Stark-selected beam of ground-state OCS molecules characterized by revivals of impulsive alignment

We make use of an inhomogeneous electrostatic dipole field to impart a quantum-state-dependent deflection to a pulsed beam of OCS molecules, and show that those molecules residing in the absolute ground state, X(1)Σ(+), |00(0)0>, J = 0, can be separated out by selecting the most deflected part of the molecular beam. Past the deflector, we irradiate the molecular beam by a linearly polarized pulsed nonresonant laser beam that impulsively aligns the OCS molecules. Their alignment, monitored via velocity-map imaging, is measured as a function of time, and the time dependence of the alignment is used to determine the quantum state composition of the beam. We find significant enhancements of the alignment ( = 0.84) and of state purity (>92%) for a state-selected, deflected beam compared with an undeflected beam.     

The thermochemistry of adsorbates on transition metal cluster ions: relationship to bulk-phase properties

In previous work, guided ion beam tandem mass spectrometry has been used to study the reactions of the cluster cations of several transition metals (V, Cr, Fe and Ni) with D2, O2, CO2 and CD4. By examining the kinetic energy dependence of these reactions and interpreting thresholds observed for various reactions, bond energies for D, O, C, CD, CD2 and CD3 can be obtained. The results of these studies are reviewed with an emphasis on the relationship between the thermochemistry obtained from this work with that for adsorbates on bulk-phase metal surfaces. It is found that in cases where quantitative comparison can be made, for example D and O atoms, modest sized clusters bind these species to approximately the same extent as the bulk-phase surface of the same metal. As there is little information available for the molecular fragments investigated here, the cluster bond energies provide some of the first experimental values for such adsorbates on surfaces.     

Ultrafast vibrational spectroscopy of water and aqueous N-methylacetamide: Comparison of different electronic structure/molecular dynamics approaches

Kwac and Cho [J. Chem. Phys. 119, 2247 (2003)] have recently developed a combined electronic structure/molecular dynamics approach to vibrational spectroscopy in liquids. The method involves fitting ab initio vibrational frequencies for a solute in a cluster of solvent molecules to a linear combination of the electrostatic potentials on the solute atoms due to the charges on the solvent molecules. These authors applied their method to the N-methylacetamide-D/D(2)O system. We (S. A. Corcelli, C. P. Lawrence, and J. L. Skinner, [J. Chem. Phys. 120, 8107 (2004)]) have recently explored a closely related method, where instead of the electrostatic potential, the solute vibrational frequencies are fit to the components of the electric fields on the solute atoms due to the solvent molecules. We applied our method to the HOD/D(2)O and HOD/H(2)O systems. In order to make a direct comparison of these two approaches, in this paper we apply their method to the water system, and our method to the N-methylacetamide system. For the water system we find that the electric field method is superior to the potential approach, as judged by comparison with experiments for the absorption line shape. For the N-methylacetamide system the two methods are comparable.     

Ultra-sensitive high-precision spectroscopy of a fast molecular ion beam

Direct spectroscopy of a fast molecular ion beam offers many advantages over competing techniques, including the generality of the approach to any molecular ion, the complete elimination of spectral confusion due to neutral molecules, and the mass identification of individual spectral lines. The major challenge is the intrinsic weakness of absorption or dispersion signals resulting from the relatively low number density of ions in the beam. Direct spectroscopy of an ion beam was pioneered by Saykally and co-workers in the late 1980s, but has not been attempted since that time. Here, we present the design and construction of an ion beam spectrometer with several improvements over the Saykally design. The ion beam and its characterization have been improved by adopting recent advances in electrostatic optics, along with a time-of-flight mass spectrometer that can be used simultaneously with optical spectroscopy. As a proof of concept, a noise-immune cavity-enhanced optical heterodyne molecular spectroscopy (NICE-OHMS) setup with a noise equivalent absorption of ~2 × 10(-11) cm(-1) Hz(-1/2) has been used to observe several transitions of the Meinel 1-0 band of N(2) (+) with linewidths of ~120 MHz. An optical frequency comb has been used for absolute frequency calibration of transition frequencies to within ~8 MHz. This work represents the first direct spectroscopy of an electronic transition in an ion beam, and also represents a major step toward the development of routine infrared spectroscopy of rotationally cooled molecular ions.     

