bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Turmeric, Turmerin and Curcumin on Ca2+, Na/K+ Atpases in Concanavalin A-Stimulated Human Blood Mononuclear Cells
Authors: Cohly Hari H. P. , Rao Maheshwara-Rajeswara , Kanji Vijaya K. , Patlolla Babu , Taylor Anelle , Wilson Melanie T. , Angel Michael F. , Das Suman K.
Published: October 2008

Ion transport enzymes may play an important role in T cell activation. This study investigates the role of turmeric and its individual components, turmerin-and curcumin-on Ca2+ and Na/K+ adenosine triphosphatases (ATPase) in the course of T cell activation. Concanavalin A (Con A) stimulated human blood mononuclear T cell proliferation paradigm was investigated for 3, 5 and 7 day periods with different concentrations of turmeric, curcumin and turmerin. Con A-stimulated cells treated with turmeric (250, 50, 5 μg/ml) for 3 and 5 days inhibited ATPase levels when compared to base levels obtained by cells in media alone. At day 7, there was a 3-fold increase for Ca2+ATPase levels and a 2-fold increase for Na/K+ATPase. Curcumin (250, 50, 5 μg/ml) showed the same pattern for ATPase activity as turmeric at 3 and 5 days with a 2-fold increase at day 7. Turmerin (2500, 1250, 250, 25 ng/ml) for Na/K+ ATPase activity showed an increase at day 3, a decrease on day 5, and a 2-fold increase on day 7. Ca2+ ATPase activity in the presence of turmerin showed an increase in ATPase levels at day 3 (except at 2500ng/ml where it decreased) and a decrease in day 5 (except at 25 ng/ml where it increased). Turmeric and curcumin generally inhibited Ca2+ATPase and Na/K+ATPases in early (day 3) and intermediate (day 5) stages of mitogen stimulation. However, the effect after 7 days incubation for turmeric, curcumin and turmerin showed a marked increase up to three fold.
Review on DFT and ab initio Calculations of Scalar Coupling Constants
Authors: Alkorta Ibon , Elguero José
Published: October 2008

The present review summarizes the information available on the ab initio calculations of spin-spin nuclear coupling constants through hydrogen bonds or in van der Waals complexes. It also reports the sources of experimental data on nhJXY scalar couplings.
Solvent Effects on the Indirect Spin–Spin Coupling Constants of Benzene: The DFT-PCM Approach
Authors: Ruud Kenneth , Frediani Luca , Cammi Roberto , Mennucci Benedetta
Published: October 2008

We present an extension of the Polarizable Continuum Model (PCM) to the calculation of solvent effects on indirect spin–spin coupling constants for Hartree–Fock wave functions and Density Functional Theory. This is achieved by implementing the PCM model for singlet and triplet linear response functions. The new code is used for calculating the solvent effects on the indirect spin–spin coupling constants of benzene. For the 1J(H13C) coupling constants, our calculated solvent shifts are in good agreement with experimental observations when geometry relaxation is taken into account. However, our results do not support the extrapolated gas-phase value for this coupling constant. A new experimentally derived 1J(H 13C) for a vibrating benzene molecule at 300 K is proposed.
Extension of the Karplus Relationship for NMR Spin-Spin Coupling Constants to Nonplanar Ring Systems: Pseudorotation of Tetrahydrofuran
Authors: Wu Anan , Cremer Dieter
Published: October 2008

coming soon
Through-Space Spin-Spin Coupling In Acetylenic Systems. Ab Initio and DFT Calculations
Authors: Bagno Alessandro , Casella Girolamo , Saielli Giacomo , Scorrano Gianfranco
Published: October 2008

coming soon
Structure–Toxicity Relationships for Aliphatic Compounds Based on Correlation Weighting of Local Graph Invariants
Authors: Toropov Andrey  A. , Duchowicz Pablo , Castro Eduardo A.
Published: October 2008

Quantitative Structure-Activity Relationships based on molecular descriptors calculated with Correlation Weights of Local Graph Invariants were developed to model the toxicity of aliphatic compounds to the 50% population growth inhibition. The relationships were computed on the basis of Labeled Hydrogen- Filled Graphs and correlation weights were obtained by an optimization to render as large as possible correlation coefficients between log(IGC50-1) and descriptors calculated with correlation weights. Morgan extended connectivity indices of zero, first, and second orders, paths of lengths two and three and valence shells of second and third ranges have been tested as local invariants of the Labeled Hydrogen-Filled Graphs. The best quantitative relationship obtained from the optimization of correlation weights is that one based on the valence shell of range two. First, second, and third order fitting equations were determined and statistical results are better than other similar data for the same molecular set.
Absolute Total Single–Electron–Capture Cross Sections of O2+ with N2 Gas
Authors: Hasan A. T. , Gray T. J.
Published: October 2008

Absolute total single-electron-capture cross sections have been measured for lowenergy O2+ + N2 system in the collision energy range between 0.50 to 2.0 keV. These cross sections are found to be in the range of 0.67 to 2.08 x10-16 cm2. The measured total cross sections for single-electron- capture display a slowly increasing behavior as a function of the incident energy. Several measurements of total cross sections for electron-capture from N2 by slow N2+ and O+ ions, and from O2 by slow O2+ ions presently exist in the literature. In the measurements reported here, we measured the total cross sections for electron-capture from N2 by slow O2+ ions, such measurements are not found in the literature. The increasing availability of data on this system may stimulate work in this direction.
Conjugated Molecules for the Smart Filtering of Intense Radiations
Authors: Dini Danilo
Published: October 2008

