A theoretical study of Zn++ interacting with models of ligands present at the thermolysin active site

Summary The binding energy and the geometrical arrangements of the complexes formed by the zinc dication with OH^–, one, four, five or six water molecules, SH^–, H₂S, formic acid, the formate anion, imidazole, its anion and formamide are calculated using the MNDO method. The comparison of the results obtained with those of ab initio computations on the same complexes induced us to propose for Zn⁺⁺ a set of parameters different from the one determined by Dewar for the neutral metal atom. Using the two MNDO parametrizations, similar calculations are carried out for Zn⁺⁺ interacting with two molecules of 2-aminoethanethiol and with models of the four ligands which are present at the thermolysin active site, in order to evaluate the possibilities and limitations of this semiempirical method for theoretical studies concerning zinc metalloenzymes. In the last case, the results obtained suggest that, in the crystal state, the water molecule could be deprotonated. This finding is discussed in relation with the mechanism of action of the enzyme which has been proposed.This laboratory is part of UA 506 of the C.N.R.S.     

Influence of the ligand structure of hafnocene polymerization catalysts: A theoretical study on chain termination reactions in ethene polymerization

Ligand effects on chain termination reactions in hafnocene-catalyzed ethene polymerization process have been systematically studied by quantum chemical methods. β-hydrogen transfer to metal, β-hydrogen transfer to monomer and hydrogenolysis were studied for 27 hafnocenes, initiating the chain termination reactions after insertion of the second ethene monomer. The results of the calculations were studied as a function of the ligand structure, focusing on the effects of various ancillary ligands, ligand substituents and bridging units. The ligand effects on chain termination reactions are strongly affected by combined effects of various structural units, in particular, in the cases of β-hydrogen transfer to monomer and hydrogenolysis. The results are expected to aid in design and development of new hafnocene polymerization catalysts.     

A theoretical study of anion-pi interactions in seven-membered rings.

Several complexes of tropylium (1) with anions are optimized at the RI-MP2(full)/6-31++G** level of theory. This binding unit can interact very favorably with anions, and it combines the strength of the electrostatic interaction with the directionality of the anion-pi interaction. The complexes of 1 with anions are characterized by means of the Bader theory of "atoms-in-molecules," and the physical nature of the interaction has been analyzed by means of the molecular interaction potential with polarization tool. Experimental evidence of anion-pi interactions involving seven-membered rings has been found in the solid state.     

A theoretical study of the interactions between N,N-dimethylformamide and xylenes

The ab initio and density functional (DFT) methods were performed on binary systems of N,N-dimethylformamide (DMF) with xylenes (o-, or m-, or p-xylene), and seven stable configurations were obtained with no imaginary frequencies. To obtain the interaction energies of these complexes, single-point energy calculations with basis set superposition error (BSSE) correction were carried out at B3LYP/6-31G* and MP2/6-31G* levels. The structures, Chelpg (charges from electrostatic potentials using a grid-based method) charge distribution and bond characteristics of the mentioned complexes were calculated. The results indicated the presence of double C–H···O hydrogen bonds between DMF and xylenes in these complexes and the interaction energies of hydrogen bonding between DMF and xylene systems decreased in the following sequence: DMF–o-xylene: a1 > DMF–m-xylene: b1 > DMF–p-xylene: c1.     

A combined experimental and theoretical study on the complexation of Li<Superscript>+</Superscript> with valinomycin

Abstract  From extraction experiments in the two-phase water–nitrobenzene system and γ-activity measurements, the stability constant of the valinomycin–lithium complex in nitrobenzene saturated with water was determined. Further, the structure of the resulting complex was indicated by means of the density functional level of theory (DFT) calculations. Graphical abstract        

A theoretical investigation on the mechanism of the α,α-diphenylprolinol trimethylsilyl ether-catalyzed oxyamination reaction

A theoretical investigation on the reaction mechanism of a chiral prolinol silyl ether-catalyzed oxyamination reaction strongly suggests that the reaction proceeds via an enol intermediate and not via an enamine intermediate. The catalyst generates the enol and forms an enol-catalyst complex. Nitrosobenzene subsequently reacts with the enol-catalyst complex to afford the (S)-N-nitroso aldol product. The proposed mechanism is able to account for the experimentally observed enantioselectivity.     

