Mechanism of Molecular Orientation by Single-cycle Pulses

Significant molecular orientation can be achieved by time-symmetric single-cycle pulses of zero area, in the THz region. We show that in spite of the existence of a combined time-space symmetry operation, not only large peak instantaneous orientations but also nonzero time-average orientations over a rotational period can be obtained. We show that this unexpected phenomenon is due to interferences among eigenstates of the time-evolution operator, as was described previously for transport phenomena in quantum ratchets. This mechanism also works for sequences of identical pulses, spanning a rotational period. This fact can be used to obtain a net average molecular orientation regardless of the magnitude of the rotational constant.Comment: Published version may be found at (URL:http://link.aip.org/link?/JCP/137/044303). Substantial changes with respect to previous versions, including new titl

XAFS Debye-Waller factors for Zn metalloproteins

An accurate and practical method for the calculation and use of thermal x-ray absorption fine structure (XAFS) Debye-Waller factors (DWFs) in active sites of metalloproteins is presented. These factors are calculated on model clusters within the local density functional approximation with nonlocal corrections. The DWFs are mapped out and parametrized as a function of the first shell distance and an angle (where applicable), for all significant single and multiple scattering paths, as well as the sample temperature. This approach is applied to the biologically essential but spectroscopically silent Zn+2 active sites composed of histidines, cysteines, and carboxylate ligands in homogeneous and heterogeneous environments. Detailed analysis of the relative scattering paths for Zn metalloproteins using projected vibrational density of states further explain why these paths are not detectable by XAFS for first shell metal-ligand distances above a “cutoff” value

APEX version 2.0: latest version of the cross-platform analysis program for EXAFS

This report describes recent progress on APEX, a free, open source, cross platform set of EXAFS data analysis software. In a previous report we described APEX 1.0 (Dimakis, N. and Bunker, G., 1999), a free and open source code suite of basic X-Ray Absorption Fine Structure (XAFS) data analysis programs for classical data reduction and single scattering analysis. The first version of APEX was the only cross platform (linux/irix/windows/MacOS) EXAFS analysis program to our knowledge, but it lacked important features like multiple scattering fitting, generic format conversion from ASCII to University of Washington (UW) binary-type files, and user friendly interactive graphics. In the enhanced version described here we have added cross-platform interactive graphics based on the BLT package, which is an extension to TCL/TK. Some of the utilities have been rewritten in native TCL/TK, allowing for faster and more integrated functionality with the main package. The package also has been ported to SunOS. APEX 2.0 in its current form is suitable for routine data analysis and training. Addition of more advanced methods of data analysis are planned

APEX: cross-platform analysis program for EXAFS

We have developed version 1.0 of a freely available (including source code) suite of basic X-Ray Absorption Fine Structure (XAFS) data analysis programs for data reduction and single scattering analysis. This package is based on the University of Washington (UW/NRL) Fortran 77 programs that are available on the International XAFS Society (IXS) database, complemented by a graphical TCL/TK scripting language based user interface which runs virtually unchanged between platforms, using the native look and feel of the corresponding platform. The package has been tested on MacOS 8.1, Linux, IRIX, Windows95 and NT. Particular emphasis is placed on simplicity, reliability, and (sup)portability. APEX 1.0 in its current form is suitable for routine data analysis and training, and systematic improvements and extensions to the underlying codes are planned

Chemical transferability of single- and multiple-scattering EXAFS Debye-Waller factors

Single- and multiple-scattering EXAFS Debye-Waller factors are amplitude reduction parameters that appear in the EXAFS x(k) equation accounting for the structural and thermal disorder of a given sample. These parameters must be known accurately in order to obtain quantitative agreement between theory and experiment. Since experimental data can only support a limited number of fitted parameters these factors must be known from another source. Although various approaches have been considered in the past with a variety of results, the self-consistent ab initio Density functional theory stands for the most accurate and reliable method regardless of molecular symmetry or other specific sample requirements. Since DFT scales as N3 where N is the number of atomic basis set, an ab initio calculation on a large structure is not feasible due to enormous CPU demand and in many cases due to hard energy/geometry convergence. In this paper we present two ways of overcoming this problem. Both they use the idea that by reducing the structure, the DWFs are still chemically transferable. In order to test this we use the Zn tetraimidazole. This molecule represents typical metalorganic ring samples that can be seen in active sites of metaloproteins. Results are compared to experimental EXAFS spectra