The practical realization of smart optical filters, i.e. devices which change their optical transmission in a suitable way to keep a working state for a general light sensitive element , can involve the use of conjugated molecules whose light absorption properties are light- intensity dependent (nonlinear optical effect). The verification of optical limiting displayed by some particular conjugated molecules, e.g. phthalocyanines, is quite noteworthy and can be successfully exploited for the realization of such smart optical devices. In the present contribution the analysis of the relevant molecular feature of a phthalocyanine are analyzed with the aim of determining useful correlations between optical limiting performance and phthalocyanine chemical structure. In particular , the electronic nature of the substituent is considered as a key factor for the explanation of some observed optical limiting trends.
Polycondensation of Tetrahydrofuran with Phthalic Anhydride Induced By a Proton Exchanged Montmorillonite Clay
Authors: Ferrahi Mohammed  Issam , Belbachir Mohammed
Published: October 2008

“Maghnite” a montmorillonite sheet silicate clay, exchanged with protons to produce “H-Maghnite” is an efficient catalyst for polymerization of many vinylic and heterocyclic monomers (Belbachir, M. U.S. Patent. 066969.0101 –2001). The structure compositions of both “Maghnite” and “H-Maghnite” have been developed. This catalyst was used for the polycondensation of the tetrahydrofuran with phthalic anhydride. The polymerization was performed under suitable conditions at temperature (40°C), in presence of acetic anhydride. Experiments revealed that polymerization induced by “H-Maghnite”, proceed in bulk and the conversion increases with increasing “H-Maghnite” proportion.
Comparative Studies on Prussian Blue or Diaquatetraaminecobalt(III) Promoted Hydrolysis of 4-Nitrophenylphosphate in Microemulsions
Authors: Tafesse Fikru
Published: October 2008

Comparative reactivities of three diaqua(tetraamine)Co(III) complexes towards hydrolysis of 4-nitrophenyl phosphate was undertaken. The results were contrasted with prussian blue promoted hydrolysis of 4-nitrophenyl phosphate. The tetraamineCobalt(III) complexes accelerated the hydrolytic reaction to varying degrees with the following reactivity order. [(tn)2Co(OH2)2]3+ < [(trpn)Co(OH2)2]3+ < [(tme)2Co(OH2)2]3+ [ tn = trimethylenediamine; tme = 1,1,2,2-tetramethyl-1,2-diaminoethane; trpn = tris(3- aminopropyl)amine].These observations are attributed to the active aquo-hydroxo forms of the tetraamineCobalt(III) complexes. The hydrolysis rate for prussian blue promoted hydrolysis was comparable to that obtained for [(tme)2Co(OH2)2]3+. The mixed valence bimetallic centers of prussian blue aid in substrate binding and organizing the nitrophenyl phosphate for effective intramolecular nucleophilic attack by coordinated hydroxide or water.
Special Issue on Proton Transfer Processes
Authors: Chojnacki Henryk
Published: October 2008

It is well established that the hydrogen bond plays crucial role in many areas of physical, chemical and biological phenomena.[...]
Ab Initio Study of the Prototropic Tautomerism of Cytosine and Guanine and Their Contribution to Spontaneous Point Mutations
Authors: Podolyan Yevgeniy , Gorb Leonid , Leszczynski Jerzy
Published: October 2008

High-level quantum-chemical and quantum-dynamics calculations are reported on the tautomerization equilibria and rate constants of isolated and monohydrated cytosine and guanine molecules. The results are used to estimate the fraction of the bases present in the cell during DNA synthesis as the unwanted tautomers that forms irregular base pairs, thus giving rise to a spontaneous GC → AT point mutation. A comparison of the estimated mutation frequencies with the observed frequency in E. coli is used to analyze two proposed mechanisms, differing in the degree of equilibration reached in the tautomerization reaction. It was found that the fraction of the rare tautomer in monohydrated complex of cytosine as well as guanine significantly exceed the amount responsible for the observed values of the GC → AT mutations. In the absence of water the equilibrium concentration of tautomeric forms is relatively large, but the barrier to their formation is high. It is possible that the mechanism in which a high tautomerization barrier keeps the tautomeric transformation far from a state of equilibrium is more likely than a mechanism in which water and/or polymerases produce a low equilibrium concentration of the tautomeric forms.
Theoretical Study of Multidimensional Proton Tunnelling in Benzoic Acid Dimer
Authors: Wójcik Marek J. , Szczeponek Krzysztof , Boczar Marek
Published: October 2008

Ab initio B3LYP/6-311++G** calculations have been carried out for the benzoic acid dimer for the stable and saddle point structures. The energy barrier for the proton tunneling amounts to 6.5 kcal/mol. The normal mode frequencies have been computed including modes coupled to the proton tunneling mode. Two-dimensional model potentials, formed from symmetric mode coupling potential and squeezed double well potential, have been fitted to the calculated energy barrier, geometries and frequencies, and used to analyze proton dynamics. The calculated proton tunneling energy splitting in the vibrationally ground states of the low-frequency modes is ~230 cm-1. The two-dimensional model PES predict monotonic increase of the tunneling splitting with the excitation of the planar modes. Depending of the sign of the coupling parameter out-of-plane modes can either suppress or promote the splittings.
Model, First-Principle Calculation of Ammonia Dissociation on Si(100) Surface. Importance of Proton Tunneling
Authors: Smedarchina Zorka K. , Zgierski Marek Z.
Published: October 2008

