Library

Notes: The performance of effective core potentials adjusted at the Hartree-Fock level but applied in density functional calculations has been tested in a set of calculations using various basis sets and/or core potentials. Test molecules have been the first-row transition-metal carbonyls Cr(CO)6, Fe(CO)5, and Ni(CO)4 and the second-row carbonyls Mo(CO)6, Ru(CO)5, and Pd(CO)4. Only “small-core” potentials have been used, and these are able to reproduce molecular structures and bond energies from all-electron calculations. Relativistic effects have been estimated for the second-row carbonyls by using quasi-relativistic core potentials. © 1996 John Wiley & Sons, Inc.

Notes: A simplified LCAO-DFT-LDA scheme for calculations of structure and electronic structure of large molecules, clusters, and solids is presented. Forces on the atoms are calculated in a semiempirical way considering the electronic states. The small computational effort of this treatment allows one to perform molecular dynamics (MD) simulations of molecules and clusters up to a few hundred atoms as well as corresponding simulations of condensed systems within the Born-Oppenheimer approximation. The accuracy of the method is illustrated by the results of calculations for a series of small molecules and clusters. © 1996 John Wiley & Sons, Inc.

Notes: No Abstracts.

Notes: No Abstracts.

Notes: Quantum chemical and molecular modeling computations on large molecular systems are defined for the computational facilities assumed to be available from now to the next 4 years. We considered a few topics which are requiring much attention. The correlation energy is discussed in some detail and we have presented two new functionals, called the J-functional and the K-functional, which make use of Coulomb or exchange-type integrals. In addition, we report new computational results for the Coulomb-Hole-Hartree-Fock approximation. Very brief summaries on new developments in relativistic Dirac-Fock computation and in density functional theory, on the advantages gained by using different basis sets in the same computation, and on the promises of parallel computing conclude the article. © 1996 John Wiley & Sons, Inc.

Notes: We investigated the dependence of the electrostatic potential on the size and the shape of various cluster models of the MgO(100) surface. Both Mg2+ and O2- adsorption sites have been considered. The clusters were embedded in a large array of point charges to provide a representation of the Madelung potential. We found that the electrostatic potential in the adsorption region shows a marked dependence on the size of the cluster, in particular, for non-stoichiometric clusters where the number of cations and anions differs considerably. These oscillations are due to (a) the different contribution to the electrostatic potential given by a point charge or by an extended ion, and (b) by the polarization of the ions at the cluster border. The effect of the oscillations in the electrostatic potential on the chemisorption properties was investigated for the case of CO2 interacting with surface and defect O2- sites of the MgO surface. © 1996 John Wiley & Sons, Inc.

Notes: This article describes the present status of the program system ASTERIX and its move toward an efficient implementation on distributed memory computers with 128 processors or more. The ASTERIX program is currently used for scf and ci calculations on what we consider to be truly large systems; polyoxometallates, metallocarbohedrenes, organometallic clusters, and polypeptides. A brief review of our projects in those fields, either recently achieved or in progress, is provided. © 1996 John Wiley & Sons, Inc.

Notes: The distinction between a finite system - however large - and an extended one is emphasized. The implications of the very different types of boundary conditions imposed on wave functions for such systems are discussed as well as the role of the long-range Coulomb potential in the two types of systems. © 1996 John Wiley & Sons, Inc.

Notes: No Abstracts.

Notes: No Abstracts.

Notes: Ab initio valence bond calculations are performed for the three lowest states of the oxygen molecule (3Σ-g, 1Δg, and 1Σ+g). One objective of the present study was to make a contribution to previous valence bond discussions about the oxygen “double” bond. Further, we study the origin of a small barrier in the potential energy surface of the ground state. Two compact models are employed to maintain the clear picture that can be offered by the valence bond method. The first model has only the Rumer structures that are essential for bonding and a proper dissociation. The second model, in addition, has structures which represent excited atoms. These prove to be important for the dissociation energies. For both models, the orbitals are fully optimized. The spectroscopic data obtained are significantly better than are the (few) valence bond results on O2 that have been published and have the quality of multiconfiguration self-consistent field calculations in which the same valence space is used. The “hump” in the potential energy surface of the ground state is shown to arise from a spin recoupling. The free atoms correspond to a spin coupling that is incapable of describing the formation of bonds. Only at short distances, an alternative spin coupling provides bonding and the repulsive curve is converted into an attractive one. Our results on this subject support a valence bond explanation previously given by McWeeny [R. McWeeny, Int. J. Quantum Chem. Symp. 24, 733 (1990)]. © 1996 John Wiley & Sons, Inc.

Notes: On statistical-mechanical grounds, a stochastic optimization technique (generalized simulated annealing) has been recently proposed which contains both classical simulated annealing (Kirkpatrick et al., 1983) and fast simulated annealing (Szu, 1986) as particular cases. This technique can be faster than both in detecting global (and also local) minima. Its utility in quantum chemistry is here illustrated, through the use of a semiempirical quantum method, on molecules of the series CH3-R (C2H6, CH3COH, CH3OH), H2X2 (H2O2, H2S2), X2Y4 (N2H4, P2H4, N2F4), for double bonds (C2H4 and CH2NH), and finally for H2O3. © 1996 John Wiley & Sons, Inc.

Notes: We report a fully self-consistent investigation of the electronic structure, relation between charge transfer and electronegativity, bonding characteristics, and alloying of Al, P, S, and Cl with silicon. The present study indicates that the charge transfer from the host Si atoms to the central impurity atom increases with electronegativity of the impurity element. The bonding between host Si atoms and the impurity atoms is ionic in nature. © 1996 John Wiley & Sons, Inc.

Notes: No Abstracts.

Notes: Alkali-doped polyacetylene is considered as an electron-transfer system. To estimate the reorganization energy due to bond-length changes when electrons are added or subtracted, we applied the (U)MP2 and CASSCF methods to small systems of the type H(CH)NH. The simple tight-binding (Hückel) model with bond-length-dependent resonance integrals has been applied to the same and larger polyenes. The bond lengths are obtained via the bond orders for the various oxidation states. The results agree very well with the ab initio results and experiments for small polyenes. Odd-N and even-N systems behave differently. In odd-N systems, a structural “soliton” exists in the neutral molecule. An electron can be added or removed without bond-length change. In even-N chains, with perfect bond alternation in the neutral molecule, the bond length changes when an electron is accepted occur over about 20 carbon atoms. The reorganization energy tends to a constant value (0.22 eV) as the chain length is increased. Soliton structure is studied as a function of out-of-plane torsional defects and it is found that an additional electron is localized primarily on a segment with an odd number of carbon atoms. In the presence of positively charged ions, electrons are attracted toward this charge and positive solitons formed at some distance from the perturbing ion. © 1996 John Wiley & Sons, Inc.

Notes: No Abstracts.

Notes: The various isomers including stable structures, carbenes, and diradicals on the C3H4 surface have been investigated. The two carbenes propenylidene and cyclopropylidene have been found to have singlet ground states. Vinylmethylene is predicted to have a triplet ground state with a planar diradical type of structure. The syn and anti forms of this state are degenerate. This is in agreement with the observation of two triplet states in the electron spin resonance (ESR) spectra. The π electrons are found to be delocalized over the three carbons. The singlet diradical structures are found to be more stable than the carbene structures, which retain the CH2 (DOUBLE BOND) CH allylic structures. The orbital compositions of the frontier orbitals of all systems have been determined to examine the nature of these orbitals. © 1996 John Wiley & Sons, Inc.

Notes: Electron orbits having a definite angular momentum in a static magnetic field are calculated with the aid of the Bohr-Sommerfeld quantization rules. The quantization gives that orbits are arranged along a straight line but the distance between the centers of two neighboring orbits decreases with increase of the absolute value of the angular momentum. With the energy correction equal to the zero-point energy of the harmonic oscillator, the distribution of orbits becomes identical to that obtained recently with the aid of a mixed semiclassical and quantum mechanical theory.   © 1996 John Wiley & Sons, Inc.

Notes: The potential barriers for the internal rotation of silole dimers are studied theoretically using the ab initio molecular orbital method at the RHF/6-31G** level of calculations. In 2,2′-bisilole, it is found that the anti-conformation is the most stable structure in the ground state and that the potential barrier height for rotation over the perpendicular conformation is 3.3 kcal/mol. © 1996 John Wiley & Sons, Inc.

