Orientational motions of vibrational chromophores in molecules at the air/water interface with time-resolved sum frequency generation

The first time-resolved experiments in which interfacial molecules are pumped to excited electronic states and probed by vibrational sum frequency generation (SFG) are reported. This method was used to measure the out-of-plane rotation dynamics, i.e. time dependent changes in the polar angle, of a vibrational chromophore of an interfacial molecule. The chromophore is the carbonyl group, the rotation observed is that of the -C=O bond axis, with respect to the interfacial normal, and the interfacial molecule is coumarin 314 (C314) at the air/water interface. The orientational relaxation time was found to be 220+/-20 ps, which is much faster than the orientational relaxation time of the permanent dipole moment axis of C314 at the same interface, as obtained from pump-second harmonic probe experiments. Possible effects on the rotation of the -C=O bond axis due to the carbonyl group hydrogen bonding with interfacial water are discussed. From the measured equilibrium orientation of the permanent dipole moment axis and the carbonyl axis, and knowledge of their relative orientation in the molecule, the absolute orientation of C314 at the air/water interface is obtained.     

Analyse conformationnelle théorique des molécules de benzylidène-aniline, stilbène et azobenzène : Partie II. Résultats de la méthode PCILO et ajustement d''un potentiel empirique

A conformational study of the benzylidene-aniline stilbene and azobenzene isoelectronic molecules has been carried out by the PCILO method in terms of torsional angles, bond lengths and valence angles. Initially, the conditions of application of this method to highly conjugated molecules were defined. The optimized geometries are in good agreement with those determined in the gas phase. Furthermore the rotation around a Ф—N or Ф—C bond can be specifically related to the variation of the second-order correction to the energy. This term was used to adjust the torsional potential in an empirical method adapted to this kind of molecule and able to account for both theoretical and experimental results.     

Theoretical modeling of energy redistribution and stereodynamics in CF scattering from Si(100) under grazing incidence

We have simulated CF scattering from Si(100) using the molecular dynamics method. Translational energy loss spectra are presented. The shape of the energy loss distribution as a result of internal energy release is analyzed. At the classical turning point, the internal energy of the molecule is mainly in the form of rotational energy. The strong rotational excitation results in additional molecule-surfaces interactions during the latter half of the collision. These additional collisions permit some molecules that initially gain internal energy exceeding the bond strength to ultimately survive the collision process via rotational de-excitation. The rotational motion exhibited by surviving molecules is determined by the combination of the molecular axis orientation and the local surface structure during the collision process. The rotation planes of the surviving molecules are preferentially aligned with the surface normal (cartwheel-like and propeller-like motions). In this study, propeller-like motion of the surviving molecules is predicted. The majority of surviving molecules exhibit a cartwheel-like motion. However, molecules that gain a propeller-like rotation exhibit a much better alignment of their planes-of-rotation compared with molecules exhibiting cartwheel-like motion.     

ESR study of molecular dynamics and orientation of TEMPO included in organic 1-D nanochannel

A mixture of 2,2,6,6-tetramethyl-1-piperidinyloxyl (TEMPO) radical and 2,2,6,6-tetramethyl-1-piperidine (TEMP) was included into organic 1-D nanochannels of tris(o-phenylenedioxy)cyclotriphosphazene (TPP) crystal. Dilution of the paramagnetic TEMPO radical was achieved with excess TEMP, thereby isolating a TEMPO molecule in the nanochannel. For inclusion compounds of TPP with TEMPO and TEMP (TEMPO/all guest compounds = 0.017, and 0.15), temperature-dependent electron spin resonance (ESR) spectra were observed to investigate their molecular dynamics and orientation. In the temperature range from 112 K to room temperature, the spectra depended remarkably on the temperature. Temperature dependence was well interpreted by uniaxial rotation, suggesting that TEMPO molecules undergo uniaxial rotation about a channel axis with a molecular orientation in which the N-O bond in the nitroxide group is perpendicular to the channel axis. The activation energy of uniaxial rotation was evaluated as 4.5 +/- 0.3 kJ mol(-1).     

The bond bundle in open systems

Much of modern chemistry is concerned with the properties and dynamics of chemical bonds. Although they have been described variously, the most familiar representation is that of a link connecting two atoms. However, no one has yet developed a scheme by which to partition a molecule into bond volumes with well‐defined properties. As a consequence, the chemical bond is left as nothing more than a heuristic devise. Here, we show molecules can be partitioned into bond‐bundles–volumes that share many of the properties associated with the conceptual bond. This partitioning follows naturally through an extension of Baders topological theory of molecular structure. Surprisingly, it also bounds regions of space containing nonbonding or lone‐pair electrons and leads to bond orders consistent with those expected from theories of directed valance. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Ultrafast electron diffraction: oriented molecular structures in space and time.