The dissociation of an ammonia molecule on a cluster of Si atoms simulating the 100 silicon crystal structure with two Si dimers has been investigated by means of the DFT and an approximate instanton methods. The model corresponds to the low coverage limit of the surface. Absolute rate constants of two different dissociation paths are evaluated together with deuterium isotope effects. It is demonstrated that, even at room temperatures, the process is dominated by tunneling and that dissociation to a silicon atom of the adjacent dimer, rather than a silicon within the same dimer, is the prevailing mechanism. This leads to creation of a metastable structure which will slowly decay through a two-step hydrogen atom migration towards the absolute minimum on the potential energy surface corresponding to the NH2 group and the hydrogen atom residing in the same dimer.
Aggregation of Non Ionic Surfactant Igepal in Aqueous Solution: Fluorescence and Light Scattering Studies
Authors: Ghosh Sujit  Kumar , Khatua Pijus  Kanti , Bhattacharya Subhash   Ch.
Published: October 2008

The association of the polyoxyethylene nonyl phenol (Igepal) in aqueous solution has been studied. The results of the fluorescence quenching of 1-Anthracene sulphonate and Safranine T in nonionic micellar solution of Igepal have been presented. The quenching process was exploited to estimate the aggregation number of surfactant monomer. In the Igepal series the micellar aggregation number systematically varied. From the dynamic light scattering studies in micellar solution the polydispersity of the medium and the diameter of the micelles have been determined. The diameters of the micelles have been increased with increase in the molar mass of surfactants. A reasonable estimation of the surface area of the head group in different micelles has been attempted.
QSAR Study of Skin Sensitization Using Local Lymph Node Assay Data
Authors: Fedorowicz Adam , Zheng Lingyi , Singh Harshinder , Demchuk Eugene
Published: October 2008

Allergic Contact Dermatitis (ACD) is a common work-related skin disease that often develops as a result of repetitive skin exposures to a sensitizing chemical agent. A variety of experimental tests have been suggested to assess the skin sensitization potential. We applied a method of Quantitative Structure-Activity Relationship (QSAR) to relate measured and calculated physical-chemical properties of chemical compounds to their sensitization potential. Using statistical methods, each of these properties, called molecular descriptors, was tested for its propensity to predict the sensitization potential. A few of the most informative descriptors were subsequently selected to build a model of skin sensitization. In this work sensitization data for the murine Local Lymph Node Assay (LLNA) were used. In principle, LLNA provides a standardized continuous scale suitable for quantitative assessment of skin sensitization. However, at present many LLNA results are still reported on a dichotomous scale, which is consistent with the scale of guinea pig tests, which were widely used in past years. Therefore, in this study only a dichotomous version of the LLNA data was used. To the statistical end, we relied on the logistic regression approach. This approach provides a statistical tool for investigating and predicting skin sensitization that is expressed only in categorical terms of activity and nonactivity. Based on the data of compounds used in this study, our results suggest a QSAR model of ACD that is based on the following descriptors: nDB (number of double bonds), C-003 (number of CHR3 molecular subfragments), GATS6M (autocorrelation coefficient) and HATS6m (GETAWAY descriptor), although the relevance of the identified descriptors to the continuous ACD QSAR has yet to be shown. The proposed QSAR model gives a percentage of positively predicted responses of 83% on the training set of compounds, and in cross validation it correctly identifies 79% of responses.
Theoretical Analysis of the Excited State Properties of Wybutine: A Natural Probe for Transfer RNA Dynamics
Authors: Lahiri Ansuman , Ulicny Jozef , Laaksonen Aatto
Published: October 2008

We have theoretically characterized the ground state and the excited state properties of wybutine, a naturally fluorescent modified base occuring in tRNAs, using configuration interaction singles (CIS) and time dependent density functional (TDDFT) methods. Both gas phase excited state properties and solvent effects, modelled through Onsager reaction field method, were considered. In addition to vertical excitation energies, the fluorescence transitions were calculated, based on S1 equilibrium geometry optimized at CIS level. Our computations show encouraging agreement with known experimental data either directly (TDDFT) or after applying empirical scaling (CIS). The fluorescence Stokes’ shift for the S0 Ã S1 transition is computed taking into account the contributions from both intramolecular and solvent reorganization processes. The results suggest that intramolecular relaxation of the S1 state accounts for the major part of the magnitude of the Stokes’ shift, while the role of solvent reorganization seems to be of less importance.
The Interpretation of the Short Range Disorder in the Fluorene-TCNE Crystal Structure
Authors: Croce Gianluca , Arrais Aldo , Diana Eliano , Civalleri Bartolomeo , Viterbo Davide , Milanesio Marco
Published: October 2008

The interpretation of the short-range static and/or dynamic disorder in a crystal structure from X-ray data is often a rather complex problem. Recently, we synthesized and characterized three co-crystalline complexes between fluorene, showing C2v symmetry, and three electron withdrawing D2h compounds, employing FTIR and Raman spectroscopy and single crystal X-ray diffraction techniques. The crystal structures of the complexes of fluorene with the three different electron withdrawing molecules are disordered in the solid state and only approximate structures were obtained by refinement of the single crystal data. Indeed, the fluorene moiety presents a very irregular geometry, showing for example C-C bonds ranging from 1.25Å to 1.75Å. Graphical inspection of the solved crystal structures indicates that the fluorene molecules in these co-crystalline complexes can assume two possible positions, both with 50% population. A two-step procedure to improve the disordered models is described. At first, the two possible ordered structures, with the fluorene molecule in only one of the two populated positions, are "separated" by molecular graphic techniques and then their geometry is fully optimized employing the periodic ab initio “CRYSTAL” code to obtain a chemically sensible model with reasonable distances and angles. The main aim of this communication is to demonstrate that ordered models can be obtained, starting from a disordered crystal structure, focusing our attention on the fluorene-TCNE molecular complex.
Ab initio Study of Alkyl-oxonium Cations CnH2n+1OH2+, n=1,2,3,4
Authors: Haitayan Frédéric , Muguet Francis   F.
Published: October 2008