Group-fitted ab initio single- and multiple-scattering EXAFS Debye-Waller factors

X-ray absorption fine structure (XAFS) spectroscopy is one of the few direct probes of the structure of metalloprotein binding that is equally applicable to proteins in crystals, solutions, and membranes. Despite considerable progress in the calculation of the photoelectron scattering aspects of XAFS, calculation of the vibrational aspects has lagged because of the difficulty of the calculations. We report here initial results that express single- and multiple-scattering Debye-Waller factors as polynomial functions of first shell radial distance for metal-peptide complexes, enabling quantitatively accurate full multiple-scattering XAFS data analysis of active sites of unknown structure at arbitrary temperatures without the use of ad hoc assumptions

Ab initio single- and multiple-scattering EXAFS Debye-Waller factors: Raman and infrared data

The extended x-ray-absorption fine structure (EXAFS) Debye-Waller factor is an essential term appearing in the EXAFS equation that accounts for the molecular structural and thermal disorder of a sample. Single- and multiple-scattering Debye-Waller factors must be known accurately to obtain quantitative agreement between theory and experiment. Since the total number of fitting parameters that can be varied is limited in general, data cannot support fitting of all relevant multiple-scattering Debye-Waller factors. Calculation of the Debye-Waller factors is typically done using the correlated Debye approximation, where a single parameter (Debye temperature) is varied. However, this procedure cannot account in general for Debye-Waller factors in materials with heterogeneous bond strengths, such as biomolecules. As an alternative procedure in this work, we calculate them ab initio directly from the known or hypothetical three-dimensional structure. In this paper we investigate the adequacy of various computational approaches for calculating vibrational structure within small molecules. Detailed EXAFS results will be presented in a subsequent paper. Analytical expressions are derived for multiple scattering Debye-Waller factors, based on the plane wave approximation. Semiempirical Hamiltonians and the ab initio density functional method are used to calculate the normal mode eigenfrequencies and eigenvectors. These data are used to calculate all single- and multiple-scattering Debye-Waller factors up to a four atom cluster. These ab initio Debye-Waller factors are compared to those calculated from experimental infrared and Raman frequencies. As an example comparison with experimental EXAFS data from GeCl4,GeH3Cl gases are also reported. Good agreement is observed for all cases tested

The Planck constant of action and the Kibble balance

It has been shown previously (P. R. Bunker and Per Jensen, J. Quant. Spectrosc. Radiat. Transf., 243 (2020) 106835) that if we choose angles to have dimension, we have to distinguish between the Planck constant h, having the dimension of action angle−1 , and the Planck constant of action hA, having the dimension of action. In the present paper, we show that a further implication that results from choosing angles to have dimension is that the Kibble balance equation relating the mass weighed to the Planck constant has to involve both of the distinct fundamental constants h and hA. We derive that new equation here and show how it compares to the equation that is obtained if one chooses angles to be dimensionless as required in SI

New methods for EXAFS analysis in structural genomics

Data analysis is one of the remaining bottlenecks in high-throughput EXAFS for structural genomics. Here some recent developments in methodology are described that offer the potential for rapid and automated XAS analysis of metalloproteins

Symmetry adapted ro-vibrational basis functions for variational nuclear motion calculations: TROVE approach

We present a general, numerically motivated approach to the construction of symmetry adapted basis functions for solving ro-vibrational Schr\"{o}dinger equations. The approach is based on the property of the Hamiltonian operator to commute with the complete set of symmetry operators and hence to reflect the symmetry of the system. The symmetry adapted ro-vibrational basis set is constructed numerically by solving a set of reduced vibrational eigenvalue problems. In order to assign the irreducible representations associated with these eigenfunctions, their symmetry properties are probed on a grid of molecular geometries with the corresponding symmetry operations. The transformation matrices are re-constructed by solving over-determined systems of linear equations related to the transformation properties of the corresponding wavefunctions on the grid. Our method is implemented in the variational approach TROVE and has been successfully applied to a number of problems covering the most important molecular symmetry groups. Several examples are used to illustrate the procedure, which can be easily applied to different types of coordinates, basis sets, and molecular systems