bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of a New Cluster Ansatz to Treat Strong Relaxation and Correlation Effects: A Direct Method for Energy Differences
Authors: Jana Debasis , Mahapatra Uttam Sinha , Mukherjee Debashis
Published: October 2008

We have presented in this paper a new cluster Ansatz for the wave operator for open-shell and/or quasidegenerate states, which takes care of strong relaxation and correlation effects in a compact and efficient manner. This Ansatz allows contraction among the various cluster operators via spectator orbitals, accompanied by suitable combinatorial factors. Since both the orbital and the correlation relaxations are treated on the same footing, it allows us to develop a very useful direct method for energy differences for open shell states relative to a closed-shell ground state, where the total charge for the two states may differ. We have discussed a new spin-free coupled cluster (CC) based direct method and illustrated its performance by evaluating electron affinity of a neutral doublet radical. We have also indicated how the scope of the theory can be extended to compute the state energies of simple open shell configurations as well. In that case, the CC equations terminate after the quartic power of cluster operators – exactly as in the closed-shell situation, which is not the case for the current methods.
On the Estimation of the Remainder Term in Møller-Plesset MP2 Theory from Limited Configuration Interaction
Authors: Hubac I. , Wilson S.
Published: October 2008

In a previous paper, we have avoided an infinite order perturbation expansion and obtained a closed expression which consists of the second-order Møller-Plesset energy component together with a remainder term. The applicabilty of second-order many-body perturbation theory with a Møller-Plesset reference hamiltonian then rests upon the magnitude of this remainder term rather than the behaviour of the higher order terms on the perturbation series. In the present work, we show how this remainder term can be estimated by limited configuration interaction.
The State-Universal Multi-Reference Coupled-Cluster Theory: An Overview of Some Recent Advances
Authors: Piecuch Piotr , Kowalski Karol
Published: October 2008

Some recent advances in the area of multi-reference coupled-cluster theory of the state-universal type are overviewed. An emphasis is placed on the following new developments: (i) the idea of combining the state-universal multi-reference coupled-cluster singles and doubles method (SUMRCCSD) with the multi-reference many-body perturbation theory (MRMBPT), in which cluster amplitudes of the SUMRCCSD formalism that carry only core and virtual orbital indices are replaced by their first-order MRMBPT estimates; and (ii) the idea of combining the recently proposed method of moments of coupled-cluster equations with the SUMRCC formalism. It is demonstrated that the new SUMRCCSD(1) method, obtained by approximating the SUMRCCSD cluster amplitudes carrying only core and virtual orbital indices by their first-order MRMBPT values, provides the results that are comparable to those obtained with the complete SUMRCCSD approach.
Higher Energy Derivatives in Hilbert Space Multi-Reference Coupled Cluster Theory : A Constrained Variational Approach
Authors: Shamasundar K. R. , Pal Sourav
Published: October 2008

In this paper, we present formulation based on constrained variational approach to compute higher energy derivatives upto third order in Hilbert Space Multi-Reference Coupled Cluster (HSMRCC) Theory. This is done through the use of a functional with Lagrange multipliers corresponding to HSMRCC method, as done by Helgaker, Jorgensen and Szalay. We derive explicit expressions upto third order energy derivatives. Using (2n + 1) and (2n + 2) rules, the cancellation of higher order derivatives of functional parameters that are not necessary according to these rules, is explicitly demonstated. Simplified expressions are presented. We discuss several aspects of the functional used and its potential implications.
State-specific Multi-reference Perturbation Theories with Relaxed Coefficients: Molecular Applications
Authors: Ghosh Pradipta , Chattopadhyay Sudip , Jana Debasis , Mukherjee Debashis
Published: October 2008

We present in this paper two new versions of Rayleigh-Schr¨odinger (RS) and the Brillouin-Wigner (BW) state-specific multi-reference perturbative theories (SSMRPT) which stem from our state-specific multi-reference coupled-cluster formalism (SS-MRCC), developed with a complete active space (CAS). They are manifestly sizeextensive and are designed to avoid intruders. The combining coefficients cμ for the model functions φμ are completely relaxed and are obtained by diagonalizing an effective operator in the model space, one root of which is the target eigenvalue of interest. By invoking suitable partitioning of the hamiltonian, very convenient perturbative versions of the formalism in both the RS and the BW forms are developed for the second order energy. The unperturbed hamiltonians for these theories can be chosen to be of both Mφller-Plesset (MP) and Epstein-Nesbet (EN) type. However, we choose the corresponding Fock operator fμ for each model function φμ, whose diagonal elements are used to define the unperturbed hamiltonian in the MP partition. In the EN partition, we additionally include all the diagonal direct and exchange ladders. Our SS-MRPT thus utilizes a multi-partitioning strategy. Illustrative numerical applications are presented for potential energy surfaces (PES) of the ground (1Σ+) and the first delta (1Δ) states of CH+ which possess pronounced multi-reference character. Comparison of the results with the corresponding full CI values indicates the efficacy of our formalisms.
Post Hartree–Fock and DFT Studies on Pyrrole···Nitrogen and Pyrrole···Carbon Monoxide Molecules
Authors: Kanakaraju R. , Kolandaivel P.
Published: October 2008