Within the framework of the itinerant radical model, the solvated electron in liquid alcohols is understood as an itinerant alkyl-oxonium ROH2. radical. As a first step in the investigation of those radicals, this study deals with the optimization of related ROH2+ alky-oxonium cations: CnH2n+1OH2+,n=1,2,3,4. The structures were optimized at the MP2/6-31G**++ level with the help of the GAMESS ab initio package. Optimized structures are reported for the following cations: MethylOxonium; EthylOxonium; 1-PropylOxonium, 2-PropylOxonium and 1-ButylOxonium, 2-ButylOxonium, IsoButylOxonium, TertButylOxonium. Optimized geometries are displayed with the help of the ChemApp Java applet. Vibrational frequencies and ZPEs have been computed, and visual depictions of expected experimental IR spectra have been simulated with the help of Lorentzian functions.
Molecular Dynamics Simulations of the O-glycosylated 21-residue MUC1 Peptides
Authors: Rubinstein A. , Kinarsky L. , Sherman S.
Published: October 2008

The conformational propensities of the 21-residue peptide and its Oglycosylated analogs were studied by molecular dynamics (MD) simulations. This polypeptide motif comprises the tandem repeat of the human mucin (MUC1) protein core that is differently glycosylated in normal and cancer cells. To evaluate the structural effects of O-glycosylation on the polypeptide backbone, conformations of the nonglycosylated peptide and its glycosylated analogs were monitored during the 1 ns MD simulations. Radius gyration for whole peptide and its fragments, as well as root-meansquare-deviation between coordinate sets of the backbone atoms of starting structures and generated structures, were calculated. It was shown that O-glycosylation promotes and stabilizes the extended conformations of the whole peptide and its central PDTRP fragment. O-glycosylation of the specific Thr residues significantly affects the conformational distributions of the flanking Ser residues. It was also shown that Oglycosylation promoted backbone conformations of the immunodominant region PDTRP that were similar to the structural features of the peptides presented by the major histocompatability complex (MHC) to T-cell receptors.
Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods
Authors: Vařeková Radka Svobodová , Koča Jaroslav , Zhang Chang-Guo
Published: October 2008

In this paper, we report a detailed comparison between the popularly used cutoff and Particle Mesh Ewald (PME) methods in terms of the time complexity and the energy convergence of the long-range electrostatic and van der Waals interaction calculations. For the comparison, we performed various calculations on various representative biological molecules, including seven peptides and proteins, eleven oligonucleotides, and three conformations of a nucleotide-sugar. The results provide useful insights into the appropriate choice of the methods (i.e. the cutoff or PME) and that of the cutoff values for the calculations on different kinds of molecules. It has also been demonstrated that for some cases using different cutoff values for calculating the electrostatic and van der Waals interaction energies will be computationally more efficient.
Intramolecular C−H···π Interactions in Metal-Porphyrin Complexes
Authors: Bogdanović Goran A. , Medaković Vesna , Milčić Miloš K. , Zarić Snežana D.
Published: October 2008

Cambridge Structural Database (CSD) was screened in order to find intramolecular C−H···π interactions with a chelate ring of coordinated porphyrin. It was found 154 crystal structures with 244 intramolecular C−H···π interactions in transition metal complexes with derivatives of porphyrin. Comparison of interacting distances indicates that interactions of hydrogen atoms in positions 2 and 6 of axially coordinated pyridine are more favorable with ruffled than with planar porphyrin.
Interactions between Physics and Biodisciplines within the Framework of Molecular Sciences
Authors: Zahradník Rudolf
Published: October 2008

In order to be able to study interactions within, between, and among biomolecules, it is highly desirable to use tools of experimental and theoretical physics, or preferably a combination thereof. Very brief comments are presented which concern biochemical reactivity, enzymatic catalysis, origin of life, experimental tools for structure elucidation and quantum chemistry methods. Additional remarks are related to ultrafast processes, experiments with individual molecules, and to symmetry considerations.
Density Functional Studies of the Dipole Polarizabilities of Substituted Stilbene, Azoarene and Related Push-Pull Molecules
Authors: Hinchliffe Alan , Nikolaidi Beatrice , Soscún Machado Humberto J.
Published: October 2008

We report high quality B3LYP Ab Initio studies of the electric dipole polarizability of three related series of molecules: para-XC6H4Y, XC6H4CH=CHC6H4Y and XC6H4N=NC6H4Y, where X and Y represent H together with the six various activating through deactivating groups NH2, OH, OCH3, CHO, CN and NO2. Molecules for which X is activating and Y deactivating all show an enhancement to the mean polarizability compared to the unsubstituted molecule, in accord with the order given above. A number of representative Ab Initio calculations at different levels of theory are discussed for azoarene; all subsequent Ab Initio polarizability calculations were done at the B3LYP/6-311G(2d,1p)//B3LYP/6-311++G(2d,1p) level of theory. We also consider semi-empirical polarizability and molecular volume calculations at the AM1 level of theory together with QSAR-quality empirical polarizability calculations using Miller’s scheme. Least-squares correlations between the various sets of results show that these less costly procedures are reliable predictors of for the first series of molecules, but less reliable for the larger molecules.
Molecular Orbital and Density Functional Study of the Formation, Charge Transfer, Bonding and the Conformational Isomerism of the Boron Trifluoride (BF3) and Ammonia (NH3) Donor-Acceptor Complex
Authors: Ghosh Dulal C. , Bhattacharyya Soma
Published: October 2008

