bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors influencing proton positions in biomolecules
Authors: Scheiner Steve , Redfern Paul , Hillenbrand Eric A. 
Published: December 2004

AbstractResults of quantum mechanical calculations are presented that suggest a number of mechanisms whereby protons may be shifted from one group to another along an H bond. The first factor to be considered is a stretching of the bond that drastically raises the energy barrier to transfer. It is possible to predict barriers for an arbitrary system based only on results for a simple system and knowledge of the relevant bond length in the isolated subsystems. Factors that increase the intrinsic basicity of the B group in A‐H‐B lead not only to a lowering of the energy of the A‐HB state relative to AH‐B but also to a reduction in the barrier to transfer of the proton from A to B. Ions in the vicinity of the H bond exert a powerful influence and can shift the proton to the less basic group across a gradient of several pK units. Rather than shielding the proton from the external ion, the H bond acts instead to amplify the effects of the electric field. Reorientation of the A and B groups relative to one another, i.e., bends of the H bond, also produce surprisingly large changes in the relative energies of the AH‐B and A‐HB states. Such bends are capable of pushing the proton across to the normally less basic group, providing a mechanism of coupling conformational changes to proton ‘pumping’ activity. It is found that the high and low pH states of a given H bond can have dramatically differnt relative populations of the AH‐B and A‐HB configurations. These observations are explained in terms of fundamental concepts involving electrostatic interaction energies.
Double symmetrization and the linearly independent spin eigenfunctions
Authors: Lim T. K. 
Published: December 2004

AbstractIt is shown that the exclusion principle merely requires the electrons to be divided into two distinct groups, then, according to our assumption of the distinguishability of electrons, its mathematical representation can be the spatial double antisymmetrization or the spatial‐spin antisymmetrization; in the latter case an auxiliary spin double symmetrization is also required in order to distinguish the two types of electrons. The second requirement is used to recognize the fact that, although all electrons can be assumed to be indistinguishable under certain condition, their natural characteristic of two distinct groups must still be preserved.It is further shown that the double antisymmetrization (or double symmetrization) determines the spin quantum number M, whereas the Löwdin spin projector for nonorthogonal eigenfunctions and the Wigner matric basis for orthogonal eigenfunctions will decide the spin quantum number S, Both the spatial double antisymmetrizer and the spin double symmetrizer will reject all the unnecessary eigenfunctions and project out only one unique set of linearly independent eigenfunctions.
Critical phenomena in isoelectronic diatomic sequences—the 14‐electron sequence
Authors: Laurenzi Bernard J. , Mall Madeline F. 
Published: December 2004

AbstractA theory of isoelectronic molecules which describes stable and metastable members of a sequence has been developed. To achieve this synthesis, it has been necessary to require that the total electronic energy surface E(R,Z,Z') for the sequence contain critical points—that is, values of the nuclear charges Z and Z' at which energy minimum, maximum [at Re(min) and Re(max)], and horizontal inflection points occur. For ground state sequences a primary physical source of these extreme points is the screened, coulombic repulsion of like‐charged atomic centers in the diatomics. With this realization, we can write analytical forms that have the correct scaling behavior and which properly model the screened, coulombic repulsion for E along certain straight‐line trajectories in the (Z,Z') plane. This leads to the observation that Re(max) values diverge logarithmically in λ‐like transitions wherever the screened coulombic repulsion becomes small as the nuclear charges vary along those trajectories.At the horizontal inflection points the E surface contains A2 folds, as required by Thom's theorem for analytical surfaces containing one control parameter. Within the isoelectronic sequence molecular subgroups have been noted and explained in terms of the underlying atomic shell structures of the molecules' constituent atoms. Using input data for seven stable molecules together with the analytical surface selected for study, we have estimated the equilibrium bond distances Re(min), dissociation energies De(min), and harmonic force constants E(2)(min) for 18 other neutral and charged species.
Usage de l'algebre de lie su(n) dans l'etude des systems à n etats. VI. Equations linéaires d'evolution positive
Authors: Van Groenendael A. 
Published: December 2004

