Showing papers in "International Journal of Quantum Chemistry in 2002"

Comparison of different atomic charge schemes for predicting pKa variations in substituted anilines and phenols

Abstract: A number of different methods have been proposed for assigning partial charges to the atoms of a molecule, including both quantum chemical and empirical schemes. A reasonable expectation for any successful calculational scheme is that the atomic charges it produces should vary in a manner consistent with chemical intuition and, more specifically, that these variations should be correlated in a sensible way with experimental observations. Seven of the most popular atomic charge schemes (Bader's AIM charges QAIM, electrostatic potential charges QESP, GAPT charges QGAPT, Gasteiger π charges QGast ,L owdin chargesQLow, Mulliken charges QMul, and charges derived from natural population analysis QNPA) were tested for their ability to represent variations in the pKa's of 19 monosubstituted anilines and 19 monosubstituted phenols. In most cases the calculations were performed at the B3LYP/6-311G ∗∗ level of theory. For the substituted anilines, the amino nitrogen, anilinium proton, and total amino group charges were taken as representative regression parameters, and for the phenols, the phenolic hydrogen, phenoxide oxygen, and hydroxyl group charges were employed. Overall, QAIM, QLow, and QNPA yielded the most successful correlations with the pKa's of these compounds, although for the phenol series, QGAPT and QMul also yielded good results. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem 90: 445-458, 2002

Ladder operators for the Morse potential

Abstract: A realization of the raising and lowering operators for the Morse potential is presented. It is shown that these operators satisfy the commutation relations for the SU(2) group. Closed analytical expressions are obtained for the matrix elements of different operators such as 1/y and d/dy. The harmonic limit of the SU(2) operators is also studied and an approach previously proposed to calculate the Franck–Condon factors is discussed. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001

The complementary roles of molecular surface electrostatic potentials and average local ionization energies with respect to electrophilic processes

Abstract: We focus upon two properties, the electrostatic potential V(r) and the average local ionization energy . When evaluated on molecular surfaces, VS(r) and can be useful tools for analyzing and predicting reactive behavior. VS(r) is most reliable with respect to noncovalent interactions; when electrophilic attack and some degree of charge transfer are involved, then the combination of VS(r) and can be quite effective. They play complementary roles: VS(r) reveals the regions of the molecule to which an electrophile would initially be attracted, and indicates the ease of charge transfer at these and other sites. Four examples of such complementarity are discussed, involving benzene derivatives, guanine and cytosine, furan and pyrrole, and binary hydrides. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2002

Local kinetic energy and local temperature in the density‐functional theory of electronic structure

Abstract: Various thermodynamic elements of the density functional theory of electronic structure are reviewed and clarified. Detailed argumentation is given for the particular “del dot del” definition of the local kinetic energy density and local temperature. The temperature measures the “nighness” of an electron pair, thus playing a key role in quantitative (exchange and kinetic energy functionals) and qualitative (electron localization functions) tools based on the electron pair density. Two different derivations are given of the Gaussian model for the phase-space distribution function, from which one obtains an approximation to the entropy of the charge distribution. The full thermodynamic description is briefly discussed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

Resistance-distance matrix: A computational algorithm and its application

Abstract: The distance matrix D, the resistance-distance matrix Ω, the related quotient matrices D/Ω and Ω/D and the corresponding distance-related and resistance-distance-related descriptors: the Wiener index W, the Balaban indices J and JΩ, the Kirchhoff index Kf, the Wiener-sum index WS, and Kirchhoff-sum index KfS are presented. A simple algorithm for computing the resistance-distance matrix is outlined. The distance-related and the resistance-distance-related indices are used to study cyclicity in four classes of polycyclic graphs: five-vertex graphs containing a five-cycle and Schlegel graphs representing platonic solids, buckminsterfullerene isomers and C70 isomers. Among the considered indices only the Kirchhoff index correctly ranks according to their cyclicity, the Schlegel graphs for platonic solids, C60 isomers, and C70 isomers. The Kirchhoff index further produces the reverse order of five-vertex graphs containing a five-cycle (which could be simply altered to the correct order by adding a minus sign to the Kirchhoff indices for these graphs). © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001