The formation of the F3B–NH3 supermolecule by chemical interaction of its fragment parts, BF3 and NH3, and the dynamics of internal rotation about the ‘B–N’ bond have been studied in terms of parameters provided by the molecular orbital and density functional theories. It is found that the pairs of frontier orbitals of the interacting fragments have matching symmetry and are involved in the charge transfer interaction. The donation process stems from the HOMO of the donor into the LUMO of the acceptor and simultaneously, back donation stems from the HOMO of acceptor into the LUMO of the donor. The density functional computation of chemical activation in the donor and acceptor fragments, associated with the physical process of structural reorganization just prior to the event of chemical reaction, indicates that BF3 becomes more acidic and NH3 becomes more basic, compared to their separate equilibrium states. Theoretically it is observed that the chemical reaction event of the formation of the supermolecule from its fragment parts is in accordance with the chemical potential equalization principle of the density functional theory and the electronegativity equalization principle of Sanderson. The energetics of the chemical reaction, the magnitude of the net charge transfer and the energy of the newly formed bond are quite consistent, both internally and with the principle of maximum hardness, PMH. The dynamics of the internal rotation of one part with respect to the other part of the supermolecule about the ‘B–N’ bond mimics the pattern of the conformational isomerism of the isostructural ethane molecule. It is also observed that the dynamics and evolution of molecular conformations as a function of dihedral angles is also in accordance with the principle of maximum hardness, PMH. Quite consistent with spectroscopic predictions, the height of the molecule’s barrier to internal rotation is very small. A rationale for the low height of the barrier has been put forward in terms of the energy partitioning analysis. On the question of origin of the barrier to internal rotation, we conclude that the conformational barrier to internal rotation does not originate from a particular region of the molecule, but rather it is a result of the subtle conjoint interplay of a number of opposing effects of one- and two-center bonded and nonbonded energy terms involving the entire skeleton of the molecule.
Vertical Ionization Energies of α-L-Amino Acids as a Function of Their Conformation: an Ab Initio Study
Authors: Dehareng Dominique , Dive Georges
Published: October 2008

Vertical ionization energies (IE) as a function of the conformation are determined at the quantum chemistry level for eighteen α-L-amino acids. Geometry optimization of the neutrals are performed within the Density Functional Theory (DFT) framework using the hybrid method B3LYP and the 6-31G**(5d) basis set. Few comparisons are made with wave-function-based ab initio correlated methods like MP2, QCISD or CCSD. For each amino acid, several conformations are considered that lie in the range 10-15 kJ/mol by reference to the more stable one. Their IE are calculated using the Outer-Valence-Green's-Functions (OVGF) method at the neutrals' geometry. Few comparisons are made with MP2 and QCISD IE. It turns out that the OVGF results are satisfactory but an uncertainty relative to the most stable conformer at the B3LYP level persists. Moreover, the value of the IE can largely depend on the conformation due to the fact that the ionized molecular orbitals (MO) can change a lot as a function of the nuclear structure.
Inductive QSAR Descriptors. Distinguishing Compounds with Antibacterial Activity by Artificial Neural Networks
Authors: Cherkasov Artem
Published: October 2008

On the basis of the previous models of inductive and steric effects, ‘inductive’ electronegativity and molecular capacitance, a range of new ‘inductive’ QSAR descriptors has been derived. These molecular parameters are easily accessible from electronegativities and covalent radii of the constituent atoms and interatomic distances and can reflect a variety of aspects of intra- and intermolecular interactions. Using 34 ‘inductive’ QSAR descriptors alone we have been able to achieve 93% correct separation of compounds with- and without antibacterial activity (in the set of 657). The elaborated QSAR model based on the Artificial Neural Networks approach has been extensively validated and has confidently assigned antibacterial character to a number of trial antibiotics from the literature.
Influence of Long-Tailed Alcohols on the Solubilisation of Cationic DHAB Bilayers
Authors: Linthorst Johan   A. , Klijn Jaap  E. , Engberts Jan   B.F.N.
Published: October 2008

The effects of n-decanol and cetyl alcohol incorporated into cationic di-n-hexadecyldimethylammonium bromide (DHAB) bilayers on the packing and the resistance against solubilisation by Triton X-100 have been investigated. Solubilisation experiments revealed that the mismatch between the C10-tail of n-decanol with the DHAB-tails does not affect the structural integrity of the vesicles. On the contrary, upon increasing amounts of cetyl alcohol, of which the tail matches in size with the DHAB-tails, breakdown of the vesicles is promoted, whereas complete solubilisation is strongly hampered. The system is further investigated by DSC and cryo-EM experiments. In addition, the effects of n-decanol and cetyl alcohol embedded into DHAB bilayers on the vesicular rate constants for the decarboxylation of 6-nitrobenzisoxazole-3-carboxylate (6-NBIC) suggest that both alcohols affect the structure of the Stern region in an equal manner, leading to a decrease in the catalysis. Therefore, it is concluded that addition of the alcohols leads to changes in properties of the interior of the bilayer, rather than the polar-apolar interface.
Thermodynamics of Water-octanol and Water-cyclohexane Partitioning of some Aromatic Compounds
Authors: Dearden J.  C. , Bresnen G.  M.
Published: October 2008