AbstractThe n‐level quantum system density‐operators evolution is not usually given by the Liouville equation, but by a more general one. This equation must keep density‐operators trace, hermiticity, and positiveness. These three conditions restrict the available kinds of evolution equations. In this paper we investigate linear equations for systems without memory effects. By using the first two conditions and the formalism we introduced in earlier papers, the evolution equation takes the form of a first order differential equation concerning the n2 – 1 dimension “coherence‐vector.” The third one is the essential object of this paper. Moreover, we obtain a cononical splitting of this equation into four parts that may be separately studied.
The spin‐projected Hartree‐Fock method: Direct optimization schemes and stability conditions
Authors: Karadakov Peter 
Published: December 2004

AbstractThe necessary theory to construct different direct orbital optimization schemes in the framework of the spin‐projected Hartree‐Fock (spin‐PHF) method for systems with an even number of electrons and for the proper characterization of the pertinent spin‐PHF solutions is developed using the formalism of second quantization. The treatment is based on a unitary transformation of a reference DODS (different orbitals for different spins) Slater determinant. The energy expectation value corresponding to the transformed DODS Slater determinant is expanded in a Taylor series about the reference DODS Slater determinant, including second‐order terms. On the basis of this expansion we propose several direct iterative approaches to optimize the spin‐PHF energy expectation value: for example, implementations of steepest descent and conjugated gradient techniques, and Newton–Raphson, Fletcher, and limited configuration interaction approaches. The analysis of the second‐order term in the Taylor series expansion of the spin‐PHF energy expectation value about a spin‐PHF solution is used to define stability conditions for spin‐PHF solutions. Explicit expressions are reported for all matrix elements between different spin‐projected DODS Slater determinants appearing in the treatment.
Theoretical calculation of electrode potentials: Electron‐withdrawing compounds
Authors: Lister Simon G. , Reynolds Christopher A. , Richards W. Graham 
Published: December 2004

AbstractThe electrode potential of 2,3‐dicyanobenzoquinone in aqueous solution has been calculated relative to parabenzoquinone using a thermodynamic cycle approach that includes accurate gasphase ab initio calculations and calculation of differences in free energies of hydration using the free‐energy perturbation method. The discrepancy between the calculated and experimental electrode potential is disappointingly large (99 mV) compared to previous studies using this approach. This, along with the experimental evidence, suggests that the experimental value itself is too large and that theoretical approaches may indeed be as reliable as experimental ones for determining redox properties of molecules such as 2,3‐dicyanobenzoquinone. In the light of this discrepancy we have examined the variation of the results with the basis set, inclusion of electron correlation and changes in the parameters used in the molecular dynamics free‐energy simulations. The results are shown to be dependent upon the torsional parameters and especially dependent upon the basis set or semiempirical method used to obtain the electrostatic potential‐derived charges. The best charge set was determined using the ab initio criteria of completeness—as far as it can be applied to large molecules—and also by studying the effect of hydration on these charges. This was done by allowing the solvent to perturb the wave function prior to the electrostatic potential determination. Thus, 3‐21G and 6‐31G* basis sets were found to give satisfactory results. Similar results were obtained using semiempirical and ab initio geometries.
Vector coupling coefficients for calculations of transition‐metal atoms and ions by the SCF coupling operator method
Authors: Plakhutin B. N. , Zhidomirov G. M. , Arbuznikov A. V. 
Published: December 2004

AbstractWe derived the necessary conditions to which the vector coupling coefficients (VCC) a and b describing atomic L,S‐multiplets of the configurations dN (1 ≤ N ≤ 9), should satisfy. Special attention is paid to the states of non‐Roothaan type for which VCC depend on the choice of degenerate d‐orbitals basis set determined within the accuracy up to an orthogonal transformation u. It is shown that for such states the direct sum of matrices ‖a‖ and ‖b‖ must be the non‐symmetric matrix. Obtained VCC were used for the ab initio calculations (basis set (14s9p5d)/[8s4p2d] from [15]) on first‐row transition atoms (from Sc to Cu) to compare to similar calculations [16], in which the Peterson's VCC have been used, and with calculations [15] carried out by the atomic SCF program [4] as well.
Molecular dynamics simulation for liquid water using a polarizable and flexible potential
Authors: Corongiu Giorgina 
Published: December 2004

