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• Atomic, Molecular and Optical Physics  (238)
• 1990-1994  (238)
• 1970-1974
• 1965-1969
• 1991  (238)
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• 1990-1994  (238)
• 1970-1974
• 1965-1969
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• 1
Electronic Resource
New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
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• 2
Electronic Resource
New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: A theoretical model based on physical, chemical, and biochemical mechanisms has been presented to evaluate the yields of DNA strand breaks (single and double) as a function of linear energy transfer (LET) or -dE/dx. Energetic heavy charged particles are considered explicitly to provide a general theory for low- as well as for high-LET radiation. There are three main features of the calculation: (a) track structure considerations for the energy deposition pattern, (b) three-dimensional structure of DNA molecules to provide information on the exact location of damage, and (c) a Monte-Carlo scheme to simulate the diffusion processes of water radicals. To avoid the complexities of a cellular medium, an aqueous solution of DNA is considered in the calculation. When the results of the calculations are compared with experimental measurements of the yields of strand breaks in mammalian DNA (exposed in a cellular complex), reasonable agreement is obtained. However, only those experimental data have been compared where there were no enzyme repair processes. The method of calculation has also been extended to study breaks in higher-order structures of DNA molecules such as chromatin. Specific limitations of the present model have been pointed out for making further improvements.
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• 3
Electronic Resource
New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
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• 4
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: An orthogonalization procedure is presented that allows construction of at least (n-m) vectors orthogonal to {Xj}, j equals; 1, m, by linear combinations solely among {ηi}, i equals; 1, n, n〉m, and 〈Xj/ηi〉≠0. An important application of the procedure is in effective core potential methods for which valence orbitals can be constructed that are orthogonal to the core orbitals and yet involve no component of the core. Thus, a separate calculation for only the valence electrons can be performed without any explicit reference to the core electrons (orbitals).
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• 5
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: We calculate a range of isotropic and anisotropic spectral moments of the dipole oscillator strength distribution for N2 in the random phase approximation. The internuclear dependence of, in particular, S∥(k) is nonnegligible and vibrationally averaged moments are reported. The results are compared to other calculations and to experiment when available, and we conclude that the scheme gives reliable results. Based on our results, we predict a 10% anisotropy in the stopping power of oriented N2 molecules.
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• 6
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: Electronic aspects of the catalytic mechanism of liver alcohol dehydrogenase (LADH) are studied with the help of ab initio analytical gradient SCF MO methods. Three points are considered: (i) role of the catalytic zinc; (ii) geometry and electronic structure of the transition state for the hydride transfer reactions; and (iii) factors affecting the energy gap for the hydride transfer step, namely, substrate binding to zinc, reaction field, and serine 48 effects on the potential energy profile. The coordination sphere of the catalytic zinc has been modeled with an ammonia molecule and two SH- groups; complexes with CH3O-, CH3OH, and CH2O have been studied; a (6, 2, 2, 2, 1/6, 2, 1/3, 2) basis set has been used for Zn++; a (5, 2, 1, 1/3, 2) was used for oxygen, carbon, and sulfur; and a (3, 1) was used for hydrogen atoms. The hydride step was studied with two model systems: pyridinium cation/1,4-dihydropyridine coupled to the CH3O-/CH2O reaction, and cyclopropenyl cation/cyclopropene coupled to the CH3O-/CH2O system. For the latter, the role of Ser48 has been studied at the supermolecule level. The calculation on the hydride transfer step has been done at a 4-31G basis set level. The results obtained shed new light on the sources of catalytic activity of liver alcohol dehydrogenases.
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• 7
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: We have adopted the uniformly charged sphere model of atomic nucleus for one-electron atoms H, Ar17+, Xe53+, Hg79+, and U91+ and calculated several energy levels by solving the matching equations of the inward and the outward radial wave functions for the Schrödinger as well as for the Dirac equations. The finite-size effect (FSE) of the atomic nucleus on the energy levels of nonrelativistic atoms has been found one order of magnitude smaller than the effect on the relativistic atoms. The FSE works mainly on s states for nonrelativistic atoms, whereas for relativistic atoms, it works on s and p1/2 states. The energy levels of p states have been calculated lower than the energies of the corresponding s states when we have included the FSE.