The hydrogen bonded and van der Waals isomers of pyrrole···nitrogen and pyrrole···carbon monoxide have been studied using ab initio and density functional theory methods. Complex geometries and total energies of the isomers have been determined at HF, MP2, B3LYP and B3PW91 levels of theory employing 6-31G* basis set. For pyrrole···nitrogen complex, only two isomers have stable structure and the more stable one is found to be the hydrogen bonded isomer. Among the five isomers of pyrrole···carbon monoxide complex, the hydrogen bonded isomer is found to be the most stable form. The interaction energy for all these isomers have been calculated after eliminating the basis set superposition errors by using the full counterpoise correction method. Chemical hardness, chemical potential have been calculated and are used to study the stability of the molecules.
Among Synthetic, Supramolecular and Theoretical Chemistry Stabilization of Short-lived Species in “Molecular’ or ‘Supramolecular Flasks’
Authors: Dodziuk Helena
Published: October 2008

The recent advances in the syntheses of short-lived species inside cages of ‘molecular’ or ‘supramolecular flasks’ lead their more involved studies. Moreover, they open prospects for much closer and fruitful cooperation among organic synthetic, theoretical and supramolecular chemists that will allow one to obtain and study numerous, exciting highly strained molecules, ions and/or radicals.
Special Issue on Recent Advances in Nuclear Magnetic Shielding Theory
Authors: Ferraro Marta
Published: October 2008

Nuclear Magnetic Resonance Spectroscopy (NMR) is one of the most important tools to elucidate structure and environment.[...]
In Vitro Metabolism of Dibenzo[a,l]pyrene, 2-Chlorodibenzo [a,l]pyrene and 10-Chlorodibenzo[a,l]pyrene - Effects of Chloro Substitution
Authors: Wu Yuh-Shen , Fang Guor-Cheng , Moody Joanna , Von Tungeln Linda S. , Fu Peter P. , Hwang Huey-Min , Yu Hongtao
Published: October 2008

Stereoselective metabolism of dibenzo[a,l]pyrene (DB[a,l]P), 2-chlorodibenzo[a,l]pyrene (2-Cl-DB[a,l]P) and 10-chlorodibenzo[a,l]pyrene (10-Cl-DB[a,l]P) by rat liver microsomes was studied and effects of the chloro substituent on the metabolism were determined. All three compounds produced trans-8,9-dihydrodiol, trans-11,12-dihydrodiol, and the 7-hydroxyl derivative as major metabolic products and several other phenolic derivatives as minor metabolites. The trans-8,9- and 11,12-dihydrodiols of DB[a,l]P and 2-Cl-DB[a,l]P preferentially adopted a quasidiequatorial conformation, whereas 10-Cl-DB[a,l]P trans-8,9- and 11,12-dihydrodiols preferentially adopted a quasidiaxial conformation. The yields of the trans-11,12-dihydrodiol metabolites are: DB[a,l]P trans-11,12-dihydrodiol > 2-Cl-DB[a,l]P trans-11,12-dihydrodiol >> 10-Cl-DB[a,l]P trans-11,12-dihydrodiol. Circular dichroism (CD) spectral analysis indicates that the trans-8,9-dihydrodiol and trans-11,12-dihydrodiol metabolites from DB[a,l]P, 2-Cl-DB[a,l]P, and 10-Cl-DB[a,l]P are optically active. Furthermore, the major enantiomeric DB[a,l]P trans-11,12-dihydrodiol and 2-Cl-DB[a,l]P trans-11,12-dihydrodiol had R,R absolute configuration. Based on the fact that DB[a,l]P trans-11,12-dihydrodiol is the proximate tumorigenic metabolite of DB[a,l]P, our results suggest that DB[a,l]P exhibits the highest tumorigenic potency followed by 2-Cl-DB[a,l]P, and 10-Cl-DB[a,l]P exhibits the lowest tumorigenicity.
Methyl Parathion Masks Withdrawal from Physical Dependence on Morphine
Authors: Zhu Hong , Ho Ing K. , Kramer Robert E. , Baker Rodney C. , Rockhold Robin W.
Published: October 2008

The cholinergic system has been proposed to participate in the development of dependence on opioids. The present study examined effects of dermal pretreatment with methyl parathion (MP), an acetylcholinesterase inhibitor, on the development of physical dependence on morphine. Opioid dependence was induced by continuous intracerebroventricular (i.c.v.) infusion of morphine (26 nmol/μl/h) for 3 days in adult male Sprague-Dawley rats. Each rat received two doses of MP, 12.5 mg/kg, dermally, initially, 3 days prior to initiation of i.c.v. morphine infusion and again on the first day of infusion. Withdrawal was precipitated after 3 days of infusion by administering an opioid antagonist, naloxone (48 nmol/5 μl, i.c.v.). Twelve of 23 MP-treated rats exhibited signs of acetylcholinesterase inhibitor intoxication (mild tremors) and showed reduced spontaneous locomotor activity (tested by an open field test), prior to naloxone. The brain cholinesterase activity in these 12 rats was 13% of levels in control rats. Eleven rats that did not show toxic signs, exhibited cholinesterase activities that were 20% of control (not significant versus toxic group). The group that showed signs of MP intoxication exhibited a significantly lower incidence of opioid withdrawal jumping, rearing and wet dog shakes compared with the non-toxic group. No differences between quantal withdrawal signs (ptosis, penis-licking, and vocalization) were noted between the two groups. The results suggest that toxic inhibition of acetylcholinesterase non-specifically reduces locomotor activity and may obscure certain behavioral signs of withdrawal from opioid dependence. This indicates that caution should be used in interpreting a direct involvement of acetylcholinesterase inhibition in preventing opioid dependence.
Meiotic and Mitotic Phenotypes Conferred by the blm1-1 Mutation in Saccharomyces cerevisiae and MSH4 Suppression of the Bleomycin Hypersusceptibility
Authors: Anyatonwu Georgia , Garcia Ediberto , Pramanik Ajay , Powell Marie , Moore Carol Wood
Published: October 2008