The technique of ultrafast electron diffraction allows direct measurement of changes which occur in the molecular structures of isolated molecules upon excitation by femtosecond laser pulses. The vectorial nature of the molecule-radiation interaction also ensures that the orientation of the transient populations created by the laser excitation is not isotropic. Here, we examine the influence on electron diffraction measurements--on the femtosecond and picosecond timescales--of this induced initial anisotropy and subsequent inertial (collision-free) molecular reorientation, accounting for the geometry and dynamics of a laser-induced reaction (dissociation). The orientations of both the residual ground-state population and the excited- or product-state populations evolve in time, with different characteristic rotational dephasing and recurrence times due to differing moments of inertia. This purely orientational evolution imposes a corresponding evolution on the electron scattering pattern, which we show may be similar to evolution due to intrinsic structural changes in the molecule, and thus potentially subject to misinterpretation. The contribution of each internuclear separation is shown to depend on its orientation in the molecular frame relative to the transition dipole for the photoexcitation; thus not only bond lengths, but also bond angles leave a characteristic imprint on the diffraction. Of particular note is the fact that the influence of anisotropy persists at all times, producing distinct differences between the asymptotic "static" diffraction image and the predictions of isotropic diffraction theory.     

The conformational properties of glycosidic linkages

The developments in stereochemistry which have made possible our present appreciation of the preferred orientation of the aglycon for a glycopyranoside are briefly reviewed. Recent studies in this laboratory are presented wherein, for model compounds, measurements were made of the coupling constant between the ¹³C-aglyconic carbons and anomeric hydrogens as an estimate of the torsion angles, of ¹³C-chemical shifts as a measure of relative steric compressions at the anomeric centers, and of contributions to the molecular rotations by units of conformational asymmetry defined by atoms about the glycosidic bond. These measurements are compared to the results of hard-sphere calculations. It is concluded that the exo-anomeric effect offers an important resistance to rotation about the anomeric carbon to glycosidic bond (φ angles) and that the preferred conformation for a glycopyranoside arise mainly from rotation about the aglyconic carbon to glycosidic oxygen bond (ψ angles).     

Microscopic origin of spontaneous polarization in ferroelectric SC* liquid crystals

The origin of spontaneous polarization in the ferroelectric smectic C* phase is investigated within a mean-field microscopic model which describes the coupling between the tilt of molecules from the normal to the smectic layers and the rotation of a molecule around its long axis. The mean-field potential is studied which takes into account a chiral polar and a non-chiral quadrupolar biasing of the rotation of molecules around the molecular long axes. Each molecule is characterized by three transverse molecular axes: the chiral axis which turns parallel to the macroscopic C₂ axis at small tilts, the polar axis in the direction of the transverse dipole moment and the quadrupolar axis which tends to be parallel to the C₂ axis at very large tilts. A numerical analysis of the model shows that there are four different types of spontaneous polarization dependent on the temperature, including the sign-reversal type. The influence of three microscopic parameters, i.e. two angles between the three characteristic axes and the relative strength of the chiral versus the non-chiral biasing, on the type of spontaneous polarization is investigated. The relationship between the microscopic and the equivalent Landau model is established and discussed.     

Statistical thermodynamics of internal rotation in a hindering potential of mean force obtained from computer simulations

A method of statistical estimation is applied to the problem of one-dimensional internal rotation in a hindering potential of mean force. The hindering potential, which may have a completely general shape, is expanded in a Fourier series, the coefficients of which are estimated by fitting an appropriate statistical-mechanical distribution to the random variable of internal rotation angle. The function of reduced moment of inertia of an internal rotation is averaged over the thermodynamic ensemble of atomic configurations of the molecule obtained in stochastic simulations. When quantum effects are not important, an accurate estimate of the absolute internal rotation entropy of a molecule with a single rotatable bond is obtained. When there is more than one rotatable bond, the "marginal" statistical-mechanical properties corresponding to a given internal rotational degree of freedom are reduced. The method is illustrated using Monte Carlo simulations of two public health relevant halocarbon molecules, each having a single internal-rotation degree of freedom, and a molecular dynamics simulation of an immunologically relevant polypeptide, in which several dihedral angles are analyzed.     

