Quantitative structure–activity relationship study on some benzodiazepine derivatives as anti-Alzheimer agents

A QSAR study was performed in an attempt to explore the pharmacophore of some benzodiazepine derivatives as anti-Alzheimer agents for the inhibition of -secretase. The study, which used the electrotopological state atom (ETSA) index, which encodes electronic and topological information, reveals the importance of two phenyl rings—one substituted and another unsubstituted, for the inhibition of the enzyme. Fluorine substitution on the substituted phenyl ring has an important contribution to the activity. R-configurations of the aliphatic chain substituents provide the exact conformation of the molecules to enter into the binding pockets of the receptor(s).Figure General structure of benzodiazepine containing -secretase inhibitors     

Determination of fuzzy logic membership functions using genetic algorithms: application to structure–odor modeling

Fuzzy logic has been used as a tool in structure–camphoraceous odor relationships. The data base studied included 99 molecules. The rules used to discriminate between camphor and non camphor molecules lead to 77% correct discrimination. Such rules account for the shape and the size of the molecule. Their adjustment by means of genetic algorithms led to 84% correct discrimination between camphor and non-camphor molecules.Figure Membership function for the chosen variables     

An ab initio study of di- and trifluorobenzene–benzene complexes as relevant to carbonic anhydrase II–drug interactions

Ab initio calculations at the MP2/6-31G* level have shown that variously substituted di- and trifluorobenzenes form non-covalent complexes with benzene that adopt either aromatic–aromatic or H---F binding, the choice being determined by the pattern of fluorination. The binding energies of these structures are from 3.4 to 4.5 kcal mol^–1. This range is large enough to account for observed variations in the binding affinity of a library of fluoroaromatic inhibitors of carbonic anhydrase. This enzyme has an aromatic amino acid at a central position in the active site. The diverse modes of binding of the dimers also suggest that aggregates of fluorobenzenes might adopt specified 3-dimensional shapes in the solid state. Figure Observed structure for 1,2-difluorobenzene     

Theoretical studies of the conformational behavior of chain molecules containing polar groups: simulations of a poly(vinylidene fluoride) model

Atomistic Monte Carlo simulations have been conducted to elucidate the conformational behavior of a single chain molecule containing polar functional groups. Here, we resort to an atomistic poly(vinylidene fluoride) (PVDF) chain model as a representative example. The model is modified in such a way that bond lengths and bond angles are fixed, aiming to manifest the role of dipolar interactions. For a given chain length, chain conformation is sensitive to two environmental parameters, temperature and dielectric constant. The mean chain size increases when temperature and/or dielectric constant are increased. The conformational behavior is further characterized by chain size distribution function, and our findings show that temperature induced conformational transition for a chain molecule can be discrete or continuous, depending on its chain length. Also, the dipolar interactions in PVDF are effectively attractive, and enhance chain contraction. As a result, when the strength of dipolar interactions is increased, the discrete conformational transition shifts toward longer chains; and for a given chain length, such a transition occurs at higher temperatures.Figure Variation of R² with temperature for different dielectric constants =1 and 8, denoted by dotted and solid lines, respectively, and for different chain lengths M=8 and 12, as marked. Lines are meant for eye guidance     

Direct ab initio dynamics studies of the hydrogen abstraction reactions of hydrogen atom with n-propyl radical and isopropyl radical