Oxidative damage can lead to a number of diseases, and can be fatal. The blm1-1 mutation of Saccharomyces cerevisiae confers hypersusceptibility to lethal effects of the oxidative, anticancer and antifungal agent, bleomycin. For the current report, additional defects conferred by the mutation in meiosis and mitosis were investigated. The viability of spores produced during meiosis by homozygous normal BLM1/BLM1, heterozygous BLM1/blm1-1, and homozygous mutant blm1-1/blm1-1 diploid strains was studied and compared. Approximately 88% of the tetrads derived from homozygous blm1-1/blm1-1 mutant diploid cells only produced one or two viable spores. In contrast, just one tetrad among all BLM1/BLM1 and BLM1/blm1-1 tetrads only produced one or two viable spores. Rather, 94% of BLM1/BLM1 tetrads and 100% of BLM1/blm1-1 tetrads produced asci with four or three viable spores. Thus, at least one copy of the BLM1 gene is essential for the production of four viable spores after meiosis. During mitotic growth, mutant blm1-1 strains grew at reduced rates and produced cells with high frequencies of unusual morphologies compared to wild-type strains. These results indicated BLM1 is also essential for normal mitotic growth. We also investigated the suppression by the MSH4 gene, a meiosis-specific MutS homolog, of the bleomycin hypersusceptibility of blm1-1 mutant cells, and the relationship of MSH4 to BLM1. We screened a genomic library, and isolated the MSH4 gene on the basis of its ability to suppress lethal effects of bleomycin in blm1-1 cells. However, genetic mapping studies indicated that BLM1 and MSH4 are not the same gene. The possibility that chromosomal nondisjunction could be the basis for the inability of blm1-1/blm1-1 mutant cells to produce four viable spores after meiosis is discussed.
Special Issue on Nuclear Magnetic Resonance Spin–Spin Coupling Constants — Calculations and Measurements
Authors: Sauer Stephan
Published: October 2008

The importance of nuclear magnetic resonance (NMR) spectroscopy for the determination of three dimensional structures of even biomolecules has again been emphasized by last years Nobel prize.[...]
Experimental Determination of Pseudorotation Potentials for Disubstituted Cyclopentanes Based on Spin–Spin Coupling Constants
Authors: Zubkov Sergei V. , Chertkov Vyacheslav A.
Published: October 2008

Complete analysis of 1H-NMR spectra of trans-1,2-dichlorocyclopentane and trans-1,2-dibromocyclopentane was performed with use of our total lineshape fitting algorithm VALISA. The resulting high precision spin-spin coupling constants were then applied to the problem of conformational analysis, yielding a continuos potential of pseudorotation for the studied compounds in CDCl3, CCl4, and CD3CN solutions.
Electronic Mechanisms of Intra and Intermolecular J Couplings in Systems with C-H···O Interactions
Authors: Giribet Claudia G. , Ruiz de Azua Martin C. , Vizioli Celia V. , Cavasotto Claudio N.
Published: October 2008

Correlation effects on the change of 1J(CH) couplings in model systems I:NCH...H2O and II:CH4...H2O as a function of the H...O distance are discussed. RPA and SOPPA results follow a similar trend in system II. In system I RPA values decrease monotonously as the H...O distance decreases, while SOPPA ones exhibit flat maximum near equilibrium. Such different behavior is ascribed to the π-transmitted component. Intermolecular couplings at the equilibrium geometry of I are analyzed by means of the CLOPPA approach. The larger absolute value of 2hJ(CO) compared to 1hJ(HO) is found to arise from contributions involving a vacant LMO localized in the C-H...O moiety.
The Effect of Substituents on Indirect Nuclear Spin-Spin Coupling Constants: Methan- and Ethanimine, Methanal- and Ethanaloxime
Authors: Provasi Patricio F. , Aucar Gustavo A. , Sauer Stephan P. A.
Published: October 2008

Ab initio calculations of the spin-spin coupling constants have been carried out for methan- and ethanimine, methanal- and ethanaloxime at the level of the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes (SOPPA(CCSD)) using the aug-cc-pVTZ-J basis sets. Previously we have shown that this method can reproduce quantitatively the coupling constants for methanimine; our new results for methanal- and ethanaloxime agree also very well with the measured couplings. A study of both purely geometrical and substituent effects on all coupling constants in the title compounds is presented. Analyzing the four contributions to the coupling constants we find that the stereoelectronic effect of the nitrogen lone pair on the one-bond C-H and C-C couplings as well as the corresponding effect for the geminal N-H and N-C couplings is affected strongly by the -OH substituent. For the one-bond C-N couplings we observe that the orbital paramagnetic (OP) contribution is comparable to the Fermi Contact (FC) contribution but opposite in sign and that the spin-dipolar (SD) term amounts to between 40% and 85% of the total coupling constants. Changes in the total one-bond C-N couplings caused by the -OH substituent are also almost entirely due to SD contribution.
A Microscopic Study of Sodium Cluster Deposition on an Insulating Surface
Authors: Ipatov A. , Suraud E. , Reinhard P.
Published: October 2008

We present microscopic calculations of the low energy deposition of small sodium clusters on NaCl surface. The substrate surface is taken as inert acting on the cluster through its interface potential. The time evolution of the cluster electronic system is described using the time-dependent density approximation. The dependence of the attachment process on the initial cluster orientation relative to the insulating surface is studied for the case of a Na6 cluster.
C- versus O-Arylation of an Enol-Lactone Using Potassium tert-butoxide
Authors: Ibrahimi Sanae , Sauvé Gilles , Essassi El  Moktar
Published: October 2008

