A DFT study of determination of the reactive sites of the acetylcholine and its agonists: In the gas phase and dielectric medium

The reactive behavior of acetylcholine and its agonist molecules have been investigated using B3LYP hybrid density functional method at the 6‐311++G** basis set level, in the gas phase and aqueous phase. The calculations have been performed to obtain optimized geometries, relative reactivities, net atomic charges, HOMO, and LUMO energies. The solvent effect has been analyzed by using the continuum model (IPCM) and, the obtained results have shown that the all molecules have been stabilized more by solvent dielectric constant. For Ach and its analogues, it has been very well known that esteratic site and quaternary ammonium group which have reflected the difference in biological activity have been the two of the most important active site for interactions between molecule and its receptor. The structures of these analogues have provided an essential foundation for subsequent structure‐activity analysis of ligand binding at acetylcholine receptors, neuronal uptake inhibitors and transporters. Molecular modeling predictions will be important initial steps toward the development of novel pharmaceuticals in the fight acetylcholine‐related neurological disorders. This work is therefore expected to facilitate the design and development of new biologically active Ach analogues to treat Ach‐related neurological disorders and, specially is used to qualitative understanding of the reactivity and related properties and, so on can be used to a preselection of new ligands which at the moment is taken essentially from empirical knowledge. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

自由基氧净电荷对过氧化物引发剂活性的影响

采用分子力学和半经验量子化学的方法 ,计算出了数十种有机过氧化物氧氧键均裂的键离解能 ,以及过氧化物生成的自由基的氧净电荷及其校正值 .数据的多重线性回归证明 ,影响有机过氧化物引发剂活性(常用 1 0h HLT表示 )的主要因素为自由基的电性和空间效应 ,这两者可以用自由基的氧净电荷及其校正值来表征 .在同种溶剂中 ,过氧化物生成的两个自由基的氧净电荷及其校正值 ,这四个因素与其半分解温度之间有较好的相关性 .这种相关性可以用来预测过氧化物的 1 0h HLT值 .     

Local and nonlocal density functional calculations of the molecular structure of isomeric thiadiazoles

The chemistry of thiadiazoles and their derivatives is of considerable interest in chemistry owing to their pharmacological and potential industrial applications. In this context, a detailed study of isomeric thiadiazole molecules has been done using local (SVWN; Slater, and Vosko, Wilk and Nusair) and nonlocal (BLYP; Becke, and Lee, Yang and Parr) density functionals and optimizing the molecular geometries by means of the gradient technique. A charge sensitivity analysis of the studied molecule has been performed by resorting to density functional theory, obtaining several sensitivity coefficients such as the molecular energy, net atomic charges, global and local hardness, global and local softness and Fukui functions. With these results and the analysis of the dipole moments, the molecular electrostatic potentials and the total electron density maps, several conclusions have been inferred about the preferred sites of chemical reaction of the studied compounds. The condensed Fukui functions are shown to be one of the best criteria for predicting chemical reactivity.     

Metalation reactions—XVII : The dimetalation of branched olefins. The question of the aromaticity of the trimethylenemethane dianion and related derivatives

Metalation of methallylbenzenes with BuLi gave dilithio derivatives which were dialkylated with methyl bromide. Derivatives of cross conjugated dianions are obtained preferentially to linear ones. The parent trimethylenemethane dianion² was obtained by metalation of isobutene. Energies and atomic net charges of these and related molecules were calcualted. The question of the aromaticity of these systems is discussed.     

A nano-confined charged layer defies the principle of electrostatic interaction

The reactivity between two charged molecules and the activity of charged biomolecules are mainly governed by the principle of electrostatic interaction, i.e., like charges repel and opposite charges attract. In the present study it is shown that the principle of electrostatic interaction is violated in the nano-confined biomimetic environment. Thus a positively charged molecule shows more preference to a positively charged surface compared to a negatively charged surface.     

A test of the Hirshfeld definition of atomic charges and moments

Summary The Hirshfeld population analysis scheme which carves the molecular density into atomic density contributions is tested. This method does not require a reference to basis sets or their respective locations, but is based on a different physical and mathematical footing. The advantage of this method is that, when the molecular deformation density converges to the true solution, the computed net charges will necessarily converge. This method also allows a straightforward definition for local moments. About 36 molecules have been used to compute the conventional Mulliken and Löwdin population analyses with STO3G, 6311G** and Dunning-Hay split valence basis sets. These results have been compared to the estimates provided by the Hirshfeld model. The charges found in the Hirshfeld method are smaller than those from the other methods.     