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• 8
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: The three azaborine isomers with the formula C4H6BN, 1,2-, 1,4-, and 1,3-azaborine (I, II, and III), have been examined using MNDO (modified neglect of diatomic overlap) calculations. The most stable azaborine was I (heat of formation -8.147 kcal/mol), followed by II (+11.60 kcal/mol) and III (+16.64 kcal/mol). Qualitatively, although the π- and π*-orbitals calculated for the azaborines exhibited an ordering similar to that in benzene and borazine, the HOMO/LUMO energy differences (9.27, 9.68, and 8.44 eV, respectively) were smaller than was the difference calculated for borazine (12.81 eV), but of the same magnitude as the difference for benzene (9.76 eV). With the exception of borazine, each molecule had a π-orbital for the HOMO and a π*-orbital for the LUMO; borazine's LUMO was a π*-orbital. The calculated shapes and atomic contributions for the π-and π*-orbitals of the azaborines were best described as “hybrids” of the π- and π*-orbitals of benzene and borazine. As was observed for the π- and π*-orbitals of borazine, the azaborines exhibited increased orbital density at the nitrogen atom in the π-bonding orbitals and at boron in the π-antibonding orbitals, as would be predicted from electronegativity considerations. Although I and II exhibited significant double- and single-bond localization, all of the ring bonds in III were delocalized. The delocalization in III was not uniform but, rather, resembled two inequivalent fused allyl systems. The cyclotrimer (IV) of 1,2-azaborine (heat of formation -44.07 kcal/mol), based purely on thermodynamic considerations, was predicted to form spontaneously from three monomer molecules with the concurrent loss of three molecules of dihydrogen. The cyclotrimers that could theoretically be produced from 1,2-azaborine without the loss of dihydrogen (IVc and IVt) were each calculated to be less stable (heats of formation +24.45, and +33.29 kcal/mol, respectively) than was the experimentally observed IV. The carbon molecules triphenylene (TP) and cis- and trans-4a,4b,8a,8b,12a,12b- hexahydrotriphenylene (TPc and TPt) (heats of formation +76.79, +101.6, and +103.1 kcal/mol, respectively) were each calculated to be less stable than were the azaborine cyclotrimer analogs, as was observed in comparisons of benzene with the azaborines and borazine.
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• 9
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: The basis-set expansion method has been applied to the nonrelativistic and relativistic ground states of one-electron atoms H, Ar17+, Xe53+, Hg79+, and U91+ in the uniformly charged sphere (UCS) and the point-change (PC) models of atomic nucleus, using the Gaussian-type basis functions. The energies and the radial expectation values, especially 1/r2, converges faster in the UCS model than in the PC model. In the PC model, larger values of the exponent parameters of the basis functions are required both in the nonrelativistic and the relativistic calculations. Even in the UCS model, the larger values of the exponent parameters are needed in the relativistic calculations.
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• 10
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: The entropy of an electronic system is defined in terms of the Husimi function, a nonnegative distribution function in phase space. The Husimi function is calculated by maximizing the entropy subject to the constraints that the Husimi function give a Gaussian convolution of the desity when integrating over the momentum coordinates and that its second moment with respect to momentum give a sum of Gaussian convolutions of the density and the kinetic energy density. The result is compared with the Wigner function. Equations are given for calculating the density matrix from the Husimi function. The resulting equation for the exchange energy requires a difficult numerical integration. An alternate method is used to obtain the density matrix from an approximate partially collapsed Husimi matrix that gives the maximum entropy Husimi function as its diagonal. The results are exact for the harmonic oscillator ground state. Exchange energies calculated for H and the He isoelectronic series through C+4 show slight improvements over those calculated using a maximum entropy Wigner function.
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• 11
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: We present a treatment of chemisorption that uses the Green matrix of the surface and the admolecule, as well as a cluster calculation of a small surface cluster. Since full HF-SCF-band structures with nonlocal exchange are available now for larger systems for a couple of years, it is possible to treat the substrate surface and the admolecule on equal footing. This offers a natural way to solve the embedding problem. We have applied the formalism to the adsorption of H2 on beryllium and show that in contrast to cluster calculations there appears a binding, which is experimentally verified.
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• 12
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
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• 13
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
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• 14
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: A new type of correlation functional derived from the second-order expression for the correlation energy of an atom is proposed. The derived correlation potential contains one free parameter, which is determined by fitting the known pair correlation energy. The calculations with this potential in the Kohn-Sham approximation give rather accurate values for the matrix elements of different operators.
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• 15
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
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• 16
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
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• 17
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: It is shown that the Heisenberg Lie algebra of the nondegenerate harmonic oscillator leads to a basis {J+, J0, J-} of LASU(2). The Hamiltonian of the system is proportional to J0, and the basis elements give rise to irreducible tensors in the associative enveloping algebra of the Heisenberg Lie algebra. The construction of these irreducible tensors is studied with special attention being paid to the case in which they act upon a single vector space spanned by the harmonic oscillator basis functions. A tensor coupling rule is developed, and useful application is made of it in the calculation of general expressions for vibrational operators and their matrix elements. Throughout, the value of the additional algebraic quantum numbers (l, m) is emphasized.
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• 18
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: A perturbation theory for normal coordinates of nonadiabatic solvation is presented by means of the “string model” of chemical reactions. The dynamic normal coordinate is introduced for the perturbational treatment of the “intrinsic” normal coordinates that are orthogonal to the reaction path. The reaction is defined as the intrinsic reaction coordinate (IRC) that is treated as a string. The string is thrown in the external force field that acts as a nonadiabatic source of perturbation. As an application of the present treatment, the effect of a water molecule for hydration reaction of formaldehyde is calculated. A second-order perturbation effect for the enhancement of the reaction rate is found.
