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91.
Molecular mechanics (MM) calculations have been performed on the title compounds. For the MM minimum energy conformation obtained by conformational analysis, molecular orbital (MO) calculations (MNDO and AM1) have also been performed. The geometries obtained have been compared with the experimental ones extracted from the Cambridge Structural Database (CSD). A qualitative structure-activity relationship has been pointed out based on the electrostatic potentials calculated at different positions on the electronic surface. 相似文献
92.
M. I. El-Barghouthi N. A. Masoud J. K. Al-Kafawein M. B. Zughul A. A. Badwan 《Journal of inclusion phenomena and macrocyclic chemistry》2005,53(1-2):15-22
The solubility of risperidone (Risp) in aqueous buffered cyclodextrin (CD) solution was investigated for α-, β-, γ- and HP-β-CD. The effects of pH, ionic strength and temperature on complex stability were also explored. Neutral Risp tends to form
higher order complexes (1:2) with both β- and HP-β-CD, but only 1:1 type complexes with α-, and γ-CD. The tendency of Risp to complex with cyclodextrins is in the order β-CD > HP-β-CD > γ-CD > α-CD. The 1:1 complex formation constant of Risp/HP-β-CD increases with increasing ionic strength in an opposite trend to the inherent solubility (S
0) of Risp, thus indicating significant hydrophobic effect. The hydrophobic effect contributes to the extent of 72% towards
neutral Risp/HP-β-CD complex stability, while specific interactions contribute only 4.7 kJ/mol. Thermodynamic studies showed that 1:1 Risp/HP-β-CD complex formation is driven by a favorable enthalpy change (ΔH
0=−31.2 kJ/mol, ΔS
0=−7 J/mol.K) while the 1:2 complex is largely driven by entropy changes (ΔH
0=−5.0 kJ/mol, ΔS
0=42 J/mol.K). Complex stability was found to vary with pH, with a higher formation constant for neutral Risp. Molecular mechanical
computations using MM (atomic charges and bond dipole algorithms) and Amber force fields, which were carried out to explore
possible sites of interactions between Risp and CDs and to rationalize complex stoichiometry, produced similar results concerning
optimal inclusion complex geometries and stoichiometries. 相似文献
93.
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. 相似文献
94.
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. 相似文献
95.
Julie A. Braatz Michael B. Bass Rick L. Ornstein 《Journal of computer-aided molecular design》1994,8(5):607-622
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. 相似文献
96.
Kinsel GR Knochenmuss R Setz P Land CM Goh SK Archibong EF Hardesty JH Marynick DS 《Journal of mass spectrometry : JMS》2002,37(11):1131-1140
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. 相似文献
97.
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 相似文献
98.
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. 相似文献
99.
A. Marongiu T. Faravelli G. Bozzano M. Dente E. Ranzi 《Journal of Analytical and Applied Pyrolysis》2003,70(2):519-553
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. 相似文献
100.
María L. López-Rodríguez María José Morcillo Bellinda Benhamú María Luisa Rosado 《Journal of computer-aided molecular design》1997,11(6):589-599
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(pKi 8.9), superimposed in pharmacophoric conformations.Six inactive analogs (pKi < 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 (pKi 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(pKi 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 (Ki(5-HT3)= 3.7 nM; Ki(5-HT4) > 1000 nM) and 25(Ki(5-HT4) = 13.7 nM;Ki(5-HT3) > 10 000 nM). 相似文献