Substituent effects on the electronic structure and pKa of benzoic acid

Abstract: The effects of substituents on the pKas of a set of 16 substituted benzoic acids have been examined using density functional theory [B3LYP/6-311G(d, p)] calculations. A variety of quantum chemical parameters were examined as indicators for the variations observed in the experimental pKas, including the Lowdin, Mulliken, AIM, and natural population analysis charges (QL, QM, QA, and Qn) on atoms of the dissociating carboxylic acid group, the energy difference (ΔEprot) between the carboxylic acid and its conjugate base, and the Wiberg bond index. Several of these calculated quantities yielded excellent correlations with the experimental pKa: ΔHprot, r2= 0.958; QL(H), r2= 0.963; Qn(CO2H), r2= 0.969; QL(CO), r2= 0.970; and QL(CO2H), r2= 0.978. The best correlation observed with the pKa, as expected, was from the empirical Hammett constants designed for this purpose (r2= 0.999). © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

Simultaneous determination of nuclear and electronic wave functions without Born–Oppenheimer approximation: Ab initio NO+MO/HF theory

Abstract: We develop a simultaneous determination method of nuclear and electronic wave functions without the Born–Oppenheimer approximation. We examine two expanding methods, namely, molecular orbital (MO)-type and valence bond (VB)-type expansions for a nuclear orbital, which is a one-particle wave function of a nucleus. The VB-type expansion is shown to be more accurate than the MO-type one because of the local nature of the nuclei. We also investigate the basis function expansion of the nuclear orbital and propose a scheme to determine the orbital exponent for the nuclear basis function. Numerical calculations confirm the accuracy and feasibility of the present method. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001

Analytical and ab initio studies of effective exchange interactions, polyradical character, unpaired electron density, and information entropy in radical clusters (R)N: Allyl radical cluster (N=2–10) and hydrogen radical cluster (N=50)

Abstract: Analytical expressions of total energies, effective exchange integrals, polyradical character, spin density, unpaired electron density, and information entropy are derived for allyl radical dimers and trimers on the basis of the Hubbard model in order to elucidate interrelationships among several broken-symmetry and symmetry-adapted approaches to molecular magnetism. Ab initio unrestricted Hartree–Fock and hybrid density functional theory (DFT) calculations of allyl radical dimers to decamers are also carried out for confirmation of characteristics revealed by the analytical investigations. A mesoscopic hydrogen radical cluster with 50 radical sites is studied by the ab initio hybrid DFT methods to elucidate functional behaviors of the above quantities with change of interatomic distance. The potential curves for the lowest and highest spin states of the cluster by these methods are depicted for the purpose. Implications of the present computational results are discussed in relation to size-consistent spin projection and size effects on effective exchange interactions in mesoscopic radical clusters. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

Link between the Kinetic- and Exchange-Energy Functionals in the Generalized Gradient Approximation

Abstract: An approximate kinetic-energy functional of the generalized gradient approximation form was derived following the conjointness conjecture of Lee, Lee, and Parr. The functional shares the analytical form of its gradient dependency with the exchange-energy functionals of Becke and Perdew, Burke, and Ernzerhof. The two free parameters of this functional were determined using the exact values of the kinetic energy of He and Xe atoms. A set of 12 closed-shell atoms was used to test the accuracy of the proposed functional and more than 30 others taken from the literature. It is shown that the conjointness conjecture leads to a very good class of kinetic-energy functionals. Moreover, the functional developed in this work is shown to be one of the most accurate despite its simple analytical form.