AbstractA molecular dynamics simulation for liquid water at room temperature is reported. A sample of 1000 water molecules has been analyzed with the Nieser–Corongiu–Clementi polarizable potential, to which is added vibrational flexibility. The sample was contained in a cubic box subject to periodic boundary conditions, a cutoff radius of 15.54 Å was used in evaluating energies and forces, the long‐range interactions were taken into account with the reaction field method, and the integration of the equation of motion has been performed using a sixth‐order Gear predictor–corrector algorithm. The simulation, after 35 ps of equilibration time, has been carried out for 10.4 ps with a time step of 1.25 × 10−16 s. The trajectories and velocities, collected in the production phase of the simulation, have been used to compute the geometry of the water molecule within the liquid, thermodynamical quantities, the pair correlation functions, the Dore neutron pair correlation function, X‐ray and neutron scattering structure functions, translational, rotational, orientational autocorrelation functions and their Fourier transforms, mean square displacements, diffusion coefficients, and NMR relaxation times. A detailed study on the spectral density is presented, and good agreement is found with the most recent infrared, Raman, and neutron scattering laboratory data. All the simulated properties so far analyzed are in good agreement with experimental data, and, with confidence, we can assess that our ab initio polarizable potential with inclusion of vibrations is the most reliable water potential in today's literature for the description of water.
Toward designing molecular‐electronics devices: A potential significance of highly mobile equilibrium interconversions
Authors: Slanina Zdeněk 
Published: December 2004

AbstractPossible applications of computational molecular‐engineering approaches to the design of bistable conformational systems, to be potentially employed in molecular electronics, have been analyzed in isomeric–thermodynamic terms. Constructing such systems led to (conflicting) requirements, viz. an easy interconversion of the two structures (the isomerization equilibrium constant close to unity). At the same time there is a need for both isomers to be sufficiently stable and mutually different (enthalpy–entropy compensation can still ensure the equilibrium‐constant requirement). Moreover, the equilibrium criteria have to be necessarily combined with considerations of kinetics. The design problems are illustrated on two model systems: Si6H6 isomeric species and deuterium‐ and hydrogen‐bonded water dimers, HOD · OHD and DOH · OHD, respectively.
Effect of hydrogen bonding and cooperativity on stretching force constants of formamide
Authors: Shivaglal M. C. , Singh Surjit 
Published: December 2004

AbstractStretching force constants for formamide and its seven associated species involving two to four molecules hydrogen‐bonded through linear and cyclic configurations and 10 structures containing formamide hydrogen‐bonded with one to five water molecules are reported. Since ab initio calculations are rather inconvenient to perform on such big clusters and are time‐consuming, CNINDO MO calculations were carried out using the gradient method. The results demonstrate, on the one hand, the feasibility of semiempirical calculations for the evaluation of trends in force constants for big clusters where generally ab initio calculations become much involved and, on the other hand, explain the effect of hydrogen bonding and cooperativity on force constants and vibrational spectra of biologically important systems composed of formamide in the condensed phase and its aqueous solutions. The CO and NH stretching force constants are found to reduce significantly on hydrogen bonding. The reduction in force constant is further enhanced when two cyclic dimers become associated through a linear hydrogen bond. The results indicate justification for the stabilization of the formamide structure with two cyclic dimers hydrogen‐bonded together. The reduction in the force constants on hydrogen bonding also reflect the cooperativity contribution. The CO and CN stretching force constants for the structures corresponding to formamide in liquid and aqueous solution phases are in agreement with the experimental vibrational frequencies reported.
AM1 calculation of hydration to aldehyde group in nitro‐substituted benzaldehydes
Authors: Shinoda Hiroyuki , Sayama Michio , Mori Masa‐Aki , Kozuka Hiroshi 
Published: December 2004