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• 19
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: Potential energy surfaces, properties, and spectra of singlet (X1A1) and triplet (a3B2) ozone are investigated by means of MCSCF/MCLR analytical response theory calculations. MCSCF analytical gradients and Hessians are used to locate equilibrium and transition-state structures and to obtain associated vibrational and rotational constants, infrared intensities, and dipole moments. By means of MC linear response functions, electronic excitation energies, and oscillator strengths, static and dynamic polarizabilities as well as dispersion (C6) coefficients are obtained. Good agreement is achieved, in some cases within experimental error margins, for properties where experimental data are known. A very low IR intensity for triplet ozone is predicted.
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• 20
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: Two possible reaction paths for the pyrolysis of the ethylester of glyoxylic acid have been studied by ab initio molecular orbital calculations. The basis sets 3-21G and 6-31G* have been used, and electron correlation has been included by Møller-Plesset calculations up to fourth order. Our calculations indicate that the reaction leading to acid and ethylene through a 6-membered ring transition state is favored relative to a process involving a formyl hydrogen transfer via a 5-membered ring to the alkyl unit leading to ethane, CO, and CO2. The predicted activation energies for these two reactions obtained at the highest level of calculation, MP4(SDTQ)/6-31G*, are 50.4 and 71.7 kcal/mol, respectively. The transition states have RHF wave functions that are stable relative to UHF solutions using the 3-21G basis. The geometry of the transition states and IRC following indicate that both reactions are strongly asynchronous: The C—O bond rupture is virtually completed before hydrogen transfer occurs. For comparative purposes, analogous calculations have been performed for the ethylester of formic acid, where it is confirmed that a 6-membered ring transition state is preferred relative to a 4-membered one by around 42 kcal/mol at the highest level of calculation.
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• 21
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: In excited states of atoms and molecules, as well as in time-dependent situations, the one-electron density no longer suffices to completely characterize the electronic state; in addition, one now requires information about the electronic phase or the current density. We show that, for a stationary electronic state, the continuity equation of quantum fluid dynamics represents a differential equation for the electronic phase, which must be solved subject to certain periodicity conditions. These periodicity conditions arise from the nodal topology of the wave function and give rise to quantized vortices of current. The consequences of writing an electronic “wave function” for a many-electron system directly in terms of the single-particle density and phase have been investigated. We have shown that such a procedure leads to the appearance of an “internal magnetic vector potential.” We also establish the connection between the electronic phase and the geometrical (“Berry”) phase accompanying the adiabatic transport of a quantal system around a closed loop in parameter space. This leads to a generalization of the current density concept and allows us to discuss the geometrical phase in terms of the circulation of this current in parameter space.
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• 22
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: Environmental effects on the electronic structure of molecules caused by external perturbations are studied by means of an expansion of molecular orbital wave functions into valence-bond (VB) wave functions. Applications are carried out to the π system of butadiene, hydroxyethylene, acrolein, and carbonyl oxide and also to the full electronic system of water. The external perturbations considered are uniform electric fields, nonuniform electric fields, and reaction fields created by solvents. A different behavior is found between nonpolar and polar species in the presence of solvents. Some consequences on the behavior of molecules under the influence of the different electric fields are discussed.
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• 23
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: The Hartree-Fock problem in two dimensions (2D) has been solved for 1 ≤ Z ≤ 24 using a Gaussian basis and assuming r-1 Coulomb interactions. The order of occupation of the one-electron states is \documentclass{article}\pagestyle{empty}\begin{document}$$1s\, \ll \,2s\, 〈 2p\, 〈 3s\, 〈 3p 〈 4s\mathop 〈 \limits^ \approx \,3d 〈 4p$$\end{document} like in the 3D case. The 1s shell is found to be particularly small and strongly bound, making the 2D hydrogen a “superhalogen” and the 2D He a “superinert gas.” In contrast to 3D, 4s13d2 and 4s23d3 configurations are preferred for the 2D “Sc” and “Cu,” respectively. The six first 2D atoms have stronger and the later ones weaker valence-bonding energies than do their 3D analogs. It is noted that the 2D Dirac energy expression for a hydrogenlike atom for mj = l + 1/2 agrees with the 3D Klein-Gordon one.
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• 24
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: A time-dependent molecular orbital method has been developed to study charge transfer in collisions of ions with metal surfaces at energies between 1 and 100 au. A set of localized basis functions consisting of generalized Wannier functions for the surface and s- and p-atomic functions for the ion, is used to separate the system into primary and secondary regions. An effective Hamiltonian and time-dependent equations for the electron density matrix are obtained in the primary region, where most charge transfer occurs. The equations for the electron density matrix are solved with a linearization scheme. The method is suitable to study atomic orbital orientation for collisions of ions and surfaces. A model calculation for Na+ + W(110) collisions with a prescribed trajectory is presented. The interaction potentials between the W(110) surface and Na+ 3s and 3p orbitals are calculated from Na+ pseudopotentials. Results show that the yield of neutralized atoms in 3p states changes as the collision energy is lowered.