New complete orthonormal sets of exponential‐type orbitals and their application to translation of Slater orbitals

Abstract: The new complete orthonormal sets of exponential-type orbitals (ETOs) are introduced in closed form as functions of the exponential, the complex or real regular solid spherical harmonic, and the generalized Laguerre polynomials, where α=1,0,−1,−2,−3,… . These Ψα-ETOs are represented as finite linear combinations of Slater-type orbitals (STOs). The Coulomb Sturmian and Lambda ETOs are the special classes of Ψα-ETOs for α=1 and α=0, respectively. By the use of Ψα-ETOs the simpler expansion formulas for translation of STOs are derived. The translation coefficients are presented by a linear combination of overlap integrals. The final results are especially useful for machine computations of arbitrary multielectron multicenter molecular integrals over STOs that arise in the Hartree–Fock–Roothaan approximation and also in the Hylleraas correlated wave function method which play a significant role in theory and application to quantum mechanics of atoms, molecules, and solids. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

On Löwdin's method of symmetric orthogonalization*

Abstract: An elementary direct proof is given for the stationarity property of Lowdin's symmetric orthogonalization scheme. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

VB2000: Pushing valence bond theory to new limits

Abstract: Full valence bond (VB) calculations for a system of N electrons have always been hindered by the rapidly growing value of N!, which effectively imposes a limit N < 20. Often, however, not all electrons in a molecule are of interest; if we focus on a “group” G of NG electrons (e.g., in an “active” region), then it is NG! that sets the limit. In this work, group function (GF) theory is used to represent a molecule as a collection of interacting electron groups, each with a many-electron wave function of any chosen form (e.g., VB, MO-SCF, MCSCF), and each GF is optimized individually in a step-by-step process. An efficient VB algorithm allows for up to 14 electrons in any VB group and this combination of GF and VB methods greatly extends the range of feasibility of molecular calculations with VB-type wave functions: Thus, (1) a large system can be divided into any number of smaller subsystems (groups); (2) each group may contain any chosen number of electrons; (3) the form of any group function (including its level of accuracy) may be chosen at will by the program user. A number of sample calculations are briefly presented. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

Ladder operators for the modified Pöschl–Teller potential

Abstract: A closed form of the normalization constants of the wave function for the modified Poschl–Teller (MPT) potential is obtained from two different methods. It is shown that the discrete spectrum of the MPT potential is associated to the su(2) algebra. This identification is achieved by means of a realization of raising and lowering operators in terms of the physical variable u=tanh (αx). Analytical expressions for the matrix elements derived from these operators are obtained for the functions and . The harmonic limit of the su(2) operators is also analyzed. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem 86: 265–272, 2002

Information distance analysis of molecular electron densities

Abstract: The information-theoretic basis of the Hirshfeld partitioning of the molecular electronic density into the densities of the “stockholder” atoms-in-molecules (AIM) is summarized. It is argued that these AIM densities minimize both the directed divergence (Kullback–Leibler) and divergence (Kullback) measures of the entropy deficiency between the AIM and their free atom analogs of the promolecule. The local equalization of the information distance densities of the Hirshfeld components, at the local value of the corresponding global entropy deficiency density, is outlined and several approximate relations are established between the alternative local measures of the missing information and the familiar function of a difference between the molecular and promolecule densities. Various global (of the system as a whole) and atomic measures of the entropy deficiency or the displacements relative to the isoelectronic promolecule, defined for densities or probabilities (shape functions) in both the local resolution and the Hirshfeld AIM discretization, are introduced and tested. This analysis is performed also for the valence electron (frozen-core) approximation. Illustrative results for representative linear molecules, including diatomics, triatomics, and tetraatomics, are reported. They are interpreted as complementary characteristics of changes in the net AIM charge distribution and of the displacements in the information content of the electron distributions of bonded atoms. These numerical results confirm the overall similarity of the stockholder AIM to their free atom analogs and reflect the information displacements due to the AIM polarization and charge transfer in molecules. They also demonstrate the semiquantitative nature of the approximate relations established between the entropy deficiency densities and the related functions involving the density difference function. This development extends the range of interpretations based on the density difference diagrams into probing the associated information displacements in a molecule accompanying the formation of the chemical bonds. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2002

Thermodynamics and kinetics of downhill protein folding investigated with a simple statistical mechanical model