AbstractHydration to the aldehyde group in nitro‐substituted benzaldehydes was studied theoretically by using an AM1 method. The calculated values of activation energy and heat of reaction showed good correlations with the experimental values of rate constants and equilibrium constants, respectively. To examine the hydration mechanism, localized molecular orbitals were calculated. Furthermore, expression of the molecular orbitals of supermolecular complexes in terms of occupied and vacant orbitals of the component molecules elucidated that the interaction between the lonepair orbital of water and the antibonding CO π‐orbital of aldehyde was important. 2,6‐DNBAl was concluded to be less reactive toward water than was 2.4‐DNBAl. This is consistent with the experimental result that the mutagenic activity of 2,4‐DNBAl depends not only on the reduction of the nitro group by a bacterial enzyme but also on the acetyl conjugation, but that in the case of 2,6‐DNBAl the mutagenic activity is manifested through the reduction by a bacterial enzyme. © 1993 John Wiley & Sons, Inc.
MBOHO calculations of CH stretching frequencies in hydrocarbons and heterosubstituted hydrocarbons
Authors: Hu Zhen‐Min , Zhan Chang‐Guo 
Published: December 2004

AbstractBased on the generalized relationship for calculating the nuclear spin–spin coupling constants and the correlation of the bond stretching frequencies with the coupling constants, a novel generalized reationship, which includes the contributions of not only the hybrid orbitals, but also the net atomic charges, is introduced for calculation of the bond stretching frequencies and employed to elucidate the CH stretching frequencies in hydrocarbons and heterosubstituted hydrocarbons on the basis of the MBOHO calculation employing the CNDO/2 approximation. By use of the obtained concrete realtionships, one can get different νCH value for the CH bonds existing in different chemical environments, which is coincident with chemical intuition. The calculated numerical results show that for hydrocarbons the contribution of the net atomic charges can be neglected, but it is necessary for heterosubstituted hydrocarbons to include the contribution of the net atomic charges to the CH stretching frequencies. The calculated CH stretching frequencies are in good ageement with the experimental data, which shows its reasonableness. © 1994 John Wiley & Sons, Inc.
Effective core potentials and the structures of metallocenes
Authors: Cook David B. 
Published: December 2004

AbstractThe use of effective core potentials in the calculation of the geometrical parameters of the ferrocene molecule and its heavier analogs is reported. It is shown that a critical factor in these calculations is the efective core–core (ECC) potential and, in the absence of ECCs for first‐row atoms that are involved in short bonds, calculations of the geometrical parameters are not reliable. Good agreement with experimental geometries may be obtained by using the Los Alamos ECPs for atoms of the second and higher rows of the periodic table at the MP2 level. DFT calculations have been performed and found to give numerical results comparable to MP2 in the same basis. © 1995 John Wiley & Sons, Inc.
The historical development of the electron correlation problem
Authors: Löwdin Per‐Olov 
Published: December 2004

AbstractA brief review is given of the historical development of the treatment of the correlation problem in solving the Schrödinger equation in modern quantum theory from the early 1930s up to now. The correlation energy for a specific state of a system is defined as the differenceEcorr=E−EHFbetween the exact eigenvalueEand the Hartree–Fock energyEHFof the same Hamiltonian for the state under consideration. From the concepts of the “Different Orbitals for Different Spins” (DODS) and the “Alternant Molecular Orbital” (AMO) methods introduced in the 1950s, the study goes to the use of transition formulas—instead of expectation values—for the Hamiltonian and the possibility to express the correlation energy exactly in terms of “double excitations” or pair functions. The main emphasis is then put on the concept of wave and reaction operators and the formulation of the results of infinite‐order perturbation theory in terms of such operators. The partitioning technique offers a simple way to derive these operators and to explore the resolvent or propagator methods in greater detail, and it replaces the original Schrödinger equation with its degeneracies and multiple roots by a reduced characteristic equation having only single roots, which is often a great simplification. Special attention is given the treatment of Schrödinger's perturbation theory in view of the importance of the linked‐cluster theorem in the applications. In the study of the splitting of degenerate levels due to a perturbation, the use of the multidimensional partitioning technique utilizing the concept of an energy‐independent wave operator is also discussed. Some developments in the coupled‐cluster methods are further briefly reviewed. Since all quantum mechanical calculations going beyond the Hartree‐Fock method imply a certain treatment of the correlation problem, a brief survey is also given of the progress in computational quantum theory, particularly in current quantum chemistry. © 1995 John Wiley & Sons, Inc.
Analytic energy derivatives for coupled‐cluster methods describing excited states: General formulas and comparison of computational costs
Authors: Szalay Péter G. 
Published: December 2004