Monte Carlo simulation of O(1D) + H2 and O(1D) + HCl — rotational excitation of product OH radicals

Experimental studies with molecular beam and LIF techniques have independently shown that the reaction O(¹D) + H₂ → OH + H passes through a long-lived complex and gives products with small translational and large rotational excitation. We have previously published a statistical algorithm, based on ordinary RRKM theory with angular momentum restrictions included, which was designed to simulate molecular beam experiments. It has now been modified and applied to simulate the experimental rotational OH distributions from O(¹D)+H₂, measured by Luntz et al. The present study also includes simulation of similar results by Luntz for O(¹D) + HCI → OH + Cl. The purely statistical algorithm successfully simulates the apparently non-statistical experimental rotational distributions. For these reactions the total angular momentum conservation. which is applied at the transition state, proves to be decisive for the product energy distributions.     

Influence of patterned concave depth and surface curvature on anodization of titania nanotubes and alumina nanopores

Vertically aligned TiO(2) nanotube and Al(2)O(3) nanopore arrays have been obtained by pattern guided anodization with uniform concave depths. There are some studies about the effect of surface curvature on the growth of Al(2)O(3) nanopores. However, the surface curvature influence on the development of TiO(2) nanotubes is seldom studied. Moreover, there is no research about the effect of heterogeneous concave depths of the guiding patterns on the anodized TiO(2) nanotube and Al(2)O(3) nanopore characteristics, such as diameter, growth direction, and termination/bifurcation. In this study, focused ion beam lithography is used to create concave patterns with heterogeneous depths on flat surfaces and with uniform depths on curved surfaces. For the former, bending and bifurcation of nanotubes/nanopores are observed after the anodization. For the latter, bifurcation of a large tube into two smaller tubes occurs on concave surfaces, while termination of existing tubes occurs on convex surfaces. The growth direction of all TiO(2) nanotubes is perpendicular to the local surface and thus is different on different facets of the same Ti foil. At the edge of the Ti foil where two facets meet, the nanotube growth direction is bent, resulting in a large stress release that causes the formation of cracks.     

Multi-way PLS modeling of structure-activity data by incorporating electrostatic and lipophilic potentials on molecular surface

We devised and elaborated a surface-based three-dimensional-quantitative structure-activity relationship (3D-QSAR) method, which had been proposed in the previous study. This approach can be applied to more general case where both the electrostatic and lipophilic potentials on molecular surface simultaneously change. The 3D coordinates of all sampling points on molecular surface are projected into a 2D map by Kohonen neural network (KNN). Each node in the map is coded by the associated molecular electrostatic potential (MEP) or molecular lipophilic potential (MLP) values. The electrostatic and lipophilic KNN maps are generated for each compound and the four-way array is constructed by collecting two KNN maps of all samples. The correlation between four-way array and biological activity is examined by four-way partial least-squares (PLS). For validation, the structure-activity data of estrogen receptor antagonists was investigated. The four-way PLS model gave the high statistics at calibration and validation stages. The coefficients of the four-way PLS model back-projected on molecular surface had a reasonable 3D distribution and it was nicely consistent with active site of the estrogen receptor which was recently made clear by X-ray crystallography.     

Multi-way PLS modeling of structure–activity data by incorporating electrostatic and lipophilic potentials on molecular surface

We devised and elaborated a surface-based three-dimensional-quantitative structure–activity relationship (3D-QSAR) method, which had been proposed in the previous study. This approach can be applied to more general case where both the electrostatic and lipophilic potentials on molecular surface simultaneously change. The 3D coordinates of all sampling points on molecular surface are projected into a 2D map by Kohonen neural network (KNN). Each node in the map is coded by the associated molecular electrostatic potential (MEP) or molecular lipophilic potential (MLP) values. The electrostatic and lipophilic KNN maps are generated for each compound and the four-way array is constructed by collecting two KNN maps of all samples. The correlation between four-way array and biological activity is examined by four-way partial least-squares (PLS). For validation, the structure–activity data of estrogen receptor antagonists was investigated. The four-way PLS model gave the high statistics at calibration and validation stages. The coefficients of the four-way PLS model back-projected on molecular surface had a reasonable 3D distribution and it was nicely consistent with active site of the estrogen receptor which was recently made clear by X-ray crystallography.     

