Molecular monolayer-mediated control over semiconductor surfaces: evidence for molecular depolarization of silane monolayers on Si/SiO(x)

We show that, for molecules with particularly strong dipoles, their organization into a monomolecular layer can lead to depolarization, something that limits the range over which the substrate's work function can be changed. It appears that, with molecules, depolarization is achieved by changes in orientation and conformation, rather than by charge transfer to the substrate as is common for atomic layers.     

Thermal hysteresis and thickness dependence of the molecular orientation of poly(di-n-hexylsilane) in the film state

Molecular orientation of poly(di-n-hexylsilane) adsorbed on poly(vinyl alcohol) film has been studied by making use of the stretching technique. Dichroic ratio, Rd, strongly depended on the thickness of poly(di-n-hexylsilane) thin film and the highest value ca. 19 was observed at the film thickness of 110 +/- 30 nm. The thermal hysteresis of the molecular orientation was observed in the heating-cooling cycles. By studying the fluorescence spectrum it was confirmed that a portion of the poly(di-n-hexylsilane) molecules were in transoid conformation even at 320 K, although most of poly(di-n-hexylsilane) molecules were in disordered conformation (conformation D). This poly(di-n-hexylsilane) in transoid conformation is formed in the stretching process and may play a role of crystallization nucleus to induce the whole orientation of the poly(di-n-hexylsilane) in the film state.     

New mechanistic insight in the thermal helix inversion of second-generation molecular motors

The introduction of dibenzocyclohepten-5-ylidene as part of a unidirectional light-driven molecular motor allows a more complete picture of the pathway of thermal helix inversion to be developed. The most stable conformation is similar to that found in related motors in that it has, overall, an anti-folded structure with the substituent at the stereogenic centre adopting an axial orientation. Photochemical cis/trans isomerisation at -40 degrees C results in the formation of an isomer in a syn-folded conformation with the methyl group in an axial orientation. This contrasts with previous studies on related molecular rotary motors. The conformation of the higher energy intermediate typically observed for this class of compound is the anti-folded conformation, in which the methyl group is in an equatorial orientation. This conformation is available through an energetically uphill upper half ring inversion of the observed photochemical product. However, this pathway competes with a second process that leads to the more stable anti-folded conformation in which the methyl group is oriented axially. It has been shown that the conformations and pathways available for second-generation molecular motors can be described by using similar overall geometries. Differences in the metastable high-energy species are attributable to the relative energy and position on the reaction coordinate of the transition states. Kinetic studies on these new molecular motors thus provide important insights into the conformational dynamics of the rotation cycle.     

Conformational and configurational analysis of 2-phenoxy-2-oxo-1,3,2-dioxaphosphorinanes. Conformational and configurational dependence upon conformation of the diol precursor

Diastereomeric 5-tert-butyl-4-methyl-2-phenoxy-2-oxo-1,3,2-dioxaphosphorinanes were synthesized, and studied by NMR and computational methods in order to determine their predominant conformations as well as their relative configurations. The study was performed assuming a novel criteria, in which, the conformation and configuration of the diastereomeric 5-tert-butyl-4-methyl-2-phenoxy-2-oxo-1,3,2-dioxaphosphorinanes depend upon the conformation of the corresponding diol precursors. In other words, the orientation or pseudo orientation of the groups into the ring framework of the heterocyclic is initially acquired by the direct phosphorylation reaction with the diol precursor in the most stable conformation, and then, once the heterocyclic is formed, the final conformation is dictated by stereoelectronic and steric effects.     

一种反铁电液晶薄膜相变过程的变温红外光谱研究

通过变温红外光谱对反铁电液晶MHOCPOOB薄膜相变过程中的分子构象、排布及相互作用的变化进行了研究.结果表明,室温时,薄膜中的分子烷基链同时含有zigzag和gauche两种构象.随着温度的升高,有序的zigzag构象转化为无序的gauche构象,链的扭曲程度增加.但S^*IA到S^*CA的转变并不引起烷基链构象和取向发生明显变化.刚性核中的羰基与相邻的苯环形成共轭体系,苯环之间相互倾斜排列,在相变过程中羰基与苯环的共平面作用逐渐被打破,且在相变点苯环间的二面角明显增大.     

