Ab initio HF-SCF study of naphthazarin: Geometries,isomerism, hydrogen bonding,and vibrational spectrum

The structural properties and intramolecular hydrogen bonding of a series of structures of naphthazarin molecule were investigated by ab initio HF-SCF methods. The geometries of theC _2v ,C _2h ,D _2h , andC _s symmetry structures were optimized using split-valence basis sets. MP2/6-31G^*// HF/6-31G single-point energy calculations indicate that theC _2v isomer (5,8-dihydroxy-1,4-naphthoquinone) is the lowest energy structure of the molecule and that theC _2h symmetry one (4,8-dihydroxy-1,5-naphthoquinone), lying 37 kJ/mol above theC _2v form, is the other stable isomer of naphthazarin. At the HF/6-31G level, the intramolecular proton exchange between two equivalentC _2v structures is a two-step process where each proton can be independently transferred through an unsymmetrical potential having a 1,5-quinone intermediate, theC _2h symmetry structure, and two equivalent transition states ofC _s symmetry, with a barrier height equal to 38 kJ/ mol (MP2/6-31G^*//HF/6-31G). The study of naphthazarin molecule is flanked by a theoretical investigation on theC _2v andC _2h isomers of the parent naphthoquinone and dihydroxynaphthalene molecules. The SCF vibrational spectrum of the ground state of naphthazarin, harmonic frequencies, and infrared and Raman band intensities were computed at the HF/6-31G level. The results of the calculations are compared with the matrix isolation FT-IR spectroscopy measurements and with the infrared and Raman spectra of the crystal molecule.     

Infia—program for rotational analysis of linear molecule spectra

A software package for spectral rotation analysis is described. The Infia a program features multiple simultaneous views of the analysis data, including a spectrum view with assignment markers; a Loomis–Wood-type view; and lists of assignments, bands, and vibrational states. Automatic combination difference prediction and parameter calculation are included for linear molecules, but the program can also be used to assign spectra for symmetric top molecules. The interactive nature of the program combined with the high level of automation makes possible rapid and reliable analyses even for difficult spectra with many overlapping bands and high peak densities. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 610–622, 1999     

Continuous symmetry measures: Finding the closest C2-symmetric object or closest reflection-symmetric object using unit quaternions

A closed-form solution is provided for the problem of finding the closest reflection-symmetric object, and its relation to the problems of finding the closest achiral object, the closest inversion-symmetric object, and the closest projection plane is discussed. The key to the solution is reducing this problem to the problem of finding the best (least squares) c₂ rotation between two sets of points, in addition to solving the problem of finding the closest C₂-symmetric object. The solution is derived using the quaternion representation of rotation. It is shown that calculation of the best c₂ rotation can be reduced to the diagonalization of the outer product matrix of the pair (between the two sets). ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 772–780, 1999     

Lie algebraic approach to multiphoton excitation of diatomic molecules in intense laser fields

The quadratic anharmonic oscillator Lie algebraic model is used to study the multiphoton transition of the diatomic molecule placed in intense laser fields. The multiphoton excitation of vibration and vibration‐rotation of diatomic molecules in intense laser fields are discussed. In the pure vibration transition we calculate the transition probability versus the frequency of the laser fields for the CO molecule. We also investigate the roles of rotational motion in multiphoton processes and compare with pure vibration for the LiH molecule. The influences of the angular quantum number l and the molecular orientations in laser fields on the multiphoton processes are discussed. The averaged absorb energy changing with the laser field's frequency is calculated. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 71: 201–207, 1999     

Theory of optical rotation,Faraday effect,and inverse Faraday effect

The Hamiltonian for these problems is arranged appropriately in the nonrelativistic limit of the Dirac Hamiltonian. The unified view is tried to elucidate the mechanisms responsible for these phenomena by connecting the polarization vector of light and molecular properties inherent in the species or the external magnetic field. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 75: 33–45, 1999     

A Review of the System-Intrinsic Nonequilibrium Thermodynamics in Extended Space (MNEQT) with Applications