Matrix-isolation FT-IR study and theoretical calculations of the vibrational, tautomeric and H-bonding properties of hypoxanthine

The neutral compound hypoxanthine is investigated using the technique of matrix-isolation FT-IR spectroscopy combined with density functional theory (DFT) and ab initio methods. Two theoretical methods (RHF and DFT/B3-LYP) are compared for vibrational frequency prediction, and four methods (RHF//RHF, MP2//RHF, DFT//DFT and MP2//DFT) for prediction of the relative energies of the tautomers and the interaction energies of the complexes. All the possible tautomeric forms have been considered theoretically, and the results indicate that two oxo forms (O17 and O19) and one hydroxy form (H9-r1) are the three most stable forms. The experimental FT-IR spectra are consistent with this prediction, and nearly all the characteristic spectral features of these forms have been identified in the spectrum. A theoretical study of the H-bonded complexes of these three tautomers with water is also performed. Several structures have been found for each form and the results demonstrate that the closed complexes with two H-bonds are the most stable systems due to the H-bond cooperative effect.     

Amide-directed arylation of sp C-H bonds using Pd(II) and Pd(0) catalysts

Protocols to effect β-arylation of sp³ C-H bonds via Pd(II)/(IV) and Pd(0)/(II) catalytic cycles have been achieved using a newly developed monodentate CONHC₆F₅ directing group. These reactions provide an unprecedented means to functionalize sp³ C-H bonds in aliphatic carboxylic acid-derived substrates.     

A theoretical study of the relative stability of the isomeric forms of N2O3

The electronic structure, geometrical parameters and relative stability of the isomeric forms of N₂O₃ are analysed by means of ab initio calculations. Total energies of the different isomers are given. The energy difference between the most stable conformers of the symmetric N₂O₃ is 4.31 Kcal mol^–1 as provided by 6–31G basis set. The height of the rotational barrier determined by the ab initio technique is 7.12 kcal mol^–1.Member of the Carrera del Investigador CICPBA, R. Argentina.Member of the Carrera del Investigador CONICET, R. Argentina.Predoctoral fellow of CONICET, R. Argentina.     

Gas phase ionization of 1,3-propanedial tautomeric forms: A theoretical study

Two stable 1,3-propanedial tautomers and three their anions have been studied theoretically at MP2 and DFT levels of theory. The energies, structural parameters, ionization potentials, and vibration frequencies have been calculated at the two theoretical levels in order to compare the accuracy of the methods used. The ionization potential of the end form of 1,3-propanedial enol form was estimated to be 752 kJ mol^?1; the first and second potentials of the diketo form of 1,3-propanedial are 661 and 1239 kJ mol^?1, respectively.     

Experimental and theoretical study of the atmospherically important O2-H2O complex

The theoretically predicted water-oxygen van der Waals adduct has been experimentally confirmed by vibrational characterization using matrix isolation spectroscopic studies at 10 K. Vibrational bands for asymmetric and symmetric OH-stretching for this adduct have been found at 3728 cm(-1) and 3639 cm(-1), respectively. Theoretical calculations performed with Gaussian 98 software at the MP2/6-311++G(2d,2p) level of theory support the alternative structure of the hydrated complex proposed by this study.     

The structural and theoretical study of 1H-3,5-di-phenyl-1,2,4-diazaphosphole in the solid state

The N-, P-containing five-membered heterocyclic compound 1H-3,5-di-phenyl-1,2,4-diazaphosphole (1) was prepared in good yield and has been structurally characterized. 1H-3,5-Di-phenyl-1,2,4-diazaphosphole (1), crystallizing in two unexpected cyclic dimers with N-H?N hydrogen bonds, presents in the solid state a dynamic proton disorder implying a dynamic equilibrium within both dimers. The conformations of the phenyl rings, the disorder of the NH protons, and the intermolecular hydrogen bond of several 1,2,4-diazaphospholes (1-5) in the solid state have been rationalized by DFT [B3LYP/6-311++G(d,p)] calculations.     