Notes: This article presents a treatment scheme of the tunneling of hydrogen between two molecular centers (Cl…Cl). The purpose is to calculate the tunneling probabilities of hydrogen atom transfer from the initial (the proceeding complex) to the final-state energy minima (the succeeding complex) in two anharmonic vibrational states (0 → 0 and 1 → 1) in terms of the time-dependent perturbation theory expression and to see whether spectroscopic signatures of tunneling persist in the form of splittings of the vibrational modes. The analysis uses the realistic potential energy function calculated at the HF/6-31 + G** self-consistent-field basis-set level for the interaction between transferred hydrogen and its molecular skeleton (Cl…H…Cl). This potential energy surface is calibrated by comparing its properties with those from sf-POLCI and the LEPS potential-energy surfaces. The anharmonic vibrational state is characterized by the corrected vibrational energy levels and a set of linear combination coefficients obtained via perturbation theory. The tunneling probabilities for two transitions (0 → 0 and 1 → 1) were calculated and compared with those from Gamow's equation. Applicability of the time-dependent perturbation theory expression and Gamow's equation to the [Cl BOND H…Cl] system is discussed. The vibrational splitting energies are obtained, and a spectroscopic signature caused by tunneling is expected and should be observable. © 1996 John Wiley & Sons, Inc.

Notes: Ab initio calculations at the scf level were carried out to compute the polarization potential map (mpp) of the nucleic acid bases: cytosine, thymine, uracil, adedine, and guanine. For this purpose, the Dunning's 9s5p basis set contracted to a split-valence, was selected to perform the calculations. The molecular polarization potential (mpp) at each point was evaluated by the difference between the interaction energy of the molecule with a unit point charge and the molecular electrostatic potential (mep) at that point. meps and mpps for the different molecules were computed with a density of 5 points/Å2 on the van der Waals surface of each molecule, defined using the van der Waals radii. Due to the symmetry of the molecules, only half the points were computed. The total number of points calculated was 558 for cytosine, 621 for thymine, 526 for uracil, 666 for adenine, and 699 for guanine. The results of these calculations are analyzed in terms of their implications on the molecular interactions between pairs of nucleic acid bases. © 1996 John Wiley & Sons, Inc.

Notes: Ultrafast dissipative dynamics of vibrational degrees of freedom in molecular systems in the condensed phase are studied here. Assuming that the total system is separable into a relevant part and a reservoir, the dynamics of the relevant part can be described by means of a reduced statistical density operator. For a weak or intermediate coupling between the relevant part and the reservoir, it is possible to derive a second-order master equation for this operator. Using a representation of the reduced statistical operator in an appropriate molecular basis set, vibrational dynamics in a variety of potential energy surfaces can be studied. In the numerical calculations, we focus on the dissipative dynamics under the influence of external laser fields. In the first example, vibrational wave-packet dynamics and time-resolved pump-probe spectroscopy of molecular systems with nonadiabatically coupled excited-state potential energy surfaces is presented. In the second part, we show how an intense laser field modifies the wave-packet motion onto two radiatively coupled potential energy surfaces. Finally, the controlled preparation of definite vibrational states in a triatomic molecule with infrared laser pulses is considered taking relaxation and dephasing processes into account. © 1996 John Wiley & Sons, Inc.

Notes: We sketch the procedure that we are using to optimize a spin-coupled wave function built with partially orthogonalized orbitals. It is shown how it is possible to parametrize the orbitals in order to deal with independent variables while maintaining the partial orthogonalization and how to calculate first- and second-order derivatives with respect to these variables. A test calculation on CH4 molecule is shown. © 1996 John Wiley & Sons, Inc.

Notes: The properties of Sturmian basis sets in d-dimensional direct space and d-dimensional momentum space are reviewed, as well as the relationship between hydrogenlike Sturmians and hyperspherical harmonics. The kernel of the reciprocal-space Schrödinger equation is expanded in terms of Strumian basis sets. This expansion allows Shibuya and Wulfman's treatment of many-center Coulomb potentials to be extended to many-center potentials of a general form, and the method is also extended to the calculation of crystal orbitals and band structures. © 1996 John Wiley & Sons, Inc.

Notes: To provide a potential energy surface (PES) for a three-dimensional vibrational model of the dissociation dynamics of ammonia in the à state, accurate MRD-CI computations were carried out for a wide range of displacements in the out-of-plane and in-plane bending coordinates along the H(bond)NH2 dissociation coordinate. Some characteristic features of the Ã-state PES, such as the height and position of the barrier to dissociation and the dependence of the PES on the out-of-plane angle, differ noticeably from earlier work on this system. The values for the height of the barrier computed from the MRD-CI extrapolation, full CI, and secular equation estimates are 0.38, 0.34, and 0.32 eV, respectively. © 1996 John Wiley & Sons, Inc.

Notes: Ab initio calculations at the MP2/6-31G*//HF/3-21G* level have been carried out to study Diels-Alder reactions of 2-substituted-1,3-dienes with sulfur dioxide. The CH ··· O electrostatic interaction detected in some of the transition structures located could be decisive in the control of the exo/endo stereoselectivity of this type of reaction. © 1996 John Wiley & Sons, Inc.

Notes: We present ab initio calculations carried out in the framework of the G2 theory on the singlet and triplet potential energy surfaces corresponding to the gas-phase between CH+2 and PO. The global minimum of both potential energy surfaces is a cyclic singlet-state cation. Oxygen attachment of PO to CH+2 in a triplet configuration is accompanied by a P(SINGLEBOND)O bond fission, with the result that the corresponding global minimum is an ion-dipole complex between P+(3P) and formaldehyde. This is also consistent with the fact that our results predict the formation of formaldehyde to be highly exothermic, either as a neutral or as radical cation. Both charge-transfer processes yielding CH2(3B1) or CH2(1A1) are also exothermic. The formation of other carbon and oxygen containing species are endothermic. © 1996 John Wiley & Sons, Inc.

Notes: Vibrational population factors for the nascent Penning ions HD+ (v′)(… He) and energy of the corresponding Penning electrons are calculated for the ionization event He(23S)(SINGLEBOND)HD(v′ = 0) → [He … HD+(v′)] + e- taking place at a range of the He*(SINGLEBOND)HD separations and orientations accessible by the system during thermal energy collisions. The vibrational population factors are obtained from the local widths of the He(23S)(SINGLEBOND)HD(v′ = 0, N) state with respect to autoionization to HD+(… He) in its v′th vibrational level. The initial overall picture of the autoionization event is consistent with the He(23S)(SINGLEBOND)H2(v′ = 0) one. On the other hand, the vibrational population factors are different from the approximate average populations used in initial model theoretical considerations about the Penning processes in the system. Variation of the calculated considerations about the Penning processes in the system. Variation of the calculated quantities with changes in the He*(SINGLEBOND)HD separations and orientations is found to be smooth enough to guarantee that the present data might form a sound basis for construction of analytical representations of the corresponding 2D surfaces and for future study of the dynamics of the collision system. © 1996 John Wiley & Sons, Inc.

Notes: The benzene … Ar2 cluster was studied by constant energy molecular dynamics simulations using the ab initio intermolecular potential for the benzene … Ar interaction. The relative population of the energetically less favorable one-sided structure was found to be higher that the population of the global minimum (two-sided structure). The preference of the energetically less stable structure was explained by the entropy effect. The thermodynamic functions (entropy, internal energy, and free energy) were calculated independently by integration of the canonical distribution function. © 1996 John Wiley & Sons, Inc.

Notes: Three specific model systems, HCo(CO)4, Na · NH3, and NO/Pt(111), are used to extend the strategy of vibrationally mediated photodissociations of organometallics, via small clusters of metal atoms and small molecules, to photodesorption of small molecules from metal surfaces. All systems and strategies are similar with respect to breaking metal-ligand bonds by means of infrared IR and visible or ultraviolet UV photons. Specific properties of the systems call, however, for different implementations of the overall tools. In the case of HCo(CO)4, traditional continuous wave (CW) IR + UV 2-photon excitations enhance the rates of HCo bond homolysis. A detailed analysis discovers three effects which result from Franck-Condon transitions in the domains of vibrationally excited wave functions: (i) ultrafast (≈ 20 fs) bond rupture starting from the steeply repulsive wall of the potential energy surface of the excited singlet state; (ii) efficient fast (≈ 200 fs) predissociation via tunneling through neighboring potential barriers; and (iii) decreasing contributions from indirect dissociations via slow (≈ 46 ps) intersystem crossing induced by spin-orbit coupling. In the case of Na · NH3, we suggest a vibrationally mediated pump-and-dump scheme, similar to the strategy of Tannor, Rice, and Kosloff, with proper control of the delay (ca. 70 fs) between ultrashort (ca. 30 fs) pump-and-dump laser pulses. Ultimately, this strategy shifts specific lobes of the vibrationally excited wave packets into a steeply repulsive wall of the potential energy surface of the electronic ground state, with subsequent fast (ca. 100 fs) ruptures of the NA(SINGLEBOND)NH3 bond, similar to effect (i) for HCo(CO)4. Finally, we show that a similar, vibrationally mediated pump-and-dump scheme may also support photodesorption of NO from Pt(111), with an intrinsic relaxation step for the electronically excited system NO/Pt(111) instead of active pump-and-dump control for Na · NH3. All strategies are simulated by fast Fourier transform propagations of representative wave packets on two potential energy surfaces. © 1996 John Wiley & Sons, Inc.