The Gibbs free energy, enthalpy and entropy of partitioning of 45 simple aromatic compounds (phenols, benzoic acids and acetanilides) from water to octanol and from water to cyclohexane have been determined using the filter-probe method. This involved the measurement of partition coefficients over the temperature range 20-45oC. The aim of the work was to explore the effects of intramolecular hydrogen bonding and steric factors on the partitioning process. It was found that the intramolecular hydrogen bond is intact in 2-nitrophenol and salicylic acid, and possibly in 2-hydroxybenzaldehyde, in all three solvents, but 2-chlorophenol is intramolecularly hydrogen bonded only in inert solution. The evidence indicates that 2-nitroresorcinol and 2,6-dihydroxybenzoic acid possess only one intramolecular hydrogen bond, although they are theoretically capable of possessing two. There is evidence of steric shielding in 2,6-dimethylphenol, whilst 2,6-dimethylbenzoic acid and ortho-substituted acetanilides show evidence of steric twisting of the carboxyl and acetamido groups respectively out of the plane of the aromatic ring. Unusual steric effects are displayed in the methyl-2-nitrophenols whereby, depending upon the position of the methyl group, the intramolecular hydrogen bond is either weakened or strengthened.
Reduction of Sulfur Dioxide on Carbons Catalyzed by Salts
Authors: Humeres Eduardo , Peruch Maria da Gloria B. , Moreira Regina F.P.M. , Schreiner Wido
Published: October 2008

The reduction of SO2 on different carbons in the presence of the nitrates and sulfides of sodium, potassium and calcium and potassium polysulfides was studied. The presence of salts increased the initial rate 2-5 fold for all of them and did not change the product distribution. The catalysis was not determined by the cation and there was no difference in the catalytic reactivity between nitrates and sulfides. The sulfur content of the activated carbon increased during the reaction on account of the stable reactive intermediates in the reduction of SO2. In the presence of NaNO3 or Na2S, the amount of sulfur incorporated was in the molar ratio Na:S = 3 ± 0.3, and the XPS spectra of the residual carbon showed an increase of ca. 9% of the non-oxidized form of sulfur in the intermediates. In the absence of salt, it is proposed that after the adsorption of SO2 on the carbon, a 1,3,2-dioxathiolane or 1,2-oxathietene 2-oxide are formed and that decompose to produce CO2 and atomic sulfur. The non-oxidized sulfur intermediate would be an episulfide 3, formed from the reaction of the atomic sulfur with the nearest double bond and followed by consecutive reactions of insertion of atomic sulfur to form a trisulfide. Extrusion of S2 from the trisulfide would regenerate the episulfide, establishing a sulfidedisulfide-trisulfide equilibrium that worked as a capture-release cycle of sulfur. In the presence of salt, the results are consistent with the assumption that the episulfide 3 reacts with the corresponding sulfide anion to form a disulfide anion, which upon reaction with atomic sulfur forms a trisulfide anion that decomposes releasing diatomic sulfur S2, transporting the sulfur and generating a thiolate that is part of the catalytic cycle.
Ab Initio Studies on the Preferred Site of Protonation in Cytisine in the Gas Phase and Water
Authors: Raczyńska Ewa D. , Makowski Mariusz , Górnicka Elżbieta , Darowska Małgorzata
Published: October 2008

Ab initio calculations (HF, MP2, DFT for isolated and PCM for solvated molecules) were performed for cytisine (1) and its model compounds: N-methyl-2-pyridone (2) and piperidine (3). Among three heteroatomic functions (carbonyl oxygen, pyridone and piperidine nitrogens) considered as the possible sites of protonation in 1, surprisingly the carbonyl oxygen takes preferentially the proton in the gas phase whereas in water the piperidine nitrogen is firstly protonated. For model compounds, the piperidine nitrogen in 3 is more basic than the carbonyl oxygen in 2 in both, the gas phase and water.
Ab initio post-HF CCSD(T) Calculations for Triplet and Singlet Methylene in Four consecutive Dunning Basis Sets with Extrapolations to Infinite Limits for Various Molecular Properties
Authors: Neugebauer Alexander , Häfelinger Günter
Published: October 2008

Stationary points for four geometrically different states of methylene: bent and linear triplet methylene, bent and linear singlet methylene were investigated using the highly reliable post-HF CCSD(T) method. Extrapolations to the CCSD(T) basis set (CBS) limit from Dunning triple to quintuple correlation consistent polarized basis sets were performed for total energies, for the equilibrium CH distances re(CH), for singlettriplet separation energies, for energy barriers to linearity and for correlation energies. Post-HF calculations with Dunning basis sets of the literature are presented for comparisons.
Synthesis and GIAO NMR Calculations for Some Novel 4-Heteroarylidenamino-4,5-dihydro-1H-1,2,4-triazol-5-one Derivatives: Comparison of Theoretical and Experimental 1Hand 13C- Chemical Shifts
Authors: Yüksek Haydar , Cakmak Ismail , Sadi Sibel , Alkan Muzaffer , Baykara Haci
Published: October 2008