A theoretical study of the Si-O bond in disiloxane and related molecules

Summary A comparison of semi-empirical (MNDO) and ab initio (GAUSSIAN) calculations for disiloxane and related molecules is given. The STO-3G^* basis set well reproduced the observed geometries of disiloxane (*), DZP, TZVP) gave much poorer agreement with the observed geometries.Comparison of the STO-3G^* and the STO-3G basis sets demonstrates the necessity of including d-orbitals on the silicon. However, the semi-empirical MNDO program gave, despite the absence of d-orbitals, a better approximation to the molecular geometry than the complex ab initio basis sets.Force field parameters have been calculated for k_SiOSi, k_OSiO, 0.089 and 0.73 mdyneÅ/rad², and the SiOSiO torsion which has a V₁ potential of –0.68 kcal/mol. In addition, the HSiOH torsion is shown to have a three-fold potential of 0.78 kcal/mol. These are profoundly different from the analogous carbon-oxygen force constants, demonstrating that C-O parameters cannot be transferred to the corresponding Si-O systems.     

A theoretical study of substituent effects on the structure of isolated and condensed three-membered rings. A comparison between radicals and parent hydrocarbons

Substituent effects on the structure of radicals and parent hydrocarbons formed by isolated or condensed three-membered rings have been investigated by Hartree-Fock, post-Hartree-Fock and density functional methods. The trends of structural parameters computed for the hydrocarbon systems are in agreement with available experimental data. Substituent effects can be rationalized in terms of interactions between localized orbitals obtained by natural bond analysis. The effects are even larger in free radicals and can be analyzed using the same model. Received: 13 March 1998 / Accepted: 13 July 1998 / Published online: 9 October 1998     

A theoretical investigation of the gas-phase oxidation reaction of the saturated tert-butyl radical.

The radical-radical reaction mechanisms and dynamics of ground-state atomic oxygen [O(3P)] with the saturated tert-butyl radical (t-C4H9) are investigated using the density functional method and the complete basis set model. Two distinctive reaction pathways are predicted to be in competition: addition and abstraction. The barrierless addition of O(3P) to t-C4H9 leads to the formation of an energy-rich intermediate (OC4H9) on the lowest doublet potential energy surface, which undergoes subsequent direct elimination or isomerization-elimination leading to various products: C3H6O + CH3, iso-C4H8O + H, C3H7O + CH2, and iso-C4H8 + OH. The respective microscopic reaction processes examined with the aid of statistical calculations, predict that the major addition pathway is the formation of acetone (C3H6O) + CH3 through a low-barrier, single-step cleavage. For the direct, barrierless H-atom abstraction mechanism producing iso-C4H8 (isobutene) + OH, which was recently reported in gas-phase crossed-beam investigations, the reaction is described in terms of both an abstraction process (major) and a short-lived addition dynamic complex (minor).     

IR, Raman and theoretical ab initio RHF study of aminoglutethimide — an anticancer drug

A comparative analysis of the IR and Raman spectra of aminoglutethimide (AG) dissolved in CCl₄, CHCl₃ and CH₃CN was performed. Most of the absorption bands were assigned to characteristic group vibrations with the use of the IR and Raman spectra of deuterated AG, glutethimide, N-methyl glutethimide and glutarimide. The AG samples very weakly interacting with the environment were studied with the use of the Ar matrix isolation IR spectra. For comparison, the IR and Raman spectra of the crystalline samples formed by hydrogen-bonded AG molecules were recorded. The spectra were analyzed also in terms of normal modes and the harmonic approximation with the use of the ab initio restricted Hartree-Fock theory. It was found that increasing the solute concentration in CCl₄ and CHCl₃ leads to formation of the autoassociates. In CH₃CN the solute–solvent AG–CH₃CN dimers occur. Possible structures of the associates were theoretically studied on the model systems: the centrosymmetric glutarimide dimer and the linear AG–CH₃CN dimer. By a comparison of the theoretical and experimental spectra we were able to identify several peaks originating from the solute–solvent interactions.     