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• 25
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
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• 26
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: The splitting method is an approach for preventing unphysical behavior of a wave-packet at the edges of its coordinate space representation grid. We examine here the possibilities and limits of using this method to perform time-resolved analysis of the products of molecular processes.
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• 27
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: The electronic structure of a 2D polyglycine network with a pleated sheet structure has been computed at the Hartree-Fock level and by including electron correlation effects within the second order of many-body perturbation theory (electron polaron model). The influence of the size of the atomic basis set and of the extension of the virtual space has been investigated both for single- and many-particle properties. Comparison with the energy of the corresponding single chains showed that interchain interactions (mainly hydrogen bonding) provide an extra stabilization for the 2D network by 7.4 and 10 kcal/mole per glycine residue at the Hartree-Fock and correlated levels, respectively. The energy dispersions are rather anisotropic for all bands whose widths are about 0.5-1 eV along the polypeptide backbones and 0.1-0.2 eV in the perpendicular direction (hydrogen bonds). The HF value of the fundamental energy gap is reduced by 4 eV to 9.2 eV for electron polarons. The wave functions and interaction integrals obtained can be used to calculate further optical and lattice vibrational properties.
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• 28
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: Local-scaling transformations are employed in order to formulate a desity functional theory where both electrons and nuclei are treated quantum mechanically. Because of the properties of these transformations, the ensuing version of density functional theory is N- and v- representable. In particular, we study the effect of these transformations on both densities and generating wave functions, and as a result, a functional for the energy expressed in terms of the electronic and nuclear densities is constructed. Plausible physical approximations for simplifying this electronic-nuclear functional are considered, and upon variation of the fuctional with respect to the electronic and nuclear densities, a system of coupled Euler-Lagrange equations is obtained.
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• 29
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: It is shown that the dispute about the conditions for physical admissibility of Schrödinger wave functions may be settled if the following two questions are clarified: (a) Are these condittions rooted in the foundations of quantum mechanics or invoked only for particular physical models? (b) Do we consider either the position-space wave function or the momentum-space wave function? Both the case of closed states and scattering states are considered. Some general remarks about these conditions are made in the Conclusion.
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• 30
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: We have attempted to optimize the cost (the total number of floating-point operations required) of using the McMurchie-Davidson RNLMj recurrence relation. Rigorous solutions of the tree-search problem inherent in the cost minimization are given for total angular momentum L ≤ 7. For L ≥ 8, the rigorous search algorithm is prohibitively expensive, and we propose an approximate algorithm that generates highly optimized trees. Cost comparisons demonstrate that the present scheme is consistently superior to two others currently in use.
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• 31
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: Methods for calculations on extended systems are proposed, in which long-range Coulombic interactions are treated classically. The basic mode of description for the system is still in a quantum mechanical language, involving wave functions, Hamiltonians, etc. The electron density in a large molecular system is divided into suitable fragments, and the electrostatic potential generated by such a fragment at some distance away from it is then expressed by a generalized multipole expansion relative to a single point in space, conveniently taken as the center of charge distribution for that fragment. The computational effort required for evaluating the interactions involving those multipoles is modest and scales favorably (quadratically) with the size of the system. The remaining interactions, which need to be treated with conventional methods, i.e., with explicit one- and two-electron integrals, scale only linearly with size in extended systems. An important characteristic of the approach is that, while the approximations and shortcuts introduced have a clear physical origin, they can be justified on strict numerical grounds, such that calculated energies and other properties are identical to those obtained with conventional methods.
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• 32
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: A distributed-memory model is adopted for the development of parallel ab initio codes with an emphasis on portability as well as efficiency. A highly portable message-passing toolkit (inspired by the Argonne ACRF PARMACS) is described. Examples and results of its use are presented.
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• 33
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
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• 34
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: An original procedure has been developed to determine the eigenvalues and the eigenfunctions of quantum-mechanical many-body systems with a harmonic oscillator interaction. Exact solutions in the explicit form have been obtained for the case of systems containing three groups of identical particles. For the system containing two groups of identical particles, a solution in the adiabatic approximation has been obtained and compared with the exact one.
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• 35
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: An exact, within the Born-Oppenheimer approximation, body-fixed Hamiltonian for the nuclear motions of a triatomic system is presented. This Hamiltonian is expressed in terms of two arbitrarily defined internal distances and the angle between them. The body-fixed axis system is related to these coordinates in a general fashion. Problems with singularities and the domain of the Hamiltonian are discussed using specific examples of axis embedding. A number of commonly used coordinate systems including Jacobi, bond-length-bond-angle, and Radau coordinates are special cases of this Hamiltonian. Sample calculations on the H2S molecule are presented using all these and other coordinate systems. The possibility of using this Hamiltonian for reactive scattering calculations is also discussed.
