bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preliminary attempt to follow the enthalpy of an enzymatic reaction by ab initio computations: Catalytic action of papain
Authors: Bolis G. , Clementi E. , Ragazzi M. , Salvaderi D. , Ferro D. R. 
Published: December 2004

AbstractA new theoretical approach to study the enthalpy variations occurring during an enzymatic reaction is presented. The structural modifications of the enzyme–substrate complex along the reaction path are distinguished as macro‐ and microdeformations. Macrodeformations, which concern primarily the approach of the substrate to the enzyme and the release of the reaction products and arise from nonbonded interactions, are treated with an empirical method for computing the energy of a macromolecule. Microdeformations, which are local displacements driven by variations of the electronic structure and its energy and involve only a limited portion of the complex, are treated with the ab initio SCF‐LCAO‐MO method. The reaction path is idealized as a sequence of major steps: at each step, first the empirical program REFINE is used to calculate the geometry of the system for that step, then the energy of an appropriate subsystem is computed ab initio with the program IBMOL, using the geometry provided by REFINE and applying small concerted atomic displacements. Thus along the entire reaction path one can obtain an energy profile computed with the ab initio method and compatible with the structure of the whole complex. This approach was applied here to the first steps of the reaction of proteolysis catalyzed by papain. The formation of an ion pair ImH+ …S− between the side chains of residues His‐159 and Cys‐25 was examined in detail. The results show that the instability of the ion pair decreases by ˜ 11.5 kcal/mol when the interactions with residues Asn‐175 and Ala‐ 160 are taken into account; the instability is further decreased by ˜2 kcal/mol after a partial geometry optimization. The energies of the noncovalent enzyme–substrate complex and of the tetrahedral intermediate were computed, considering N‐methyl acetamide (NMA) as model substrate and representing papain with the residues Cys‐25, His‐159, Gln‐19, and Ala‐160. The interaction energy of the noncovalent complex is ‐3.8 kcal/mol, compared to the value of +7.4 kcal/mol for the CH3S− ‐NMA complex. The tetrahedral intermediate is found to be less stable than the noncovalent complex by 27 and 38.5 kcal/mol, respectively, for the papain–NMA and the CH3S− ‐NMA systems. While these rather large energy differences are possibly due to the incorrect geometry of the tetrahedral intermediate and optimization of the structure is required, it appears that the interactions with the various protein residues represent a very important stabilization factor, which lowers the onthalpy variations during the reaction.
Excited electronic states of a hydrogen bond: Bifluoride ion
Authors: Lozes Richard , Sabin John R. 
Published: December 2004

AbstractWe report here a summary of a limited CI calculation carried out on the C∞v and D∞h electronically excited states of bifluoride ion. This species is interesting as the prototype of a hydrogen‐bonded system. It is determined that the lowest‐lying excited states of the system are dissociative and/or autoionizing.
Heme proteins and metalloporphyrins: Redox chemistry and oxygen binding
Authors: Dolphin David , Addison Anthony W. , Cairns Max , Dinello Robert K. , Farrell Nicholas P. , James Brian R. , Paulson Donald R. , Welborn Curtis 
Published: December 2004

AbstractMetalloporphyrins perform a variety of functions in nature from the storage and transport of electrons and molecular oxygen to the decomposition of hydrogen peroxide and the activation of oxygen. The chemistry of both the centrally coordinated metal and the porphyrin macrocycle play important roles in these reactions. The use of model systems and metalloporphyrins, other than iron porphyrins, is described for the elucidation of the mechanism of action of the natural systems.
Assessment of reaction center special‐pair chlorophyll models
Authors: Maggiora Gerald M. 
Published: December 2004