Ab initio study of a purine nucleoside: Adenosine

The ab initio SCF LCAO-MO method is used to compute the main electronic properties of a purine nucleoside, adenosine, in two specific conformational arrangements (3′-endo conformation of the ribose, gt orientation of the extracyclic CH₂OH group, anti orientation of the base with respect to the sugar and 3′-endo conformation of the ribose, gg orientation of the extra-cyclic CH₂OH group, syn orientation of the base with respect to the sugar). The results are compared with those performed for the isolated component fragments, adenine and 3′-endo riboses.     

Orientation in nylon 6 films as determined by the three-dimensional polarized infrared technique

A three-dimensional polarized infrared technique was used to obtain information about molecular orientation in both uniaxially and biaxially drawn nylon 6 films. The 835 and 930 cm^?1 bands were used to describe the orientation of the A (extended chain) conformation while absorptions at 1175 cm^?1, and 1120 cm^?1 and 1075 cm^?1 were used to give some information about orientation of the B (twisted chain) conformation. On the basis of the 835 and 930 cm^?1 bands, it was shown that the hydrogen-bonded sheets made up of chains in the A conformation are parallel to the film surface in the biaxially drawn film. Uniaxially drawn films obtained by drawing both at 100 and 150°C showed a high degree of chain alignment in the draw direction for the A conformation at draw ratios greater than 2.5. Some planar orientation was also observed in these uniaxially drawn films for both the A and B conformations at high draw ratios.     

Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity

Canonical duplex RNA assumes only the A-form conformation at the secondary structure level while, in contrast, a wide range of noncanonical, tertiary conformations of RNA occur. Here, we show how the 2'-hydroxyl controls RNA conformational properties. Quantum mechanical calculations reveal that the orientation of the 2'-hydroxyl significantly alters the intrinsic flexibility of the phosphodiester backbone, favoring the A-form in duplex RNA when it is in the base orientation and facilitating sampling of a wide range of noncanonical, tertiary structures when it is in the O3' orientation. Influencing the orientation of the 2'-hydroxyl are interactions with the environment, as evidenced by crystallographic survey data, indicating the 2'-hydroxyl to sample more of the O3' orientation in noncanonical RNA structures. These results indicate that the 2'-hydroxyl acts as a "switch", both limiting the conformation of RNA to the A-form at the secondary structure level and allowing RNA to sample a wide range of noncanonical tertiary conformations.     

Synthesis of Piperidine Nucleosides as Conformationally Restricted Immucillin Mimics

The de novo synthesis of piperidine nucleosides from our homologating agent 5,6-dihydro-1,4-dithiin is herein reported. The structure and conformation of nucleosides were conceived to faithfully resemble the well-known nucleoside drugs Immucillins H and A in their bioactive conformation. NMR analysis of the synthesized compounds confirmed that they adopt an iminosugar conformation bearing the nucleobases and the hydroxyl groups in the appropriate orientation.     

Ab initio determination of the flexibility of 2'-aminoribonucleosides and 2'-aminoarabinonucleosides inserted in duplexes

The sugar puckering of adenosine and uridine nucleosides with an amino group at 2' in the ribo or arabino orientations are determined using high-level quantum mechanical calculations Only the conformations that have dihedrals compatible with their insertion into a duplex are retained. The amino group has always been found to be pyramidal and its orientation governs the conformation of the sugar. The energetically most favorable conformation of the 2'-aminoribonucleosides has the south puckering but must be discarded. For another orientation of the 2'-amino group, the conformation is energetically less favorable but has the north puckering. Calculations performed in the presence of a water molecule give similar results but with a smaller energy gap. The model then explains why the insertion of a 2'-aminoribonucleotide destabilizes double-stranded RNAs and also double-stranded DNAs. In the arabino orientation, an NH(2) substituent at 2' favors north puckering. In contrast to 2'-aminoribonucleosides, deoxynucleosides inserted into a duplex remain in the most energetically favorable conformation compatible with the canonical values of the torsion angles. The whole relaxed potential map, in the amplitude/pseudorotation space, shows that for natural deoxyadenosine there is only one valley in the east running from south to north puckering.     