The melting points of oligomethylenes

Quantitative structure-property relationships (QSPR) between the melting points of oligomethylenes and quantum chemical data calculated by the semiempirical method CNDO/2 were investigated. A linear relationship between the average net charges of hydrogen and carbon atoms in the molecules and the melting points could be established, achieving good fit as well as predictability. Further, the relation between the net charges and the chain length was evaluated. The evaluated net charges of polyethylene lead to a calculated melting point of 141.4°C (experimental: 141.4°C). © 1996 John Wiley & Sons, Inc.     

DFT and Ab initio computational study on the reactivity sites of the GABA and its agonists,such as CACA,TACA, DABA,and muscimol: In the gas phase and dielectric media

The reactive behavior of GABA and its agonist molecules have been investigated using B3LYP hybrid density functional method at the 6‐311++G** basis set level, in the gas phase and dielectric media. The calculations have been performed to obtain optimized geometries, relative energies, net atomic charges, HOMO, and LUMO energies. Solvent effects have been analyzed using isodensity polarized continuum model (IPCM) for four different solvents, which are chloroform, ethanol, DMSO, and H₂O. The results have suggested that both the amino group and carboxyl group have been two of the most important active site for interactions between all compounds and their receptors. In addition they have suggested that the amino group reflects the difference in biological activity for each all molecules. The structures of these agonists have provided an essential foundation for subsequent structure‐activity analysis of ligand binding at GABA receptors, neuronal uptake inhibitors and transporters. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Aqueous solution properties of polyampholytes: Effect of the net charge distribution

Viscometric and light scattering studies have been performed on aqueous solutions of polyampholyte terpolymers based on sodium-2-acrylamido-2-methylpropanesulfonate (Na-AMPS), 2-(methacryloyloxy)-ethyltrimethylammonium chloride (MADQUAT), and acrylamide (AM), prepared by an inverse microemulsion polymerization technique. The distribution of net charges among the chains was varied by adjusting the initial monomer composition and the degree of conversion. The effect of this distribution on the solubility of the samples and on the chain conformation was studied. It was found that samples with a narrow distribution of net charges were soluble in pure water even if the average net charge is small. Addition of salt induces a transition from an extended conformation to a more compact one, in qualitative agreement with theoretical predictions. A practically alternated NaAMPS-MADQUAT copolymer prepared by polymerization in homogeneous solution and with a small average net charge shows a behavior quite similar to that of the terpolymers. © 1996 John Wiley & Sons, Inc.     

Investigation of the role of the C-PCM solvent effect in reactivity indices

It has been shown recently, how the coupling between electronic degrees of freedom and vibrational modes is reflected in the properties of molecules. The necessary derivatives have been analyzed and their thermodynamic relations were demonstrated. This present work is focused on the analysis of a molecular system, under the influence of C-PCM induced solvent effect. The analysis is based on reactivity indices derived from DFT. The shift of frequency for diatomic molecules has been obtained. It has been identified as chemical force effect. The role of nuclear reactivity indices has been emphasized. This concept has been extended to obtain regional chemical potential values within C-PCM model for polyatomic molecules.     

The effective nuclear charge model—IX. On the transferability of effective nuclear charges defined from homonuclear diatomic molecules

Effective nuclear charges of many triatomic molecules have been calculated inversely by the least squares method (Jacobian matrix method) from the experimental force constants which are determined by normal coordinate analyses using the observed vibrational data. The values of effective nuclear charges thus obtained are compared with those defined from homonuclear diatomic molecules. The results show that the transferability of effective nuclear charges from homonuclear diatomic molecules to triatomic molecules is moderately good. This gives support to the utility of the effective nuclear charge model.     

Geometry optimization and electronic structures of molecules H_3AXAH_3

The geometries of molecules H_3AXAH_3(X=O,S,Se and A=C,Si)have been optimizedusing STO-3G ab initio calculations and gradient method and the results are in good agreement withreported experimental values.From the STO-3G optimized geometries,we have also calculated theelectronic structures of these molecules using 4-31G and 6-31G basis sets to obtain the MO energies.atomic net charges and dipole moments.The ionization potentials calculated by 6-31G basis set are ingood agreement with experimental values.     