Notes: A proposal for the classification of molecular open-shell states is presented. This classification can be applied to most standard situations, well described within the Born-Oppenheimer and nonrelativistic approximations. The main idea is to consider electronic configurations important in the CI-type expansion of the state wave function at the equilibrium conformation, as well as along any generalized coordinate describing a physically realistic conformational transformation, in particular, the system separation in the state considered. The states are generally divided into single- and multireference ones. On the basis of the conformational dependence of the multireference character, the states are further divided into locally, asympotically, globally, and strongly multiconfigurational ones. The proposed classification is an attempt at a unifying view of such well-known phenomena, like avoided crossings, Woodward-Hoffman forbidden processes, conical intersections, Jahn-Teller stabilizations, and van der Waals minima. A comparison with the classification of Kutzelnigg and Smith [Int. J. Quantum Chem. 2, 531 (1968)], based on an analysis of natural orbital occupation numbers, is made wherever possible. © 1996 John Wiley & Sons, Inc.

Notes: Using density functional theory with Becke's gradient correction for the exchange part and Vanderbilt's ultrasoft pseudopotentials, we investigated [Be(H2O)n]2+ clusters for n = 1 and 3. A new scheme implemented with the Car-Parrinello method is used, upon which no periodic boundary conditions are imposed so that isolated and possibly charged molecules can also be treated dynamically in a plane-wave basis. Harmonic vibrational frequencies are obtained via a fit of the molecular dynamics trajectory in terms of harmonic oscillators, for which we use a fragmentation scheme to analyze complex spectra. Based on this combination of techniques, we find good agreement with data from SCF calculations and correlated methods. © 1996 John Wiley & Sons, Inc.

Notes: To elucidate the physical origin of relativistic changes of molecular properties, exact theorems, perturbation theory, and Hartree-Fock-Slater-Pauli calculations are exploited. The relativistic molecular virial theorem offers insight into the relativistic and nonrelativistic, kinetic, and potential energy contributions to the bond energy. In general, there exist two contributions to the relativistic correction of a molecular property: the relativistic change at the nonrelativistic equilibrium geometry and the change of the nonrelativistic property due to the relativistic change of the equilibrium geometry. Sometimes the first and sometimes the second contribution is the dominant one. Accurate numerical results for H+2-like systems are obtained using direct relativistic double perturbation theory. In some cases, near-degenerate perturbation theory is mandatory. Relativistic changes of chemical bond energies are often proportional to the density change in the K-shell when the bond is formed. Relativistic corrections to many properties (and also to the 1s2-correlation energy) are often proportional to Z2α2. © 1996 John Wiley & Sons, Inc.

Notes: A review is given of many-body perturbation methods, particularly in the all-order and coupled-cluster forms. Relativistic many-body schemes are analyzed in terms of one- and two-photon potentials, derived by means of QED. A complete second-order (nonradiative) calculation for He-like ions is presented, including repeated Breit interactions as well as the effects of retardation and of negative-energy states, but omitting the Lamb shift. Numerical results of some Lamb-shift calculations are also given. From the analysis, conclusions can be drawn concerning the accuracy of certain relativistic many-body approaches. © 1996 John Wiley & Sons, Inc.

Notes: Three isoelectronic reactions, proton transfer (PT), hydrogen abstraction (HA), and electron transfer (ET), of NH+3 with NH,3 H2O, and HF have been studied using ab initio molecular orbital calculations. For the reaction of NH+3 + H2O, the energy of the transition state (TS) is higher than that of the reactants. This is consistent with the experimental observation that the rate constant is less than the average dipole orientation (ADO) rate constant. It seems reasonable that the reaction rate for the reaction NH+3 + H2O would hardly depend on the v2 mode of NH+3 at least for low-lying excited states (Eint≤ 0.714 eV) of the v2 mode, because the v2 mode contributes mainly to the normal mode orthogonal to the reaction coordinate at the TS. This is consistent with experimental observation. A similar prediction can be made for the NH+3 + HF reaction. The electron-transfer processes for the HA reactions have been examined in terms of the intrinsic reaction coordinate (IRC). The order of reactivity with NH+3 is NH3 〉 H2O 〉 HF. It is found that the degree of the electron transfer and the reactivity are correlated with the absolute hardness (η) of NH3, H2O, and HF. This is in accord with the softness as the chemical reactivity index in the density functional theory. © 1996 John Wiley & Sons, Inc.

Notes: The dependence of the rotational energy of small argon clusters on the magnitude and direction of their rotational angular momenta is obtained by two different methods, namely, by analytic descriptions parametric in structural variables (centrifugal displacements) and by classical simulations carried out in rotating frames so that rotational angular momenta are conserved. Potential energies are taken as additive Ar2 pair potentials [R. A. Aziz, J. Chem. Phys. 99, 4518 (1993)], augmented in some cases by three-body Axilrod-Teller interactions, thus complementing our earlier studies of rare-gas clusters modeled by additive Lennard-Jones oscillator (LJO) pair potentials [L. L. Lohr and C. H. Huben, J. Chem. Phys. 99, 6369 (1993)]. Quartic and sextic spectroscopic constants are found to be approximately 10% smaller when the Aziz pair potential is used, reflecting its greater stiffness as compared to the LJO potential. The sign of the sextic tensor coefficient for both tetrahedral Ar4 and octahedral Ar6 is such that for sufficiently high J the C2v (or D2h) structures with J parallel to a pseudo-C2 (or true C2) axis (saddle points on the rotational energy surface at low J) become local energy maxima, the D2d (or D4h) structures with J parallel to an S4 (or C4) axis representing the energy minima. The trigonal bipyramidal cluster Ar5 resembles both Ar3 and Ar4 in its rotational characteristics but with reduced manifestations of nonrigidity. As found with an LJO pair potential [D. H. Li and J. Jellinek, Z. Phys. D 12, 177 (1989)], the icosahedral Ar13 cluster displays a very slight preference for D3d structures with J parallel to a C3 axis, while the D5d structures with J parallel to a C5 axis are energy maxima and the D2h structures with J parallel to a C2 axis are saddle points on the rotational energy surface. The scalar quartic spectroscopic coefficient for Ar13 is found to be 2.15 × 10-14 times that for the reference diatomic Ar2. A variety of structural instabilities are described for Ar13 clusters with very high rotational energies. © 1996 John Wiley & Sons, Inc.

Notes: Post-Hartree-Fock calculations were carried out to predict the stabilities and properties of four HClCO … HCl, HClCO … HF, HFCO … HCl, and HFCO … HF molecular complexes. Full geometry optimizations and vibrational frequency calculations were performed for all systems using standard 6-311G(d, p) and 6-311G(2d,2p) basis sets at the MP2 level of theory. Single-point calculations of the interaction energies were carried out for all complexes at the MP4(SDTQ) level with the 6-311G(d, p) basis set. All systems were found to be stable and their predicted molecular parameters match well available (very scarce) experimental data. © 1996 John Wiley & Sons, Inc.

Notes: A computer modeling of events that occurred under the scanning tunneling microscope (STM) tip was considered from a chemical standpoint. The DYQUAMOD, semiempirical dynamical-quantum chemical program system, which well manifested itself in a quantitative studying of nano-sized objects, was transformed into the DYQUAFIELD program system involving an external electrostatic field. The fields of changeable configurations were simulated by a set of up to 200 point charges. Atomic system modeling was focused on obtaining local electron density (LED) as well as on the object chemical transformations caused by the field. This article presents the results of simulating LED of differently originated graphite films, of a field action on a set of stable molecules, and of an irreversible in-field reconstruction of the diamondlike film surface, which demonstrates a possible nano-sized memory element creation. © 1996 John Wiley & Sons, Inc.

Notes: The energetically possible ways of water condensation at the molecular level were considered. The quantum chemical calculations of the relative stability of elementary modules of the fractal structure without external fields using AM1, CNDO/2, and MNDO methods were done. It was shown that CNDO/2 gives the most adequate results for simple water clusters. Condensation energy per molecule was chosen as a criterion of the cluster stability. It was shown that the twisted modules are the stable structures with respect to the water dissociation. In comparing the energies of the icelike and twisted structures, we conclude that the latter may exist under certain conditions. © 1996 John Wiley & Sons, Inc.

