Point scattering: a new geometric invariant with applications from (nano)clusters to biomolecules

A new geometric invariant is defined from "first principles" for a point ensemble, which can represent clusters, molecules, crystals, and biomolecules. The scattering of a point ensemble is defined in terms of the Euclidean distance matrix and a vector measuring the weighted departure of the points from the cluster centre. Using the Rayleigh-Ritz theorem this function is maximized obtaining the point scattering of the ensemble. The point scattering shows several properties which are useful for studying clusters, molecules, crystals, and biomolecules. We examined different natural clusters of hard spheres such as colloidal particles and fullerenes, as well as protein-peptide complexes and the effect of temperature on protein structure. In all cases point scattering differentiates point ensembles with different structures, which are not distinguished by other geometric invariants, such as the second moment of mass distribution, surface areas, and volumes. Point scattering also shows better correlation with thermodynamic parameters of binding and describes the interior cavities of hollowed ensembles better than the other geometric measures.     

Thermal detection laser spectroscopy of molecular beams

We describe the experimental methods used in carrying out high resolution infrared spectroscopy of molecular beams using bolometric thermal detection. The main applications of this technique are also described and include: studies on molecular internal vibrational relaxation, radiationless transition after “visible” excitation, photodissociation spectroscopy of van der Waals molecules, the study of coherent excitation of molecules in the infrared, multiphoton infrared spectroscopy, overtone spectroscopy and the study of large molecular clusters.     

Water dynamics in silica nanopores: the self-intermediate scattering functions

The dynamics of water molecules confined in approximately cylindrical silica nanopores is investigated using molecular simulation. The model systems are pores of diameter varying between 20 and 40 ? containing water at room temperature and at full hydration, prepared using grand canonical Monte Carlo simulation. Water dynamics in these systems is studied via molecular dynamics simulation. The results of the basic characterization of these systems have been reported in A. A. Milischuk and B. M. Ladanyi [J. Chem. Phys. 135, 174709 (2011)]. The main focus of the present study is the self-intermediate scattering function (ISF), F(S)(Q, t), of water hydrogens, the observable in quasi-elastic neutron scattering experiments. We investigate how F(S)(Q, t) depends on the pore diameter, the direction and magnitude of the momentum transfer Q, and the proximity of water molecules to the silica surface. We also study the contributions to F(S)(Q, t) from rotational and translational motions of water molecules and the extent of rotation-translation coupling present in F(S)(Q, t). We find that F(S)(Q, t) depends strongly on the pore diameter and that this dependence is due mainly to the contributions to the ISF from water translational motion and can be attributed to the decreased mobility of water molecules near the silica surface. The relaxation rate depends on the direction of Q and is faster for Q in the axial than in the radial direction. As the magnitude of Q increases, this difference diminishes but does not disappear. We find that its source is mainly the anisotropy in translational diffusion at low Q and in molecular reorientation at higher Q values.     

On the determination of absolute vibrational excitation probabilities in molecule-surface scattering: Case study of NO on Au(111)

We describe a method to obtain absolute vibrational excitation probabilities of molecules scattering from a surface based on measurements of the rotational state, scattering angle, and temporal distributions of the scattered molecules and apply this method to the vibrational excitation of NO scattering from Au(111). We report the absolute excitation probabilities to the v = 1 and v = 2 vibrational states, rotational excitation distributions, and final scattering angle distributions for a wide range of incidence energies and surface temperatures. In addition to demonstrating the methodology for obtaining absolute scattering probabilities, these results provide an excellent benchmark for theoretical calculations of molecule-surface scattering.     

Interference effects in resonance raman spectroscopy

We show that resonance Raman excitation profiles are not generally expected to superimpose on the profile of the absorption spectrum. The discrepancy is due to interference between transition amplitudes of preresonant and more nearly resonant states. Two cases are outlined: in the first the amplitudes have similar magnitudes, and in the second they are quite different. Examples discussed include hemeproteins, visual pigments and resonant scattering from triplet states of molecules. A main point is that qualitative aspects of these interferences may be used to assign states and vibrations. Some new experiments are reported for ferrocytochrome-c scattering.     