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• 36
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New York, NY : Wiley-Blackwell
ISSN: 0020-7608
Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: The correct description of energetic separations between atomic states arising from s2dn, s1dn+1, and dn+2 electronic configurations is known to be essential to treat transition metals. Effective core potentials calculations for first-row transition elements with an Ar core show important errors in these energies when compared with all-electron values. A procedure to eliminate errors while maintaining the formalism unaltered and retaining the ar core is proposed.
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Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: The electronic absorption spectra of 2-, 3-, and 4-vinylpyridines and 1,2-(2,3-dipyridyl), 1,2-(2,4-dipyridyl), 1,2-(3,4-dipyridyl), and 1,2-(4,4-dipyridyl) ethylenes have been investigated in polar and nonpolar solvents. A correlation has been made between the geometry of the molecule and the observed spectrum. Molecular orbital calculations have been carried out using the INDO/S—CI procedure and a limited geometry optimization. The solvent effect at the MO level has been calculated. MO calculations predicted the existence of nπ* transitions that were not observed experimentally. The wave functions of the different CI states were calculated. The experimental transition energy as well as oscillator strength corresponded satisfactorily with the calculated ones. The observed transitions were assigned according to the results of MO calculations.
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Source: Wiley InterScience Backfile Collection 1832-2000
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Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: The novel B-DNA dodecamer sequence d(CGCGTTAACGCG) and its complex with the anticancer drug netropsin have been determined using single crystal X-ray diffraction methods. The DNA conformations in both structures are compared to understand drug-induced conformational changes. The dodecamers crystallize in isomorphous orthorhombic space group P212121 with cell constants a = 25.49 Å, b = 40.84 Å, and c = 67.02 Å for the DNA itself, and a = 25.70 Å, b = 40.50 Å, and c = 67.00 Å for the complex. X-ray intensity data were collected on a Siemens area detector, and the structures were refined to R factors of about 19%. The DNA molecule is bent 18° in the native structure and 24° in the netropsin complex. The narrow “cleft” formed by the T2A2 sequence at the center serves as the binding site for the drug and on binding expands the cleft from about 4 to 4.3 Å. The drug is engaged in hydrogenbonding interactions with the adenine N3 and thymine O2 atoms in the floor of the minor groove covering the entire tetranucleotide stretch TTAA/AATT.
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Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: The synthetic polytetrapeptide using the repeating sequence VPGG found in the fibrous protein, elastin, exhibits a reversible inverse temperature transition, i.e., the molecular order increases on raising the temperature of the polypeptide in aqueous solutions. The matrices formed from the coacervate by γ-irradiation-induced cross-linking exhibit an elastic modulus and temperature dependence of elastomeric force with similarity to that of fibrous elastin. As demonstrated on poly(VPGVG), which forms a β-spiral structure with recurring Type II β-turns, the molecular structure of the elastin-based polypeptides is fundamental to an understanding of the mechanism of elasticity.It was found previously that the repeating unit VPGG in the polytetrapeptide forms a Type II β-turn with a hydrogen bond between Val1 C=O and Gly4 NH. This secondary structural feature is confirmed in this report by 2D NMR data as indicated by specific NOE cross-peaks, particularly, dNN(3,4), dαN(2,3), dαN(2,4), and dγN(1,4). The same secondary structural feature is found in the 2D NMR data for its analog polypeptide, poly(IPGG).The NMR data provide conclusive evidence for the Type II β-turn secondary structure. Molecular mechanics computations were performed to develop a more detailed tertiary structure for the polytetrapeptides. The ECEPP/2 potential field and build-up strategy were employed in mapping conformational space of VPGG and its high polymer. In addition, helical structures are sought using the Go-Scheraga condition, on the assumption that the repeated sequence would preferentially adopt a helical or nearhelical conformation on optimization of intramolecular hydrophobic contacts. A number of structures with helically recurring β-turns was obtained and can be used as starting structures in future studies that are to include hydration. The structures were also evaluated in terms of potential energy using the CHARMm force field.
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Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: An empirical approach for the computation of log P for flexible molecules has been developed. This approach is based upon the use of fragmental parameters for obtaining the free energy of solvation of a given molecular conformation in both water and octan-1-ol. Two parametrization methods have been investigated, and the quality of the fragment parameters obtained assessed by computation of log P values for a number of compounds which can only adopt a single conformation. Comparison of these calculated log P values with experimental measurements revealed that simple empirical models which assume a linear relationship of transfer free energy and fragment solvent accessible area do not adequately represent the interaction of polar fragments with water molecules. In the second parametrization method, therefore, a novel step function was introduced, based upon physical models of the specific hydration of polar fragments able to participate in hydrogen bonding, by water molecules. Fragment parameters derived by the second approach gave excellent agreement between calculated and experimental log P values for rigid molecules containing several classes of functional group.