Notes: We describe by approximate MO calculation a number of species for which high spin states are either the ground state or lie very low in energy. These are models for the spin coupling in projected ferromagnetic organic materials. The theory guiding their construction is based on planar conjugated systems, while experimentally realized systems are often far from planarity. We can by appeal to steric decoupling explain the failure of the prediction that methoxy subsitution on metaphenylene-coupled nitroxides should stabilize the triplet. However, we find in general that the qualitative rules derived from discussion of planar systems are robust; drastic departures from planarity are required before they lose their value. © 1996 John Wiley & Sons, Inc.

Notes: A general ab initio package using Slater-type atomic orbitals is presented. This package, called STOP, uses the one-center two-range expansion method to evaluate the multicenter electronic integrals. Thoroughly optimized numerical techniques, in particular, convergence accelerators and suitable Gauss quadratures, are used in the algorithms which provide accurate numerical values for all these integrals. STOP thus provides wavefunctions for general molecular structures at the self-consistent field level for the first time over a Slater-type orbital basis. © 1996 John Wiley & Sons, Inc.

Notes: In this article, an attempt was made to develop an activation process model. The average energy of the translational motion of the atoms, taking part in the elementary activation process and being in the thermodynamic equilibrium with thermal radiation, was obtained using the quantum canonical Gibbs distribution and the model principles of elementary activation. The degeneracy and exclusion of some excited vibrational levels were taken into consideration, the result being a strong dependence of the probability of surmounting the activation barrier on the behavior of the excited vibrational states of the quantum subsystems. As an application of the development model, the formulas of the preexponential factor for solid-state atomic diffusivity and first-order chemical reaction rate constants were derived. Quantitative analysis of the atomic diffusion in solids in the framework of our model has made it possible to describe the diffusion processes in metals, covalent semiconductors, as well as diffusion anomalies, connected with the “nonclassical” behavior of the empirical Arrhenius dependence. A possible physical essence of a kinetic compensation effect is discussed. It was shown that compensation may be caused by only changing the degeneracy of the vibrational levels of the quantum subsystems. © 1996 John Wiley & Sons, Inc.

Notes: Based on a cluster operator formulation of sixth-order Møller-Plesset (MP6) perturbation theory equations for the calculation of MP6 in terms of spin-orbital two-electron integrals are derived. Efficiency has been gained by systematically using intermediate arrays for the determination of energy contributions resulting from disconnected cluster operators. In this way, the maximum cost factor of O(M12) (M being number of basis functions) is reduced to O(M9). The implementation of MP6 on a computer is described. The reliability of calculated MP6 correlation energies has been checked in three different ways, namely (a) by comparison with full configuration interaction (CI) results, (b) by using alternative computational routines that do not involve intermediate arrays, and (c) by taking advantage of relationships between fifth-order and sixth-order energy contributions. First applications of the MP6 method are presented. © 1996 John Wiley & Sons, Inc.

Notes: Generalized overlap amplitudes (GOAS) are calculated between the lithium atom and several states of Li+. An examination of the long-range behavior of the GOAS indicates that they are coupled, appearing to have the same exponential decay at large r. At intermediate distances from the nucleus, the GOAS decay with their unique exponential rate and the decay rates only merge at large r. Although many of the GOAS appear to be similar, their distinctness indicates that they may, in fact, be linearly independent. © 1996 John Wiley & Sons, Inc.

Notes: The wave function of a system may be expanded in terms of eigenfunctions of the N -1 electron Hamiltonian times one-particle functions known as generalized overlap amplitudes (GOAS). The one-electron operator whose eigenfunctions are the GOAS is presented, without using an energy-dependent term as in the one-particle Green function or propagator approach. It is shown that this operator and the extended Koopmans' theorem (EKT) one-electron operator are of similar form, but perform complementary roles. The GOA operator begins with one-electron densities and total energies of N -1 electron states to generate the two-matrix and total energy of an N-electron state. The EKT operator begins with the two-matrix of an N-electron state to generate one-electron densities and ionization potentials (or approximations thereto) for N -1 electron states. However, whereas the EKT orbitals must be linearly independent, no such restriction applies to the GOAS. © 1996 John Wiley & Sons, Inc.

Notes: We applied general quantum mechanical ideas in order to establish the form of the many-electron wave functions suitable for analysis of catalytic processes. This led us to the conclusion that the relevant wave functions for the electrons of the catalytic complexes must be taken as superpositions of the antisymmetrized products of the wave functions of electrons in excited and ionized states of the catalyst and reactants. With use of the trial wave function for the electrons of the catalytic complex in such a form, it becomes possible to construct model potential energy surfaces of catalytic reactions as a superposition of the potential energy surfaces of the reactants in different electronic states. We formulate the criteria which when satisfied make it possible to implement a catalytic version of a desired chemical transformation. We also propose an approach to the explanation of the frequently observed correlations between the catalytic activity and other physical properties of a catalyst. © 1996 John Wiley & Sons, Inc.

Notes: The 17O and 2H quadrupole coupling constants of rovibrational levels of 17O1H+, 17O2H+, and 16O2H+ in their X3Σ- state have been calculated from molecular wave functions that explicitly describe nuclear motion. The 17O quadrupole coupling is predicted to be strong and its vibrational dependence differs from that known for other nuclei A in the first-row hydrides AH or AH+. The deuterium coupling in 17O2H+ and 16O2H+ is found to be weak and its behavior is similar to that of other first-row hydrides. The change with rotational excitation is unimportant. The quadrupole hyperfine patterns of 17O2H+ in its ground state are dominated by the strong oxygen coupling. © 1996 John Wiley & Sons, Inc.

Notes: Nonlocal density functional calculations and a semiempirical modified Born method for computing free energies of hydration were used to calculate the electrode potentials for a series of nitroimidazoles to a mean accuracy of about 80 mV. The density functional calculations used the nonlocal Becke '88 functional for exchange and either the nonlocal Lee-Yang-Parr or the local Vosko-Wilk-Nusair functionals for correlation and were performed at the HF/3-21G geometry. The most suitable geometry for these calculations was determined from a survey of various semiempirical, Hartree-Fock (HF) and density functional methods, with a variety of basis sets. The HF/3-21G method was found to yield a very favorable compromise between speed and accuracy in the determination of the geometry of 2-nitroimidazole, but the small basis set density functional calculations performed very badly. Density functional atom-optimized basis sets were found to give better overall results than traditional Pople-type basis sets. The free energy of hydration calculations employed the AM1 SM2 method. Both the gas-phase energies and the free energies of hydration made a significant contribution to the computed electrode potential. Indeed, an inverse relationship was found between the gas-phase electron affinity and the difference in free energy of hydration between the neutral nitroimidazole and its radical anion. The protocol established here may be useful for investigating novel bioreductive agents. © 1996 John Wiley & Sons, Inc.

Notes: Theoretical calculations of the potential energy surface (PES) for the [NH3 + HCl] system are presented using several standard ab initio methods such as Hartree-Fock (HF), second-order Møller-Plesset perturbation theory (MP2), coupled cluster (CC), complete active space self-consistent-field (CASSCF), density functional theory (DFT), and less traditional ab initio approaches such as Dirac-Fock four-components and the use of effective Hamiltonian techniques, such as the recently proposed K functional. All calculations predict a single minimum for the complex, corresponding to a hydrogen-bonded structure, confirming early studies. The dynamical and nondynamical contributions to the correlation energy are discussed for different cuts of the PES, involving different N(SINGLE BOND)Cl distances. The complex has also been characterized by performing a full geometry optimization within the HF and DFT schemes; with the latter we have performed also the vibrational analysis. The predicted binding energies and infrared (IR) spectrum are compared with other theoretical and experimental results. For the gas phase, we propose a binding energy of -5.3 ± 0.5 kcal/mol, thus revising the experimental value of -8.0 ± 2.8 kcal/mol; for the minimum, the predicted N(SINGLE BOND)H and H(SINGLE BOND)Cl distances are 5.91 ± 0.05 and 2.46 ± 0.05 a.u., respectively. When the computation is done with approximate inclusion of solvent effects (Onsager reaction field), the minimum is shifted and it corresponds to the ion pair NH+4·Cl- structure, similar to Mulliken's outer complex. Since the first ab initio computation for the NH4Cl complex is the pioneer work in 1967 by E. Clementi, the present work provides us with an opportunity to comment on some aspects of the evolution in computational chemistry, particularly for energy determinations. We have concluded our comments with the invitation to use four-components Fock-Dirac for molecules both with high and low Z atoms, rather than the traditional Hartree-Fock and related methods. In other words, we are of the opinion that the time is ready in quantum chemistry to switch from the Schrödinger to the Dirac representation, due to new developments in computer hardware and software. In addition, the use of effective Hamiltonians, like the recently proposed “K functional,” seems to deserve attention, because of their computational simplicity and physical reliability in predicting correlation corrections. © 1996 John Wiley & Sons, Inc.