3-Alkyl(aryl)-4-amino-4,5-dihydro-1H-1,2,4-triazol-5-ones (1) reacted with 5-methylfuran-2-carboxyaldehyde to afford the corresponding 3-alkyl(aryl)-4-(5-methyl-2-furylmethylenamino)-4,5-dihydro-1H-1,2,4-triazol-5-ones (2). Four newly synthesized compounds have been characterized by elemental analyses, IR, 1H-NMR, 13C-NMR and UV spectral data. In addition, isotropic 1H- and 13C-nuclear magnetic shielding constants of compounds 3 were calculated by employing the direct implementation of the gaugeincluding-atomic-orbital (GIAO) method at the B3LYP density functional and HF levels of the theory. The geometry of each compound has been optimized using a 6-311G basis set. Nuclear shielding constants were also calculated by using 6-311G basis set. Theoretical values are compared to the experimental data.
Studies on the Interaction between Zinc-Hydroxybenzoite Complex and Genomic DNA
Authors: Arslantas Ali , Devrim A.  Kadir , Kaya Neceti , Necefoglu Hacali
Published: October 2008

Zinc-Hydroxybenzoite ([Zn (H20)6] (p-HO-C6H4COO)22H20) complex which wassynthesized and characterized by instrumental methods and the DNA samples which hadbeen isolated from cattle were allowed to interact at 37 oC for different time periods. Theinteraction of genomic DNA with this complex has been followed by agarose gelelectrophoresis at 50 V for 2 h. When DNA samples were allowed to interact with this metalcomplex, it was found that band intensities changed with the concentrations of the complex.In the result of interaction between this complex and genomic DNA samples, it wasdetermined that the intensities of bands were changed at the different concentrations of thecomplex. The brightness of the bands was increased and mobility of the bands wasdecreased, indicating the occurrence of increased covalent binding of the metal complexwith DNA. In this study it was concluded that the damage effect of ascorbate was reducedby Zinc-Hydroxybenzoite.
QSAR of Some N1-Aryl/Heteroarylaminomethyl/ethyl-1,2,4-Triazoles Part II: Antimicrobial Activity Against BacillusSubtilis
Authors: Dimova Vesna , Ragenovic Katica  Colanceska , Kakurinov Vladimir
Published: October 2008

QSAR analysis of a series of previously synthesized N1-aryl-amino/methyl/ethyl-1,2,4-triazole and N1-heteroarylamino/methyl/ethyl-1,2,4-triazolederivatives tested for growth inhibitory activity against Bacillus subtilis, was performedusing the computer-assisted multiple regression procedure. Using the Hansch and FreeWilson approaches the activity contribution for either the aminomethyl/aminoethyl unitor the aromatic/heteroaromatic ring was determined from the correlation equation.
Characteristic and Synthetic Approach of Molecularly Imprinted Polymer
Authors: Yan Hongyuan , Row Kyung  Ho
Published: October 2008

Molecularly imprinted polymers (MIP) exhibiting high selectivity and affinity tothe predetermined molecule (template) are now seeing a fast growing research. However,optimization of the imprinted products is difficult due to the fact that there are manyvariables to consider, some or all of which can potentially impact upon the chemical,morphological and molecular recognition properties of the imprinted materials. This reviewpresent a summary of the principal synthetic considerations pertaining to good practice in thepolymerization aspects of molecular imprinting, and is primarily aimed at researcher familiarwith molecular imprinting methods but with little or no prior experience in polymersynthesis. The synthesis, characteristic, effect of molecular recognition and differentpreparation methods of MIP in recent few years are discussed in this review, unsolvedproblems and possible developments of MIP were also been briefly discussed.
Self-Organizing Molecular Field Analysis on a New Series of COX-2 Selective Inhibitors: 1,5-Diarylimidazoles
Authors: Li Shunlai , Zheng Yan
Published: October 2008

Self-organizing molecular field analysis (SOMFA), a simple three-dimensionalquantitative structure–activity relationship (3D-QSAR) method is used to study the correlationbetween the molecular properties and the anti-inflammatory biological activities of a new series of1,5-Diarylimidazoles that act as selective COX-2 inhibitors. The statistical results, cross-validated rCV2 (0.507) and non cross-validated r2 (0.546), show a satisfied predictive ability.
A Comparative X-ray Diffraction Study and Ab Initio Calculation on RU60358, a New Pyrethroid
Authors: Hamzaoui Fodil , Chouaih Abdelkader , Lagant Philippe , Belarbi Ouassila , Vergoten Gérard
Published: October 2008

The crystal structure of RU60358, C20H21NO3, has been determined using X-raydiffraction to establish the configuration and stereochemistry of the molecule around theC15-C16 triple bond. The compound crystallises in the orthorhombic space group P212121, a= 7.7575, b = 11.3182, c = 21.3529å, V = 1874.80å3 and Z = 4. The structure has beenrefined to a final R = 0.068 for the observed structure factors with I ≥ 3σ (I). The refinedstructure was found to be significantly non planar. A comparative study, using the ab initiocalculations of the structure at B3LYP/6-31G** levels of theory, shows good geometricalagreement with the X-ray diffraction data. Standard deviations between the calculated andexperimental bond values have been shown to be 0.01 å and 0.5° for bond angles.Vibrational wavenumbers were obtained from a normal mode analysis using the ab initiocalculations.
A Quest for the Origin of Barrier to the Internal Rotation ofHydrogen Peroxide (H2O2) and Fluorine Peroxide (F2O2)
Authors: Ghosh Dulal C.
Published: October 2008