Abstract: The possibility of downhill protein folding is one of the most intriguing predictions of the energy landscape approach. Finding examples of downhill folding has important practical implications because in the absence of a free energy barrier the mechanism of folding is amenable to experimental observation. Here, a simple statistical mechanical model of protein folding is used to analyze the thermodynamic and kinetic properties of downhill and two-state folding. Folding free energy surfaces with and without a barrier separating denatured and native states can be generated with this model by simply modifying the curvature of the energy as a function of the order parameter, i.e., number of amino acids in incorrect conformation. Thermodynamic and kinetic analysis of surfaces with a barrier show the typical properties of two-state folding: a first-order equilibrium unfolding transition and exponential biphasic folding kinetics. In contrast, in downhill surfaces the unfolding process is noncooperative, and the apparent transition depends on the structural probe used to measure it. Therefore, this inherent behavior can be used as an experimental criterion for the identification of downhill folding. Surprisingly, the kinetics of downhill folding do not greatly deviate from exponential behavior unless the effective diffusion coefficient is assumed to decrese as folding progresses, exemplifying the increase in the roughness of the landscape. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

Structure and spin-state energetics of an iron porphyrin model: An assessment of theoretical methods

Abstract: The ability of unrestricted Hartree–Fock (UHF), Moller–Plesset (MP2), density functional theory (DFT), and hybrid density functional/Hartree–Fock methodologies to describe the structure and spin-state energetics of iron porphyrins was assessed. In the first place, these techniques have been applied to Fe, Fe+, Fe2+, and Fe3+ for which HF calculations overestimate energy gaps, favoring stabilization of higher multiplicity states. DFT shows the opposite trend at the GGA level, with some improvement using the hybrid schemes B3LYP and half-and-half. We use the hybrid functionals to explore the dependence of the spin state with the iron displacement out of the porphyrin plane in the five-coordinate system, for which a high-spin ground state has been experimentally determined. The possibility of spin crossover, proposed in previous studies, is examined. Finally, the hybrid methodologies are applied to the computation of the oxyhemoglobin model. The B3LYP description of the electronic structure of both penta and hexa coordinate model systems is consistent with previous theoretical calculations and with experimental information of deoxy and oxy hemoglobin. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2002

Fully relativistic density functional calculations on hydroxylated actinide oxide surfaces

Abstract: The linear combinations of Gaussian-type orbitals-fitting function (LCGTO-FF) method has been used to investigate the cohesive properties of three fluorite structure actinide oxides (ThO 2 , UO 2 , and PuO 2 ), and their clean and hydroxylated (111) surfaces, within the generalized gradient approximation (GGA) to density functional theory (DFT). Relativistic effects have been considered at both the scalar-relativistic and the fully relativistic (spin-orbit coupling included) levels of approximation. It is found here that the 5f states have only a minimal effect on the cohesive properties of these systems, despite the fact that the two heavier actinide oxides (both Mott-Hubbard-type insulators) are incorrectly predicted to be good metals. The cause of this insensitivity to the spurious metallic nature of the 5f states is elucidated.

High‐precision Hy–CI variational calculations for the ground state of neutral helium and helium‐like ions

Abstract: Hylleraas-configuration interaction (Hy-CI) method variational calculations with up to 4648 expansion terms are reported for the ground 1 S state of neutral helium Convergence arguments are presented to obtain estimates for the exact nonrelativistic energy of this state The nonrelativistic energy is calculated to be -29037 2437 7034 1195 9829 99 au Comparisons with other calculations and an energy extrapolation give an estimated nonrelativistic energy of -29037 2437 7034 1195 9830(2) au, which agrees well with the best previous variational energy, -29037 2437 7034 1195 9829 55 au, of Korobov (Phys Rev A 2000, 61, 64503), obtained using the universal (exponential) variational expansion method with complex exponents (Frolov, A M; Smith, V H Jr J Phys B Atom Mol Opt Phys 1995, 28, L449) In addition to He, results are also included for the ground IS states of H - , Li + , Be + + , and B + 3

Toward a computed peptide structure database: The role of a universal atomic numbering system of amino acids in peptides and internal hierarchy of database