The use of potassium tert-butoxide as the base in arylation reactions of an enollactone with a series of benzyl halides was explored. Our work demonstrates that the ratio of C-arylation to O-arylation varies with the substitution pattern of the aryl halide.
Structure, Stability and Interaction Studies on Nucleotide Analogue Systems
Authors: Kolandaivel P. , Kanakaraju R.
Published: October 2008

Most of the biological molecules have a good interaction with water molecules. The hydrogen bonding interactions with the structural analogues of nucleic acid phosphate group namely dimethyl phosphate anion (DMP) and diethyl phosphate anion (DEP) are studied employing the ab initio and density functional theory methods. Inspections have been made to locate the reactive sites for the interactions of isomeric forms of mono, di and tri hydrates of alkyl phosphate anion using the above theories. It reveals, water molecules have a very strong interaction with the phosphate group in both the molecules and their interactions induce the changes in the structural parameters of the PO4 group for both the DMP and DEP anions. The optimized structural parameters, total energy, dipole moment and rotational constants are calculated and are compared with the available experimental values. The chemical hardness and chemical potential for these complexes have been calculated at HF/6-31G* level of theory and discussed the conformational stability of these complexes.
Total and Local Quadratic Indices of the “Molecular Pseudograph’s Atom Adjacency Matrix”. Application to Prediction of Caco-2 Permeability of Drugs
Authors: Ponce Yovani  Marrero , Pérez Miguel   Angel Cabrera , Zaldivar Vicente  Romero , Ofori Ernest , Montero Luis  A.
Published: October 2008

The high interest in the prediction of the intestinal absorption for New Chemical Entities (NCEs) is generated by the increasing rate in the synthesis of compounds by combinatorial chemistry and the extensive cost of the traditional evaluation methods. Quantitative Structure–Permeability Relationships (QSPerR) of the intestinal permeability across the Caco-2 cells monolayer (PCaco-2) could be obtained by the application of new molecular descriptors. In this sense, quadratic indices of the “molecular pseudograph’s atom adjacency matrix” and multiple linear regression analysis were used to obtain good quantitative models to determine the PCaco-2. QSPerR models found are significant from a statistical point of view. The total and local quadratic indices were calculated with the TOMO-COMD software. A leave-one-out cross-validation procedure (internal validation) and the evaluation of external test set of 20 drugs (external validation) revealed that regression models had a good predictive power. A comparison with results derived from other theoretical studies shown a quite satisfactory behavior of the present method. The descriptors included in the prediction models permitted the interpretation in structural terms of the permeability process, evidencing the main role of H-bonding and size properties. The models found were used in virtual screening of drug intestinal permeability and a relationship between PCaco-2 calculated and percentage of human intestinal absorption for the 72 compounds was established. These results suggest that the proposed method is able to predict PCaco-2, being a good tool for screening of PCaco-2 for large sets of NCEs synthesized via combinatorial chemistry approach.
Thermodynamic, Structural and Transport Properties of Lennard-Jones Liquid Systems. A Molecular Dynamics Simulations of Liquid Helium, Neon, Methane and Nitrogen
Authors: Tchouar N. , Benyettou M. , Kadour F.  Ould
Published: October 2008

Molecular dynamics calculations are carried out in order to find the properties of Lennard Jones liquids in different state points of their phase diagram. The spherical shape and the stability of the helium, neon, methane and nitrogen make the liquids easily accessible to numerical simulation. Thermodynamic, structural, and transport properties are studied and compared with both experimental data and recent theoretical investigations. In the present work, up to 22 state points are covered, some of which are near or at the triple point. It will be shown that the classical approach leads to data that are in very good agreement with experiments and other types of calculations. At high temperatures and low densities, we observe a decrease in the uncertainties in the stress autocorrelation function by increasing the number of iterations.
Lubrication Chemistry Viewed from DFT-Based Concepts and Electronic Structural Principles
Authors: Shenghua Li , He Yang , Yuansheng Jin
Published: October 2008

Fundamental molecular issues in lubrication chemistry were reviewed under categories of solution chemistry, contact chemistry and tribochemistry. By introducing the Density Functional Theory(DFT)-derived chemical reactivity parameters (chemical potential, electronegativity, hardness, softness and Fukui function) and related electronic structural principles (electronegativity equalization principle, hard-soft acid-base principle, and maximum hardness principle), their relevancy to lubrication chemistry was explored. It was suggested that DFT, theoretical, conceptual and computational, represents a useful enabling tool to understand lubrication chemistry issues prior to experimentation and the approach may form a key step in the rational design of lubrication chemistry via computational methods. It can also be optimistically anticipated that these considerations will gestate unique DFT-based strategies to understand sophisticated tribology themes, such as origin of friction, essence of wear, adhesion in MEMS/NEMS, chemical mechanical polishing in wafer manufacturing, stress corrosion, chemical control of friction and wear, and construction of designer tribochemical systems.
Scalar Relativistic Study of the Structure of Rhodium Acetate
Authors: Williams Stephen D. , Edwards Emily E.
Published: October 2008