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Source: Wiley InterScience Backfile Collection 1832-2000
Topics: Chemistry and Pharmacology
Notes: In distinction to the classical strategy of molecular modeling minimizing the energy of a small number of molecules, a procedure (FLATER) is developed to treat an aggregate of molecules organized in an array. The molecular energy of a unit cell in the array is minimized relative to a set of general coordinates defining the conformations and arrangement of molecules and the global geometry of the lattice, while allowing complete flexibility of the system. A test performed on the 1,2-dilauroyl-DL-phosphatidylethanolamine:acetic acid crystal of known structure shows that the molecular structures obtained by the procedure are reliable. An application of the procedure to the study of the copacking of lipids and hydrophobic polypetide α-helices in membranes is reported. Its results indicate that the interplay of the interactions that exist in the hydrocarbon region of a membrane concur to favor the assemblage of the helices rather than their dispersion in the lipid phase. This situation springs from the dominance of the helix-helix interactions, insured by the nature and number of the hydrophobic amino acid involved. This program is particularly well suited to studies of the interactions and architecture of molecules in multicomponent membranes.
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Source: Wiley InterScience Backfile Collection 1832-2000
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• 45
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Source: Wiley InterScience Backfile Collection 1832-2000
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Notes: The angular and energy dependence of minima of the differential scattering cross section (DCS) for electrons scattered elastically by selected target atoms is studied using the nonrelativistic Hartree-Fock wavefunction for the static field and local energy-dependent function for the exchange and polarization potentials for the target atoms. The parameters contained in the polarization potential are varied to determine the minima of the DCS with respect to the scattering angle and incident energy with the constraint that the integral cross section agrees with the experimental value within the uncertainty of 5% at a selected energy. The resulting effective interaction potential is then used to compute the DCS over the intermediate energy range for the target atoms. The computed values are in good agreement with recently published experimental and theoretical cross section for helium and neon atoms.
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Topics: Chemistry and Pharmacology
Notes: From ab initio SCF-MO calculation using a 6 - 31G** basis set, the relationship between the topology of the charge distribution and the electric field gradient (EFG) at the nuclei of the two-coordinated N atoms was determined in imines with R = H2C =, HFC =, NCHC =, and H3CHC =; di-imides with R = H, F, and CN; and the monocyclic azines with one and two N atoms in it. It was found that the N nuclear quadrupole coupling constant was determined by the nonbonded concentration of N valence shell while the asymmetry parameter has contributions from this shell and also from the rest of the molecule.
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Topics: Chemistry and Pharmacology
Notes: Using computational SCF and MCSCF followed by extensive variational and perturbational CI calculations, we study the insertion routes of a copper atom into the carbon-hydrogen bond of a methane molecule. Here we show the importance of the initial reaction routes of the interaction for obtaining the final products of maximal probability. Because of the initial conditions of this reaction, our study shows that not all of the HCuCH3 intermediate complex dissociation channels in Part I can be easily reached. Another important result presented is the nonlinearity of the intermediate product HCuCH3. Finally, the results are discussed in light of low temperature matrix photoexcitation experiments and a comparison of this Cu—CH4 interaction with previous studies of the activation of the hydrogen molecule by copper is presented.
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Notes: The restricted Hartree-Fock formalism applied to quasi one-dimensional translational systems embodies slowly convergent Coulomb and exchange lattice summations. In this contribution, an algorithm based on a Filon like quadrature procedure to carry out the k-space integration of density matrix elements is analyzed and its efficiency is illustrated by its application to the linear chains of hydrogen molecules. It allows the computation of Coulomb and exchange lattice sums to their asymptotic limit, and renders obsolete the empirical procedure of guessing the number of interactions to be included in the calculations.
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Notes: The hybrid method having features of ab-initio crystal orbital and ab-initio molecular cluster methods is proposed. In the approach presented the molecular crystal is treated as an infinite chain in a direction z, while two other directions are simulated by finite interactions of the molecular type. The new approach is especially useful for an investigation of anisotropic crystals. Test calculations for the carbon dioxide crystal are presented. The method was also employed for the investigation of a dissociation pathway of C—N bond in nitromethane in nitromethane crystal.
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Notes: A quantum mechanical time-dependent method was used to study the dynamics of dissociative adsorption and associative desorption of H2 on a flat, static surface. We used a two-dimensional model in which the molecular axis was held parallel to the surface and the diatom internuclear separation and distance above the surface were the dynamic variables. A modified London-Eyring-Polanyi-Sato (LEPS) potential described the molecule-surface interactions. The wave function for the molecule was represented by its values on a spatial grid of points. The wave function was propagated by expanding the time evolution operator in a series of Chebyshev polynomials and using the properties of the Fourier transform to calculate the kinetic energy. The computational requirements of the problem were significantly reduced by using an L-shaped grid which deletes a large number of points where it is known a priori that the wave-function amplitude vanishes. State-to-state transition probabilities were calculated as a function of the initial translational and vibrational energy for potentials with early, late, and intermediate barriers. The location of the barrier has a strong effect on the energy threshold for reaction and on the distribution of energy between vibration and translation in the products.