Notes: Molecular orbital calculations are reported on the structure and electronic properties of both 2-nitrophenylcyanate and 2-nitrophenylthiocyanate using both the semiempirical AM1 and PM3 methods and the ab initio 3-21G and 6-31G** basis sets. The resulting structures are compared with crystallographic data where available. The marked difference in biological activity observed between the two molecules appears to be attributable to large differences in their electronic properties rather than to any geometric factors. © 1996 John Wiley & Sons, Inc.

Notes: We investigated the adsorption and heterolytic dissociation of H2O and H2 molecules on a (ZnO)22 cluster corresponding to ZnO (0001), (000(OVERBAR)1), and (10(OVERBAR)10) surfaces using MNDO, AM1 and PM3 semiempirical procedures. The geometry of the adsorbed molecule has been optimized in order to analyze binding energies, charge transfer, and preferential sites of interaction. The adsorbed species interact most strongly when it is bonded to the twofold coordinated zinc atom of the cluster surface. The interaction of the H2O molecule with the surface of ZnO has a charge transfer from H2O to the surface ranging between 0.17 and 0.27 au. The neighboring atoms of the surface are the main receptors during the process of charge transfer. Our results indicate that there is a weak bonding of the hydrogen atom from OH with the oxygen surface atom that could produce the O(SINGLE BOND)H·O band. The interaction of the H2 molecule with the surface is generally weak and only the PM3 method yields a strong binding energy for this interaction. There is a charge transfer from the H2 molecule to the surface. The chemisorption of H on oxygen atom of the surface transfer charge from the surface to the H. We also calculated the vibrational analyses for these interactions on ZnO surface and compared our results with available experimental data. © 1996 John Wiley & Sons, Inc.

Notes: The energy eigenvalues of coupled oscillators in two dimensions with quartic and sextic couplings have been calculated to a high accuracy. For this purpose, unbounded domain of the wave function has been truncated and various combination of trigonometric functions are employed as the basis sets in a Rayleigh-Ritz variational method. The method is applicable to the multiwell oscillators as well. © 1996 John Wiley & Sons, Inc.

Notes: An improved scheme to accelerate the convergence in the calculations of N-electron atoms, which is based on the exact method we proposed before in hyperspherical coordinates, is presented. The factors influencing the rate of convergence in both parts of expansions in wave function with the hyperspherical harmonics (HHs) of hyperangles and the generalized Laguerre polynomials (GLPs) of hyperradius were investigated. A reselected asymptotic term was introduced by including more structural features in it to accelerate the convergence in the expansion part with the HHs, and a transformation of the hyperradius was used to keep the convergence going properly in the expansion part with the GLPs. Calculations with this scheme for the helium atom were given and compared with some other ones. More accurate results were obtained by considering a simple cusp parameter. © 1996 John Wiley & Sons, Inc.

Notes: A series of the d6 iron(II) complexes with bulky organic ligands (like [Fe(bipy)2(NCS)2]) can exist in two spin forms: in the low-spin (S = 0) form at low temperature and in the high-spin (S = 2) form at high temperature. In the crystal phase, the transition between these two forms may be either smooth or abrupt. Recently, the abrupt spin transitions were identified with the first-order transitions between different ordered phases occurring in the binary mixtures of the two spin forms of the complex. Here, we apply the method widely used in the field of binary metal alloys to the analysis of the spin transitions. The molecules undergoing the spin transition are modeled by octahedra of variable size which interact when they are immediate neighbors in the crystal lattice. We show that some simple assumptions concerning the intermolecular interaction and crystal geometry relaxation allows one to get the desired first-order phase transitions together with a satisfactory description for the crystal compressibility as a function of temperature. © 1996 John Wiley & Sons, Inc.

Notes: All the possible rotamers of 2-aminoethanol and 2-amino-ethanethiol were fully optimized at the ab initio level using the 6-31G** basis with correlation energy inclusion and zero-point energy evaluation. Thirteen local minima for the former and 14 for the latter compound were found. In both molecules, the gauche′-gauche-gauche′ (g′Gg′) is the prevailing conformation, but in the sulfurated compound, it is accompanied by relevant percentages of other conformers, owing to the very low ΔE values. The stability of the g′Gg′ accommodation derives mainly from the presence of weak hydrogen bridges (O(SINGLE BOND)H···N and S(SINGLE BOND)H···N, respectively). The rotation barriers around the C(SINGLE BOND)C and C(SINGLE BOND)N bonds are higher than those around the C(SINGLE BOND)O and C(SINGLE BOND)S ones. © 1996 John Wiley & Sons, Inc.

Notes: The impact of the choices of the complete model space (CMS) and of the orbital basis set on the existence, attainability, and properties of the nonstandard solutions of the valence-universal coupled-cluster (VU-CC) methods has been studied for the case of nonlinear equations corresponding to the atomically oriented form of these methods accounting for one- and two-electron excitations (VU-CCSD/R method) and applied to the Be atom. The results for five 1S states are discussed. In addition to the previously applied CMS defined by the orbital set (2s, 2p) and (2s, 3s), we have employed the CMSs defined by the (2s, 2p, 3s) set. For each of the CMSs several nonstandard solutions are documented. It is found that the energies of the individual states corresponding to standard and nonstandard solutions differ very little. These energies are also almost independent on the choice of CMS. On the other hand, the energies of excited states disclose a strong dependence on the radial structure of the orbital basis set. It is also demonstrated that the magnitudes of the cluster amplitudes representing a set of states depend both on the choice of the CMS and whether they correspond to the standard or nonstandard solutions. © 1996 John Wiley & Sons, Inc.

Notes: We employ a dynamical configuration interaction approach to study the transport of charge along the polyacetylene chain axis when placed in an external electric field. The steady-state wave function in this approach is constructed as a linear combination of solitonic wave functions weighted by nuclear vibrational functions. We retain the Born-Oppenheimer approximation, i.e., we neglect the terms involving the differentiation of the electronic configurations with respect to the nuclear coordinates. We also use basis functions that follow the nuclei. A solution of the time-dependent Schrödinger equation in terms of the wave functions of the above kind is obtained, leading to a closed formula for estimating mobilities of the soliton transport. © 1996 John Wiley & Sons, Inc.

Notes: Two different approaches were used to explain the distribution of water coordinates in the crystallographically invisible part of the unit cell. Monte Carlo calculations were done starting from different initial water structures. Extended Monte Carlo calculations using equal initial structures were also used to obtain two further water structures. The differences between the Monte Carlo water structures were used to calculate the mean-square displacements of the water molecules. Monte Carlo calculations starting from different structures lead to a mean-square displacement of 0.58 Å2, whereas extended Monte Carlo moves using the same initial structure only show a mean-square displacement of 0.17 Å2. The mean-square displacement of 0.58 Å2 can be used to explain the experimental data. © 1996 John Wiley & Sons, Inc.

Notes: The diffusion constant of dynamics simulation data evaluated by the time-dependent displacement or the velocity autocorrelation function provides equivalent results. The diffusion constant (D) increases with the cutoff distance for electrostatic energy. An extended version of the TIP3P water model provides a proper value of D at small cutoff distance (8.5 Å); the SPC/E water model requires a larger cutoff distance (11.0 Å). Considering Langevin dynamics with a total friction γ, the Einstein relation (D ∼ 1/γ) is valid for large enough friction (γ 〉 5 ps-1) only. Heating of a protein-water system by stochastic dynamics at the boundary is studied in detail. The calculated thermal conductivity of water agrees with experiment. The thermal conductivity of a protein molecule is about a factor of two smaller. © 1996 John Wiley & Sons, Inc.

Notes: Continuing the search for a broader interpretation of hemeprotein behavior, we give preliminary results showing that there are electric and dynamic couplings between the heme group and amino acid residues within the protein matrix. EPR and X-ray absorption spectroscopy studies on azidometmyoglobin show that both magnetic and geometric properties of Fe—N3 evolve in the same nonlinear way as pH is increased and are tightly correlated to the strains on the helical segments of the protein. Flash photolysis of carbon monoxide hemoglobin, in the presence of ethanol or formamide, allows the study of cosolvent effects on geminate and nongeminate recombinations of the CO ligand trapped within the protein matrix. Data clearly show that cosolvents alter the statistic fluctuations of the protein, as well as the ligand partition between different protein matrix domains. From these studies, it is concluded that alterations occurring at particular sites give way to global protein perturbations. Then, each perturbated protein domain - binding site included - evolves with its own sensitivity to a new metastable state of the protein. The amplification of the initial perturbation which - instead of regressing - progressively propagates through the whole macromolecule is typical of a dissipative structure in the Prigogine sense. Biological properties of hemeproteins largely involve the surrounding solvent, via permanent or temporary exchanges of water molecules, protons, and small ligands. These fluxes along with their entropic corollary are not quite compatible with a conservative system. These works present the current trends developed in our laboratory in association with the European network “The Dynamics of Protein Structure.” In this framework, our laboratory collaborates with Dr. W. Doster and T. Kleinert (Munich, Germany) for the CO recombination studies in hemoglobin and with Dr. J. Hutterman (Homburg, Germany) and Drs. A. Bianconi and S. Della Longa (Rome and L'Aquila, Italy) for the magnetic and geometric properties of the myoglobin iron site. © 1996 John Wiley & Sons, Inc.