Rhodium acetate, related rhodium carboxylates, and rhodium amide complexes are powerful catalysts for carbene chemistry. They readily promote the decomposition of diazo compounds and transfer the resulting carbene to a variety of substrates. There have been several quantum chemistry studies of these compounds, particularly of the acetate. These have all used non-relativistic methods, and all have shown optimized Rh-Rh bond lengths significantly longer than the experimental value. In this study we have surveyed several scalar relativistic DFT methods using Gaussian, Slater, and numerical basis functions (in DGAUSS, ADF, and DMOL3). Several combinations of exchange-correlation functionals with relativistic and non-relativistic effective core potentials (ECP) were investigated, as were non-relativistic and all electron scalar relativistic methods. The combination of the PW91 exchange and PW91 correlation functional with the Christiansen-Ermler ECP gave the best results: 2.3918 Å compared to the experimental value of 2.3855±0.0005 Å.
Preface
Authors: Burda Jaroslav , Leszczynski Jerzy , Sokalski W.
Published: October 2008

This special Issue of the International Journal of Molecular Sciences contains selected papers from the US-Czech-Polish workshop on Modeling Interaction in Biomolecules that took place between 15-th and 20-th September, 2003 in Nové Hrady, Czech Republic.[...]
Visualization of the Differential Transition State Stabilization within the Active Site Environment
Authors: Kedzierski Pawel , Wielgus Pawel , Sikora Adrian , Sokalski W. Andrzej , Leszczynski Jerzy
Published: October 2008

Increasing interest in the enzymatic reaction mechanisms and in the nature of catalytic effects in enzymes causes the need of appropriate visualization methods. A new interactive method to investigate catalytic effects using differential transition state stabilization approach (DTSS) [1, 2] is presented. The catalytic properties of the active site of cytidine deaminase (E.C. 3.5.4.5) is visualized in the form of differential electrostatic properties. The visualization was implemented using scripting interface of VMD [3]. Cumulative Atomic Multipole Moments (CAMM) [4,5,6] were utilized for efficient yet accurate evaluation of the electrostatic properties. The implementation is efficient enough for interactive presentation of catalytic effects in the active site of the enzyme due to transition state or substrate movement. This system of visualization of DTTS approach can be potentially used to validate hypotheses regarding the catalytic mechanism or to study binding properties of transition state analogues.
Estimation of Electron Spectra Transitions of Free-Based Porphin and Mg-Porphin Using Various Quantum Chemical Approaches
Authors: Šeda Josef , Burda Jaroslav V. , Brázdová Veronika , Kapsa Vojtěch
Published: October 2008

For optimized molecules of free-base porphin and magnesium-porphin (at Hartree-Fock level and 6-31G* basis set) excitation spectra were determined using several ab initio methods: CIS, RPA, CASSCF, and TDDFT. Obtained values were compared with semiempirical ZINDO method, other calculations found recently in literature and experimental data. It was demonstrated that for qualitatively correct spectra description the AO basis must include both the polarization and diffuse functions. The later play an important role in formation of Rydberg MOs. Estimated energies of the spectra transitions using the CIS method remain relatively far from the measured values. RPA method can be already considered as a quantitatively accurate method when sufficiently large basis set is used. For CASSCF approach, it was shown that even the lowest energy transitions are insufficiently described in CAS formalism and much larger active space or inclusion of more inactive orbitals in correlation treatment would be necessary for obtaining sufficient accuracy. It can be stated that without sufficiently large correlation contributions, the determined spectra are not able to reach quantitative agreement with experimental data. From the methods treated in this study, only TDDFT can be considered as a useful tool for spectra prediction, at least for calculations of lower excited states. It is relatively fast and feasible for calculation of middle-size molecules. ZINDO approximation is also relatively successful for such large systems. Acceptable predictions of experimentally observed energy transitions in the range of Q and B bands were obtained. Until higher (UV) part of spectra is examined where the excitations to Rydberg orbital will happen, it can be considered as a good candidate for electron spectra calculations.
Enol and Enethiol Occurrence for Some Ketones and Thioketones. Mass Spectrometry and Theoretical Calculations
Authors: Allegretti Patricia  E. , Schiavoni María de las Mercedes , Cortizo María  Susana , Castro Eduardo   A. , Furlong Jorge   J. P.
Published: October 2008

The mass spectra of ketones can provide valuable information with regards to keto-enol equilibria occurring in the gas phase. Mass spectra of selected ketones and thioketones have been analysed and specific fragmentation assignments have been done to characterised and weigh co-existing keto and enol tautomers. Thioketones are of particular interest due to their tendency to shift the tautomeric equilibrium towards the enethiol form. The predictive value of this methodology is not only supported by the influence of these compound’s nature and size of the substituent on these equilibria but also by the good correlation found between the selected fragments abundances ratio and semi-empirical calculation (AM1) of the corresponding heats of tautomerization.
Substituent Effects in the 13C-NMR Spectra of Six-Membered Nitrogen Heteroaromatic Compounds
Authors: Oszczapowicz Janusz
Published: October 2008

It is shown that the 13C-NMR chemical shifts of carbon atoms in substituted sixmembered heteroaromatic compounds correlate with the correponding "additivity parameters" for substituted benzene derivatives. Thus, for precalculation of chemical shifts in such compounds, just one set of parameters can be used. The differences between experimental chemical shifts and those calculated from correlation with the common set may provide insights into intramolecular interactions not reported in the literature.
Re-examination of Steric Substituent Constants by Molecular Mechanics
Authors: Hirota Minoru , Sakakibara Kazuhisa , Yuzuri Tomoaki , Kuroda Shin-ichi
Published: October 2008

Statistical analysis employing the set of the steric constants Ωj,k(Rc) is shown to be very effective in characterizing the substituent steric effect on organic reactions. Ωj,k(Rc) contains several variable parameters which are useful for the diagnosis of the character of steric effect. The parameters controlling the angular, or directional, weight (j,k) and the size of reaction center atom X(Rc) are varied in order to elucidate the characteristics of several steric substituent constants.
How the Substituent Effect Influences π-Electron Delocalisation in the Ring of Reactants in the Reaction Defining the Hammett Substituent Constants σm and σp
Authors: Krygowski Tadeusz M. , Stępień Beata   T. , Cyrański Michał   K.
Published: October 2008