Scattering resonances in slow NH3-He collisions

We theoretically study slow collisions of NH(3) molecules with He atoms, where we focus in particular on the observation of scattering resonances. We calculate state-to-state integral and differential cross sections for collision energies ranging from 10(-4) cm(-1) to 130 cm(-1), using fully converged quantum close-coupling calculations. To describe the interaction between the NH(3) molecules and the He atoms, we present a four-dimensional potential energy surface, based on an accurate fit of 4180 ab initio points. Prior to collision, we consider the ammonia molecules to be in their antisymmetric umbrella state with angular momentum j = 1 and projection k = 1, which is a suitable state for Stark deceleration. We find pronounced shape and Feshbach resonances, especially for inelastic collisions into the symmetric umbrella state with j = k = 1. We analyze the observed resonant structures in detail by looking at scattering wavefunctions, phase shifts, and lifetimes. Finally, we discuss the prospects for observing the predicted scattering resonances in future crossed molecular beam experiments with a Stark-decelerated NH(3) beam.     

Incoherent subharmonic light scattering in isotropic media

Incoherent subharmonic light scattering in isotropic media is a new kind of nonlinear light scattering, which involves single input photon and multiple output photons of equal frequency. We investigate theoretically the dependence of the subharmonic scattering intensity on the hyperpolarizability of molecules and the incident intensity using nonlinear optics theory similar to that used for Hyper-Rayleigh scattering and degenerate optical parametric oscillators. It is derived that the subharmonic scattering intensities grow exponentially or superexponentially with the hyperpolarizability of molecules and the incident intensity.     

Anisotropic Picosecond X-ray Solution Scattering from Photo-selectively Aligned Protein Molecules

Anisotropic X-ray scattering patterns of transiently aligned protein molecules in solution are measured by using pump-probe X-ray solution scattering. When a linearly polarized laser pulse interacts with an ensemble of molecules, the population of excited molecules is created with their transition dipoles preferentially aligned along the laser polarization direction. We measured the X-ray scattering from the myoglobin protein molecules excited by a linearly polarized, short laser pulse and obtained anisotropic scattering patterns on 100 ps time scale. An anisotropic scattering pattern contains higher structural information content than a typical isotropic pattern available from randomly oriented molecules. In addition, multiple independent diffraction patterns measured by using various laser polarization orientations will give substantially increased amount of structural information compared with a single isotropic pattern. By monitoring the temporal change of the anisotropic scattering pattern from 100 ps to 1 μs, we observed the orientational dynamics of photo-generated myoglobin with the rotational diffusion time of ～15 ns.     

Can the transition from tunneling to hopping in molecular junctions be predicted by theoretical calculation?

The electron transport mechanism changes from tunneling to hopping as molecular length increases. To validate the theoretical simulation after the transition point and clarify influence of electronic structures on the transition, we calculated the conductance of a series of conjugated molecules by density functional theory together with the nonequilibrium Green's function. We found that the highest occupied molecular orbital energy level, transmission spectrum, and the reorganization energy are good indicators for the transition of the electron transport mechanism. The calculated resistances of short junctions (<50 Å, before the transition point) are consistent with the experimental result, following the tunneling mechanism. However, the theoretical predication failed for long molecules, indicating the limitation of the theoretical framework of elastic scattering when the electron transport mechanism changes to hopping. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Rotational predissociation of extremely weakly bound atom-molecule complexes produced by Feshbach resonance association

We study the rotational predissociation of atom-molecule complexes with very small binding energy. Such complexes can be produced by Feshbach resonance association of ultracold molecules with ultracold atoms. Numerical calculations of the predissociation lifetimes based on the computation of the energy dependence of the scattering matrix elements become inaccurate when the binding energy is smaller than the energy width of the predissociating state. We derive expressions that represent accurately the predissociation lifetimes in terms of the real and imaginary parts of the scattering length and effective range for molecules in an excited rotational state. Our results show that the predissociation lifetimes are the longest when the binding energy is positive, i.e., when the predissociating state is just above the excited state threshold.     

