considering the second order perturbation energies, vicinal stereoelectronic interactions between the Si–X and adjacent C–H, C–S, and C–C bonds proved responsible. Copyright © 2010 John Wiley & Sons, Ltd.     

Dynamic mechanism for encapsulating two HIV replication inhibitor peptides with carbon nanotubes

Encapsulation of biomolecules inside a carbon nanotube(CNT) has attracted great interest because it could enable the delivery of nanoscale pharmaceutical drugs with CNT-based devices.Using a molecular dynamics simulation,we investigate the dynamic process by which human immunodeficiency virus(HIV) replication inhibitor peptides(HRIPs) are encapsulated in a water solution contained inside a CNT.The van der Waals attraction between the HRIPs and the CNT and the root-mean-square deviation are used to analyse the evolution of the encapsulation.It is found that the interaction between the HRIPs and the CNT is the main driving force for the encapsulation process,which does not cause an obvious conformational change to the HRIPs.     

Substituent effects on the conformational stability of allyl fluorides

By the B3P86/6‐311G(3d,2p) method, remote substituent effects on trans‐YCH?CHCH₂F were investigated by examining their conformational stabilities, molecular geometries, and stereoelectronic interactions in this paper. The cis conformer is favored for Y?H, Cl, Me, Vinyl, CF₃, CN, CHO, and NO₂, whereas the gauche is favored for Y?OMe, OH. A correlation of ΔH with the substituent constants σ⁺(Y) shows that the increasing electron‐withdrawing ability of the substituent Y increases the relative stability of the cis conformer. It was found that the substituent effect on the molecule stabilization energies (relative to CH₂?CHCH₂F) is more significant in the gauche conformers than in the cis conformers. In agreement, molecular structures of the gauche conformers were also observed to vary more significantly with the substitution than those of the cis conformers. By the second‐order perturbation energy (E(2)) in NBO analysis, it was found that the total C₂–C₃ vicinal hyperconjugation is determinant in the enthalpy difference and consequently controls the conformational stability. Further analysis shows that the substituent effect on the C₂–C₃ vicinal hyperconjugations is much higher in the gauche conformers than in the cis conformers. The highly sensitive π_C?C→σ*_{C? F} interaction to the substitution in the gauche conformers, is the leading factor in variation of molecular stability and geometry. Copyright © 2010 John Wiley & Sons, Ltd.     

Isomer Structural Transformation in Au–Cu Alloy Nanoclusters: Water Ripple‐Like Transfer of Thiol Ligands

Structure isomerism is observed in noble metal nanoclusters; however, the mechanism study of this process is rarely reported. Herein, by using the biphosphine ligands instead of phosphine ligands, the high symmetry of the Au₂Cu₆(PPh₃)₂(SAdm)₆ nanocluster is successfully broken and [Au₄Cu₄(L₁)₂(SAdm)₅]Br (where, L₁ is bis(diphenylphosphine)methane, DPPM) nanocluster is obtained with chiral arrangement. This newly obtained nanocluster contains a total of four isomers in crystal unit cell. Interestingly, these isomers undergo rapid isomorphism in solution, which is confirmed by ¹H‐¹H COSY spectrum. Density functional theory calculations demonstrate that the water ripple–like transfer of the thiol ligands results from the isomorphism of nanoclusters.     

Formic acid in deuterium and hydrogen matrices

ABSTRACT

Formic acid (HCOOH, FA) was studied experimentally, by infrared spectroscopy, in H₂ and D₂ matrices, with focus on the preparation and characterisation in these matrix media of structures containing the higher-energy (cis) conformer. The cis-FA monomer and the cis-FA^?…?N₂ complex were successfully produced by selective vibrational excitation of corresponding trans-FA based species, and vibrationally characterised. The tunneling-induced conversion of the cis-FA^?…?N₂ complex in the studied matrices into the corresponding trans-FA complex was also investigated, and the found tunnelling properties discussed, in particular in comparison with those observed for the spontaneous conversion of cis-FA monomer into trans-FA. This article constitutes the first report on the infrared spectrum of FA conformers and stability of cis-FA monomer in a D₂ matrix, and on the structure, spectroscopy and stability of the cis-FA^?…?N₂ complex in both H₂ and D₂ matrices. Different attempts to prepare the cis-FA^?…?H₂O complex in the two investigated matrices are also described in detail, both from previously in situ generated cis-FA monomer followed by thermal mobilisation and by direct selective vibrational excitation of the trans-FA-H₂O complex.     