Ultrafast 2D IR anisotropy of water reveals reorientation during hydrogen-bond switching

Rearrangements of the hydrogen bond network of liquid water are believed to involve rapid and concerted hydrogen bond switching events, during which a hydrogen bond donor molecule undergoes large angle molecular reorientation as it exchanges hydrogen bonding partners. To test this picture of hydrogen bond dynamics, we have performed ultrafast 2D IR spectral anisotropy measurements on the OH stretching vibration of HOD in D(2)O to directly track the reorientation of water molecules as they change hydrogen bonding environments. Interpretation of the experimental data is assisted by modeling drawn from molecular dynamics simulations, and we quantify the degree of molecular rotation on changing local hydrogen bonding environment using restricted rotation models. From the inertial 2D anisotropy decay, we find that water molecules initiating from a strained configuration and relaxing to a stable configuration are characterized by a distribution of angles, with an average reorientation half-angle of 10°, implying an average reorientation for a full switch of ≥20°. These results provide evidence that water hydrogen bond network connectivity switches through concerted motions involving large angle molecular reorientation.     

Fast clustering of equivalent structures in crystal structure prediction

Most methods of crystal structure prediction generate many trial structures. Because these may differ in choice of unit cell, it is not always immediately obvious whether or not two such structures are equivalent. A method to answer this question is described for the case where the asymmetric unit contains one molecule in a general position, defined by the rotation and translation of that molecule with respect to some reference geometry. In the comparison of two structures, the rotation needed to transform one orientation into the other is determined first. Then it is checked whether this rotation corresponds to a transformation that is compatible with the imposed space group symmetry. A final test compares the cell lengths, the cell angles, and the molecular centers of gravity after the transformation of one structure into the other. The method is implemented for triclinic, monoclinic, and orthorhombic systems and is found to be very fast in tests on hypothetical crystal structures of acetic acid. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 :1036–1042, 1997     

透射电镜薄样品倾转过程中的附加旋转及其计算

模拟透射电镜双倾台进行样品位向调整过程,推导出反映样品倾转前后其合成倾转轴(即共有菊池线对的法线)方向变化规律的计算公式,称为附加旋转角计算公式。指出,实现样品位向调整的双倾操作,等效于样品绕其合成倾转轴的倾转及该倾转轴绕Z轴(平行入射束方向)的旋转之和。利用双倾台对薄膜样品进行的系列倾转实验表明,由附加旋转角公式计算的附加旋转角和实测值相一致。还根据双倾操作过程导出了合成倾转角的计算公式,它可用于判断样品位向调整的准确度。     

Absolute orientation of molecules at interfaces

A method to determine the absolute orientation of molecules at liquid interfaces by sum frequency generation (SFG) is reported. It is based on measurements of the orientations of two nonparallel vibrationally active chromophores in the molecule of interest combined with a rotation matrix formulation to obtain the absolute molecular orientation. We chose m-tolunitrile, a planar molecule adsorbed to the air/water interface, as a proof-of-method experiment. Quantitative analysis of different polarization sum frequency intensities facilitate unique peak assignments of the methyl and nitrile groups of m-tolunitrile. The SFG analysis of the measurement yields a nitrile group tilting at 53 degrees to the surface normal, and the C3 axis of the methyl group is almost upright at 23 degrees with respect to the surface normal. Using a rotation matrix formulation, we found that the angle between the surface plane and the m-tolunitrile molecular plane is 70 degrees.     

Efficient algorithm for quantitative assessment of similarities among atoms in molecules

A new algorithm for quantitative assessment of similarity between two atoms in molecules is presented. Both the atomic similarity index and its derivatives with respect to the three Euler angles that describe the mutual orientation of the atoms under comparison are computed efficiently by taking advantage of the recently developed analytical representations for atomic zero-flux surfaces. The use of such representations makes it possible to substantially enhance the accuracy of the computed similarity indices without increasing the cost of their evaluation. Numerical tests involving oxygen atoms in several carbonyl compounds demonstrate the ability of the new algorithm to discern small changes in atomic similarity that are brought about by second-neighbor effects. Comparisons among hydrogen atoms in the acrolein molecule reveal the usefulness of the similarity index in detection and quantification of the effects of steric interactions on atomic shapes. © 1996 by John Wiley & Sons, Inc.     