Application of the geometry (HOMA, EN, GEO) and magnetism based (NICS, NICS(1)) indices of aromaticity to optimised geometry of the ring in 12 meta – and 12 para – substituted benzoic acids and their anions by use of DFT computations at B3LYP/6-311+G(d,p) level has shown a very low substituent effect on the π-electron delocalisation. This resembles (qualitatively) the resistance of benzene (and typical aromatic systems) against reactions leading to the change of π-electron delocalisation.
13C-NMR Based Evaluation of the Electronic and Steric Interactions in Aromatic Amines
Authors: Zakrzewska Anna , Gawinecki Ryszard , Kolehmainen Erkki , Ośmiałowski Borys
Published: October 2008

Chemical shifts of the para carbon atoms, δ(13C-4), in a series of aromatic amines were used to calculate the σp, σR and σOR substituent constants for different amino groups. 1-Pyrrolidino, N,N-di-n-butylamino and N,N-diethylamino groups were found to be the most strong electron-donors. ortho-Substitution decreases the donor properties of the amino group. The amino groups in 2,6-di-i-propylaniline and N,N-2,6-tetramethylaniline have very weak electron-donor properties. The nitrogen atom in benzoquinuclidine and N,N-dimethyl-2,6-di-i-propylaniline have an electron-acceptor character. The calculated substituent constants of the amino groups studied are consistent with the spectral and reactivity data available in literature. Values of δ(15N) cannot be used as a direct measure of electronic effects of the N atom in anilines.
Jubilite: A 4-,8-connected Cubic Structural Pattern in Space Group Pm3
Authors: Bucknum Michael J. , Castro Eduardo A.
Published: October 2008

In the course of investigating structural modifications of the 3-,4-connected net known as the Pt3O4 structure-type (waserite), a novel 4-,8-connected structure-type was discovered. This lattice is generated by replacing the 3-connected trigonal planar vertices of the Pt3O4 structure-type with 4-connected tetrahedral vertices, to achieve a structure which possesses a generic empirical formula of JK6L8. In such a topological modification, the four 3-fold axes of the parent cubic, Pm3n, Pt3O4 structure-type are retained. Thus the 4-connected tetrahedral vertices are oriented so as to preserve cubic symmetry in the resulting Pm3, JK6L8 (jubilite) lattice. The unit cell contains a single 8-connected cubecentered vertex, six 4-connected distorted square planar vertices and eight 4-connected distorted tetrahedral vertices. It is a Wellsean structure with a Wells point symbol given by (4166484)(4282)6(4383)8 and a Schläfli symbol of (53/4, 4.2667). This latter index reveals a decrease in the lattice’s polygonality and concomitant increase in the connectivity through the transformation from waserite to jubilite. The topology of the parent waserite lattice (Pt3O4) corresponds to that of the Catalan structures with the Wells point symbol (84)3(83)4, which has the Schläfli symbol (8, 3.4285). Finally, it can be seen that a sequence of structure-types starting with waserite (Pt3O4) and moving to jubilite (JK6L8) and finally to fluorite (CaF2) represents a continuous crystallographic structural transformation in which the symmetry and topology undergo concomitant changes from one structure-type (waserite) to the other structure-types. The topology of the fluorite lattice, represented by the Wells point symbol (424)(46)2, and the Schläfli symbol (4, 51/3), indicates a discontinuous topological transformation from the intermediate jubilite lattice; like the discontinuous topological transformation from Pt3O4 to JK6L8; in which the polygonality is again reduced, in this step from 53/4 to 4, and the connectivity is concomitantly increased, from 4.2667 to 51/3, during the continuous structural transformation. The l index, a topological measure of the form of a structure-type in terms of the ratio of the weighted average polygonality to the weighted average connectivity in the unit cell, decreases in the sequence from Pt3O4 (2.3333) to jubilite (1.3476) to fluorite (0.7500). This indicates the discontinuous, though monotonic, appearance of more closed networks upon increasing the connectivity and concomitantly decreasing the polygonality in the structural sequence. Interestingly, the ratios of the form indexes of the adjacent members in this series: lwaserite/ljubilite and ljubilite/lfluorite, are approximately equal to each other.
Study on the XPS-ESCA of Aluminum Phosphide Products
Authors: Pan Canping , Li Weixi , Jiang Shuren
Published: October 2008

XPS-ESCA analysis showed small signal for phosphorus in fresh specimens of aluminum phosphide (AlP). After removal of a layer of about 0.5 – 1.0 μm by argon ion sputtering, it was observed that signal intensities from oxygen and aluminum increased. The oxygen signal decreased as a function of sputtering time, synchronously with the increase of the phosphorous signal from the AlP nucleus. The aluminum signal, which was considered to be mainly due to AlP and Al(OH)3, remained constant. Other impurity elements including N, Mg, etc., were identified in the technical 85% AlP and AlP tablet formulated products.
Relation of Certain Quantum Chemical Parameters to Lubrication Behavior of Solid Oxides
Authors: Erdemir Ali , Li Shenghua , Jin Yuansheng
Published: October 2008