Abstract: With the construction and implementation of a logical and standardized numbering of atomic nuclei, to define mono-, di-, and oligo-peptide systems, automation of input file generation and data extraction could greatly improve the efficiency of the search for the structural energy minima on the potential energy hypersurface of these systems. The internal hierarchy of the database covering constitutional structures, protective groups, levels of theory, and basis sets used, as well as the variety of possible conformations, is also discussed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

Density functional complete study of hydrogen bonding between the water molecule and the hydroxyl radical (H2O · HO)

Abstract: The hydrogen bonding complexes formed between the H2O and OH radical have been completely investigated for the first time in this study using density functional theory (DFT). A larger basis set 6-311++G(2d,2p) has been employed in conjunction with a hybrid density functional method, namely, UB3LYP/6-311++G(2d,2p). The two degenerate components of the OH radical 2Π ground electronic state give rise to independent states upon interaction with the water molecule, with hydrogen bonding occurring between the oxygen atom of H2O and the hydrogen atom of the OH radical. Another hydrogen bond occurs between one of the H atoms of H2O and the O atom of the OH radical. The extensive calculation reveals that there is still more hydrogen bonding form found first in this investigation, in which two or three hydrogen bonds occur at the same time. The optimized geometry parameter and interaction energy for various isomers at the present level of theory was estimated. The infrared (IR) spectrum frequencies, IR intensities, and vibrational frequency shifts are reported. The estimates of the H2O · OH complex's vibrational modes and predicted IR spectra for these structures are also made. It should be noted that a total of 10 stationary points have been confirmed to be genuine minima and transition states on the potential energy hypersurface of the H2O · HO system. Among them, four genuine minima were located. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

Brueckner orbitals and density‐functional theory

Abstract: By means of many-body perturbation theory (MBPT) it is shown that minimizing the energy expectation value of a closed-shell system in a certain order of the perturbation expansion by varying the partitioning of the Hamiltonian leads to a zeroth-order function, which—as the order of perturbation increases and provided the expansion converges properly—approaches a determinant of Brueckner orbitals. It is also shown that the energy eigenvalues of the Brueckner orbitals represent the corresponding ionization energies of the system, including orbital-relaxation and correlation effects to all orders of perturbation theory. This is a generalization of the Koopmans theorem in Hartree–Fock theory. The MBPT treatment is used for a discussion of the density-functional theory, and a new model is proposed—referred to as the Brueckner–Kohn–Sham scheme—where also the electron correlation is included in the functional. This leads to a nonlocal exchange-correlation potential, quite similar to that of Brueckner orbitals (BO), implying that the orbitals of the new scheme are essentially BO. Arguments are given that also the orbitals of other schemes with a purely local potential, such as the standard Kohn–Sham (KS) scheme, would be close to BO. This has been conjectured by Heselmann and Jansen ( J Chem Phys 2000, 112, 6949), and the present work gives more direct evidence of that. This might explain the recent observations that the KS orbitals and energy eigenvalues do have more physical significance than was originally anticipated. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

The hydration of the uranyl dication: Incorporation of solvent effects in parallel density functional calculations with the program PARAGAUSS

Abstract: The parallel density functional program PARAGAUSS has been extended by a tool for computing solvent effects based on the conductor-like screening model (COSMO). The molecular cavity in the solvent is constructed as a set of overlapping spheres according to the GEPOL algorithm. The cavity tessellation scheme and the resulting set of point charges on the cavity surface comply with the point group symmetry of the solute. Symmetry is exploited to reduce the computational effort of the solvent model. To allow an automatic geometry optimization including solvent effects, care has been taken to avoid discontinuities due to the discretization (weights of tesserae, number of spheres created by GEPOL). In this context, an alternative definition for the grid points representing the tesserae is introduced. In addition to the COSMO model, short-range solvent effects are taken into account via a force field. We apply the solvent module to all-electron scalar-relativistic density functional calculations on uranyl, UO22+, and its aquo complexes in aqueous solution. Solvent effects on the geometry are very small. Based on the model [UO2(H2O)5]2+, the solvation energy of uranyl is estimated to be about −400 kcal/mol, in agreement with the range of experimental data. The major part of the solvation energy, about −250 kcal/mol, is due to a donor–acceptor interaction associated with a coordination shell of five water ligands. One can interpret this large solvation energy also as a compounded effect of an effective reduction of the uranyl moiety plus a solvent polarization. The energetic effect of the structure relaxation in the solution is only about 8 kcal/mol. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001