Notes: To investigate the backbone dynamics of proteins 15N longitudinal and transverse relaxation experiments combined with {1H, 15N{ NOE measurements together with molecular dynamics simulations were carried out using ribonuclease T1 and the complex of ribonuclease T1 with 2′GMP as a model protein. The intensity decay of individual amide cross peaks in a series of (1H, 15N)HSQC spectra with appropriate relaxation periods was fitted to a single exponential by using a simplex algorithm in order to obtain 15N T1 and T2 relaxation times. The relaxation times were analyzed in terms of the “model-free” approach introduced by Lipari and Szabo. In addition, a nanosecond molecular dynamics (MD) simulation of ribonuclease T1 and its 2′GMP complex in water was carried out. The angular reorientations of the backbone amide groups were classified with several coordinate frames following a transformation of NH vector trajectories. In this study, NH librations and backbone dihedral angle fluctuations were distinguished. The NH bond librations were found to be similar for all amides as characterized by correlation times of librational motions in a subpicosecond scale. The angular amplitudes of these motions were found to be about 10°-12° for out-of-plane displacements and 3°-5° for the in-plane displacement. The contributions from the much slower backbone dihedral angle fluctuations strongly depend on the secondary structure. The dependence of the amplitude of local motion on the residue location in the backbone is in good agreement with the results of NMR relaxation measurements and the X-ray data. The protein dynamics is characterized by a highly restricted local motion of those parts of the backbone with defined secondary structure as well as by a high flexibility in loop regions. Comparison of the MD and NMR data of the free liganded enzyme ribonuclease T1 clearly indicates a restriction of the mobility within certain regions of the backbone upon inhibitor binding. © 1996 John Wiley & Sons, Inc.

Notes: NMR techniques can give insight into a wide variety of motional events that occur in proteins over a range of timescales. In the first section of this article an overview of the results of dynamics studies, using NMR methods, on both small globular and larger multi-domain proteins is presented including the findings from investigations of non-native partly folded states. The second section of the article then concentrates on two topics where NMR can give residue specific quantitative data, namely coupling constant measurements and relaxation studies, including comparisons of these NMR data with results from crystallographic studies and theoretical molecular dynamics simulations. Finally the possible functional significance of the experimentally observed motions in proteins is discussed. © 1996 John Wiley & Sons, Inc.

Notes: We measured the νFe-His Raman band of horse heart deoxymyoglobin and human deoxyhemoglobin as a function of temperature between 10 and 300 K. A self-consistent spectral analysis of the deoxymyoglobin Raman band reveals that it is underlied by three different sublines with frequencies at Ο1 = 209 cm-1, Ο2 = 217 cm-1, and Ο3 = 225 cm-1 and an identical half-width of 13 cm-1. All these parameters were found to be independent of temperature. These sublines were attributed to different conformational substates of the Fe2+-His F8 linkage, which comprise different out-off-plane displacements of the heme iron and tilt angles of the Fe2+-Ng(His F8) bond. The intensity ratio I3/I2 exhibits a van't Hoff behavior between 150 and 300 K, bends over in a region between 150 and 80 K, and remains constant at lower temperature. In contrast, I2/I1 shows a maximum at 170 K and approaches a constant value at 80 K. These data can be fitted by a modified van't Hoff expression, which accounts for the freezing into nonequilibrium distributions of substrates in a temperature interval ΔT around a distinct temperature Tf and also for the linear temperature dependence of the protein's specific heat. The fits to the above intensity ratios yield a freezing temperature of Tf = 117 K and a transition region of ΔT = 55 K. The νFe-His Raman band of human deoxyhemoglobin was decomposed into seven sublines with frequencies at 195, 202, 211, 218, 226, 234, and 240 cm-1, with half-widths of 12 cm-1. While the low-frequency sublines are strong at 300 K, the high-frequency sublines dominate the band at cryogenic temperatures. In comparison, we also investigated the temperature dependence of the near-infrared band III at 760 nm. Band III of deoxymyoglobin can be decomposed into two subbands which are 165 cm-1 apart. The ratio of their absorption cross sections shows a temperature dependence which parallels that of the ratio I3/(I2 + I1) of the corresponding Raman sublines. Band III of deoxyhemoglobin was decomposed into three subbands, the absorption cross sections of which also depend on temperature, similar to what has been observed for the νFe-His subbands. These observations provide strong evidence that the frequency positions of the subbands of band III and the νFe-His sublines are governed by the same coordinates. For both proteins investigated, the frequency positions and the half-widths of the band III subbands depend significantly on temperature. This is rationalized in terms of an earlier proposed model (Cupane et al., Eur. Biophys. J. 21; 385 1993) which assumes that the corresponding electronic transition is coupled to a bath of low-frequency modes. Our data indicate that these modes are harmonic below 134 K but become anharmonic above this temperature. This onset of anharmonic motions is interpreted as resulting from conformational transitions within the protein which affect the prostethic group via heme-protein coupling. © 1996 John Wiley & Sons, Inc.

Notes: The interaction between the R2R3 DNA binding domain of the oncoprotein c-Myb and oligodeoxynucleotides was investigated by 1H-NMR spectroscopy and fluorescence anisotropy assays. Titration of 12 and 16 base-pair DNA fragments containing the TAACGGTC sequence with R2R3 revealed the presence of two complexed forms (in a 40/60 ratio): either two complexes or two conformations in slow exchange at the NMR chemical shift time scale. The largest variations of imino proton chemical shifts were observed for the imino proton of the base pairs 2, 3, 4 and 6 of the DNA sequence, suggesting a direct involvement of these base pairs in the interaction. Using fluorescence anisotropy measurements, a dissociation constant of 5.12 ± 1.49 nM for the specific DNA-R2R3 complex was found, whereas a value of 2.7 ± 0.1 μM was determined for the nonspecific complex. © 1996 John Wiley & Sons, Inc.

Notes: 131Xe-NMR longitudinal relaxation rates have been measured by the inversion recovery method for xenon in presence of lecithin vesicles or a small protein charybdotoxin. The transverse relaxation rates in the same spectra have been obtained by spectral deconvolution. The results show that xenon in lecithin vesicles is in a rapid exchange between free and bound sites and that averaging of the electric-field gradient at the Xe nucleus is a two-step process. From these results, estimates have been obtained for the parameters entering the 131Xe quadrupolar interaction. © 1996 John Wiley & Sons, Inc.

Notes: In a novel approach to molecular shape representation, molecular electronic density functions are treated as 3D hypersurfaces in a 4D Euclidean space, spanned by the three spatial coordinates and an electronic density threshold variable. The general objects resulting from this approach are topological spheres with handles, modeling the electron density. Based on this model, a new, simple representation of molecular topology of electron density is proposed, using a tree describing the evolution of topological spheres with handles as function of a varying density threshold. The vertices of the tree are characterized by nonnegative integers (the genea of the topological objects). This representation is compared to earlier, detailed 3D topological descriptions of molecular shape as well as to the more conventional molecular network (bond skeleton) representation. A variety of relevant topological equivalence relations of molecules are discussed and a new, global, molecular similarity measure is proposed. © 1996 John Wiley & Sons, Inc.

Notes: An ab initio procedure for the calculation of atomic and molecular electronic wave functions, the Optimized-Basis-Set Multi-Configuration Spin-Coupled (OBS-MCSC) method, is generalized by introducing a separate linear combination of spin functions for each configuration, turning it into the OBS-GMCSC method. The ability to use a second-order minimization procedure in the computation of the wave function is maintained through appropriate generalization of the analytic expressions for the first and second derivatives of the energy with respect to the optimization parameters, as is the optional inclusion among the latter of the basis-function exponential parameters. The generalization, a variational improvement of the wave function, strengthens the connection with classical VB theory, of which the method can now be considered an optimized-orbitals variant, while maintaining the link with single-configuration Spin-Coupled theory, of which it may still be considered a multiconfiguration extension. The method can also be viewed as a nonorthogonal variant of the MCSCF approach. To demonstrate its practical feasibility and usefulness, the OBS-GMCSC method is applied to a study of the electronic structure and electron affinity of boron. © 1996 John Wiley & Sons, Inc.