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Notes: In this work we deal with ab initio and semiempirical calculations of single and multiple Al → Si replacements in the ZSM-5 structure. Substitutional energies for single replacements were obtained for cluster models of monomers, hexamers, and for the secondary building unit (SBU) of the zeolite by means of nonempirical SCF calculations, as well as the modified neglect of differential overlap (MNDO) method for extended clusters. The choice of the semiempirical methods for the study of multiple Si replacements by Al in the extended cluster model of the SBU is justified from the results with monomers and hexamers where the replacement energies obtained with MNDO are qualitatively the same as those from ab initio calculations. According to the results, a site occupancy order in the unit cell of the ZSM-5 network is derived from multiple Al → Si substitutions in the SBU, providing a theoretical basis for the Loewenstein-Dempsey Al sitting avoidance rules. Likewise, a Si/Al limit ratio in the Mobil FIve (MFI) zeolite, along with the corresponding Al distribution pattern in the unit cell, are also obtained.
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Notes: Due to the mass effect, muonic molecular ions are about 200 times smaller than their electronic counterparts. The proximity of the nuclei in the tdμ ion results in fusion taking place within a picosecond. The properties of this ion are central to understanding the phenomenon of muon catalysis. We developed a computational method of solving the nonadiabatic Schrödinger equation for the bound and resonant states of tdμ and its isotopic analogues. The method takes into account both the Coulomb interactions and the strong nuclear forces responsible for the fusion reaction. The wave functions obtained from our method were used to predict very accurately branching ratios and transition rates relevant for various stages of the muon catalytic cycle. Knowledge of these quantities will guide the experiments and help to answer the question of feasibility of net energy production via muon catalysis.
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Notes: This article describes the computation of the tunnel current in a scanning tunneling microscope (STM). The calculation accounts for the three-dimensional scattering taking place simultaneously in the first atomic layers of the sample and in the apex of the probing tip. The model is built with the following ingredients: (a) the tip is represented by a cluster of atoms attached to an otherwise planar, free-electron metal surface, and (b) the analyzed sample is a planar free-electron metal with a local potential corrugation induced by an isolated molecule or adatom. The potential barrier includes the strong bending effect due to the image-charge formation occurring as the tunneling electron crosses the gap between the tip and the sample. The specific theoretical approach designed to solve this scattering problem exploits the fast Fourier transform algorithm to construct a transfer matrix in a mixed real- and momentum-spaces representation. The total current is obtained by summing the contributions of all scattered waves traveling in the barrier between the tip and the sample, and it is studied in this article for various positions of the tip relative to the adsorbed atomic cluster. The theory is used here to simulate the scan of a model-aluminum atom on a free-electron metal substrate using electrons focused by a single-atom tungsten tip.
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Notes: Drawing on the results of an analysis of the nature of the pulse that generates complete transfer of population from one to another level in a system with a discrete spectrum, a generalization of the method of stimulated emission pumping is proposed. It is shown that a small subset of the Fourier components of the optimal pulse will, if their relative amplitudes are the same as in the optimal pulse, generate almost as efficient a population transfer, thereby generating the opportunity to prepare a system in a selected state with a selected population.
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Notes: Model studies are reported aimed at accounting for the abrupt dependence of radiationless decay-rate constants on excess energy (known as channel-three decay in the case of S1 benzene) in singlet and triplet manifolds of benzene and azabenzenes. The favored model involves La(ππ*) state, strongly distorted along an out-of-plane coordinate, crossing the ground-state potential at an energy close to the minimum of the lowest excited state. The results are compared with experimental observations on benzene and three azabenzenes. Implications for photochemical reactions are also discussed.
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Notes: The near-ultraviolet spectrum of a dinaphthonorbornadiene is reported and is interpreted using simple exciton theory that treats this molecule as a dimer of naphthalene. It shows examples of weak, intermediate, and strong coupling for the interaction of the three observed bands of naphthalene.
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Notes: Coherent dynamics of multilevel systems is of interest for the elucidation of energy disposal and multiphoton chemistry of polyatomic molecules. We compare the analytical solutions for coherent multiphoton excitation of two sparse multilevel model systems: (1) The spin-J system consisting of N = (2J + 1) equally spaced levels with the radiative coupling being determined by the xth component of the angular momentum. (2) The equally coupled N level system. The transition amplitudes for system (1) are always periodic, which is in contrast to the nonperiodic behavior exhibited by system (2) for N 〉 3.