It is well-documented that certain oxides (such as Re2O7, B2O3, MoO3, V2O5, etc.) can provide friction coefficients of 0.1-0.3 to sliding surfaces at elevated temperatures and thus they are often referred to as lubricious oxides in the tribology literature. In a recently proposed crystal chemical model, Erdemir was able to establish a close correlation between the reported friction coefficients of such oxides and their ionic potentials [1]. In the present paper, we expand on this original concept and explore the relevance of two other quantum chemical parameters, electronegativity and chemical hardness, to the lubricity of solid oxides. These parameters have already been used by scientists to explain the nature of tribochemical interactions between various oil additives and sliding surfaces. It is conceivable that electronegativity and chemical hardness may also be strongly related to the extent of adhesive interactions and shear rheology of solid oxides and hence to their lubricity. The new results have confirmed that electronegativity, like ionic potential, is indeed a valid quantum chemistry parameter that can be used in predicting the lubrication behavior of solid oxides. Generally, the higher the electronegativity of the solid oxides is, the lower the friction coefficients will be. However, chemical hardness did not yield a similar trend. In light of these new findings, we propose some guidelines for the formulation of novel oxide or alloy systems that can lead to the formation of lubricious oxides at elevated temperatures. The findings of this study may pave the way for designer-based tribosystems in general and smart tribochemical systems in particular in future tribological applications such as dry machining.
Structural Stability and Vibrational Analyses of Haloselenonyl Azides, XSeO2-NNN, where X is F, Cl, Br
Authors: Förner Wolfgang , Badawi Hassan M. , Seddigi Zaki S.
Published: October 2008

The structural stability of haloselenonyl azides was investigated by quantum mechanical Møller-Plesset perturbation theory of second order and density functional theory calculations. The 6-311+G** basis set was used to include polarization and diffuse functions in the calculations at the DFT-B3LYP level. The potential scans for the rotation of the -NNN rotor were calculated and found to be consistent with a single minimum that corresponds to a gauche conformation (-NNN moiety nearly eclipses one of the two selenonyl Se=O bonds) for the three halogens at ambient temperature. The structural parameters for the minima calculated by MP2 and DFT turned out to be very similar. The vibrational modes, infrared and Raman intensities as well as depolarization ratios were calculated at DFT-B3LYP/6-311+G** level for the three molecules in their gauche conformations. The potential energy distributions among symmetry coordinates of the normal modes of the molecules in their gauche conformation were then computed from normal coordinate analyses.
Acidity Study on 3-Substituted Pyridines
Authors: Güven Alaattin
Published: October 2008

A comprehensive theoretical study for the protonation of some 3-substituted pyridines has been carried out in aqueous solution (e=78.4) by semi empirical AM1 method in MOPAC2000 and PM5 method in MOPAC2002. Solvent effect was accounted for implicitly by means of the conductor like screening model (COSMO). The acidity constants of these pyridine derivatives have been calculated. The tautomeric and/or conformational equilibria for these compounds, where available, were also taken into account to find out the mol fractions of the species in aqueous media. The results obtained from the calculations were compared with the available experimental values, and the results indicate a considerable agreement with available experimental data.
Facile Interfacial Electron Transfer of Hemoglobin
Authors: Zhou Bo , Sun Runguang , Hu Xiaofang , Wang Lihua , Wu Haiping , Song Shiping , Fan Chunhai
Published: October 2008

We herein describe a method of depositing hemoglobin (Hb) and sulfonated polyaniline (SPAN) on GC electrodes that facilitate interfacial protein electron transfer. Well-defined, reproducible, chemically reversible peaks of Hb and SPAN can be obtained in our experiments. We also observed enhanced peroxidase activity of Hb in SPAN films. These results clearly showed that SPAN worked as molecular wires and effectively exchanged electrons between Hb and electrodes.Mediated by Conjugated Polymers
Theoretical Study of the Diastereofacial Isomers of Aldrin and Dieldrin
Authors: Nestorovska-Krsteska Aleksandra , Zdravkovski Zoran
Published: October 2008

The Diels-Alder reaction of hexachlorocyclopentadiene with norbornadiene givesaldrin but theoretically three other diastereofacial isomers are possible. On oxidation theseisomers can generate eight adducts one of which is known as dieldrin. All these, as well asthe corresponding reactions with hexafluorocyclopenadiene were studied by semiempirical(AM1 and PM3) and hybrid density functional (B3LYP) methods. Besides the energy levels,the transition states were calculated for the reactions leading to the diastereofacial isomers ofaldrin, which indicate that aldrin is the favored product of the reaction both fromthermodynamic and kinetic point of view.
Downregulation of the Expression of GLUT1 Plays a Role in Apoptosis Induced by Sodium Butyrate in HT-29 Cell Line
Authors: Li Xi , Luo He-Sheng , Paul Shelley  C. , Tang Tao , Yuan Guang-Jin
Published: October 2008

The regulation of glucose and sodium butyrate transporters(glucose transporter1-5 and Monocarboxylate transporter 1) and their relationship with cell apoptosis induced bysodium butyrate in colonic caner cell line HT-29 were studied. Cell apoptosis was detectedby flow cytometric assay. The expression of MCT1 and GLUT1-5 mRNA were detected byRT-PCR and the uptake of glucose was detected using 2-deoxy-[3H]glucose. The expressionof bax and bcl-x/l were detected by westernblot assay. We found that sodium butyrateinduced apoptosis in HT-29 cell line. The expression of GLUT1 mRNA, bcl-x/l, as well theuptake of glucose was inhibited by sodium butyrate. The expression of MCT1 and GLUT2,GLUT3, GLUT5 was not regulated by sodium butyrate. However, the concentration ofglucose had positive correlation with the expression of bcl-x/l protein and negativecorrelation with the apoptosis induced by sodium butyrate. All the results suggested thatdownregulation of the expression of GLUT1 was associated with the apoptosis induced bysodium butyrate in HT-29 cell line.
The Principle of Substance Stability Is Applicable to All Levels of Organization of Living Matter
Authors: Gladyshev Georgi P.
Published: October 2008

