New translation method for STOs and its application to calculation of two-center two-electron integrals

The new translation method for Slater-type orbitals (STOs) previously tested in the case of the overlap integral is extended to the calculation of two-center two-electron molecular integrals. The method is based on the exact translation of the regular solid harmonic part of the orbital followed by the series expansion of the residual spherical part in powers of the radial variable. Fair uniform convergence and stability under wide changes in molecular parameters are obtained for all studied two-center hybrid, Coulomb, and exchange repulsion integrals. Ten-digit accuracy in the final numerical results is achieved through multiple precision arithmetic calculation of common angular coefficients and Gaussian numerical integration of some of the analytical formulas resulting for the radial integrals. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 79: 91–100, 2000     

Analysis of the relaxations on polymers from the real part of a general complex susceptibility. Application to dielectric relaxations

From a thermodynamic relation that involves the generalized relaxation function, an approximated method that allows estimation of the thermal dependence of the imaginary part of the general complex susceptibility from the real part is discussed. Several conditions such as broad distribution of relaxation times, the applicability of the time–temperature superposition principle, and the temperature dependence of the relaxation strength are considered and analyzed, together with the expected thermal behavior of the relaxed and unrelaxed susceptibilities. The method is tested by means of dielectric measurements on the poly(vinyl acetate) polymer in the temperature range corresponding to the segmental dynamics and the secondary relaxation. An acceptable agreement respect with the maximum temperature of the ε″(T) and the width and shape of the loss peak is obtained between the experimental and estimated imaginary part. This comparison gives validity to the method when the imaginary part is experimentally not well resolved due to the signal–resolution ratio or to the presence of other contributions that mask the thermal behavior of the imaginary part. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 1337–1349, 1999     

Superlinearly converging dimer method for transition state search

Algorithmic improvements of the dimer method [G. Henkelman and H. Jonsson, J. Chem. Phys. 111, 7010 (1999)] are described in this paper. Using the limited memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) optimizer for the dimer translation greatly improves the convergence compared to the previously used conjugate gradient algorithm. It also saves one energy and gradient calculation per dimer iteration. Extrapolation of the gradient during repeated dimer rotations reduces the computational cost to one gradient calculation per dimer rotation. The L-BFGS algorithm also improves convergence of the rotation. Thus, three to four energy and gradient evaluations are needed per iteration at the beginning of a transition state search, while only two are required close to convergence. Moreover, we apply the dimer method in internal coordinates to reduce coupling between the degrees of freedom. Weighting the coordinates can be used to apply chemical knowledge about the system and restrict the transition state search to only part of the system while minimizing the remainder. These improvements led to an efficient method for the location of transition states without the need to calculate the Hessian. Thus, it is especially useful in large systems with expensive gradient evaluations.     

High-throughput capillary gas chromatography for the determination of polychlorinated biphenyls and fatty acid methyl esters in food samples

High-throughput capillary gas chromatography (CGC) methods, developed during the Belgian 1999 "dioxin" food crisis, for the determination of the contaminating polychlorinated biphenyls (PCBs) and the fatty acid composition of the lipids are described. For PCB analysis, the fat obtained by ultrasonic extraction is fractionated by matrix solid-phase dispersion, and the PCBs are analyzed by CGC-electron capture detection on a 10-mL x 100-microm-i.d. HP-5MS column. Analytical conditions for the high-speed column are deduced from analyses on conventional CGC columns using the method translation software. The concept of retention time locking is implemented to facilitate the elucidation of the PCB markers. The fatty acid methyl esters (FAMEs) are prepared by the sodium methylate procedure on part of the ultrasonic extract followed by analysis on 10-mL x 100-microm-i.d. HP-WAX or BPX-70 capillary columns. By optimizing both the sample preparation and CGC analysis, the throughput is more than fifty PCB and FAME samples per day with the same robustness as conventional methods.     

FTIR spectroscopy of monomolecular layers and multilayers of organic molecules on solid substrates

A method for measuring grazing incidence reflection spectra of monomolecular organic layers is presented which involves the use of a stepmotor-driven translation stage to alternately measure the covered and uncovered part of a metal substrate and averaging of the spectra from several such cycles. The method is applied to Langmuir-Blodgett films of poly(octadecylmethacrylate).     