Simulation of EPR and time resolved EPR lineshapes in partially ordered glasses

Simulation of magnetic resonance spectra of probes in partially ordered glasses requires in principle a numerical integration on the full set of three Euler angles omega=(alpha beta gamma) from a laboratory fixed to a molecule fixed reference frame. It is shown that it is possible to manage efficiently this problem by using the algebraic properties of the Wigner matrix elements. This analysis is applied to time resolved EPR (TREPR) spectra of a series of bis-adducts of C60 in the ordered glass of a nematic liquid crystal solvent. A paramagnetic triplet state is created by light excitation and TREPR spectra are obtained with the external magnetic field set parallel or perpendicular to the director n of the mesophase. The preferred orientation in the mesophase of the triplet state zero field tensor is determined.     

4‐(Pyrrol‐1‐yl)‐1,2,4‐triazole

The asymmetric unit of the title compound, C₆H₆N₄, comprises one and a half molecules with a C₂ axis through the second molecule. Each molecule consists of two planar five‐membered rings connected by a triazole–pyrrole N—N bond with the triazole ring close to being at right angles to the pyrrole ring. The molecules are linked by C—H...N hydrogen bonds and weaker offset face‐to‐face π–π interactions.     

The influence of layer curvature on switching in ferroelectric B2 phases of liquid crystals having bent-shape molecules

In the B₂ phase of liquid crystalline compounds with bent-shape molecules ferroelectric switching can occur either by molecular rotation on the cone or by rotation of the molecule about its long axis (so-called chirality flipping), or by both mechanisms simultaneously. When the smectic layers of the B₂ phase are non-deformed and parallel the rotation of molecules under an external electric field occurs readily on the surface of the cone, while rotation around the long molecular axis is hindered by an energy barrier. Imposed deformation of smectic layers leads to interaction between local layer curvatures and molecular orientation, which results in the energy barrier hindering the molecular rotation by a cone. For appropriate constants describing this interaction the energy barrier can be so high that chirality flipping becomes the principal switching mode. An increase in the electric field can eliminate layer curvature, and therefore the energy barrier, so that switching with molecular rotation on the cone becomes possible. In the present contribution these mechanisms of switching are discussed and the influence of layer curvature on the switching mode is demonstrated.     

偶氮共轭聚合物光电特性研究进展

芳香环或杂环通过NN双键连接形成的化合物如偶氮苯、偶氮吡咯等具有π共轭结构,此类分子有顺反两种构型,他们可以在光照条件下相互转换。分子构型转变会影响电子的共轭程度及其离域特性,因此含环结构的偶氮共轭分子具有光调制特性。反式偶氮苯分子为平面结构,顺式构型分子两个苯环有一定角度的扭转分子不在同一平面,实验和理论计算结果表明偶氮苯分子的键长、键角等受溶剂和取代基影响;光照可以实现偶氮苯分子的导电性改变,目前认为其导电性改变的原因主要是光致顺反异构而改变分子尺寸而引起。通过氮氮双键连接的杂环共轭分子能显著地降低分子的能隙,并使共轭化合物在更宽的波长范围内有强吸收,能提高太阳能光伏电池的转换效率,是理想的有机光伏材料。文章还对偶氮共轭聚合物的合成方法做了介绍,分析了含偶氮结构的共轭聚合物的光相应研究现状及其未来发展趋势。     

苯-卤素(X2, X=F, Cl, Br, I)相互作用本质的对称性匹配微扰理论研究

在MP2水平下对被定义为"电荷转移复合物(CTC)"的苯(C6H6)-卤素分子X2(X＝F, Cl, Br, I)相互作用体系进行了量子化学研究. 在优化所得C6H6-X2(X＝F, Cl, Br, I)复合物的平衡几何结构中, 卤素分子X2接近垂直指向苯环上碳-碳双键的中心. 自然键轨道(NBO)分析结果表明, 苯-卤素体系中电荷转移的数量很少. 对称性匹配微扰理论(Symmetry-adapted perturbation theory, SAPT) 能量分解结果显示, 在4个复合物体系中, 静电作用的贡献相对较小(只占总吸引作用的20%左右), 对于C6H6-F2体系, 色散作用是其主要吸引作用, 对于C6H6-Cl2, C6H6-Br2和C6H6-I2 体系, 诱导作用则是其主要的吸引作用, 从F到I, 色散作用逐渐减弱, 诱导作用逐渐增强, 表明在电子相关水平上将苯-卤素体系称为"电荷转移复合物"的说法并不确切.