The kinetics of the hydrogen abstraction reactions of hydrogen atom with n-propyl radical and isopropyl radical were studied using the direct ab initio dynamics approach. BHandHLYP/cc-pVDZ method was employed to optimize the geometries of stationary points as well as the points on the minimum energy path (MEP). The energies of all the points for the two reactions were further refined at the QCISD(T)/cc-pVTZ level of theory. No barrier was found at the QCISD(T)/cc-pVTZ//BHandHLYP/cc-pVDZ level of theory for both reactions. The forward and reverse rate constants were evaluated with both canonical variational transition state theory (CVT) and microcanonical variational transition state theory ( VT) in the temperature range of 300–2,500 K. The fitted three-parameter Arrhenius expression of the calculated CVT rate constants at the QCISD(T)/cc-pVTZ//BHandHLYP/cc-pVDZ level of theory are k^CVT (n – C₃H₇)=1.68×10^–14 T^0.84 e^(319.5/T) cm³ molecule^–1 s^–1 and k^CVT (iso-C₃H₇)=4.99×10^–14 T^0.90 e^(159.5/T) cm³ molecule^–1 s^–1 for reactions of n-C₃H₇ + H and iso-C₃H₇ + H, respectively, which are in good agreement with available literature data. The variational effects were analysed.Figure Comparison of the calculated forward rate constants at the QCISD(T)/cc-pVTZ//BHandHLYP/cc-pVDZ level of theory and the available experimental and theoretical data of the reaction vs 1,000/T for the two reactions.     

A computational approach to the synthesis of dirithromycin

Dirithromycin is a macrolide antibiotic derived from erythromycin A. Dirithromycin is synthesized by the condensation of 9(S)-erythromycylamine with 2-(2-methoxyethoxy)-acetaldehyde. To gain insight into the synthesis, the condensation mechanism has been analyzed computationally by the AM1 method in the gas phase. First, the formation of the Schiff bases of dirithromycin and epidirithromycin from 9(S)-erythromycylamine and 2-(2-methoxyethoxy)-acetaldehyde were modeled. Then, the tautomerization of the Schiff bases to dirithromycin and epidirithromycin were considered. Finally, the epimerization of the Schiff base of epidirithromycin to the Schiff base of dirithromycin was investigated. Our results show that, even though carbinolamine forms faster for epidirithromycin than the corresponding structure for dirithromycin, dirithromycin is the major product of the synthesis. Figure Synthesis of dirithromycin     

AIPAR: ab initio parametrization of intermolecular potentials for computer simulations

An unambiguous, fully ab initio and automated technique denoted AIPAR (ab initio parametrization) implemented in the SJBR program has been proposed to yield intermolecular interaction potentials between polar molecules and water. The AIPAR procedure has been applied to several organic molecules covering a wide range of structure and functional groups, namely methanol, acetone (propanone), methanethiol (methyl mercaptan), imidazole (1,3-diazole), oxazole and furan. The AIPAR-derived sets of parameters compare well with the empirical OPLS ones, mainly when the all-atoms model is employed in the OPLS procedure. Monte Carlo simulations were performed for an aqueous solution of methanol and for an equimolar binary mixture methanol–water using the AIPAR and OPLS parameters. The thermodynamic and geometric results obtained with the parameters obtained with the AIPAR procedure compare favorably with the OPLS simulations, even for the binary mixture, demonstrating the precision, robustness and transferability of the parameters obtained with the AIPAR procedure.Figure Superimposed configurations of water (without the hydrogen atoms) around the methanol molecule obtained with the AGOA procedure.     

Nuclear reactivity indices within regional density functional theory

Regional chemical potential values- _R have been obtained with the use of nuclear reactivity indices. Perturbational formulae use values of reactivity indices of isolated molecular fragments. The changes of the parameters (N_R,{ Q_i }_{i R}) within each fragment determine the value of the regional chemical potential after a chemical reaction. The computational scheme has been tested numerically along the chemical reaction path. We have studied a set of chemical reactions to obtain regional chemical potentials ( ) and regional transfer potentials ( ) for transition states of the following chemical reactions: HF+CO=HFCO, HCl+CO=HClCO, HF+SiO=HFSiO and HF+GeO=HFGeO. The results are reasonable and encouraging. Values of these indices show the possible reactivity directions of the transition states examined.     

Reinvestigation of molecular structure and barrier to internal rotation of pyridinium N-phenolate betaine dye

In the present paper, the results of a systematic theoretical study of the molecular structure of 4-(1-pyridinium-1-yl)phenolate betaine are reported. The ground-state molecular structure and the barrier to internal rotation of the betaine dye molecule were calculated ab inito (with Hartree–Fock theory and the second-order of Möller–Plesset method) and with density functional theory (DFT). In order to estimate the complete basis set limit, the calculations of barriers to internal rotations were performed using correlation–consistent basis sets with a maximal cardinal number of four. It was determined that electron correlation is crucial in order to obtain reliable geometries and rotational barriers of the molecule investigated. For the sake of comparison, the results of calculations using the AM1 Hamiltonian are also presented.Figure Investigated betaine dye.     

