Modeling of H2 and H2/CH4 Moderate-Pressure Microwave Plasma Used for Diamond Deposition

One-dimensional transport models of moderate-pressure H ₂ and H ₂ /CH ₄ plasmas obtained in a diamond deposition microwave reactor are presented. These models describe the plasma as a thermochemically nonequilibrium flow with three different energy modes. The solution of the one-dimensional plasma transport equations enabled the estimation of plasma species concentrations and temperatures on the axis of the reactor. As far as pure H ₂ plasmas are concerned, results showed that the model predictions of gas and vibration temperatures are in good agreement with experimental measurements. The model also yields a relatively good qualitative prediction of the variations of H-atom mole fraction with the power density absorbed by the plasma. The results obtained for H ₂ /CH ₄ discharges showed that the model prediction on the variations of H-atom mole fraction with methane percentage in the discharge is in good qualitative agreement with experimental results. They also showed that methane is rapidly converted to acetylene before reaching the discharge zone. The concentrations of neutral hydrocarbon species in the reactor are mainly governed by thermal chemistry. The addition of methane strongly affects the ionization kinetics of the plasma. Three major ions are generally obtained in H ₂ /CH ₄ plasmas: C ₂ H ₂ ⁺ , C ₂ H ₃ ⁺ , and C ₂ H ₅ ⁺ . The relative predominance of these ions depends on the considered plasma region and on the discharge conditions. The ionic species concentrations are also mainly governed by chemistry, except very near the substrate surface. Finally the use of this transport model along with the surface chemistry model of Goodwin ⁽¹⁾ enabled us to estimate the diamond growth rate for several discharge conditions.     

THE STRUCTURAL BASIS OF THE POOR FIBRIN SPECIFICITY OF UROKINASE(Ⅰ)——KNOWLEDGE-BASED PREDICTION OF KRINGLE STRUCTURES OF UROKINASE AND ITS RELATED PROTEINS

The Kringle-1 structure of plasminogen (PGK-1), the Kringle-2 structure of tissue plasminogen activator (PAK-2) and the Kringle structure of prourokinase (UKK) has been modeled on the basis of the three-dimensional structure of Kringle-1 of prothrombin (PTK-1) at 2.8 resolution. The predicted three-dimensional structure of these Kringles shows that the binding site of PGK-1 is characterized by an apparent dipolar site, the polar parts of which are separated by a hydrophobic region. PAK-2 possesses the anionic center but has not a cationic binding center which might be provided by a guanidinium group from Arg-69 located adjacent to the Arg-71 position. UKK possesses neither the anionic binding center nor the cationic center which are probably the main reason for the poor fibrin specificity of urokinase.     

Modeling and simulation of free radical polymerization of styrene under semibatch reactor conditions

The first part of this approach is concerned with the elaboration of a radical polymerization model of styrenne, based on a kinetic diagram that includes chemical and thermal initiation, propagation, termination by recombination and chain transfer to the monomer. Furthermore, volume contraction during polymerization is considered, as well as the gel and glass effects. The mathematical formalism that describes the model in terms of moments is explored in detail. The model was then used to predict the changes in monomer conversion and molecular weight after intermediate addition of initiator and monomer. The results of this operation are dependent on the conditions of the reaction mass, quantity, and moment of substance addition. Therefore, the simulations were performed at different times with respect to the gel effect; before, during and after this phenomenon, and also with respect to different temperatures and initiators. Increasing the initiator concentration before the gel effect leads to an earlier appearance of the phenomenon and to a decrease in molecular weight. The ratio reveals a polydispersity index smaller for the intermediate addition of initiator. No significant changes take place during or after the gel effect. If along with the initiator, unreacted monomver (used to dissolve the initiator) enters the reactor, a small dip in conversion is observed. The general conclusion of this paper reveals the intermediate addition of initiator as a method to control polymer properties and to prevent the “dead-end” polymerization of styrene.     

An evaluation of molecular models of the cytochrome P450 Streptomyces griseolus enzymes P450SU1 and P450SU2

Summary P450SU1 and P450SU2 are herbicide-inducible bacterial cytochrome P450 enzymes from Streptomyces griseolus. They have two of the highest sequence identities to camphor hydroxylase (P450cam from Pseudomonas putida), the cytochrome P450 with the first known crystal structure. We have built several models of these two proteins to investigate the variability in the structures that can occur from using different modeling protocols. We looked at variability due to alignment methods, backbone loop conformations and refinement methods. We have constructed two models for each protein using two alignment algorithms, and then an additional model using an identical alignment but different loop conformations for both buried and surface loops. The alignments used to build the models were created using the Needleman-Wunsch method, adapted for multiple sequences, and a manual method that utilized both a dotmatrix search matrix and the Needleman-Wunsch method. After constructing the initial models, several energy minimization methods were used to explore the variability in the final models caused by the choice of minimization techniques. Features of cytochrome P450cam and the cytochrome P450 superfamily, such as the ferredoxin binding site, the heme binding site and the substrate binding site were used to evaluate the validity of the models. Although the final structures were very similar between the models with different alignments, active-site residues were found to be dependent on the conformations of buried loops and early stages of energy minimization. We show which regions of the active site are the most dependent on the particular methods used, and which parts of the structures seem to be independent of the methods.     

Ionization energy reductions in small 2,5-dihydroxybenzoic acid-proline clusters

The photoionization of (pro)(n)DHB (pro = proline, DHB = 2,5-dihydroxybenzoic acid, n = 0, 1, 2 or 4) clusters was studied both experimentally and computationally. Experimentally the (pro)(n)DHB clusters are generated in the gas phase by laser desorption and supersonic jet entrainment. The photoionization thresholds are then determined by the mass-selective measurement of both one- and two-color photoionization efficiency curves. These experiments demonstrate that the ionization energies (IEs) of the (pro)(n)DHB clusters are substantially reduced in comparison with the IE of free DHB. Computational studies of the (pro)(n)DHB clusters provide insights into the mechanism of IE reduction. For the (pro)DHB system the IE reduction results from spin delocalization in the ion state of the cluster. In contrast, for the (pro)(2)DHB and (pro)(4)DHB clusters the IE reduction results from an inductive delocalization of electron density from pro to DHB in the ground state of the cluster. This latter effect, which is a result of the specific hydrogen-bonding interactions occurring in the mixed clusters, leads to IE reductions of >1 eV. Finally, determination of the energetics of the (pro)(2)DHB radical cation demonstrate that the DHB-to-proline proton transfer reaction is a barrierless, exoergic process in the ion state and that energetic demands for cluster dissociation to protonated (pro)(2) plus a deprotonated DHB radical are substantially lower than those for cluster dissociation to (pro)(2) plus DHB(+*). Cumulatively, these studies provide new energetic and mechanistic insights into both primary and secondary MALDI ionization processes.     

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).