Negative collision energy dependence of Br formation in the OH + HBr reaction

The reaction between HBr and OH leading to H(2)O and Br in its ground state is studied by means of a crossed molecular beam experiment for a collision energy varying from 0.05 to 0.26 eV, the initial OH being selected in the state |JOmega> = |3/2 3/2> by an electrostatic hexapole field. The reaction cross-section is found to decrease with increasing collision energy. This negative dependence suggests that there is no barrier on the potential energy surface for the formation pathway considered. The experimental results are compared with the previously reported quantum scattering calculations of Clary et al. (D. C. Clary, G. Nyman and R. Hernandez, J. Phys. Chem., 1994, 101, 3704), and briefly discussed in the light of skewed potential energy surfaces associated with heavy-light-heavy type reactions.     

In situ surface-enhanced infrared absorption spectroscopy for the analysis of the adsorption and desorption process of Au nanoparticles on the SiO2/Si surface

The adsorption and desorption of Au nanoparticles (AuNP) in colloidal D2O suspension on the (3-aminopropyl)triethoxysilane treated SiO2/Si surface was investigated by in situ attenuated total reflection surface enhanced infrared absorption (ATR-SEIRA) spectroscopy with a liquid flow cell. With increasing surface density of AuNP, the absorption of the vibrational modes of D2O and of the citrate molecules covering the AuNP increases due to SEIRA. Repulsive electrostatic Coulomb forces between the AuNP lead to the saturation of the AuNP surface density at submonolayer coverage. We show that the adsorption kinetics can be investigated by monitoring in situ the molecular vibrational modes of D2O and the citrate molecules. Furthermore, we clarify that the adsorption process can be described very well by a diffusion-limited first-order Langmuir kinetics model. When exposing a saturated AuNP submonolayer to 2-aminoethanethiol (AET)/D2O solution, the AuNP are removed from the surface and the IR absorption of the D2O vibrational modes become weaker again. Taking into account the time dependencies of the OD and the CH peaks, we propose a microscopic model where the AET molecules quickly adsorb on the AuNP by replacing most of the precovering citrate molecules exposed to the AET solution. As this takes place, the AuNP agglomerate-as we could detect with scanning electron microscopy-and are finally removed from the surface.     

On the role of nonbonded interactions in vibrational energy relaxation of cyanide in water

The vibrationally excited cyanide ion (CN(-)) in H2O or D2O relaxes back to the ground state within several tens of picoseconds. Pump-probe infrared spectroscopy has determined relaxation times of T1 = 28 ± 7 and 71 ± 3 ps in H2O and D2O, respectively. Atomistic simulations of this process using nonequilibrium molecular dynamics simulations allow determination of whether it is possible at all to describe such a process, what level of accuracy in the force fields is required, and whether the information can be used to understand the molecular mechanisms underlying vibrational relaxation. It is found that, by using the best electrostatic models investigated, absolute relaxation times can be described rather more qualitatively (T1(H2O) = 19 ps and T1(D2O) = 34 ps) whereas the relative change in going from water to deuterated water is more quantitatively captured (factor of 2 vs 2.5 from experiment). However, moderate adjustment of the van der Waals ranges by less than 20% (for NVT) and 7.5% (for NVE), respectively, leads to almost quantitative agreement with experiment. Analysis of the energy redistribution establishes that the major pathway for CN(-) relaxation in H2O or D2O proceeds through coupling to the water-bending plus libration mode.     

Production of a positron microprobe using a transmission remoderator.

A production method for a positron microprobe using a beta+-decay radioisotope (22Na) source has been investigated. When a magnetically guided positron beam was extracted from the magnetic field, the combination of an extraction coil and a magnetic lens enabled us to focus the positron beam by a factor of 10 and to achieve a high transport efficiency (71%). A 150-nm-thick Ni(100) thin film was mounted at the focal point of the magnetic lens and was used as a remoderator for brightness enhancement in a transmission geometry. The remoderated positrons were accelerated by an electrostatic lens and focused on the target by an objective magnetic lens. As a result, a 4-mm-diameter positron beam could be transformed into a microprobe of 60 microm or less with 4.2% total efficiency. The S parameter profile obtained by a single-line scan of a test specimen coincided well with the defect distribution. This technique for a positron microprobe is available to an accelerator-based high-intensity positron source and allows 3-dimensional vacancy-type defect analysis and a positron source for a transmission positron microscope.     