Characterization of molecular structures and properties of polyurethanes using molecular dynamics simulations

Thermotropic polyurethanes with mesogenic groups in side chains were prepared from two diisocyanates and four diols with stoichiometric ratios of reactive isocyanate (NCO) and hydroxy (OH) groups. Their thermal behavior was determined by differential scanning calorimetry. The effect of structure modifications of the diisocyanates and diols, in particular changes in the mesogen, were investigated. Introduction of mesogenic segments into the polymers suppresses the ordering. Stiff end substituents (phenyl and alkoxy groups) of the mesogens stabilize the mesophases to such an extent that the negative influence of long polymer chains is compensated and the liquid-crystalline properties are recovered. All-atom molecular dynamics simulations in the Cerius² modeling environment were carried out to characterize the structures of the polymers. Analysis of the dynamic trajectories at 20, 100, 120 and 170 °C revealed changes in conformation of macromolecules, which correlate with DSC measurements.Figure Example of structure relaxation of D4/TDI molecule at indicated simulation times (temperature 20 °C): a complete structure; b backbone structure; c top view of molecule     

Modeling of adsorption in nanopores

Adsorption in nonporous materials has been studied using Grand Canonical Monte Carlo simulations. We discuss three types of materials: (a) a model of cylindrical pores with smooth walls, representing MCM-41 like materials, (b) a model of cylindrical pores with regular structured walls (model of carbon nanotubes) and (c) a material with crystalline wall structure (zeolites). Typical problems related to the stability of adsorbed layers have been analyzed. We have shown that the mechanism of adsorption is strongly dependent on the structure of the pore walls. In the case of amorphous walls it may lead to metastable configurations. In nanotubes, the ordered corrugation structure of walls determines the low temperature structure of the adsorbed system. In 3D ordered porous system, such as zeolites, the mechanism of adsorption is mostly determined by characteristic sites of adsorption.Figure Adsorbed atoms and energy fluctuations at the pressure of the first layer formation of krypton atoms: (a) instantaneous numbers of adsorbed atoms (per nm² of the pore wall) as a function of the time of simulation (Monte Carlo steps) observed in a relatively long run, (b) the bimodal distribution of the energy fluctuations is a consequence of the behavior of the systems as shown in (a).     

Ab initio study of phenyl benzoate: structure,conformational analysis,dipole moment,IR and Raman vibrational spectra

The molecular structure (bond distances and angles), conformational properties, dipole moment and vibrational spectroscopic data (vibrational frequencies, IR and Raman intensities) of phenyl benzoate were calculated using Hartree–Fock (HF), density functional (DFT), and second order Møller–Plesset perturbation theory (MP2) with basis sets ranging from 6-31G* to 6-311++G**. The theoretical results are discussed mainly in terms of comparisons with available experimental data. For geometric data, good agreement between theory and experiment is obtained for the MP2, B3LYP and B3PW91 levels with basis sets including diffuse functions. The B3LYP/6-31+G* theory level estimates the shape of the experimental functions for phenyl torsion around the Ph–O and Ph–C bonds well, but reproduces the height of the rotational barriers poorly. The B3LYP/6-31+G* harmonic force constants were scaled by applying the scaled quantum mechanical force field (SQM) technique. The calculated vibrational spectra were interpreted and band assignments were reported. They are in excellent agreement with experimental IR and Raman spectra.Figure Calculated and experimental (GED) potential energy functions for torsional motion of phenyl benzoate relative to the minimum value. a The potential function for torsion about the O₃–C₄ bond. b The potential function for torsion about the C₂–C₁₀ bond.     