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Topics: Chemistry and Pharmacology
Notes: In this paper, the density matrix formalism has been applied to treat ultrafast time-resolved absorption spectroscopy. We have shown that in the femto-second (fs) pump-probe experiments, the observed time-resolved absorption spectra consist of the contributions from the population (i.e., incoherent contribution) and the coherence (i.e., the phase of the system). The adiabatic approximation has been used to derive the expressions for ultrafast time-resolved spectra. We have also shown that the dynamics of the coherence will result in quantum beat. Numerical calculations have been performed to demonstrate the theoretical results.
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Notes: We propose 10 desirable features or criteria for general purpose methods to be applied to the calculation of a range of spectroscopic properties. We discuss the second-order polarization propagator approximation (SOPPA) in light of these criteria by giving the actual computational expression used as well as a few numerical examples taken from the theory of NMR spectra (magnetic shieldings and spin-spin coupling constants). We demonstrate that SOPPA comes close to fulfilling these criteria.
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Notes: The effects of perturber gases, partial pressures in the range 0-50 atm, on the absorption spectra of high-n Rydbergs, n ≥ 10, in methyl iodide and benzene have been investigated. The perturbers were rare gases and H2. It has been shown that the spectroscopic energy shift Δ = Δ(ρ, n) is given by Δ = Δ°ρ, where ρ is the number density of the perturber, for n ≥ 10. The shift data can be interpreted using a Fermi model, and values of scattering lengths for perturbers can be extracted. These scattering lengths are internally consistent, independent of the absorber, and in excellent agreement with electron-swarm results. Given that the Fermi model is nonspecific and microscopic, scattering shifts and lengths for mixtures of perturber gases can be predicted. These predictions, having been verified by experiment for He/Ar mixtures, provide a means of “tailoring” any required scattering length. Finally, it is shown empirically that the determinative scattering parameter is the polarizability of the perturber, and a universal relationship a = -0.26α + 1.18 between scattering length a, in Bohr radii, and polarizability α is found to exist.
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Notes: C6H6 Raman scattering activities calculated from harmonic model ab initio Hartree-Fock 6-311 ++ G(d, p) polarizability derivatives (and harmonic force fields calculated at the same level) accurately simulate experiment (to within 1% for the a1g modes). Accurate predictions are also made for the e2g modes (to within 5% for ν7 and ν9, and more poorly for ν6 and ν8 [in Fermi resonance with ν6 + ν1]) and for the e1g out-of-plane mode, ν10. Only the ν6 in-plane CCC bending mode scattering activity is found to be anomalous. Systematic variation of the basis set indicates that the benzene scattering activities and depolarization ratios are strongly dependent on inclusion of both carbon and hydrogen atom diffuse functions in the basis set. Predictions are also made for 12C6D6 and for unmeasured intensities in 13C6H6. Measurements of a1g mode scattering activities in the latter molecule are predicted to be useful in testing the harmonic Hartree-Fock Raman intensity model.
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Notes: A formulation is presented of the effects of van der Waals interaction on infrared intensities. The theory takes account of induction and dispersion interactions (including charge interpenetration) and is applicable to fluids of arbitrary density. The transition moments are developed from generalized van der Waals-induced moments, and expressions are obtained for the adsorption coefficient in terms of generalized charge densities and charge-density (hyper)susceptibilities. Explicit expressions are given also of the integrated absorption coefficient in terms of multipoles, and (hyper)polarizabilities and their derivates, and the usefulness of this formulationin interpreting experimental data is illustrated by several examples. The relevance of the induction and dispersion interactions to allowed and to forbidden transitions made allowed is discussed.
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Notes: A method for analyzing asymmetric top rovibrational bands displaying both blended and resolved features is described. The two-phase computational procedure uses a modified version of the asymmetric rotor-band contour program FASTPLOT to generate a preliminary set of upperstate spectroscopic constants. The parameters are subsequently refined by employing the assigned line-fitting formalism of the ASYROT program using both resolved and blended features. The technique is detailed in a comprehensive analysis of the ν17 band of pyridine. Inclusion of quartic centrifugal distortion constants was found to satisfactorily model a high-resolution (0.004 cm-1) spectrum of this band, yielding a standard deviation of 0.00137 cm-1. The variation in the rotational parameters with vibrational quantum number is examined in terms of possible weak rovibrational perturbations to the ν17 state. An ab initio calculation of the ν17/ν27 Coriolis coupling constant indicates the observed results are consistent with the interaction of these two vibrational states.
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Notes: The intermolecular modes of the bifurcated water dimer are determined at the HF level using an extended basis set. In these computations, the donor libration frequency is found to be real and the bifurcated structure does not collapse toward the linear dimer. This result is contrary to all previous ab initio computations, which have predicted a Hessian with one negative eigenvalue. A good representation of other intermolecular modes, such as the libration of the acceptor, also requires an extended basis set. An interesting infrared active transition is predicted around 444 cm-1. This transition, which corresponds to the donor wag, is found in the low-temperature spectrum of water in a N2 matrix.
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