Single Molecules as Optical Nanoprobes for Soft and Complex Matter

The optical signals of single molecules provide information about structure and dynamics of their nanoscale environment, free from space and time averaging. These new data are particularly useful whenever complex structures or dynamics are present, as in polymers or in porous oxides, but also in many other classes of materials, where heterogeneity is less obvious. We review the main uses of single molecules in studies of condensed matter at nanometer scales, especially in the fields of soft matter and materials science. We discuss several examples, including the orientation distribution of molecules in crystals, rotational diffusion in glass‐forming molecular liquids, polymer studies with probes and labeled chains, porous and heterogeneous oxide materials, blinking of single molecules and nanocrystals, and the potential of surface‐enhanced Raman scattering for local chemical analysis. All these examples show that static and dynamic heterogeneities and the spread of molecular parameters are much larger than previously imagined.     

Helium atom scattering from oxide surfaces.

Many experimental methods of surface science employ electrons or photons of considerable incident energy as probe particles. However, insulating surfaces or delicate physisorbed layers may be damaged by these particles and should, therefore, be analyzed with a gentler probe: He atom scattering allows to determine the symmetry of the unit cell and the detection of phase transitions from diffraction measurements as well as the determination of surface and adsorbate vibrations by time-of-flight resolved detection. Herein, the application of He atom scattering to oxide surfaces is demonstrated on the basis of the examples of MgO and ZnO. MgO(001) is a very inert and stable surface, whereas hydrogen atoms are chemisorbed on the mixed-terminated ZnO(1010) and on both polar faces: ZnO(0001) and ZnO(0001). He atom scattering is very sensitive to the presence of hydrogen on surfaces. In addition ZnO reacts with molecules such as water, CO and CO(2). It is demonstrated that in combination with photoelectron spectroscopy and thermal desorption spectroscopy He atom scattering can also contribute to studies of surface chemistry.     

Silver Nanowire-Templated Molecular Nanopatterning and Nanoparticle Assembly for Surface-Enhanced Raman Scattering

Developing simple and cost-efficient methods for fabricating molecular patterns is of great importance in the field of nanoscience and nanotechnology. Here, a simple and convenient method was developed for fabricating nanopatterns composed of positively charged silane molecules by using silver nanowires as templates. The as-obtained silane pattern copies the shape of the silver nanowires and is only 0.7 nm thick, which can later be used for templated assembly of small molecules and nanoparticles of opposite charges. As a proof of concept, the resultant assembly could be further used for surface-enhanced Raman scattering.     

The Story Behind the Link between Molecular Chirality and Crystal Shape

Here we describe the story behind the link between molecular chirality and macroscopic phenomena, the latter being a probe for the direct assignment of absolute configuration of chiral molecules. First, a brief tour of the history of molecular stereochemistry, starting with the classic experiment reported by Pasteur in 1848 on the separation of enantiomorphous crystals of a salt of tartaric acid, and his conclusion that the molecules of life are chiral of single-handedness. With time, this study raised, inter alia, two fundamental questions: the absolute configuration of chiral molecules and how a molecule of given configuration shapes the enantiomorphous morphology of its crystal. As for the first question, following the beginning of crystal structure determination by X-ray diffraction in 1912, it took almost 40 years before Bijvoet assigned molecular chirality through the esoteric method involving anomalous X-ray scattering. We have been able to address and link both questions through ‘everyday concepts of left and right’ (in the words of Jack Dunitz) by the use of ‘tailor-made’ auxiliaries. By such means, it proved possible to reveal, through morphology, etch patterns, epitaxy and symmetry reduction of both chiral and, paradoxically, centrosymmetric crystals, the basic chiral symmetry of the molecules of life, the α-amino acids and sugars.     

Enhanced Raman scattering as a probe for 4-mercaptopyridine surface-modified copper oxide nanocrystals.