Notes: Based on the charge density functional theory, a simple method is proposed to calculate the parallel electron correlation coefficient, correlation charge, and exchange correlation energy. In contrast to the result in the literature, our analysis reveals that the Fermi hole has its fine structure which is different from the model suggested in the literature. © 1996 John Wiley & Sons, Inc.

Notes: The electron localization function (ELF) was calculated for the atoms Li to Sr. The ELF maxima reveal the atomic shell structure for all these atoms. The shells are separated from each other by ELF minima. The integration of the electron density in a shell gives electron numbers. For the valence shell those are in good agreement with the ones expected from the Periodic Table of Elements. © 1996 John Wiley & Sons, Inc.

Notes: The valence isomerization of the 1,2-dithiete parent compound to the open-chain dithial was studied by CASSCF multiconfiguration methods including the CASPT2 perturbational treatment. The isomerization energy remains small at the highest level of theory. In agreement with Jonas and Frenking, the cyclic structure is only then preferred over the acyclic ones if f-functions on the sulfur atoms are considered. If they are included, the 1,2-dithiete is more stable by 3.8 kcal/mol and the barrier amounts to 24.9 kcal/mol at the CASPT2(8,8)/6-31G(2df)//MP2/6-31G* level of theory. According to MP2/6-31G* geometry optimizations, substitution of H by NH2 and CH3 reduces the stability of the 1,2-dithiete ring structures relative to the open-chain dithiocarbonyl structures, whereas the inverse holds for acceptor substitution by CN and CF3. A higher stability of benzodithiete relative to ortho-dithiobenzoquinone is predicted at all employed levels of theory. This is in good agreement with conclusions drawn from experimental results. Whereas the experimental microwave geometry of 1,2-dithiete is well reproduced theoretically, the experimental electron diffraction geometry of 3,4-bis-(trifluoromethyl)-1,2-dithiete differs from the calculated one. © 1996 John Wiley & Sons, Inc.

Notes: The variational method proposed earlier has been generalized, using a trial function of the form: ψ = (Λ0 + ΣsΛsms)ψ0 in which ms = r2p+1Cml, s standing for a triplet (p, l, m) and implemented into the program Hondo-8.4. The second-order density matrices are used to take into account the mono and bi-excited states (DM1 and DM2 matrices, GUGA Algorithm). This allows us to compute the dipole (α), dipole-quadrupole (A) and quadrupole (C) polarizability tensors at the CISD level. The results obtained for a series of test molecules: CO, HF, NH3, and methane with various gaussian basis sets are compared with experimental results (when available for A and C) and those obtained with other theoretical methods. The correlation is found to lower the values of the dipole polarizability which was generally too high when computed by the variational method at the RHF level and the values obtained here are in good agreement with the experimental ones. © 1996 John Wiley & Sons, Inc.

Notes: We previously studied the first stable conformations of flavone acetic acid and related compounds. In this article, a similar investigation was carried out on the second stable conformation of the same compounds. Emphasis is on the conformation dependence of the hydrogen-bonding effects, the molecular electrostatic potential (MEP), and the antitumor activity shown by these compounds. The results show that the second conformation is about 7.0 kcal mol-1 higher in energy and possibly is an inactive conformation as no correlation has been found between the antitumor activity and the MEP features. In addition, a detailed comparison with the first conformation, which is probably the active conformation, has been made of the geometry, the total energy, the Mulliken charges on some important atoms, hydrogen-bonding effects, and the MEP minima and isosurfaces. The role of the hydrogen-bonding effects, which was unclear in our previous work, is clarified in this work. The possible molecular basis of the antitumor activity is suggested. © 1996 John Wiley & Sons, Inc.

Notes: The mivazerol and three of its methylated derivatives are studied at the ab initio SCF level within the MINI-1 and 6-31G basis sets. This study aimed at determining some probable conformations, either neutral or protonated, that could interact with the α2 adrenoceptors. The solvent effect was also studied within the Onsager's solvent model at the two dielectric constant (ε) values of 4 and 80. The interaction with the environment (either solvent or receptor) is schematically studied by positioning either two water molecules or one formamide or/and one formic acid near the amide and the imidazole for few isomers. The medium polarization, through ε, and the solvation effect, through the interaction with the solvent molecules or the receptor side chains, stabilize the same isomers. Post-SCF calculations are performed at the CISD level, the first excited singlet and triplet states energies are determined, and the question of the wave-function stability is addressed. The results indicate the probability of a spin-orbit coupling with the first excited triplet state, thus opening the question of such a possibility within an enzyme active site. © 1996 John Wiley & Sons, Inc.

Notes: The calculation of group electronegativity and hardness for amino acid “functional groups,” considered as a biradical taken out of their protein environment, is performed for both the α-helix and β-sheet geometry of these amino acids. Group electronegativity and hardness are then used to interpret the experimental gas-phase proton affinity sequence of the amino acids. Group hardness was found to play the dominant role, whereas group electronegativity only had a minor influence on the sequence, thereby stressing the importance of the charged form in the acid-base equilibrium. An explanation for the deviations, seen for some of the amino acids, from the correlation between these group properties and the proton affinity was sought. © 1996 John Wiley & Sons, Inc.

Notes: The Wiener index is a graphical invariant that has found extensive application in chemistry. We define a generating function, which we call the Wiener polynomial, whose derivative is a q-analog of the Wiener index. We study some of the elementary properties of this polynomial and compute it for some common graphs. We then find a formula for the Wiener polynomial of a dendrimer, a certain highly regular tree of interest to chemists, and show that it is unimodal. Finally, we point out a connection with the Poincaré polynomial of a finite Coxeter group. © 1996 John Wiley & Sons, Inc.

Notes: A recursive method for enumeration of linearly independent and minimal conjugated circuits of benzenoid hydrocarbons had previously been given which is valid for several classes of benzenoid hydrocarbons. In the present article, the properties and constructions of unique minimal conjugated circuits and pairs of minimal conjugated circuits of a ring s in a benzenoid hydrocarbon B are investigated. An analytical expression for the count of LM-conjugated circuits of B is given which is based on the counts of Kekulé structures of selected subgraphs of B. By using the method, the LMC expression of any benzenoid hydrocarbon can be obtained. © 1996 John Wiley & Sons, Inc.

Notes: A study of π-electron systems confined by impenetrable surfaces is presented. The study results in a nonempirical-based approach to obtain confinement-adapted semiempirical π-Hamiltonians including repulsive terms (PPP or Hubbard). The impenetrable surface confinement of a physical system involves changes in the boundary conditions that the eigenvectors of its differential Hamiltonian operator have to fulfill, while the Hamiltonian itself remains unchanged. However, if this Hamiltonian is written in second quantization language, then confinement only involves changes of the Hamiltonian scalar factors (integrals). Semiempirical Hamiltonian integrals are replaced by parameters; therefore, confinement involves only changes of these parameters. It is shown that confinement changes Coulomb (αi) and exchange (βij), while repulsion (γij) parameters remain unaffected. Next, the influence of confinement upon the electron correlation of (i) π-electron molecular systems, (ii) atoms, and (iii) an electron gas is discussed. The behaviour of the correlation energy vs. the confinement size is found to be different for each type of system. A neat explanation of this variety is given in terms of the Coulomb attractive fields of the systems. Some chemical confinement effects such as an increase in the reactivity of π-electron systems is also outlined. © 1996 John Wiley & Sons, Inc.

Notes: A spin-free method is presented for evaluating electronic matrix elements over a spin-independent many-electron Hamiltonian. The spin-adapted basis of configuration state functions is obtained using a nonorthogonal spin basis consisting of projected spin eigenfunctions. The general expressions for the matrix elements are given explicitly, and it is demonstrated how the matrix elements may be obtained simply from the knowledge of the irreducible characters of the permutation group ℒN. The presented formulas are very general and may be applied in connection with both spin-coupled valence bond studies and in conventional configuration interaction (CI) methods based on an orthonormal orbital basis. © 1996 John Wiley & Sons, Inc.

Notes: A simple method of calculation of the integrals of the Hylleraas-Ore wave function, used in the description of the four-particle system analogous to the H2 molecule, is presented. The integrals corresponding to the kinetic energies of particles, to the Coulomb energy terms, and to the interparticle distances are given by the appropriate partial derivatives of a functional depending on the wave-function parameters. © 1996 John Wiley & Sons, Inc.

Notes: A method of selection of basis functions for the quantum chemical description of atoms and molecules inside spherical and cuboidal cavities is presented. The method consists of two independent steps. First, the appropriate GTO or STO exponents are chosen by fitting the basis functions to cutoff orbitals. The criterion of maximal orbital density inside the cavity is next applied to form the final model orbital space. The method presents the fundamental advantage over many other methods of being trivially applicable in standard quantum chemical progam packages. As an illustration, the method is applied to the hydrogen atom in a spherical box. The use of contracted basis functions is also discussed. © 1996 John Wiley & Sons, Inc.