Structural motifs as functional microdomains in G-protein-coupled receptors: Energetic considerations in the mechanism of activation of the serotonin 5-HT2A receptor by disruption of the ionic lock of the arginine cage*

Abstract: Studies of the structural changes associated with the activation of several G-protein coupled receptors (GPCRs) have suggested that the cytoplasmic ends of transmembrane helices 6 and 3 move apart, but the molecular mechanisms involved in the helix rearrangements are not known. The cytoplasmic end of helix 3 contains the structural motif DRY that is universally conserved in the sequences of GPCRs in the rhodopsin family. Using computational modeling of the 5-HT2A receptor, we find that an interaction of the central arginine in this motif, R3.50, with the conserved acidic side chain of the neighboring Asp (D3.49) is supplemented by a concomitant interaction with the conserved glutamate in helix 6, E6.30. Thus, R3.50 is caged in the inactive state of the receptor by its interaction with D3.49 and other conserved residues including E6.30. In the model, these interactions support the close packing of the ends of helices 3 and 6 that contributes to the stabilization of the inactive receptor state. To understand the energetic determinants for the stabilization of the inactive form of the receptor, and the mode in which activation can free the caged R3.50, we compared the electrostatic properties of the conserved residues in the conformations corresponding to the active and inactive forms of the receptor. These comparisons were analyzed with respect to a hypothesis about the role of protonation of D3.49 and E6.30 in the activation mechanism. The inferences from the computational analysis were used to design mutations to probe the mechanistic hypothesis. The experiments with mutant receptor constructs show that the removal of the acidic side-chain at either position 3.49 or 6.30, or both, increases the level of ligand-independent (constitutive) activity of the receptor. These results support the hypothesis regarding the role of these acidic residues in stabilizing the inactive state, because mutations that weaken the interactions should facilitate the receptor's transition to the active conformation. Hence we find a constitutively active state for receptor constructs in which E6.30 is mutated to N, Q, or L. The weakening of the helix 3–helix 6 link that results from these substitutions allows the helices to move apart in the activated state of the receptor. From the results of the computational analysis combined with related experimental probing of receptor function we thus propose a general molecular model for the role of the structural motif that include D3.49, R3.50, and E6.30, as a functional microdomain in the receptor activation mechanism. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem 88: 65–75, 2002

Hydrogen molecular ion inside penetrable prolate spheroidal boxes: Electronic and vibrational properties

Abstract: The exact solution of the Schrodinger equation for the hydrogen molecular ion confined inside penetrable prolate spheroidal boxes is constructed within the Born–Oppenheimer approximation.The pressure dependence of physical properties such as ground-state energy, equilibrium bond length, vibrational force constant, polarizability and quadrupole moment are examined for different barrier heights. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001

Comparative studies on the structures, infrared spectrum, and thermodynamic properties of phthalocyanine using ab initio Hartree-Fock and density functional theory methods

Abstract: The molecular structure, vibrational spectrum, standard thermodynamic functions, and enthalpy of formation of free base phthalocyanine (Pc) have been studied using the density functional theory B3LYP procedure, as well as the ab initio Hartree–Fock method. Various basis sets 3-21G, 6-31G*, and LANL2DZ have been employed. The results obtained at various levels are discussed and compared with each other and with the available experimental data. It is shown that calculations performed at the Hartree–Fock level cannot produce a reliable geometry and related properties such as the dipole moment of Pc and similar porphyrin-based systems. Electron correlation must be included in the calculations. The basis set has comparatively less effect on the calculated results. The results derived at the B3LYP level using the smaller 3-21G and LANL2DZ basis sets are very close to those produced using the medium 6-31G* basis set. The geometry of Pc obtained at the B3LYP level has D2h symmetry and the diameter of the central macrocycle is about 4 A. The enthalpy of formation of Pc in the gas phase has been predicted to be 1518.50 kJ/mol at the B3LYP/6-311G(2d,2p)//B3LYP/6-31G* level via an isodesmic reaction. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001