The review deals with a novel approach (MNEQT) to nonequilibrium thermodynamics (NEQT) that is based on the concept of internal equilibrium (IEQ) in an enlarged state space SZ involving internal variables as additional state variables. The IEQ macrostates are unique in SZ and have no memory just as EQ macrostates are in the EQ state space SX⊂SZ. The approach provides a clear strategy to identify the internal variables for any model through several examples. The MNEQT deals directly with system-intrinsic quantities, which are very useful as they fully describe irreversibility. Because of this, MNEQT solves a long-standing problem in NEQT of identifying a unique global temperature T of a system, thus fulfilling Planck’s dream of a global temperature for any system, even if it is not uniform such as when it is driven between two heat baths; T has the conventional interpretation of satisfying the Clausius statement that the exchange macroheatdeQflows from hot to cold, and other sensible criteria expected of a temperature. The concept of the generalized macroheat dQ=deQ+diQ converts the Clausius inequality dS≥deQ/T0 for a system in a medium at temperature T0 into the Clausius equalitydS≡dQ/T, which also covers macrostates with memory, and follows from the extensivity property. The equality also holds for a NEQ isolated system. The novel approach is extremely useful as it also works when no internal state variables are used to study nonunique macrostates in the EQ state space SX at the expense of explicit time dependence in the entropy that gives rise to memory effects. To show the usefulness of the novel approach, we give several examples such as irreversible Carnot cycle, friction and Brownian motion, the free expansion, etc.     

Numerical simulation of three-dimensional free surface flow in isopycnal co-ordinates

In this paper a semi-implicit method for three-dimensional circulation in isopycnal co-ordinates is derived and discussed. It is assumed that the flow is hydrostatic and characterized by isopycnal surfaces which can be represented by explicit, single-valued functions. The hydrostatic pressure is determined by using the conjugate gradient method to solve a block pentadiagonal linear system. The horizontal velocities are determined by solving a large set of tridiagonal systems. The stability of the resulting algorithm is shown to be independent of the surface and internal gravity wave speeds. © 1997 John Wiley & Sons, Ltd.     

Characterization of the surface of­bulk‐molded compounds

The automotive industry more and more frequently uses composite materials such as molded compounds (sheet‐molded compounds, SMC, or bulk‐molded compounds, BMC). Bonding is then the only way of assembling two pieces. Consequently, and in order tentatively to predict the adhesive behavior of such materials, it is necessary to have a good knowledge of their surface properties. Here, different complementary techniques of surface analysis allowed us, on the one hand, to reach this aim for BMCs prepared by compression molding and, on the other hand, to show the influence on the surface properties of the concentration and composition of the internal release agent added to the blend. The surface heterogeneity and the organic nature of the surface of the compounds are shown and no phase separation occurs there as in the bulk. Mold release agents remain in the surface layer and induce some acid–base character to the surface material which depends on the type of stearate introduced in the blend. Copyright © 1999 John Wiley & Sons, Ltd.     

Graphical approach for defining natural internal coordinates

A simple, customizable connectivity scheme is rigorously defined in which pairs of atoms are classified into three categories. The tools of graph theory are used to analyze the molecular graph and to efficiently find rings and ring assemblies through a combination of pruning and homeomorphic reduction. The definition of natural internal coordinates is extended in a nonredundant fashion for the various cases of weakly interacting components and for fused ring systems. The ring system coordinates were tested and found to be superior to Z-matrix coordinates. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 504–511, 1998     

Parallel algorithm for efficient calculation of second derivatives of conformational energy function in internal coordinates

A parallel algorithm for efficient calculation of the second derivatives (Hessian) of the conformational energy in internal coordinates is proposed. This parallel algorithm is based on the master/slave model. A master processor distributes the calculations of components of the Hessian to one or more slave processors that, after finishing their calculations, send the results to the master processor that assembles all the components of the Hessian. Our previously developed molecular analysis system for conformational energy optimization, normal mode analysis, and Monte Carlo simulation for internal coordinates is extended to use this parallel algorithm for Hessian calculation on a massively parallel computer. The implementation of our algorithm uses the message passing interface and works effectively on both distributed-memory parallel computers and shared-memory parallel computers. We applied this system to the Newton–Raphson energy optimization of the structures of glutaminyl transfer RNA (Gln-tRNA) with 74 nucleotides and glutaminyl-tRNA synthetase (GlnRS) with 540 residues to analyze the performance of our system. The parallel speedups for the Hessian calculation were 6.8 for Gln-tRNA with 24 processors and 11.2 for GlnRS with 54 processors. The parallel speedups for the Newton–Raphson optimization were 6.3 for Gln-tRNA with 30 processors and 12.0 for GlnRS with 62 processors. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1716–1723, 1998