Density functional theory investigation of electrophilic addition reaction of bromine to tricyclo[4.2.2.22,5]dodeca-1,5-diene1

The geometry and the electronic structure of tricyclo[4.2.2.2^2,5]dodeca-1,5-diene (TCDD) molecule were investigated by DFT/B3LYP and /B3PW91 methods using the 6-311G(d,p) and 6-311++G(d,p) basis sets. The double bonds of TCDD molecule are syn-pyramidalized. The structure of π-orbitals and their mutual interactions for TCDD molecule were investigated. Potential energy surface (PES) of the TCDD-Br₂ system was studied by B3LYP/6-311++G(d,p) method and the configurations [molecular charge-transfer (CT) complex, transition states (TS1 and TS2), intermediate (INT) and product (P)] corresponding to the stationary points (minima or saddle points) were determined. Initially, a molecular CT-complex forms between Br₂ and TCDD. With a barrier of 22.336 kcal mol^-1 the CT-complex can be activated to an intermediate (INT) with energy 15.154 kcal mol^-1 higher than that of the CT-complex. The intermediate (INT) then transforms easily (barrier 5.442 kcal mol^-1) into the final, N-type product. The total bromination is slightly exothermic. Accompanying the breaking of Br-Br bond, C1-Br, C5-Br and C2-C6 bonds are formed, and C1 = C2 and C5 = C6 double bonds transform into single bonds. The direction of the reaction is determined by the direction of intramolecular skeletal rearrangement that is realized by the formation of C2-C6 bond.

An extended aqueous solvation model based on atom-weighted solvent accessible surface areas: SAWSA v2.0 model

A new method is proposed for calculating aqueous solvation free energy based on atom-weighted solvent accessible surface areas. The method, SAWSA v2.0, gives the aqueous solvation free energy by summing the contributions of component atoms and a correction factor. We applied two different sets of atom typing rules and fitting processes for small organic molecules and proteins, respectively. For small organic molecules, the model classified the atoms in organic molecules into 65 basic types and additionally. For small organic molecules we proposed a correction factor of hydrophobic carbon to account for the aggregation of hydrocarbons and compounds with long hydrophobic aliphatic chains. The contributions for each atom type and correction factor were derived by multivariate regression analysis of 379 neutral molecules and 39 ions with known experimental aqueous solvation free energies. Based on the new atom typing rules, the correlation coefficient (r) for fitting the whole neutral organic molecules is 0.984, and the absolute mean error is 0.40 kcal mol^–1, which is much better than those of the model proposed by Wang et al. and the SAWSA model previously proposed by us. Furthermore, the SAWSA v2.0 model was compared with the simple atom-additive model based on the number of atom types (NA). The calculated results show that for small organic molecules, the predictions from the SAWSA v2.0 model are slightly better than those from the atom-additive model based on NA. However, for macromolecules such as proteins, due to the connection between their molecular conformation and their molecular surface area, the atom-additive model based on the number of atom types has little predictive power. In order to investigate the predictive power of our model, a systematic comparison was performed on seven solvation models including SAWSA v2.0, GB/SA_1, GB/SA_2, PB/SA_1, PB/SA_2, AM1/SM5.2R and SM5.0R. The results showed that for organic molecules the SAWSA v2.0 model is better than the other six solvation models. For proteins, the model classified the atoms into 20 basic types and the predicted aqueous free energies of solvation by PB/SA were used for fitting. The solvation model based on the new parameters was employed to predict the solvation free energies of 38 proteins. The predicted values from our model were in good agreement with those from the PB/SA model and were much better than those given by the other four models developed for proteins.Figure The definition of hydrophobic carbons. Here CA, CB and CD are three carbon atoms; X represents a heteroatom. According to our definition, CB is a hydrophobic carbon, CA is not a hydrophobic carbon because a heteroatom is within four atoms and CD is not a hydrophobic carbon because CD is sp²- hydridized and in a six-member ring.Electronic Supplementary Material Supplementary material is available for this article at     

Theoretical potential scans and vibrational spectra of vinyl selenonyl halides CH2=CH–SeO2X (X is F, Cl and Br)