Routine analysis of ultra pure water by ICP-MS in the low- and sub-ng/L level

The chemical analysis with inductively coupled plasma-mass spectrometry (ICP-MS) can help to examine the purity of ultra pure water (UPW) down to 10 part per trillion (ng/L) and lower. For a proper determination of a high number of samples per week the analysis must be divided into two parts: the routine analysis and the reference water analysis. The routine analysis is done by direct measurement of the ultra pure water samples. Applying a standard addition method under particular clean conditions, the reference water analysis leads to the definition of the accurate zero. A quick evaluation scheme is also presented for the reference water analysis. The method is tested for its fitness for application by examining LOD (for relevant element < 2 ng/L), reproducibility and linearity of calibration. The ICP-MS was optimized according to the methodology of G. Taguchi to improve reproducibility and LOD. Received: 16 June 1999 / Revised: 2 August 1999 / Accepted: 6 August 1999     

Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide

Methodology is discussed for mixed ab initio quantum mechanics/molecular mechanics modeling of systems where the quantum mechanics (QM) and molecular mechanics (MM) regions are within the same molecule. The ab initio QM calculations are at the restricted Hartree–Fock level using the pseudospectral method of the Jaguar program while the MM part is treated with the OPLS force fields implemented in the IMPACT program. The interface between the QM and MM regions, in particular, is elaborated upon, as it is dealt with by “breaking” bonds at the boundaries and using Boys-localized orbitals found from model molecules in place of the bonds. These orbitals are kept frozen during QM calculations. Results from tests of the method to find relative conformational energies and geometries of alanine dipeptides and alanine tetrapeptides are presented along with comparisons to pure QM and pure MM calculations. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1468–1494, 1999     

Determination of aluminium in the edible part of fish by GFAAS after sample pretreatment with microwave activated oxygen plasma

An analytical method for the determination of aluminium in the edible part of fish was developed using a new pre-treatment method in a microwave activated oxygen plasma and graphite furnace atomic absorption spectrometry. The linearity of the calibration line as well as of different standard addition lines were very good within the measurement area of 0–60 μg Al/L. The recovery with spiked ocean perch fillet was good. The unsatisfactory recovery of aluminium with the reference-material (mussel tissue) may be due to high quantities of insoluble aluminium-silicates. An installed quality-control-card indicated that the method showed no significant fluctuation as well as contamination over the complete analysis time. The limit of detection calculated as 3 times the standard deviation of the blank absorbance divided by the slope of the calibration line was 1 μg Al/L. Received: 7 December 1998 / Revised: 14 February 1999 / Accepted: 24 February 1999     

Determination of aluminium in the edible part of fish by GFAAS after sample pretreatment with microwave activated oxygen plasma

An analytical method for the determination of aluminium in the edible part of fish was developed using a new pre-treatment method in a microwave activated oxygen plasma and graphite furnace atomic absorption spectrometry. The linearity of the calibration line as well as of different standard addition lines were very good within the measurement area of 0–60 μg Al/L. The recovery with spiked ocean perch fillet was good. The unsatisfactory recovery of aluminium with the reference-material (mussel tissue) may be due to high quantities of insoluble aluminium-silicates. An installed quality-control-card indicated that the method showed no significant fluctuation as well as contamination over the complete analysis time. The limit of detection calculated as 3 times the standard deviation of the blank absorbance divided by the slope of the calibration line was 1 μg Al/L. Received: 7 December 1998 / Revised: 14 February 1999 / Accepted: 24 February 1999     

The Gaussian and augmented-plane-wave density functional method for ab initio molecular dynamics simulations

A new algorithm for density-functional-theory-based ab initio molecular dynamics simulations is presented. The Kohn–Sham orbitals are expanded in Gaussian-type functions and an augmented-plane-wave-type approach is used to represent the electronic density. This extends previous work of ours where the density was expanded only in plane waves. We describe the total density in a smooth extended part which we represent in plane waves as in our previous work and parts localised close to the nuclei which are expanded in Gaussians. Using this representation of the charge we show how the localised and extended part can be treated separately, achieving a computational cost for the calculation of the Kohn–Sham matrix that scales with the system size N as O(NlogN). Furthermore, we are able to reduce drastically the size of the plane-wave basis. In addition, we introduce a multiple-cutoff method that improves considerably the performance of this approach. Finally, we demonstrate with a series of numerical examples the accuracy and efficiency of the new algorithm, both for electronic structure calculations and for ab initio molecular dynamics simulations. Received: 15 December 1998 /Accepted: 18 February 1999 /Published online: 14 July 1999     

Integrating quantum and molecular mechanics

A computer algorithm is developed for integrating density functional quantum mechanics into a molecular mechanics program. The computationally infeasible aspects of the standard LCAO-MO approach (the iterative calculation of eigenvectors and the requirement of orthogonal expansions for the orbitals) are replaced with an efficient use of optimization via the trace theorem of linear algebra. The construction of a basis is also described for expanding the electron density that transforms with the molecular geometry. The combination of the trace method and the basis allow the solution for one configuration of atoms and electrons to be tracked over a wide range of internal conformations. The approach is readily adaptable to being used in the context of an imposed classical field that allows it to be used on part of a macromolecular complex. The initial implementation in the program AMMP is described. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1618–1633, 1999     

Quantum molecular similarity. 3. QTMS descriptors.