Switching extended 1,3-diequatorial and bent 1,3-diaxial states of a disubstituted hinge sugar by ligand exchange reactions on Pt(II)

The bent conformation of a trisaccharide containing 2,4-diaminoxylopyranoside, in which both end sugars are presented in 1,3-diaxial orientation, is fixed by chelation of the diamino groups to Pt(II) and unfixed by a ligand exchange reaction with NaCN or thiourea giving its extended conformation.     

Weak attractive interactions between methylthio groups and electron-deficient alkenes in peri-naphthalenes: a competition with conjugative effects

The solid-state conformations of five peri-disubstituted naphthalenes bearing a methylthio group and an electron-deficient alkene indicate a weak attractive interaction between the functional groups in four cases in which out-of-plane displacements lead to a common orientation of the MeSsp(2)-C vector to the alkene bond. In some cases the interaction is not strong enough to outweigh the tendency of the alkene to conjugate with the aromatic ring, and in one case this optimisation of conjugation alone controls the molecular conformation. The methylthio group lies close to the aromatic plane in all but one example for which the plane of the sulfide group is presented to the alkene.     

Matrix-isolation FT-IR spectroscopic study and theoretical DFT(B3LYP)/6-31++G** calculations of the vibrational and conformational properties of tyrosine

The complicated conformational isomerism of tyrosine is studied by experimental matrix-isolation FT-IR spectroscopy combined with theoretical DFT(B3LYP)/6-31++G** calculations. Not less than 18 possible conformations of tyrosine have been considered theoretically. The results revealed that the most and the less stable forms of neutral tyrosine have the same conformation of the main part of amino acid (conformation II) but they differ in orientation of the phenyl ring. The calculated values of the relative energies suggest that all conformations would be detectable in the experimental spectrum. However, it appeared that it is not possible to distinguish in the experimental spectrum between the bands due to the forms with the same conformation of the main part of amino acid but a different orientation of the phenol ring.     

Influence of N(1) protonation on the orientation of the N(6) substituent in hypermodified nucleic acid base N6-(N-glycylcarbonyl) adenine

The influence of protonation at N(1) on the conformational preferences of the N(6) substituent in the modified nucleic acid base N⁶-(N-glycylcarbonyl) adenine, gc⁶Ade, was investigated by the quantum chemical perturbative configuration interaction using localized orbitals (PCILO) method. The preferred orientation of the glycylcarbonyl substituent changes on the protonation of N(1). In the preferred conformation, the carbonyl oxygen O(10) is placed on the same side as N(1)H and provides stabilization through intramolecular hydrogen bonding of O(10) with HN(1). The amino acid component is so oriented that the carboxyl oxygen O(13b) is aligned closely with the N(6)H direction. Thus, the preferred molecular orientation is further stabilized by intramolecular hydrogen bonding involving HN(6) with O(13b). The alternative conformation has 0.5 kcal/mol higher energy than has the preferred conformation. The preferred conformation is about 1 kcal/mol more stable than is the conformation obtained by the flipping of torsion angle β alone, from the favored orientation for the unprotonated gc⁶Ade. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 62: 551–556, 1997     

Inverting Small Molecule–Protein Recognition by the Fluorine Gauche Effect: Selectivity Regulated by Multiple H→F Bioisosterism

Fluorinated motifs have a venerable history in drug discovery, but as C(sp³)?F‐rich 3D scaffolds appear with increasing frequency, the effect of multiple bioisosteric changes on molecular recognition requires elucidation. Herein we demonstrate that installation of a 1,3,5‐stereotriad, in the substrate for a commonly used lipase from Pseudomonas fluorescens does not inhibit recognition, but inverts stereoselectivity. This provides facile access to optically active, stereochemically well‐defined organofluorine compounds (up to 98 % ee). Whilst orthogonal recognition is observed with fluorine, the trend does not hold for the corresponding chlorinated substrates or mixed halogens. This phenomenon can be placed on a structural basis by considering the stereoelectronic gauche effect inherent to F?C?C?X systems (σ→σ*). Docking reveals that this change in selectivity (H versus F) with a common lipase results from inversion in the orientation of the bound substrate being processed as a consequence of conformation. This contrasts with the stereochemical interpretation of the biogenetic isoprene rule, whereby product divergence from a common starting material is also a consequence of conformation, albeit enforced by two discrete enzymes.     