Electronic properties of 3,3'-dimethyl-5,5'-bis(1,2,4-triazine): towards design of supramolecular arrangements of N-heterocyclic Cu(I) complexes

A new efficient and safe synthesis of 3,3'-dimethyl-5,5'-bis-(1,2,4-triazine) is presented. The electron-density distribution and electrostatic properties (charge, electrostatic potential) of this molecule were analyzed. These properties were derived from a high-resolution single-crystal X-ray diffraction experiment at 100 K and compared to the results obtained from ab initio DFT quantum-mechanical calculations. Comparisons of its electrostatic potential features and integrated atomic charges (quantum theory of atoms in molecules, QTAIM) have been made with those of related molecules such as bipyrimidine ligands. Two methods were used to derive integrated charges: one is based on the conventional analytical procedure and the second uses a steepest-ascent numerical algorithm. Excellent agreement was obtained between these two methods. Charges and electrostatic potential were used as predictive indices of metal chelation and discussed in the light of complexation abilities of the title compound and related molecules. The crystal structure of a Cu(I) complex of 3,3'-dimethyl-5,5'-bis(1,2,4-triazine) is reported here. In the solid state, this complex forms a three-dimensional multibranch network with open channels in which counterions and solvent molecules are located. This architecture involves both cis and trans isomers of the title compound.     

Predicting the activity of single isolated Lewis acid sites in solid catalysts

An experimental study of the activity of Ti-, Zr- and Sn-beta catalysts in different types of oxidation reactions is combined with a quantum-chemical analysis of the electronic properties of the active sites and the adsorbed reactants. The differences observed in the catalytic behaviour of the three materials are explained in terms of the molecular orbital distribution of each system. The intrinsic Lewis acid strength of the isolated active site, the degree of back-donation from the catalyst to the empty orbitals of the organic reactant and the net atomic charges on selected atoms are proposed as predictors of reactivity.     

On the definition of the atomic charge in a molecule

Atomic charges calculated by various methods for model two-center molecules have been compared with corresponding electron-count functions. Varying the overlap and polarity conditions in the model system, it could be found out under what conditions the individual definitions fail to predict physically reasonable values of atomic charges.     

Accuracy of free energies of hydration for organic molecules from 6-31g*-derived partial charges

Absolute free energies of hydration have been computed for 13 diverse organic molecules using partial charges derived from ab initio 6-31G* wave functions. Both Mulliken charges and charges fit to the electrostatic potential surface (EPS) were considered in conjunction with OPLS Lennard–Jones parameters for the organic molecules and the TIP4P model of water. Monte Carlo simulations with statistical perturbation theory yielded relative free energies of hydration. These were converted to absolute quantities through perturbations to reference molecules for which absolute free energies of hydration had been obtained previously in TIP4P water. The average errors in the computed absolute free energies of hydration are 1.1 kcal/mol for the 6-31G* EPS charges and 4.0 kcal/mol for the Mulliken charges. For the EPS charges, the largest individual errors are under 2 kcal/mol except for acetamide, in which case the error is 3.7 kcal/mol. The hydrogen bonding between the organic solutes and water has also been characterized. © John Wiley & Sons, Inc.     

Novel guests for porous columnar thin films: the switchable perchlorinated trityl radical derivatives

TiO(2) and SiO(2) porous thin films consisting of tilted nanocolumns prepared by glancing angle evaporation (GLAD) have been infiltrated with guest derivatives belonging to the family of perchlorinated trityl radicals, novel guest molecules presenting an open-shell electronic configuration associated with paramagnetism, fluorescence, and electroactivity. The main driving forces for infiltration from aqueous solutions of the carboxylate-substituted radical derivatives are the electrostatic interactions between their negative charge and the net positive charges induced on the film pores. Positive charges on the internal surface of the films were induced by either adjusting the radical solution pH at values lower than the point of zero charge (PZC) of the oxide or passivating the nanocolumns oxide surface with a positively charged aminosilane. The infiltrated composite thin films are robust and easy to handle thanks to the physical protection exerted by the film columns. They also keep the multifunctionality of the used guests, as confirmed by electron paramagnetic resonance (EPR), UV-vis spectroscopy, and fluorescence spectroscopy. To prove the electroactivity of the infiltrated porous films, a porous TiO(2) host layer was supported onto conductive indium tin oxide (ITO). By application of an appropriate redox potential, the guest radical molecules have been reversibly switched from their open-shell electronic configuration to their diamagnetic state and hence changed their optical properties. On the basis of these results, it is herein proposed that the appropriate surface functionalization of the pore internal surface of GLAD thin films can be used to prepare novel radical-oxide composite thin films usable for the development of robust switchable electrically driven photonic and magnetic devices.