AbstractA discussion of the experimental evidence for the existence of special‐pair chlorophyll in the reaction centers of plants and photosynthetic bacteria is presented, and an assessment of the adequacy of various in vitro chemical model systems designed to mimic the properties of these reaction centers is given. For plant systems it appears that the in vitro models successfully mimic almost all measured in vivo properties, whereas in bacterial systems a similar situation does not obtain. Possible structural models of special‐pair chlorophyll derived primarily from in vitro model studies are described. Their suitability as models of the photooxidizable pigment in plant and bacterial reaction centers is analyzed, and alternative structures for the bacterial case, which is the least well characterized structurally, are considered.
Molecular electrostatic potential of the B‐DNA helix. I. Region of the guanine–cytosine base pair
Authors: Pullman Alberte , Zakrzewska Chrystyna , Perahia David 
Published: December 2004

AbstractThe electrostatic molecular potential minima around the guanine–cytosine base pair within a B‐DNA minihelix are computed, taking into account the contributions of the sugar‐phosphate backbone and of the adjacent base‐pairs. The calculations are based on ab initio SCF wave functions of the different constituents of the nucleic acid. The results point to significant differences in the potential between the isolated nucleic acid bases or base‐pairs and those within the DNA. Altogether the minima in the G–C regions are strongly enhanced in the minihelix. They benefit from the field created by the neighboring phosphates. From the purely electrostatic viewpoint an ambiguity remains as concerns the relative affinity of N7 and N3 of guanine for electrophiles. On the other hand, guanine should altogether be more susceptible than cytosine to such reagents, this ordering concerning also its NH2 group compared to that of cytosine.
Subduction coefficients for 〈2N/2–S, 12S〉 ↓ 〈2, 1〉 ⊗ 〈2, 1〉 of U(n) ↓ U(n1) ⊗ U(n2)
Authors: Sarma C. R. , Dinesha K. V. 
Published: December 2004

AbstractThe determination of the subduction coefficients for states of the unitary group U(n) under the restrictions U(n) ↓ U(n1) ⊗ U(n2) have been considered for the spin free states of many electron systems. Using the transformation properties of the tensor basis spanning the irreducible representation 〈2N/2–S, 12S〉 of U(n) under the permutations of electron coordinates, a simple programmable procedure has been developed for the determination of these coefficients. The procedure has been illustrated using a simple example.
Theoretical description of fluidity in biological membranes: Rotational motion in lipid hydrocarbon chains
Authors: Hosur Ramakrishna V. , Joshipura Anjan S. 
Published: December 2004

AbstractA mathematical model to relate order and rotational motion in lipid hydrocarbon chains in biological membranes is proposed. Schrödinger equations with suitable potential functions for CC rotations in lipid hydrocarbons chains have been solved to obtain wave functions characterizing these motions. For a free chain a threefold potential function has been assumed. The effect of collisions between neighboring chains in a membrane is considered by including another term (δ function) in the potential function.
Improvement of an integral approximation scheme based on semiorthogonalized orbitals
Authors: Osanai You , Kashiwagi Hiroshi 
Published: December 2004

AbstractIn a previous paper, a scheme of integral approximation was proposed, in which a large number of two‐electron integrals containing a certain kind of orbital pairs, i.e., weakly related pairs, can be neglected. A new criterion for partitioning orbital pairs into two groups, i.e., strongly and weakly related pairs, is introduced in order to allow for neglect of more integrals without sacrificing the accuracy of a computation. Test calculations on the BH3C2H4 complex show that by the use of the new version, results of roughly the same accuracy as was obtained by the old version is obtained by retaining 80% of the integrals used in the old version. This kind of saving is more significant for larger molecules. For example, in a calculation on Cu‐porphine with 203 CGTO'S, the revised version will require about 2.0 × 106 integrals, while the original version will require about 4.5 × 106. And these two approximate calculations are expected to give the results of roughly the same accuracy.
Projected surface energy bands, Shockley surface states, and bonding in transition‐metal monocompounds with rock‐salt structure: Example of NbC
Authors: Tomášek Mojmír , Pick Štěpán 
Published: December 2004