The structure and conformational stability of vinyl selenonyl fluoride, chloride and bromide CH₂=CH–SeO₂X (X is F, Cl and Br) were investigated using density functional B3LYP/6-311+G** and ab initio MP2/6-311+G** calculations. From the calculations the molecules were predicted to exist only in the non-planar gauche conformation with the vinyl C=C group almost eclipsing one of the selenonyl Se=O bonds as a result of conjugation between the two moieties. Single-minimum potential scans were calculated at the DFT level for the molecules. The vibrational frequencies were computed using B3LYP/6-311+G**. Normal coordinate calculations were then carried out and potential energy distributions were calculated for the three molecules in the gauche conformation.Figure Potential function for the asymmetric torsion in vinyl selenonyl fluoride (dotted line), chloride (dashed line) and bromide (solid line) as determined at the DFT-B3LYP/6-311+G** level     

Effects of concentration and treatment duration upon dwarf pea response to gibberellic acid root treatments in solution culture

Gibberellic acid (GA₃) root treatments stimulated internode elongation of hydroponically grown dwarf pea seedlings (Pisum sativum L.,cv. Little Marvel) When the GA₃ concentration in the solution was at least 2.9 M.Both GA₃ concentration and the duration of the root-treatment period significantly affected internode elongation. This is attributed to a limited availability or saturation of active sites for gibberellin-induced cell elongation. The amount of GA₃ taken up through the roots in 1 day from a 29 M GA₃ solution apparently equaled or exceeded the amount which could be metabolized during the first four days after treatment, although higher concenrations and longer treatment periods produced a more prolonged response, conceivably due to 1) initial saturation of gibberellin active sites, 2) storage of surplus gibberellin in the plant, and 3) subsequent utilization of the stored gibberellin. GA₃-induced stem elongation in hydroponically grown Little Marvel peas seemed to be limited initially by apparent saturation of active sites when the GA₃ concentration exceeded 29 M.     

Predicting anti-HIV activity of 2,3-diaryl-1,3-thiazolidin-4-ones: computational approach using reformed eccentric connectivity index

The eccentric connectivity index, which has recently been employed successfully for the development of numerous mathematical models for the prediction of biological activities of diverse nature, has been reformed to overcome its limitations caused by degeneracy and insensitivity towards heteroatoms. The reformed eccentric connectivity index, termed the eccentric connectivity topochemical index, overcomes the limitations of the eccentric connectivity index by exhibiting very low degeneracy and displaying sensitivity to both the presence and relative position of heteroatoms without compromizing the discriminating power of the eccentric connectivity index. The relationship of the eccentric connectivity topochemical index, eccentric connectivity index and Wieners index with regard to the anti-HIV activity of 2, 3-diaryl-1, 3-thiazolidin-4-one derivatives was subsequently investigated. The values of the eccentric connectivity topochemical index, the eccentric connectivity index and Wieners index of each of 31 analogues comprizing the data set were computed using in-house computer program. Resultant data was analyzed and suitable models developed after identification of active ranges. Subsequently, each derivative was assigned a biological activity using these models, which was then compared with the reported anti-HIV activity. The accuracy of prediction using these models was found to vary from 81 to 90%. The proposed index offers a vast potential for virtual screening of combinatorial libraries, structure property/activity studies and drug design.Figure Basic structure of 2,3-diaryl-1, 3-thiazoidin-4-ones.     

Cellular chloride depletion inhibits cAMP-activated electrogenic chloride fluxes in HT29-18-C1 cells