Notes: The Cl2CO … Cl2 complex was studied using ab initio post-Hartree-Fock theory at the MP2 and MP4 levels and, for comparison, the DFT method with 6-311G(2d), 6-311 + G(2d), and Sadlej's medium-size polarized (MSPBS) basis sets. A potential energy search recovered a planar minimum-energy structure characterized by a bent conformation. For this weakly bound complex, the interaction energy corrected for the basis set superposition error amounted to - 0.88, - 1.09, - 1.43, and - 0.38 kcal/mol at the MP4(SDTQ)/6-311G(2d), MP4(SDTQ)/6-311 + G(2d), MP4(SDTQ)/MSPBS, and DFT(Becke3LYP)/6-311 + G(2d) levels of theory, respectively. Two highly symmetrical forms, linear and T-shaped, correspond to transition-state conformers. The analysis of harmonic vibrational frequencies and potential energy distribution was performed at the MP2 and DFT levels with the 6-311 + G(2d) basis set. © 1996 John Wiley & Sons, Inc.

Notes: The effective core potential (ECP), using a basis set of different qualities, and ab initio full-electron (FE) calculations were carried out for MoS-24, MoO-24, and MoOCl4 molecules. The topology of - ▿2p(rcp) (the negative Laplacian of the charge density at its critical points) in the atomic valence shell was studied. Results clearly indicate that semicore (ECP2) approaches are able to reproduce, in a qualitative way, the topology of the Laplacian distribution with respect to those obtained by the FE method. Modifications of basis sets, such as introduction of polarization functions on the ligands, affect the electronic charge distribution (number of critical points in MoOCl4) for FE as well as for ECP2 approaches. The ECP2 scheme predicts correctly the order of - ▿2px(rcp) (X = O, S, Cl, Mo) in the valence shell; nevertheless, it fails in the relative magnitudes of - ▿2pMo(rcp) between Mo compounds in respect to FE calculations. A scaling factor consistently improves the values of - ▿2p(rcp) and p(rcp), which are larger than those obtained with FE, particularly the - ▿2p(rc) values. © 1996 John Wiley & Sons, Inc.

Notes: The efficiency of modified virtual orbitals (MVO) of ionic type and of approximate orthogonalized natural orbitals (ONO) in the CI-SD calculations was studied for O3 and SO2 molecules and compared with the commonly used canonical virtual orbitals (CVOs). The systems studied represent a class of electron-rich molecules, in which the number of valence electron pairs exceeds substantially the number of formal chemical bonds. We found that the modified orbitals of the types studied appear to be less effective for these systems than in the similar calculations for the AHn type molecules. Physical reasons for this difference were discussed. The evolution of spatial properties of virtual orbitals within the modification process was analyzed. © 1996 John Wiley & Sons, Inc.

Notes: The geometries and the energies of conformers of PnHn + 2 (n = 2-9) have been studied with PM3 method. To test the quality of the semiempirical results, ab initio calculations have been carried out on P3H5. All results of P2H4 and P3H5 with PM3 are consistent with the experimental and ab initio data. According to the analysis of P3H5 and P4H6 results, it is concluded that gauche interaction between adjacent lone electron pairs and gauche interaction between polar P-H bond with adjacent polar P-P bond are important for predicting the stable conformer of open-chain phosphoanes. The calculations of PnHn + 2 (n 〉 4) give further support to this conclusion. © 1996 John Wiley & Sons, Inc.

Notes: The electronic energy band structures of the La-doped superconductors TlBa1.2 La0.8 CuO5 + δ were calculated. The effect of the oxygen content on their electronic structures was studied. The results show that compared with those for TlBa2CuO5, the La doping at the Ba site results in the moderate change in the band structures and the decrease in the densities of states, but the increase in the oxygen content caused by the La doping results in the great change in the band structures and the densities of states near the Fermi surface. The low oxygen content causes the degree of complexity of the band structures and the densities of states near the Fermi level Ef to increase and the high oxygen content causes them to decrease. The oxygen content plays a dominant role in TlBa1.2La0.8CuO5 + δ. In addition, the Cu-O planes are most sensitive to the increase in the oxygen content. © 1996 John Wiley & Sons, Inc.

Notes: Numerical experiments were carried out to determine the timewise self-consistency of different physical processes involved in the energy transfer in green plant photosynthetic units. A 6 × 6 × 6 array of chlorophyll-a with cubic lattice constants a = b = c = 20 Å was chosen as a model of the thylakoid disc. Another model aggregate was obtained by substituting chlorophyll-b molecules for some of the chlorophyll-a molecules. In both models, a reaction center occupied a central site in the last xy plane. Two extreme arrangements were considered for the orientation of molecules. In one, the transition moments of all molecules were directed along the y-axis. The other had chlorophyll molecules randomly oriented. The four resulting model systems were used in our investigation on exciton generation, transport, decay by fluorescence, and trapping. All excitons were assumed to be generated by a 20 ms exposure to sunlight at high altitudes. The general trends noticed from these computations are as follows: The number of excitons generated is influenced by lattice disorders. Disorders also increase the time for the establishment of an equilibrium distribution. The decay of excitons by fluorescence is always a monotonic function of time. The energy transfer is adversely affected by a lower degree of orientation in the crystal: The trapping time increases with disorder. The number of trappings decreases with the onset of fluorescence of the host molecules and the trap. From these investigations, we also made three specific observations: (1) The efficiency of exciton utilization varies from 12% for a completely random arrangement of transition dipoles to 46% for a perfectly ordered arrangement. This agrees with the experimental efficiency, about 20%. (2) The number of excitons trapped varies from one to six. This tallies with the time scale of electron transfer along the Z-scheme that requires at least two excitons trapped in about 20 ms. Thus, the photon density and the exciton transfer rate are consistent with the rates of electron transfers. (3) The trapping rate also indicates that the thylakoid disc must resemble a considerably ordered system. © 1996 John Wiley & Sons, Inc.

Notes: A discussion is presented for possible diamond-lattice-based structures containing holes that can be filled with metal atoms or ions. To allow the formation of coordinative bonds to the metal, some carbon atoms should be replaced by heteroatoms (with nitrogen preferred, but in some cases oxygen or other heteroatoms may be considered). Two types of holes that may lead to the formation of coordinative bonds are discussed in detail: tetrahedral holes for four such bonds and quasi-octahedral holes for six such bonds. In turn, when suitably arranged in a translationally symmetric manner, these holes may resemble open or closed pores in foams; when they are open, the “channels” may lead to interesting properties with regard to metallic conductivity or superconductivity. © 1996 John Wiley & Sons, Inc.

Notes: Platelet-activating factor (PAF) is an autacoid derived from cellular membrane phospholipids in response to chemical or physical stimuli. It has been identified as 1-O-alkyl-2-acetyl-sn-glyceryl-3-phosphocholine; the alkyl group is composed of 16 or 18 carbon atoms in human cells. PAF can cause a series of pathophysiological effects, related to inflammatory and allergic diseases such as asthma, gastric ulcerations, transplant rejections, psoriasis, cerebral, renal, and myocardial ischemia. As PAF biological action is a result of interactions with specific receptors on target cells, several specific PAF receptor antagonists have been proposed for therapeutic control of the pathological states in which PAF is implicated. In this work we have calculated at AM1 level 16 conformations of a model (alkyl = octyl) of (R)-PAF. We have used these conformations and calculated structures of two hetrazepines (WEB 2086 and E 6123), FR 128998 and RP 59227, known antagonists of PAF activity currently under development, to test a recently proposed pharmacophore map. Our results suggest that the model is too rigid. Having this in mind, we used the pharmacophore model to evaluate the potential activity of a new series of proposed PAF receptor antagonists based on bicyclo[3.3.0]-2-oxaoctane. The results were used to decide which compounds should receive priority in synthesis. The synthetic results and pharmacological profiles of the new derivatives will be published elsewhere. © 1996 John Wiley & Sons, Inc.

Notes: Electrostatic and hydrophobic complementarities between chymotrypsin and its inhibitor, avian ovomucoid third domains, were evaluated for eight species, which have different amino acid sequences, using molecular electrostatic potential (MEP) and MEP correlation, and the enzyme-inhibitor interaction was analyzed. The changes in the electrostatic and hydrophobic complementarities caused by the amino acid replacements were reflected clearly in the calculated MEP correlation, and it explained the observed binding association constants correctly. The electrostatic complementarity due to arginine at P′3 strongly promotes the binding process of the inhibitor, while the hydrophobic complementarity in the P1 and P′2 positrons also affects the binding process. It was demonstrated that our method is an effective molecular modeling tool in drug design and protein engineering. © 1996 John Wiley & Sons, Inc.