AbstractThe qualitative theory of Shockley surface states is used to discuss the existence of surface states on three faces of niobium carbide: (001), (011), and (111). The results obtained for NbC are generalized to include other simple transition metal compounds MX, X = C, N, O. Surface states of these and related materials are of interest in chemisorption and catalysis. The qualitative theory of Shockley states appears to be useful tool in detecting strong covalency effects in solids.
Quantum model for transport through membranes
Authors: Ibáñtez‐Mengual J. A. , Tejerina‐García A. F. 
Published: December 2004

AbstractIn the present paper a new model for the transport through membranes, introduced previously by Hosur, is considered. In this model, the membrane is assimilated to a potential barrier, and the material flow through the membrane is determined from the transmission coefficient of the barrier, assuming the existence of an energy difference among the molecules placed at both sides of the membrane. An equation for the transport, in the case of small energy differences, is obtained, which is particularized to the cases that the energy difference is caused by a temperature gradient, a concentration gradient, and both gradients acting together. In all cases, under certain limitations, formally identical equations to those of the thermodynamics of irreversible processes are obtained.
Shellwise virial scaling: Approximation for atomic hole states
Authors: Katriel J. , Davidson E. R. 
Published: December 2004

AbstractA partitioning of the kinetic and potential energies of atoms within the SCF framework into shell components is proposed. It is demonstrated that this partitioning nearly satisfies a shellwise viral theorem for SCF wave functions. This property is used in order to generate approximate relaxed wave functions for atomic hole states by scaling each shell of the frozen description of the hole in terms of the neutral‐atom ground‐state orbitals. Very good estimates of ΔSCF relaxation energies and reasonable estimates of the overlap integrals between the frozen and relaxed hole wave functions are obtained.
Reduced hamiltonian orbitals. III. Unitarily invariant decomposition of hermitian operators
Authors: Coleman A. J. , Absar I. 
Published: December 2004

AbstractA decomposition of an N‐particle operator as a sum of N + 1 components is defined such that, in the case of a model system employing a finite one‐particle basis set, the decomposition is invariant under unitary transformations of the basis set. Applied to a two‐particle Hamiltonian, this decomposition gives rise to the distinction between the independent‐particle energy and the coupling energy defined in previous papers. Applied to the reduced density operator for a quantum state, the decomposition corresponds to partitioning the density into irreducible components. This partitioning is illustrated by graphs of electron density for the water molecule.
The coupled‐cluster method with a multiconfiguration reference state
Authors: Banerjee Ajit , Simons Jack 
Published: December 2004

AbstractThe coupled‐cluster approach to obtaining the bond‐state wave functions of many‐electron systems is extended, with a set of physically reasonable approximations, to admit a multiconfiguration reference state. This extension permits electronic structure calculations to be performed on correlated closed‐ or open‐shell systems with potentially uniform precision for all molecular geometries. Explicit coupled cluster working equations are derived using a multiconfiguration reference state for the case in which the so‐called cluster operator is approximated by its one‐ and two‐particle components. The evaluation of the requisite matrix elements is facilitated by use of the unitary group generators which have recently received wide attention and use in the quantum chemistry community.
The kernel of DWBA transition amplitude in atom–diatom reactive scattering
Authors: Suck Sung Ho 
Published: December 2004

AbstractThe kernel of the distorted‐wave Born approximation (DWBA) transition amplitude will be explored with attention to the atom–diatomic molecule reactive scattering process of A + BC → AB + C. Our study of the kernel reveals valuable intrinsic properties regarding the state‐to‐state reactive scattering process. In particular, such a study will help us to better understand (i) the favored geometric configuration during collision, (ii) the spatial domain of contribution to the differential and total cross sections, and (iii) the structural dependence of the kernel distribution on the mass ratio of the reactant molecule BC and the departing atom C, particularly in the case of colinear rearrangement collisions. In this study we choose the FH2 system as an illustration.
Magnesium and calcium cation–ligand interactions within the pseudopotential approach. II. Cation–GABA interactions
Authors: Blake I. Ortega , Leś A. 
Published: December 2004