Analytic energy gradient for second-order Møller-Plesset perturbation theory based on the fragment molecular orbital method

The first derivative of the total energy with respect to nuclear coordinates (the energy gradient) in the fragment molecular orbital (FMO) method is applied to second order M?ller-Plesset perturbation theory (MP2), resulting in the analytic derivative of the correlation energy in the external self-consistent electrostatic field. The completely analytic energy gradient equations are formulated at the FMO-MP2 level. Both for molecular clusters (H(2)O)(64) and a system with fragmentation across covalent bonds, a capped alanine decamer, the analytic FMO-MP2 energy gradients with the electrostatic dimer approximation are shown to be complete and accurate by comparing them with the corresponding numeric gradients. The developed gradient is parallelized with the parallel efficiency of about 97% on 32 Pentium4 nodes connected by Gigabit Ethernet.     

Molecular simulation of carbon dioxide/methane/hydrogen mixture adsorption in metal-organic frameworks

This work performs a systematic computational study toward a molecular understanding of the separation characteristics of metal-organic frameworks (MOFs), for which the purification of synthetic gas by two representative MOFs, MOF-5 and Cu-BTC, is adopted as an example. The simulations show that both geometry and pore size affect largely the separation efficiency, complex selectivity behaviors with different steps can occur in MOFs, and the electrostatic interactions that exist can enhance greatly the separation efficiency of gas mixtures composed of components with different chemistries. Furthermore, the macroscopic separation behaviors of the MOF materials are elucidated at a molecular level to give insight into the underlying mechanisms. The findings as well as the molecular-level elucidations provide useful microscopic information toward a complete understanding of the separation characteristics of MOFs that may lead to general design strategies for synthesizing new MOFs with tailored properties, as well as guiding their practical applications.     

An electrostatic elliptical mirror for neutral polar molecules

Focusing optics for neutral molecules finds application in shaping and steering molecular beams. Here we present an electrostatic elliptical mirror for polar molecules consisting of an array of microstructured gold electrodes deposited on a glass substrate. Alternating positive and negative voltages applied to the electrodes create a repulsive potential for molecules in low-field-seeking states. The equipotential lines are parallel to the substrate surface, which is bent in an elliptical shape. The mirror is characterized by focusing a beam of metastable CO molecules and the results are compared to the outcome of trajectory simulations.     

Rotational state-resolved reaction cross section in the reactions of state-selected CH with NO and with O2

A pure and highly intense state-selected pulsed supersonic CH(X (2)Pi) radical beam source was developed by use of the C((1)D)+H(2) reaction with the combination of the state selection and purification by an electrostatic hexapole field. Under the beam-cell condition, the elementary reactions of CH+NO and CH+O(2) were studied by using this state-selected CH beam. NH(A (3)Pi) [and NCO(A (2)Sigma(+))] formations and OH(A (2)Sigma(+)) formation were directly identified in the elementary reaction of CH+NO and CH+O(2), respectively. For the CH+NO reaction, the relative branching ratio sigma(NCO*)sigma(NH) of NCO(A (2)Sigma(+)) formation to NH(A (3)Pi) formation was determined to be 0.35+/-0.15. The state-selected reaction cross sections were determined for each rotational state of CH. In the CH+NO reaction, a remarkable rotational state dependence of the reactive cross section was revealed, while the CH+O(2) reaction showed little rotational state dependence.     