In order to understand the structure-property relationship, SPR, an energy-partitioning quest for the origin of the barrier to the internal rotation of two iso-structuralmolecules, hydrogen peroxide, H2O2, and fluorine peroxide, F2O2 is performed. Thehydrogen peroxide is an important bio-oxidative compound generated in the body cells tofight infections and is an essential ingredient of our immune system. The fluorine peroxideis its analogue. We have tried to discern the interactions and energetic effects that entail thenonplanar skew conformation as the equilibrium shape of the molecules. The physicalprocess of the dynamics of internal rotation initiates the isomerization reaction and generatesinfinite number of conformations. The decomposed energy components faithfully display thephysical process of skewing and eclipsing as a function of torsional angles and hence aregood descriptors of the process of isomerization reaction of hydrogen peroxide (H2O2) anddioxygen difluoride (F2O2) associated with the dynamics of internal rotation. It is observedthat the one-center, two-center bonded and nonbonded interaction terms are sharply dividedin two groups. One group of interactions hinders the skewing and favours planar cis/transforms while the other group favours skewing and prefers the gauche conformation of themolecule. The principal energetic effect forcing the molecules into the nonplanar gaucheform is the variation “O–O’ bond energy with torsion in both the molecules. It isdemonstrated that the barrier is not a regional effect rather it is made by the conjoint actionof all one- and two-center bonding and nonbonding interactions comprising the entireframework of the molecule. The present study claims to reveal one amazing feature of non-bonded interactions. Computed results of nonbonding interactions demonstrate that thenature of interaction between two formally positively charged non-bonding H atoms (Hδ+ ----Hδ+ ) is not always repulsive and it is attractive as well; the nature of the non-bondinginteraction between formally negatively charged atom (‘O’) and formally positively charged(‘H’) atom, (Oδ−----Hδ+ ), is not always attractive but repulsive too; it is also demonstrated that the nature of the nonbonding interaction between strongly electronegative atoms, ( Fδ−-- --Fδ−), is not always repulsive and it may be attractive as well.
In Silico Design in Homogeneous Catalysis Using Descriptor Modelling
Authors: Burello Enrico , Rothenberg Gadi
Published: October 2008

This review summarises the state-of-the-art methodologies used for designing homogeneous catalysts and optimising reaction conditions (e.g. choosing the right solvent). We focus on computational techniques that can complement the current advances in high-throughput experimentation, covering the literature in the period 1996-2006. The review assesses the use of molecular modelling tools, from descriptor models based on semiempirical and molecular mechanics calculations, to 2D topological descriptors and graph theory methods. Different techniques are compared based on their computational and time cost, output level, problem relevance and viability. We also review the application of various data mining tools, including artificial neural networks, linear regression, and classification trees. The future of homogeneous catalysis discovery and optimisation is discussed in the light of these developments.
Preparation of Cyclic Urethanes from Amino Alcohols and Carbon Dioxide Using Ionic Liquid Catalysts with Alkali Metal Promoters
Authors: Fujita Shin-ichiro , Kanamaru Hiroshi , Senboku Hisanori , Arai Masahiko
Published: October 2008

Several ionic liquids were applied as catalysts for the synthesis of cyclicurethanes from amino alcohols and pressurized CO2 in the presence of alkali metalcompounds as promoters. A comparative study was made for the catalytic performanceusing different ionic liquids, substrates, promoters, and pressures. The optimum catalyticsystem was BMIM-Br promoted by K2CO3, which, for 1-amino-2-propanol, produced cyclicurethane in 40% yield with a smaller yield of substituted cyclic urea and no oligomericbyproducts. For other amino alcohols, cyclic urethanes, cyclic ureas, and/or undesiredbyproducts were produced in different yields depending on the substrates used. Possiblereaction mechanisms are proposed.
Self-assembly and Fractal Feature of Chitosan and Its Conjugate with Metal Ions: Cu (II) / Ag (I)
Authors: Hu Yi , Wu Yangzhe , Cai Jiye , Ma Yufeng , Wang Bin , Xia Ke , He Xiaoqing
Published: October 2008

In this paper, we investigated the self-assembly and fractal feature of chitosan andAg (I), Cu (II)-chitosan due to the theoretical and practical importance of chitosan inbiomedical engineering, biomaterials and environmental sciences etc. The self-assembly andfractal structures of chitosan and Ag (I), Cu (II)-chitosan were observed using atomic forcemicroscope (AFM), and the fractal dimensions of chitosan and Ag (I)-chitosan werecalculated. The results indicate that their fractal dimension is approximate 2 and relates withthe accumulation degree: the fractal dimension decreases with the accumulation degreeincreases. In addition, a new self-assembly strategy was presented to study the lyotropicliquid crystals (LLC) of chitosan and the formation mechanism of LLC was primarilyanalyzed and discussed. All of these results are valuable for the structure/functionrelationship study of chitosan and useful for application in biomedical materials.
Electrochemical Studies of Camptothecin and Its Interaction with Human Serum Albumin
Authors: Zhao Jing , Zheng Xiaofeng , Xing Wei , Huang Junyi , Li Genxi
Published: October 2008

Camptothecin, an anticancer component from Camptotheca acuminate, mayinteract with human serum albumin (HSA) at the subdomain IIA (site I), and then convert toits inactive form(carboxylate form). In this paper, the detailed electrochemical behaviors ofcamptothecin at a pyrolytic graphite electrode is presented. The interaction betweencamptothecin and HSA is also studied by electrochemical technique. By comparing withbovine serum albumin (BSA), which is highly homologous to HSA, we prove thatcamptothecin can specifically bind to HSA. Meanwhile, the inhibitory influence of sodiumsalicylate to this binding is also discussed.