Single long-polymer translocation through a long pore

This paper theoretically studies the free energy and conformational entropy of a long polymer threading a long nanopore (n₀/N \ge 0.1) on external electric field. The polymer expanded model is built in this paper, that is, a single long polymer chain with N monomers (each of size a) threading a pore with n₀ monomers can be regarded as polymer with N+n_{0} monomers translocating a 2-dimension hole embedded in membrane. A theoretical approach is presented which explicitly takes into account the nucleation theory. Our calculations imply that, the structure of polymer changes more acutely than other situation, while its leading monomer reaches the second vacuum and its end monomer escapes the first vacuum. And it is also shown that the length scale of polymer and pore play a very important role for polymer translocation dynamics. The present model predicts that the translocation time depends on the chemical potential gradient and the property of the solvent on sides of pore to some extent.     

Conformational analysis and inversion process in some perhydrodipyrido[1,2‐b;1′2′‐e]‐1,4,2,5‐ dioxadiazines

The stereoselectivity in the cyclodimerization of several six‐membered cyclic nitrones has been investigated. The configurational/conformational analysis of the dimers (i.e. perhydrodipyrido[1,2‐b;1′2′‐e]‐1,4,2,5‐dioxadiazines) has been carried out by NMR spectroscopy. The NMR spectra of the dimers at lower temperatures indicated the presence of either a single or two invertomer(s). The nitrogen inversion barriers are determined using complete line–shape analysis. The invertomer ratios have been used to estimate the relative energies associated with the cis and trans ring fusion in these tricycles. A mechanistic rationale for the observed stereochemistry of the dimerization process has been presented. Copyright © 2009 John Wiley & Sons, Ltd.     

Substituent effects on conformational preference in α‐substituted α‐fluorophenylacetic acid methyl ester model systems for chiral derivatizing agents

In connection with study of chiral derivatizing agents (CDAs) for NMR determination of absolute configuration of organic compounds, factors controlling the conformational preference between syn‐ and anti‐forms in α‐substituted α‐fluorophenylacetic acid methyl ester (FC(X)(Ph)COOMe) model systems were theoretically investigated. Substituents X at the stereogenic carbon atom were X = H, C?CH and CH₃, the electronic and steric properties of which were significantly different from each other. The model system with X = C?CH and that with X = CH₃ were found to be possible candidates for fluorine‐containing CDAs. The syn conformation is stable compared with the anti one by 0.7 kcal mol^?1 for the ester with X = C?CH. On the other hand, the anti conformation is stable compared with the syn one by 0.5 kcal mol^?1 for the ester with X = CH₃. Both natural bond orbital (NBO) analysis and deletion of selected orbitals based on the donor–acceptor NBO scheme were adopted for semi‐quantitative estimation of factors responsible for the conformational preference as well as a qualitative inspection of occupied canonical molecular orbitals (MOs). It was shown that [σ–(σ* + π*)(C?O)] and [σ–σ*(Ph) and π(Ph)–σ*] hyperconjugations are the main factors controlling the conformational preferences between the syn and anti conformations. Other types of effects such as electrostatic effects were also investigated. The role of the fluorine atom was also clarified. Copyright © 2009 John Wiley & Sons, Ltd.     

Activated dynamics of semiflexible polymers on structured substrates

We study the thermally activated motion of semiflexible polymers in double-well potentials using field-theoretic methods. Shape, energy, and effective diffusion constant of kink excitations are calculated, and their dependence on the bending rigidity of the semiflexible polymer is determined. For symmetric potentials, the kink motion is purely diffusive whereas kink motion becomes directed in the presence of a driving force. We determine the average velocity of the semiflexible polymer based on the kink dynamics. The Kramers escape over the potential barriers proceeds by nucleation and diffusive motion of kink-antikink pairs, the relaxation to the straight configuration by annihilation of kink-antikink pairs. We consider both uniform and point-like driving forces. For the case of point-like forces the polymer crosses the potential barrier only if the force exceeds a critical value. Our results apply to the activated motion of biopolymers such as DNA and actin filaments or of synthetic polyelectrolytes on structured substrates.