The origin of spontaneous point mutations in DNA via Löwdin mechanism of proton tunneling in DNA base pairs: Cure with covalent base pairing*

Abstract: The key aim of the present work is twofold. On the one hand, we propose a novel model of the tautomerization of the A⋅T base pair leading to its mismatches and supporting thus the Lowdin mechanism of the proton transfers taking place within the valley formed by its mispairs. Its specific novelty is actually in that the existing barrier of ca. 23 kcal/mol is not directly related to the proton transfer. Rather, it governs a shift of the bases within the Watson–Crick A⋅T base pair relative to each other and separates it from the valley in its potential energy surface where the mispairing occurs quite easily due to lower barriers of the proton transfers therein. On the other hand, aiming to cure the DNA double helix of generating hydrogen-bonded mispairs, which lead to the spontaneous point mutations in the genetic alphabet, by inserting covalent base pairs into the DNA architecture, we subject the covalent bond base pair designed recently by Gao and Orgel (Proc Natl Acad Sci USA 1999, 96, 14837) to the high-level performance computational study. Its three tautomeric forms are found and it is shown that the most stable one is characterized by the amide-type hydrogen bond. The comparison of the properties such as rotational constants, dipole moment, polarizability, and quadrupole moment is carried out for the Gao–Orgel covalent base pair and the canonical A⋅T one. We demonstrate that the former one can be easily inserted into the double helix DNA without any significant perturbations of the double helix architecture. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

Agonist alkyl tail interaction with cannabinoid CB1 receptor V6.43/I6.46 groove induces a helix 6 active conformation

Abstract: Our modeling studies have suggested that β branched amino acids Val, lle, or Thr located (i, i + 3) or (i, i + 4) apart on an alpha helix can form a groove into which a ligand alkyl chain can fit. Experimental support forthis idea comes from the crystal structure of adipocyte lipid binding protein complexed with stearic acid (Xu et al. J Biol Chem 1993, 268, 7874). We hypothesized that the transmembrane helix 6 (TMH 6) βXXβ motif of the CB1/CB2 receptors (V6.43/I6.46), which immediately precedes the conserved TMH 6 CWXP motif, serves as an interaction site for the alkyl tail of cannabinoid (CB) ligands and that interaction with this motif may trigger receptor activation. Conformational memories (CM) calculations on TMH 6 of CB1 and CB2 were used to explore the conformation of TMH 6 in unbound and complexed states. The conserved Pro 6.50 generated a kink in the α-helical structure that behaved as a flexible hinge. In the context of a three-dimensional model of the CB1 receptor, a helix from the more kinked family of CB1 TMH 6 conformers calculated by CM brought the intracellular portion of TMH 6 in proximity to TMH 3, analogous to the inactive state TMH 3/6 conformation seen in the X-ray crystal structure of rhodopsin (Palczewski et al. Science 2000, 289, 739). A CM study of CB1 TMH 6 in which a pentane molecule (as a model system for the CB ligand side chain) interacts with the V6.43/I6.46 groove was also conducted. The results of this calculation showed that alkyl chain interaction with the V6.43/I6.46 groove directly modulates the overall conformation of TMH 6, biasing the population of TMH 6 conformers toward the family of less kinked CB1 TMH 6 conformations calculated by CM. In the context of the CB1 bundle, this conformational change would cause the intracellular end of TMH 6 to move away from TMH 3. Such a movement is consistent with recent experimental results for agonist induced conformational changes at the intracellular side of TMH 6 in the β 2 -adrenergic receptor (Jensen et al. J Biol Chem 2001, 276, 9279). In contrast to results for CB1, CB2 TMH 6 showed a smaller range of kink angles possible for unbound TMH 6, with no significant shift in the populations of TMH 6 when the V6.43/I6.46 groove was occupied by pentane. We hypothesized that the profound flexibility differences between wild-type (WT) CB1 vs. WT CB2 TMH 6 revealed by CM calculations may be due to the size of residue 6.49 which immediately precedes P6.50 of the CWXP motif (G6.49 in WT CB1 and F6.49 in WT CB2). To test this hypothesis, using CM, we compared the flexibilities of WT CB1 and CB2 TMH 6 with those of the switch mutants, CB1 G6.49F and CB2 F6.49G. Consistent with results reported above, the degree of kinking (average of 100 conformers) was distinctly different between CB1 (40.9°; std. dev. ′16.9°) and CB2 (24.6°; std. dev. ′ 4.3°), with CB1 TMH 6 exhibiting a noticeably wider range of kink angles than CB2. These flexibilities were essentially switched in the mutants [CB1 G6.49F mutant (25.3°; std. dev. ′ 5.7°) and a CB2 F6.49G mutant (44.3°; std. dev. ′ 21.4°]. Taken together, these results suggest that TMH 6 in CB1, but not in CB2, is sensitive to conformational modulation by an alkyl chain bound in the V6.43/I6.46 groove. Furthermore, results suggest that the small size of residue 6.49 in CB1 facilitates the P6.50 flexible hinge motion of CB1 TMH 6.