以构象概念为主线的高分子物理教学实践

提出以构象概念作为教学主线,论述了构象概念的意义以及构象概念与力学状态、橡胶弹性、取向态、流变性和凝聚态的内在关系。     

NMR spectra of 1,2-difluoroethane in nematic solvents

In 1,2-difluoroethane, the gauche conformation predominates strongly. This circumstance allows the determination of its relative geometry by NMR in liquid crystals, though certain assumptions have still to be made, e.g. neglect of intermediate conformations. The principal result of the structure determination is the value of 69–70° for the dihedral angle ∠FCCF, which is quite insensitive to variations of the other internal coordinates. The value is, within the limits of error, equal to that obtained by microwave spectroscopy, but deviates from results of electron diffraction measurements.It is impossible to describe the average orientation of 1,2-difluoroethane using less than three orientation parameters. This indicates that the interconversion of the two gauche rotamers is slow compared with the reorientational motion.In an attempt to explain the lower energy of the gauche conformation relative to the trans conformation, and the high value of the dihedral angle, ∠FCCF, some explorative empirical calculations were carried out. These could not, however, reproduce the experimental data.     

Effects of chromophore orientation and molecule conformation on surface-enhanced Raman scattering studied with alkanoic acids and colloidal silver nanoparticles

Experimental studies have been carried out to gain a better understanding of the effects of chromophore orientation and molecular conformation on surface-enhanced Raman scattering (SERS) based on metal nanostructures. A series of alkanoic acids that contain a phenyl ring separated by methylene groups from the carboxylic acid, including phenylacetic acid, 3-phenylpropionic acid, 4-phenylbutyric acid, 5-phenylvaleric acid, and 6-phenylhexanoic acid, was investigated as model molecules with colloidal silver nanoparticles as SERS substrates. As the number of methylene groups increases, the molecules display an interesting zigzag intensity pattern of the phenyl ring bending mode around 1000 cm(-1) as well as a trend of appearance and disappearance of either the degenerate ring breathing mode or C[Double Bond]O vibrational mode near 1585 and 1630 cm(-1), respectively. Molecules containing an odd number of methylene units display a higher ring bending intensity and degenerate ring breathing mode and are suggested to have a trans conformation on the particle surface. Molecules with an even number of methylene units show a C[Double Bond]O vibrational mode and weaker ring bending in their SERS spectra and are suggested to have a gauche conformation on the silver nanoparticle surface. The different conformation is attributed to the varying interactions of the carboxylic group or the phenyl ring pi electrons with the silver surface. The SERS intensity was found to change little as the length between the phenyl ring and the carboxylic group was increased by adding CH(2) spacers. This is possibly because the effective distance between the phenyl ring and the silver surface does not change much with increasing number of CH(2) spacers as a result of changes in molecular conformation and variations in the phenyl ring orientation with CH(2) addition. The insight gained from this study is important for understanding SERS of complex molecules for which chromophore orientation and molecular conformation must be taken into careful consideration.     

微过氧化物酶水溶液的ABEEM/MM动力学模拟

应用原子-键电负性均衡浮动电荷分子力场(ABEEM/MM), 对微过氧化物酶水溶液进行了分子动力学模拟. 研究了水溶液对微过氧化物酶的结构, 血红素的皱裂构象以及轴配体咪唑基的取向的影响. 结果表明, 在水溶液中微过氧化物酶的骨架氨基酸是稳定的, 而血红素的皱裂构象在水分子的作用下趋于平面. 与血红素轴配体咪唑基键连的组氨酸决定着咪唑基的空间取向, 而咪唑基与血红素侧链的丙酸基的静电作用对其取向仅起次要作用.     

Insertion d'allenes : IV. Complexes η3-allylcyclopentenones coordines par une phosphine ou un phosphite

Synthesis, and stereochemical and dynamical studies of phosphine and phosphite η³-allylcyclopentenone complexes are described. One diastereoisomer (I) is obtained in a major part. The orientation of conformational equilibrium towards the B conformation for the two diastereoisomers can be explained by steric interaction of cyclopentenone and phosphine or phosphite ligands in the conformation A.