AbstractWe performed ab initio pseudopotential and CNDO calculations on γ‐aminobutyric acid (GABA) and its Ca2+ and Mg2+ clathrates. We were particularly interested in the rotational barrier existing between two extreme conformers of GABA and its modification upon metal complexing. We found that the pseudopotential method predicts a coordination of the ions to GABA and that this coordination inverts the rotational barrier observed for the isolated molecule. We also looked into the adequacy of CNDO for the study of this type of coordination and found several shortcomings in its predictions. The biological implications of these findings are discussed and a hypothesis on the role of a GABA–Ca2+ complex is presented.
Algebraic structure of fermion density matrices. II
Authors: Dyadyusha G. G. , Kryachko Eugene S. 
Published: December 2004

AbstractThe properties of the algebraic structure of fermion density matrices are studied. The algebraic structure of a density matrix leads to a more varied and detailed classification scheme than that offered by the usual shell structure approach. Investigation of the algebraic structure of fermion density matrices by the methods of algebraic topology leads to a classification scheme based on Betti numbers.
Self‐Consistent methods in Hückel and extended Hückel theories
Authors: Mukhopadhyay A. K. , Mukherjee N. G. 
Published: December 2004

AbstractA self‐consistent procedure for the Hückel theory, first indicated by Harris [J. Chem. Phys. 48, 4027 (1968)] has been fully developed. To avoid time consuming repeated orthogonal‐nonorthogonal transformations and diagonalization of large matrices, a steepest descent technique has been suggested.
Basis set generation for the SCF calculation
Authors: Adamowicz Ludwik 
Published: December 2004

AbstractA method for basis set generation for SCF calculations is proposed. Using SCF orbitals and orbital energies obtained in the extended basis set the Fock operator can be expressed as its spectral resolution. The sum of differences between occupied orbital energies and corresponding eigenvalues obtained by the diagonalization of this operator in the new smaller basis set is a criterion of the quality of this new set. The present method consists of the minimization of this sum by changing the parameters that determine the new basis functions. An example of the optimization of the different Gaussian basis sets for the LiH molecule is described.
Exact formulas for overlap integrals of Slater‐type orbitals with equal screening constants
Authors: Jones Herbert W. 
Published: December 2004

AbstractExact formulas for 147 overlap integrals between Slater‐type orbitals with equal screening constants are presented in the most simplified form. This represents all combinations of orbitals with quantum numbers: 1 ≤ N ≤ 5, 0 ≤ L ≤ 3, and M ≤ L. The formulas are automatically generated by computer using the “C‐matrix” single‐center expansion method. There are no limitations to the applicability of this method to orbitals of higher quantum numbers.
Automatic geometry optimization for molecules with d orbitals. III. The EHT method with electrostatic corrections
Authors: Beran S. , Slanina Z. , Zidarov D. C. 
Published: December 2004

AbstractA procedure has been developed for automatic optimization of molecular structures in the EHT method with possible inclusion of electrostatic correction terms, operating with analytical formulas for the first derivative of the total energy in Cartesian coordinates in the s, p, d basis of Slater orbitals. Illustrative examples are given of optimization of the structural parameters of FeCl3, Fe2Cl6, FeCl4, FeCl4−, FeCl2, and FeCl and of optimization of the reaction pathways of the dissociation of Fe2Cl6 yielding the other species of the above set. The values are in good argreement with the available experimental data; this agreement is discussed briefly in connection with the general applicability of the EHT method combined with automatic geometry optimization to theoretical study of compounds containing transition metal atoms.
Information theory interpretation of the Pauli principle and Hund rule
Authors: Bonchev D. 
Published: December 2004

