Modeling η5‐C5Me4SiMe3 with η3‐C3H5 for DFT study of a tetranuclear yttrium polyhydrido complex [(η5‐C5Me4SiMe3)YH2]4

π‐Allyl (η³‐C₃H₅), a four‐electron donor, was used as a ligand model to replace η⁵‐C₅Me₄SiMe₃ in DFT calculations on the tetranuclear yttrium polyhydrido complex (η⁵‐C₅Me₄SiMe₃)₄Y₄H₈ containing a Y₄H₈ tetrahedral core structure, which may separate the four π‐allyl groups and hence suppress the allyl ligand coupling during the computation. In terms of the calculated core geometry, isomerization energy barrier, charge population, and frontier orbital features of the complex, the η³‐C₃H₅ ligand model is comparable to η⁵‐C₅H₅. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Molecular modeling of cytochrome P450 3A4

The three-dimensional structure of human cytochrome P450 3A4 was modeled based on crystallographic coordinates of four bacterial P450s: P450 BM-3, P450cam, P450terp, and P450eryF. The P450 3A4 sequence was aligned to those of the known proteins using a structure-based alignment of P450 BM-3, P450cam, P450terp, and P450eryF. The coordinates of the model were then calculated using a consensus strategy, and the final structure was optimized in the presence of water. The P450 3A4 model resembles P450 BM-3 the most, but the B helix is similar to that of P450eryF, which leads to an enlarged active site when compared with P450 BM-3, P450cam, and P450terp. The 3A4 residues equivalent to known substrate contact residues of the bacterial proteins and key residues of rat P450 2B1 are located in the active site or the substrate access channel. Docking of progesterone into the P450 3A4 model demonstrated that the substrate bound in a 6-orientation can interact with a number of active site residues, such as 114, 119, 301, 304, 305, 309, 370, 373, and 479, through hydrophobic interactions. The active site of the enzyme can also accommodate erythromycin, which, in addition to the residues listed for progesterone, also contacts residues 101, 104, 105, 214, 215, 217, 218, 374, and 478. The majority of 3A4 residues which interact with progesterone and/or erythromycin possess their equivalents in key residues of P450 2B enzymes, except for residues 297, 480 and 482, which do not contact either substrate in P450 3A4. The results from docking of progesterone and erythromycin into the enzyme model make it possible to pinpoint residues which may be important for 3A4 function and to target them for site-directed mutagenesis.     

Thermal degradation of poly(vinyl chloride)

This paper presents an initial attempt at describing poly(vinyl chloride) (PVC) thermal degradation through a semi-detailed and lumped kinetic model. A mechanism of 40 species and pseudocomponents (molecules and radicals) involved in about 250 reactions permits quite a good reproduction of the main characteristics of PVC degradation and volatilization. The presence of the two step mechanism—the first step of which corresponds to dehydrochlorination and the second to the tar release and residue char formation—are correctly predicted both in quantitative terms and in the temperature ranges. The model was validated by comparison with several thermo gravimetric analyses, both dynamic at different heating rates, and isothermal. When compared with the typical one step global apparent degradation models, the approach proposed here spans quite large operative ranges, especially when it comes to predicting product distributions. The initial results of these product predictions, even though quite preliminary, are encouraging and confirm the validity of the model.     

A genetic algorithm for the automated generation of small organic molecules: Drug design using an evolutionary algorithm

Rational drug design involves finding solutions to large combinatorial problems for which an exhaustive search is impractical. Genetic algorithms provide a novel tool for the investigation of such problems. These are a class of algorithms that mimic some of the major characteristics of Darwinian evolution. LEA has been designed in order to conceive novel small organic molecules which satisfy quantitative structure-activity relationship based rules (fitness). The fitness consists of a sum of constraints that are range properties. The algorithm takes an initial set of fragments and iteratively improves them by means of crossover and mutation operators that are related to those involved in Darwinian evolution. The basis of the algorithm, its implementation and parameterization, are described together with an application in de novo molecular design of new retinoids. The results may be promising for chemical synthesis and show that this tool may find extensive applications in de novo drug design projects.     