Building on the ideas of a previous paper [part 1, J. Phys. Chem. A 1999, 103, 2883] we present a new molecular similarity method based on the topology of the electron density. This method is directly applicable to QSARs and is called quantum topological molecular similarity (QTMS). It has been tested for five sets of carboxylic systems including para- and meta-benzoic acid, para-phenylacetic acid, 4-X-bicyclo[2.2.2]octane-1-carboxylic acids, and polysubstituted benzoic acids. In combination with the partial least squares (PLS) procedure QTMS is able to produce excellent and statistically valid regressions. It is shown that QTMS avoids certain challenges of traditional Carbó-like similarity indices. Finally, QTMS is able to suggest a molecular fragment that contains the active center or the part of the molecule that is responsible for the QSAR.     

Low-mode conformational search elucidated: Application to C39H80 and flexible docking of 9-deazaguanine inhibitors into PNP

We previously described a new conformational search method, termed low-mode search (LMOD), and discussed its utility for conformational searches performed on cycloalkanes and a cyclic penta-peptide. 1 In this report, we discuss a rigorous implementation of mode following (c-LMOD) for conformational searching, and we demonstrate that for a conformational search involving cycloheptadecane, this rigorous implementation is capable of finding all of the previously known structures. To the best of our knowledge, this is the first computational proof that mode following can be used for conformational searches conducted on a complex molecular system. We show, however, that, as expected, it is generally inefficient to perform a conformational search in this manner. Nonetheless, c-LMOD has been shown to be an excellent method for conducting conformational analyses involving conformational interconversions, where the location of saddle points is important. We also describe refinement to our original LMOD procedure (l-LMOD) and discuss its utility for a difficult conformational search problem, namely locating the global minimum energy conformation of C₃₉H₈₀. For this search, l-LMOD combined with limited torsional Monte Carlo movement was able to locate the lowest energy structures yet reported, and significantly outperformed a pure torsional Monte Carlo and a genetic algorithm-based search. Furthermore, we also demonstrate the utility of l-LMOD combined with random translation/rotation of a ligand for the extremely difficult problem of docking flexible ligands into flexible protein binding sites on a system that includes 9-deaza-guanine-based inhibitors docked into the flexible biding site of PNP. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1671–1684, 1999     

New views on hydrazone-enehydrazine tautomerism

A new proton transfer mechanism is proposed for hydrazone-enehydrazine tautomerism through the cyclic dimer of the phenylhydrazones that take part in the E. Fischer indolization process. The energy, structural, and electronic indices of the proposed dimers were calculated by the AM1 quantum-chemical method. The calculated data were used to derive a new equations for the constant of the hydrazone-enehydrazine tautomeric equilibrium in terms of the orders of the breaking and forming bonds.I. Dzhavakhishvili Tbilisi State University, Tbilisi, Georgia Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 6, pp. 752–756, June, 1999.     

Cubic-grid Gaussian basis sets for electron scattering calculations. III. Effect of basis-set translation and size on the calculated cross section

Previously developed cubic-grid basis sets of various sizes were used for the calculation of cross sections for elastic and inelastic electron scattering by the He and Ne atoms and the H₂O molecule by the T-matrix expansion method. The aim was to test the invariance of calculated cross sections with respect to the translation of the target molecule and to examine the effect of basis-set size on the results. We also present a simple procedure for accounting for long-range interactions from the part of space that lies outside the volume that contains the cubic-grid basis set. © 1995 John Wiley & Sons, Inc.     

Cycloaddition of CO2 and CS2 to a cyclic phosphazene

Carbon dioxide and carbon disulfide give crystalline cycloadducts with the phosphazene bond of a 1,2λ⁵‐azaphosphole. The CO₂‐adduct fully dissociates in solution, the CS₂‐adduct on short heating only to a small part. On longer heating, the latter rearranges in two successive 1,3‐shifts to give a thiophosphinylimino dihydrothiophene, the structure of which is revealed by X‐ray analysis. © 1999 John Wiley & Sons, Inc. Heteroatom Chem 10:167–170, 1999     

Remarks on large-scale matrix diagonalization using a Lagrange–Newton–Raphson minimization in a subspace

We present a matrix diagonalization method where the diagonalization is carried out through a normal Lagrange–Newton–Raphson method solved in a subspace. The subspace is generated using the correction vector that predicts the standard Lagrange–Newton–Raphson formula in the full space. Some numerical examples and the performance of the algorithm are given. Received: 16 February 1999 / Accepted: 10 May 1999 / Published online: 9 September 1999