AbstractMaking use of different information measures, the Pauli exclusion principle and the first Hund rule were found to be related to a trend toward acquiring a maximum information content of the atoms and molecules, and more generally, for any fermion system. The bosons conversely always have a minimum (zero) information content with respect to the permutation symmetry of their wave functions. Some new interpretations of the Pauli principle are presented.
Interactions between nucleic acid bases in hydrogen bonded and stacked configurations: The role of the molecular charge distribution
Authors: Langlet J. , Claverie P. , Caron F. , Boeuve J. C. 
Published: December 2004

AbstractSome aspects of the use of simplified formulas for the evaluation the interaction energy between two molecules is discussed. This energy is obtained as the sum of four terms: electrostatic, polarization, dispersion, and short‐range (exponentially decreasing) repulsion. The effect of using several approximations is considered (i) for representing the charge distributions of the isolated molecules (which determine the electrostatic and polarization terms), and (ii) for evaluating the short‐range repulsion term. The various charge distributions considered are semiempirical atomic net charges (Del Re + Pariser‐Parr), atomic charges and dipoles (CNDO) and corresponding “effective” atomic charges, and many‐centered multipole distributions obtained from ab initio SCF calculations (charges, dipoles, and quadrupoles located on the atoms and the middles of segments joining pairs of atoms, whether chemically bonded or not). As concerns the short‐range repulsion, the various procedures considered are a sum of atom‐atom terms, a sum of bond‐bond terms, and the use of anisotropic van der Waals radii for heteroatoms (oxygen and nitrogen). In all cases, the dispersion energy is obtained as a sum of atom‐atom terms (of the R−6 type). These various procedures are checked in the case of the interactions between nucleic acid bases, for two rather different kinds of configurations, namely, hydrogen bonded and stacked. This comparison reveals a rather complicated picture, namely the results got from the various levels of approximation of the molecular charge distribution lead to different degrees of agreement according to different situations, e.g., for guanine‐cytosine interactions, qualitative agreement is found between the various methods as concerns the relative order of stacked and hydrogen bonded situations, while agreement is much less satisfactory for adenine‐uracile interactions. One of the main conclusions is that a sufficiently sophisticated representation of the molecular charge distribution is required in order to get reliable results for all possible configurations of a complex. Such comparative studies should bring significant help as concerns the development of the reliable simplified procedures for evaluating intermolecular interaction energies.
Potential energy curves in complementary base pairs and in model hydrogen bonded systems
Authors: Chojnacki Henryk , Lipiński J´zef , Sokalski W. Andrzej 
Published: December 2004

AbstractThe potential energy curves for the intermolecular proton transfer in complementary base pairs and respective hydrogen bonded model systems have been studied at the semiempirical all‐valence and ab initio STO‐3G level. The proton transfer probability was found to be markedly greater in excited electronic states than that of the ground state. Substantial lowering of the potential barrier height for the coupled double proton transfer in model (HCOOH)2 system has been observed when the dynamics of zero‐point vibrational deformations of the heavy atom skeleton and the environmental effects were taken into account in nonempirical STO‐3G calculations. The results of quantum‐chemical calculations indicate on the possibility of the double proton transfer in complementary base pairs corroborating the submolecular Löwdin hypothesis on the mechanism of spontaneous mutations.
Comparative studies on drug‐receptor binding of phenylethylamine derivatives using calculated group contribution constants
Authors: Lukovits I. 
Published: December 2004

AbstractGroup contribution constants of phenylethylamine derivatives were calculated using a modified version of the Free‐Wilson approach and data published on group contributions were also collected. The biological activity indices used to extract these contributions are the inhibition of phenylethanolamine N‐methyl transferase, inhibition of norepinephrine uptake, dopamine β‐hydroxylase substrate activity, phenylethanolamine N‐methyl transferase substrate activity, and antagonism to the pressor activity of epinephrine. The different sets of calculated group contributions were compared. Correlation could be demonstrated between sets of group contributions, except those extracted from the antipressor activity data. It is concluded that the interaction mechanism between the receptor site and the aromatic ring might be similar in the systems considered. Methylation of the nitrogen atom appearently does not cause any change in specificity at the molecular level.