Comparative receptor mapping of serotoninergic 5-HT3 and 5-HT4 binding sites*

The clinical use of currently available drugs acting at the5-HT₄ receptor has been hampered by their lack of selectivityover 5-HT₃ binding sites. For this reason, there is considerableinterest in the medicinal chemistry of these serotonin receptor subtypes, andsignificant effort has been made towards the discovery of potent and selectiveligands. Computer-aided conformational analysis was used to characterizeserotoninergic 5-HT₃ and 5-HT₄ receptorrecognition. On the basis of the generally accepted model of the5-HT₃ antagonist pharmacophore, we have performed a receptormapping of this receptor binding site, following the active analog approach(AAA) defined by Marshall. The receptor excluded volume was calculated as theunion of the van der Waals density maps of nine active ligands(pK_i 8.9), superimposed in pharmacophoric conformations.Six inactive analogs (pK_i < 7.0) were subsequently used todefine the essential volume, which in its turn can be used to define theregions of steric intolerance of the 5-HT₃ receptor. Five activeligands (pK_i 9.3) at 5-HT₄ receptors wereused to construct an antagonist pharmacophore for this receptor, and todetermine its excluded volume by superimposition of pharmacophoricconformations. The volume defined by the superimposition of five inactive5-HT₄ receptor analogs that possess the pharmacophoric elements(pK_i 6.6) did not exceed the excluded volume calculated forthis receptor. In this case, the inactivity may be due to the lack of positiveinteraction of the amino moiety with a hypothetical hydrophobic pocket, whichwould interact with the voluminous substituents of the basic nitrogen ofactive ligands. The difference between the excluded volumes of both receptorshas confirmed that the main difference is indeed in the basic moiety. Thus,the 5-HT₃ receptor can only accommodate small substituents inthe position of the nitrogen atom, whereas the 5-HT₄ receptorrequires more voluminous groups. Also, the basic nitrogen is located at ca.8.0 Å from the aromatic moiety in the 5-HT₄ antagonistpharmacophore, whereas this distance is ca. 7.5 Å in the5-HT₃ antagonist model. The comparative mapping of bothserotoninergic receptors has allowed us to confirm the three-componentpharmacophore accepted for the 5-HT₃ receptor, as well as topropose a steric model for the 5-HT₄ receptor binding site. Thisstudy offers structural insights to aid the design of new selective ligands,and the resulting models have received some support from the synthesis of twonew active and selective ligands: 24 (K_i(5-HT₃)= 3.7 nM; K_i(5-HT₄) > 1000 nM) and 25(K_i(5-HT₄) = 13.7 nM;K_i(5-HT₃) > 10 000 nM).     

Localized Orbitals vs. Pseudopotential-Plane Waves Basis Sets: Performances and Accuracy for Molecular Magnetic Systems

 Density functional theory, in combination with a) a careful choice of the exchange-correlation part of the total energy and b) localized basis sets for the electronic orbitals, has become the method of choice for calculating the exchange-couplings in magnetic molecular complexes. Orbital expansion on plane waves can be seen as an alternative basis set especially suited to allow optimization of newly synthesized materials of unknown geometries. However, little is known on the predictive power of this scheme to yield quantitative values for exchange coupling constants J as small as a few hundredths of eV (50–300 cm⁻¹). We have used density functional theory and a plane waves basis set to calculate the exchange couplings J of three homodinuclear Cu-based molecular complexes with experimental values ranging from +40 cm⁻¹ to −300 cm⁻¹. The plane waves basis set proves as accurate as the localized basis set, thereby suggesting that this approach can be reliably employed to predict and rationalize the magnetic properties of molecular-based materials. Corresponding author. E-mail: Carlo.Massobrio@ipcms.u-strasbg.fr Received August 5, 2002; accepted August 9, 2002     

Isoindole Cycloadditions. Part III: The Synthesis of "Windscreen Wiper" and Other N-Bridged Cavity Systems