AbstractIt is possible to derive energy derivatives for nonvariational (e.g., coupled‐cluster) methods invoking the generalized Hellmann–Feynman theorem. In such a procedure, one constructs a functional which, besides the usual wave‐function parameters, contains new ones. One set of stationary conditions will reproduce exactly the original equations of the method, while the others will determine the value of the new parameters. We applied this straightforward procedure to derive analytic energy derivatives for several coupled‐cluster (CC) methods applicable to excited states such as the Hilbert‐space CC method, two‐determinetal (TD) CC method, Fock‐space CC method, and equation‐of‐motion–CC (EOM–CC) method. Finally, we compared the computational requirements for the different methods. © 1995 John Wiley & Sons, Inc.
Unitary group approach to spin‐adapted open‐shell coupled cluster theory
Authors: Jeziorski Bogumił , Paldus Josef , Jankowski Piotr 
Published: December 2004

AbstractWe show that the irreducible tensor operators of the unitary group provide a natural operator basis for the exponential Ansatz which preserves the spin symmetry of the reference state, requires a minimal number of independent cluster amplitudes for each substitution order, and guarantees the invariance of the correlation energy under unitary transformations of core, open‐shell, and virtual orbitals. When acting on the closed‐shell reference state with nc doubly occupied and nv unoccupied (virtual) orbitals, the irreducible tensor operators of the group U(nc) ⊗ U(nV) generate all Gelfand‐Tsetlin (GT) states corresponding to appropriate irreducible representation of U(nc + nv). The tensor operators generating the M‐tuply excited states are easily constructed by symmetrizing products of M unitary group generators with the Wigner operators of the symmetric group SM. This provides an alternative to the Nagel‐Moshinsky construction of the GT basis. Since the corresponding cluster amplitudes, which are also U(nc) ⊗ U(ns) tensors, can be shown to be connected, the irreducible tensor operators of U(nc) ⊗ U(nv) represent a convenient basis for a spin‐adapted full coupled cluster calculation for closed‐shell systems. For a high‐spin reference determinant with n, singly occupied open‐shell orbitals, the corresponding representation of U(n), n=nc + nv + ns is not simply reducible under the group U(nc) ⊗ U(ns) ⊗ U(nv). The multiplicity problem is resolved using the group chain U(n) ⊃ U(nc + nv) ⊗ U(ns) ⊃ U(nc) ⊗U(ns)⊗ U(nv) ⊗ U(nv). The labeling of the resulting configuration‐state functions (which, in general, are not GT states when nc > 1) by the irreducible representations of the intermediate group U(nc + nv) ⊗U(ns) turns out to be equivalent to the classification based on the order of interaction with the reference state. The irreducible tensor operators defined by the above chain and corresponding to single, double, and triple substitutions from the first‐, second‐, and third‐order interacting spaces are explicitly constructed from the U(n) generators. The connectedness of the corresponding cluster amplitudes and, consequently, the size extensivity of the resulting spin‐adapted open‐shell coupled cluster theory are proved using group theoretical arguments. The perturbation expansion of the resulting coupled cluster equations leads to an explicitly connected form of the spin‐restricted open‐shell many‐body perturbation theory. Approximation schemes leading to manageable computational procedures are proposed and their relation to perturbation theory is discussed. © 1995 John Wiley & Sons, Inc.