The influence of the ligand structure on activation of hafnocene polymerization catalysts: A theoretical study

The influence of ligand structure of hafnocenes on activation of the polymerization catalysts has been studied by quantum chemical methods. Altogether 54 hafnocenes were included in the analysis, supplemented by four zirconocenes for comparison. The trends in structural and electronic parameters relevant in the catalyst activation step were studied for the dichloride, dimethyl and cationic monomethyl forms of the catalysts. The effects of ligand modifications were analyzed as functions of the metal, ancillary cyclopentadienyl-based ligand, ligand substituent and the ligand bridge, making comparisons to experimental data. Generally, large aromatic ligands together with electron donating ligand substituents stabilize the catalytically active species, thus facilitating the catalyst activation process. The obtained trends are expected to aid in the development of new high-performance polymerization catalysts.     

Synthesis and Characteristics of Bis(2, 2‐dinitroethyl‐N‐nitro)ethylenediamine‐Based Energetic Salts

New energetic bis(2, 2‐dinitroethyl‐N‐nitro)ethylenediamine‐based salts exhibiting moderate physical properties, good detonation properties, and relatively low impact sensitivities were synthesized in high yield by direct reactions of bis(2, 2‐dinitroethyl‐N‐nitro)ethylenediamine with organic bases. The resulting salts were fully characterized by multinuclear NMR spectroscopy (¹H and ¹³C), vibrational spectroscopy (IR), differential scanning calorimetry (DSC), and elemental analysis. Solid‐state ¹⁵N NMR spectroscopy was used as an effective technique to further determine the structure of some products. Thermal decomposition kinetics and several thermodynamic parameters of some salts were obtained under non‐isothermal conditions by DSC. The densities of the energetic salts paired with organic cations were in the range 1.60–1.89 g · cm^–3 as measured with a gas pycnometer. Based on the measured densities and calculated heats of formation, detonation pressures and velocities were calculated using Explo 5.05 and found to be 23.6–44.8 GPa and 7790–9583 m · s^–1, respectively, which make them potentially useful as energetic materials.     

Binding mechanism of RGD and its mimetics to receptor GPIIb/IIIa. A theoretical study

In order to better understand, at a sub-molecular level, the minimal structural requirements for the recognition process in the platelet aggregation inhibitory activity, a series of RGD mimetics were examined as fibrinogen receptor antagonists variants. We simulate the electronic interactions between RGD with its biological receptor in terms of smaller molecules. MeCOO⁻ was used to mimic the side chain of deprotonated Asp and Meguanidinium group mimicked the side chain of the protonated Arg. Alternative moieties present on the RGD mimetics were also studied in this report. AM1; RHF/3-21G; B3LYP/6-31++G^** in the gas phase. Also, B3LYP/6-31++G^** calculations using the IPCM solvation model were carried out for all the complexes. Our results indicate that high level of theory calculations and the inclusion of solvent effects are crucial in order to obtain satisfactory of accuracy in the electronic distributions of these compounds.     

Hydration of inorganic phosphates in crystal lattices and in aqueous solution. An experimental and theoretical study

B3LYP/6-31G* and 6-311++G** calculations have been carried out in order to study the hydration of phosphates in aqueous media. Optimized geometries and relative stabilities for PO4(-3), HPO(4)-2, H2PO4(-1) have been calculated considering the interaction with one, two, three, four and five discrete water molecules and taking into account the solvent effect by using the self-consistent reaction field theory (Onsager and PCM methods). The role of specific and bulk contributions of solvent effect on the observable properties of phosphate compounds is analysed. Good agreement between theoretical and available experimental results of harmonic vibration frequencies is found. Significant effects on the geometrical and vibrational frequencies are found for those studied phosphate anions. The results presented here provide a first step toward the understanding of the phosphate group as a hydration sensor in lipid bilayers.