The thermal addition of N-carbobenzyloxyisoindole (N-Z isoindole) 11a, generated by the reaction of 3,6-di(2-pyridyl)-s-tetrazine 9 with N-Z 7-azabenzonorbornadiene 8a, onto dimethyl tricyclo[4.2.1.0^2.5]nona-3,7-diene-3,4-dicarboxylate 17 occurred site selectively at the cyclobutene -bond to form a stereoisomeric mixture of 1 : 1-adducts 18 and 19, in which the bent-frame isomer 19 was dominant (ratio 5 : 1). In contrast, N-benzyl tetrafluoroisoindole 11c reacted with 17 only under high-pressure conditions (14 kbar, RT, 4 days) to afford 1 : 1-adducts at the cyclobutene site, in which the extended-frame isomer 18c was dominant and the accompanying bent-frame product 19c reverted to starting materials soon after isolation. These same stereoselectivities were used to prepare "windscreen wiper" compound 28c having two mobile N-benzyl substituents attached to a rigid scaffold by the reaction of N-benzyl tetrafluoroisoindole 11c with tetramethyl tetracyclo[4.4.1.0.^2,5.0^7.10]undeca-3,8-diene-3,4,7,8-tetracarboxylate 23. Cavity bis-(cyclobutene-1,2-diester) 6 reacted with N-benzyl tetrafluoroisoindole 11c twice over to produce cavity structure 36 with two O- and two N-benzyl bridges on the inner face, whereas the narrower cavity bis-alkene 32 stopped at the 1 : 1-addition stage. The dynamics of the Z-group in the dual adducts 26a–28a are discussed briefly and key adducts and cavity systems have been structurally evaluated by X-ray crystallography, VT NMR, and molecular modeling.     

Interaction of chromophore, 11-<Emphasis Type="Italic">cis</Emphasis>-retinal,with amino acid residues of the visual pigment rhodopsin in the region of protonated Schiff base: A molecular dynamics study

A molecular dynamics study of the dark adapted visual pigment rhodopsin molecule was carried out. The interaction of the chromophore group, 11-cis-retinal, with the nearest amino acid residues in the chromophore center of the molecule, namely, in the region of the protonated Schiff base linkage, was analyzed. Most likely, the interaction of the CH=NH bond with the negatively charged amino acid residue Glu113 cannot be described as a simple electrostatic interaction of two oppositely charged groups. One can propose that not only Glu113 but also Glu181 and Ser186 are involved in stabilization of the protonated Schiff base linkage. Accord-ing to calculations, Glu181 interacts, as the counter-ion, with the Schiff base indirectly via Ser186. The intramolecular mechanisms of protonated Schiff base stabilization in rhodopsin are discussed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 19–27, January, 2007.     

Modeling of an inductively coupled plasma at reduced pressures

Plasma sintering experiments in this laboratory at reduced pressures revealed efficient heating of the ceramic sample due to recombination of dissociated and/or ionized species on the surface. For establishing a model for this plasma sintering process, it is necessary to first consider the plasma itself. Therefore, a suitable model for an RF inductively coupled plasma has been developed considering reduced pressures. As the pressure decreases, the electron density also decreases at a fixed electron temperature, causing substantial deviations from chemical equilibrium. Due to the poor collisional coupling between electrons and heavy particles at reduced pressures, large deviations from kinetic equilibrium have also to be expected. The model is based on a rotationally symmetric plasma contained in a quartz tube. The power level ranges from 1.5 to 3 kW and the operating pressure is varied from 1 to 0.01 atm. Both deviations from chemical and kinetic equilibrium are included in this model. Thermodynamic and transport properties for two-temperature plasmas are used for this modeling work. The results indicate that for pressures below 0.1 atm, there is a strong ambipolar flux of charge carriers to the confining walls, leading to significant variations of the temperature across the tube. The electron temperature increases rapidly as the pressure decreases, whereas the heavy-particle temperature decreases.     

X-ray, Raman and FTIRS studies of the microstructural evolution of zirconia particles caused by the thermal treatment

Genesis of the structure of zirconia particles prepared by precipitation of amorphous hydrated zirconia by ammonia from the ZrO(NO₃)₂ solution followed by a mild hydrothermal treatment (HTT) of precipitate, washing and calcination under air up to 1000 °C has been studied by X-ray diffraction (XRD), Raman and FTIRS. As revealed by FTIRS of lattice modes, the local structure of amorphous zirconia subjected to HTT is close to that in m-ZrO₂. This helps to obtain nearly single-phase monoclinic nanozirconia (particle size 5-15 nm) already after a mild calcination at 500 °C. Stability of this phase with nanoparticles sizes below the critical value determined by thermodynamic constraints is due to its excessive hydroxylation demonstrated by FTIRS. Dehydroxilation and sintering of these nanoparticles at higher (600-650 °C) temperatures of calcination leads to reappearance of the (111) “cubic” reflection in XRD patterns. Modeling of XRD patterns revealed that this phenomenon could be explained by polysynthetic (001) twinning earlier observed by HRTEM.