The principle of substance stability – the feedback principle – is applicable to allbiological systems. It boils down for different temporal hierarchies to the following: duringthe formation (self-assembly) of the most thermodynamically stable structures at the highesthierarchical level (j), e.g., the supramolecular level, in accordance with the second law,Nature spontaneously uses predominantly the (available for the given local part of thebiological system) least thermodynamically stable structures belonging to a lower level, forexample, the molecular level (j-1). The principle can be also applied to understructurehierarchical levels of any temporal hierarchy. It helps in understanding the causes of cancerformation and the origin of some other diseases.
Synthesis and Structure of a Binuclear Cu(II) Complex of 1,3- bis [N,N-bis(2-picolyl)amino]propan-2-ol
Authors: Marvey Bassie  B. , Gultneh Yilma , Butcher Ray
Published: October 2008

The synthesis and crystal structure of Cu(II) complex of a binucleating tridentateligand 1,3-bis [N,N-bis(2-picolyl)amino]propan-2-ol (I) is being reported. The two chelatingbispicolylamine arms in I are tethered by a 2-hydroxypropyl group with Cu(II) coordinatingin a slightly distorted square planar geometry to give [Cu2(I)(OH2)(Cl)](ClO4)3·2H2O (II).The crystal data for II: Triclinic, space group Pī with cell dimensions of a = 13.345 (4) å,b = 13.873 (4) å, c = 12.867 (2) å, α = 111.68 (2)°, β = 100.34 (2)°, γ = 65.83 (2)°, V =2018.4 (9) å3, F.W. = 962.46, ρcalc = 1.583 g cm-3 for Z = 2, μ = 13.93 cm-1
Rate and Product Studies of Solvolyses of Benzyl Fluoroformate
Authors: Kyong Jin  Burm , Ryu Seung  Han , Kevill Dennis  N.
Published: October 2008

The specific rates of solvolysis of benzyl fluoroformate have been measured inseveral hydroxylic solvents at 25.0 °C. For methanolysis, the solvent deuterium isotopeeffect and activation parameters were determined and activation parameters were alsodetermined for solvolyses in ethanol and 80% ethanol. For several of the binary hydroxylicsolvents, measurement of product ratios allowed selectivity values to be determined. Anextended Grunwald–Winstein treatment of the data led to sensitivities to changes in solventnucleophilicity and ionizing power. Comparison with previously determined specific ratesfor solvolysis of the chloroformate gave fluorine/chlorine rate ratios greater than unity. Allof the determinations made were consistent with an addition–elimination (association–dissociation) mechanism, with addition rate-determining.
Molecular Structure of Human Transferrin – Transferrin Receptor Complex
Authors: Wiwanitkit Viroj
Published: October 2008

Transferrin receptor (TfR) is a glycoprotein mediating the entry of ferrictransferrin (Tf) from the extracellular compartment into the cells. TfR are present on thesurface of many cell types but they are most abundant on cells active in hemoglobinsynthesis. However, the knowledge on the complex, recombination, between Tf and sTfR islimited. Here, the author performs an analysis to study the molecular structure of human Tf- sTfR complex. The output 3D molecular structure from the combination between Tf andTfR is derived. The property as well as geometry of the derived complex was also presented.
Determination of Trace Level of cAMP in Locusta Migratoria Manilensis Meyen by HPLC with Fluorescence Derivation
Authors: Zhang Lujun , Zhang Huiting , Wang Jinfang , Pan Canping
Published: October 2008

A sensitive and rapid method was developed for the determination of cAMP inLocusta migratoria manilensis Meyen by high-performance liquid chromatography withfluorescence detection. The cAMP was derivatized using chloroacetaldehyde and TBASbuffer/methanol was used as the mobile phase. A detection quantification of 40 fmol/mlcould be achieved when using fluorescence detection. An HPLC-MS method using DMHAas an ion-pair agent to analyze cAMP was also demonstrated. We studied the effect ofdopamine and other stimulants on cAMP levels from isolated locust central nervoussystems. The new method is well suited for the analysis of cAMP in small biologicalsamples.
Enzyme Chemiluminescence Immuno Assay of Free hCGβ in Serum Based on Superparamagnetic Polymer Microbeads
Authors: Guo Xiaoying , Guan Yueping , Yang Bin , Wang Yongning , Lan Hualong , Shi Wentang , Yang Zhenghui , Lu Zuhong
Published: October 2008

Superparamagnetic polymers (SPMP) microbead was an excellent form fornanosized magnetic particles less than 10nm to realize their potential applications in manyfields. We developed a novel modified suspension polymerization method for the productionof superparamagnetic poly (methacrylate divinylbenzene) (PMA-DVB) microbeads, withamino groups on their surface after simple modifications. We applied these SPMPmicrobeads to establish a sandwich enzyme chemiluminence immuno (ECLIA) procedure ofdetecting the free hCGβ in serum. It was proved to a better method compared to the ELISA,since it need half of the sample volume, simpler protocols, and the time it need wasshortened from 2 hours to 1 hour. The detection limit was 0.22 mIU•m-1, one order lowerthan the ELISA assay. Its linear range was between 0.45—185.2 mIU•m-1. And in thedetections of clinical serum samples, the related coefficient between the two methods’results was 0.955.