Cyclic AMP-activated chloride fluxes have been analyzed in HT29-18-C₁ cells (a clonal cell line derived from a human colon carcinoma) using measurements of cell volume (electronic cell sizing), cell chloride content (chloride titrator) and intracellular chloride activity (6-methoxy-N-(3-sulfopropyl)quinolinium; SPQ). HT29-18-C₁ was shown to mediate polarized chloride transport. In unstimulated cells, the apical membrane was impermeable to chloride and net chloride flux was mediated by basolateral furosemide-sensitive transport. Forskolin (10) (m) increased furosemideinsensitive chloride permeability of the apical membrane, and decreased steady-state intracellular chloride concentration approximately 9%. Cellular chloride depletion (substitution of medium chloride by nitrate or gluconate), caused greater than fourfold reduction in cellular chloride concentration. When chloride-depleted cells were returned to normal medium, cells regained chloride and osmolytes via bumetanide-sensitive transport, but forskolin did not stimulate bumetanideinsensitive chloride uptake. The inhibition of cAMP-activated chloride reuptake was not explained by limiting cation conductance, cell shrinkage, choice of substitute anion, or decreased generation of cAMP in chloridedepleted cells. When cells with normal chloride content were depolarized (135 mm medium potassium + 10 m valinomycin), cAMP activated electrogenic chloride uptake permselective for Cl^–Br^–>NO ₃ ^– >I^–. The electrogenic transport pathway was inhibited in chloridedepleted cells. Results suggest that chloride depletion limits activation of electrogenic chloride flux.The technical assistance of Dwight Derr is gratefully acknowledged. We also thank Dr. Chahrzad Montrose-Rafizadeh for help in performance of the chloride efflux experiments. This work was supported by National Institutes of Health grants RO1-DK42457 and PO1-DK44484.     

Mechanistic insight into effect of doping of Ni on CO<Subscript>2</Subscript> reduction on the (111) facet of Cu: thermodynamic and kinetic analyses of the elementary steps

A systematic mechanistic investigation of CO₂ reduction on a Ni-modified Cu(111) surface is performed based on an extensive set of density functional theory (DFT) calculations by focusing on the hydrocarbon CH₄ formation pathways. By carefully analyzing reduction pathways on the Ni-modified Cu(111) surface, some important mechanistic information is deduced. The presence of Ni stabilizes all reaction intermediates, and thus reduces the activation barrier for almost all CO₂ reduction steps. Most importantly, it can considerably lower than the activation barrier of CO₂ hydrogenative dissociation into CO, which is the rate-determining step of CO₂ reduction on a pure Cu(111) surface. Thus, the doping of Ni atom is able to activate CO₂, leading to enhanced surface activity of CO₂ reduction into hydrocarbons. Notably, the activation barriers that are required for CH₄ and CH₃OH formation are almost all easily overcome through the thermoactive process at ambient temperatures after doping of Ni atom. Thus, a higher CH₄ and CH₃OH yield may be expected in the presence of the doped Ni atom. Thermodynamic analyses indicate that doping of Ni may reduce the overpotential of CO formation through CO₂ hydrogenative dissociation. On this basis, two decriptors may be proposed in order to describe the catalytic activity of Cu-based catalysts for CO₂ reduction, and a perfect Cu-based alloy in CO₂ reduction should moderately bind CO and form and reduce CO more easily. Simutaneously, CO hydrogenation occurs more easily on the (111) facet of Ni-modified Cu than dimerization, thereby the selectivity of (111) facet of Cu on production CH₄ is further confirmed to some degree. The present study reveals a rich reaction chemistry and provides new insights to guide the rational design of Cu-based alloy catalysts for hydrocarbons formation from CO₂ reduction.

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Graphical Abstract Reduction pathways of CO₂ into hydrocarbons?

     

Improving the hydrogen storage properties of metal-organic framework by functionalization

Based on the structure of MOF-808, different substituents were introduced to replace hydrogen atom on the phenyl ring of MOF-808. The GCMC method was used to study the effect of functional groups on the hydrogen storage properties of MOF-808-X (X?=??OH, ?NO₂, ?CH₃, ?CN, ?I). The H₂ uptakes and isosteric heat of adsorption were simulated at 77 K. The results indicate that all these substituents have favorable impact on the hydrogen storage capacity, and –CN is found to be the most promising substituent to improve H₂ uptake. These results may be helpful for the design of MOFs with higher hydrogen storage capacity.

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Graphical abstract Atomistic structures of MOFs. (a) The structures of MOF-808-X. (b) Model of organic linker. Atom color scheme: C, gray; H, white; O, red; X, palegreen (X?=??OH, ?NO₂, ?CH₃, ?CN, ?I)