We report on the application of Raman scattering as a probe to study 4-mercaptopyridine (4-Mpy) surface-modified CuO nanocrystals. Enhanced Raman scattering from 4-Mpy adsorbed on CuO nanocrystals was observed. The Raman signals displayed 10(2) enhancement compared with those of 4-Mpy in solution. We compared the Raman spectra of 4-Mpy molecules adsorbed on CuO nanocrystals and Ag, Cu substrate. A particular feature of the semiconductor substrate that was different from the metal substrate was revealed. The excitation wavelength-dependent behavior was clearly observed.     

The use of polarized light scattering for the study of the dynamics of the spinodal decomposition

Due to the fact that in a system undergoing spinodal decomposition the long wavelength fluctuations are enhanced, we expect that multiple events can be observed when the passage of light through the sample is measured. We study here the intensity of double scattering for both polarized and depolarized measurements, as a function of time and angle of detection. The time dependence is nonexponential and the dependence on the scattering wave vector is less pronounced than in the case of single scattering. For systems with spherical molecules it is possible to separate double and single scattering contributions if both polarized and depolarized measurements are made. This increases the amount and quality of information about the dynamics of the spinodal decomposition that can be obtained from light scattering experiments.     

A fixed-nuclei,ab initio treatment of low-energy electron-H2O scattering

We report the results of a theoretical study of low-energy electron-H₂O scattering. The calculations employ the complex Kohn variational technique and are undertaken at both the static-exchange and polarized-SCF levels. Target polarization effects are included by using an ab initio optical potential. Particular attention is paid to the complications attending electron scattering from target molecules that possess a permanent dipole moment. We describe the steps necessary to extract meaningful differential cross sections from fixed-nuclei calculations that ignore the rotational motion of the target. Comparison is made with experiment as well as other recent theoretical treatments.     

Scattering theory for Stark Hamiltonians

We give an introduction to the spectral and scattering theory for Schr?dinger operators. An abstract short range scattering theory is developed. It is applied to perturbations of the Laplacian. Particular attention is paid to the study of Stark Hamiltonians. The main result is an explanation of the discrepancy between the classical and the quantum scattering theory for one-dimensional Stark Hamiltonians.     

Advantages of time-resolved difference X-ray solution scattering curves in analyzing solute molecular structure

Time-resolved X-ray solution scattering provides a powerful method for investigating reaction dynamics in the solution phase. Since X-rays scatter from all atoms in the solution sample, the scattering intensity is contributed from not only the solute but also the solvent and the solute–solvent cross terms. For a typical concentration the solvent molecules outnumber the solute molecules and thus the relative sensitivity of the scattering intensity to the solute structure is extremely low. To increase the structural sensitivity to the solute and to extract only the signal from structural changes, time-resolved difference scattering signal is obtained by subtracting the original raw scattering curve at a negative reference time delay from that at a positive time delay. Here we show and emphasize that time-resolved difference X-ray scattering curves generally exhibit higher structural sensitivity to the solute molecular structure and lower influence from experimental background and imperfection of theory than original raw scattering curves. These characteristics justify the validity of fitting models to difference curves to obtain transient structural information even when the magnitude of the time-resolved difference curves is smaller than the discrepancy between the theory and experiment for the original scattering curve. We considered small molecules and proteins in solution probed by time-resolved X-ray solution scattering.     

氨基甲酸酯型脱氧胆酸分子钳对中性分子的识别性能研究

利用差紫外光谱法考察了新型分子钳1～6对苯胺、对硝基苯胺、对甲氧基苯胺等中性分子的识别性能, 测定了25 ℃下, 在CHCl₃中主客体间的结合常数(K_a)和自由能变化(ΔG⁰). 结果表明, 所有分子钳主体对所考察的客体分子显示良好的识别作用, 主客体间形成1∶1型主客体络合物. 识别作用的主要推动力为多重氢键和π-π重叠等的作用. 讨论了主客体间形状、大小匹配和几何互补及识别模式等因素对识别能力的影响, 并利用核磁共振氢谱与计算机模拟作为辅助手段对实验结果进行了解释.