Vibrational spectroscopic determination of local solvent electric field, solute-solvent electrostatic interaction energy, and their fluctuation amplitudes

IR probes have been extensively used to monitor local electrostatic and solvation dynamics. Particularly, their vibrational frequencies are highly sensitive to local solvent electric field around an IR probe. Here, we show that the experimentally measured vibrational frequency shifts can be inversely used to determine local electric potential distribution and solute-solvent electrostatic interaction energy. In addition, the upper limits of their fluctuation amplitudes are estimated by using the vibrational bandwidths. Applying this method to fully deuterated N-methylacetamide (NMA) in D(2)O and examining the solvatochromic effects on the amide I' and II' mode frequencies, we found that the solvent electric potential difference between O(═C) and D(-N) atoms of the peptide bond is about 5.4 V, and thus, the approximate solvent electric field produced by surrounding water molecules on the NMA is 172 MV/cm on average if the molecular geometry is taken into account. The solute-solvent electrostatic interaction energy is estimated to be -137 kJ/mol, by considering electric dipole-electric field interaction. Furthermore, their root-mean-square fluctuation amplitudes are as large as 1.6 V, 52 MV/cm, and 41 kJ/mol, respectively. We found that the water electric potential on a peptide bond is spatially nonhomogeneous and that the fluctuation in the electrostatic peptide-water interaction energy is about 10 times larger than the thermal energy at room temperature. This indicates that the peptide-solvent interactions are indeed important for the activation of chemical reactions in aqueous solution.     

Unraveling the mechanisms of O2 activation by size-selected gold clusters: transition from superoxo to peroxo chemisorption

The activation of dioxygen is a key step in CO oxidation catalyzed by gold nanoparticles. It is known that small gold cluster anions with even-numbered atoms can molecularly chemisorb O(2) via one-electron transfer from Au(n)(-) to O(2), whereas clusters with odd-numbered atoms are inert toward O(2). Here we report spectroscopic evidence of two modes of O(2) activation by the small even-sized Au(n)(-) clusters: superoxo and peroxo chemisorption. Photoelectron spectroscopy of O(2)Au(8)(-) revealed two distinct isomers, which can be converted from one to the other depending on the reaction time. Ab initio calculations show that there are two close-lying molecular O(2)-chemisorbed isomers for O(2)Au(8)(-): the lower energy isomer involves a peroxo-type binding of O(2) onto Au(8)(-), while the superoxo chemisorption is a slightly higher energy isomer. The computed detachment transitions of the superoxo and peroxo species are in good agreement with the experimental observation. The current work shows that there is a superoxo to peroxo chemisorption transition of O(2) on gold clusters at Au(8)(-): O(2)Au(n)(-) (n = 2, 4, 6) involves superoxo binding and n = 10, 12, 14, 18 involves peroxo binding, whereas the superoxo binding re-emerges at n = 20 due to the high symmetry tetrahedral structure of Au(20), which has a very low electron affinity. Hence, the two-dimensional (2D) Au(8)(-) is the smallest anionic gold nanoparticle that prefers peroxo binding with O(2). At Au(12)(-), although both 2D and 3D isomers coexist in the cluster beam, the 3D isomer prefers the peroxo binding with O(2).     

Velocity map imaging of a slow beam of ammonia molecules inside a quadrupole guide

Velocity map imaging inside an electrostatic quadrupole guide is demonstrated. By switching the voltages that are applied to the rods, the quadrupole can be used for guiding Stark decelerated molecules and for extracting the ions. The extraction field is homogeneous along the axis of the quadrupole, while it defocuses the ions in the direction perpendicular to both the axis of the quadrupole and the axis of the ion optics. To compensate for this astigmatism, a series of planar electrodes with horizontal and vertical slits is used. A velocity resolution of 35 m s(-1) is obtained. It is shown that signal due to thermal background can be eliminated, resulting in the detection of slow molecules with an increased signal-to-noise ratio. As an illustration of the resolving power we have used the velocity map imaging system to characterize the phase-space distribution of a Stark decelerated ammonia beam.     

Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals

The electrostatic interaction among molecules solvated in ionic solution is governed by the Poisson-Boltzmann equation (PBE). Here the hypersingular integral technique is used in a boundary element method (BEM) for the three-dimensional (3D) linear PBE to calculate the Maxwell stress tensor on the solvated molecular surface, and then the PB forces and torques can be obtained from the stress tensor. Compared with the variational method (also in a BEM frame) that we proposed recently, this method provides an even more efficient way to calculate the full intermolecular electrostatic interaction force, especially for macromolecular systems. Thus, it may be more suitable for the application of Brownian dynamics methods to study the dynamics of protein/protein docking as well as the assembly of large 3D architectures involving many diffusing subunits. The method has been tested on two simple cases to demonstrate its reliability and efficiency, and also compared with our previous variational method used in BEM.