Use of promolecular ASA density functions as a general algorithm to obtain starting MO in SCF calculations

Abstract: Atomic shell approximation (ASA) constitutes a way to fit first-order density functions to a linear combination of spherical functions. The ASA fitting method makes use of positive definite expansion coefficients to ensure appropriate probability distribution features. The ASA electron density is sufficiently accurate for the practical implementation of quantum similarity measures, as was proved in previous published work. Here, a new application of the ASA density formalism is analyzed, and employed to obtain an initial guess of the density matrix for SCF procedures. The number of cycles needed to assess the convergence criterion in electronic energy calculations appears comparable to or less than those obtained by other means. Several molecular structures of different classes, including organic systems and metal complexes, were chosen as representative test cases. In addition, an ASA basis set for atoms Sc-Kr fitted to an ab initio 6-311G basis set is also presented. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001

N-H· · ·F improper blue-shifting H-bond†

Abstract: The MP2/6-31G** calculations reveal a different pattern of H-bonding in F2NH· · ·Y (Y = FH, OH2, NH2) complexes. Whereas the blue-shifted H-bonding was found for F2NH· · ·FH complex (the first known case of NH· · ·Y improper blue-shifting H-bonding), standard H-bonding exists for F2NH· · ·OH2 and F2NH· · ·NH3 complexes. A different character of H-bonding is explained by natural bond orbital analysis showing a systematic increase of electron density in the σ* antibonding orbital of the NH bond as well as in the lone-electron pairs of fluorine atoms of proton the acceptor. Whereas the former effect leads to elongation of the NH bond and a red shift of NH stretch frequency, the latter effect gives the opposite, that is, contraction of the NH bond and a blue shift of NH stretch frequency. Existence of a red- or blue-shifted H-bonding is explained by the dominance of the former or latter effect. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

Quantum-chemical prediction of the adsorption conformations and dynamics at HCOOH covered ZnO(10-10)

Abstract: Results from ab initio Hartree–Fock and gradient-corrected density functional theory calculations of formic acid interactions with ZnO (1010) surfaces are reported. Surface relaxation is found to affect equilibrium geometries and adsorption energies significantly. Large variations in adsorption energy with coverage and ordering of the adsorbates are revealed and explained in terms of strong and highly anisotropic electrostatic adsorbate–adsorbate interactions. The results are compared to published experimental and theoretical results, and differences in suggested binding geometries from the different studies are discussed. Dynamic properties of the adsorption, surface mobility, and surface reactivity are inferred from key elements of the potential energy surface obtained from the quantum chemical computations and supported by ab initio molecular dynamics simulations. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002