Modeling of serine protease prototype reactions with the flexible effective fragment potential quantum mechanical/molecular mechanical method

A complete cycle of chemical transformations for the serine protease prototype reaction is modeled following calculations with the flexible effective fragment quantum mechanical/molecular mechanical (QM/MM) method. The initial molecular model is based on the crystal structure of the trypsin–bovine pancreatic trypsin inhibitor complex including all atoms of the enzyme within approximately 15–18 Å of the oxygen center O of the catalytic serine residue. Several selections of the QM/MM partitioning are considered. Fractions of the side chains of the residues from the catalytic triad (serine, histidine and aspartic acid) and a central part of a model substrate around the C–N bond to be cleaved are included into the QM subsystem. The remaining part, or the MM subsystem, is represented by flexible chains of small effective fragments, whose potentials explicitly contribute to the Hamiltonian of the QM part, but the corresponding fragment–fragment interactions are described by the MM force fields. The QM/MM boundaries are extended over the C–C bonds of the peptides assigned to the QM subsystem in the enzyme, C–C and C–N bonds in model substrates. Multiple geometry optimizations have been performed by using the RHF/6-31G method in the QM part and OPLSAA or AMBER sets of MM parameters, resulting in a series of stationary points on the complex potential-energy surfaces. All structures generally accepted for the serine protease catalytic cycle have been located. Energies at the stationary points found have been recomputed at the MP2/6-31+G^* level for the QM part in the protein environment. Structural changes along the reaction path are analyzed with special attention to hydrogen-bonding networks. In the case of a model substrate selected as a short peptide CH₃(NHCO-CH₂)₂ – HN–CO–(CH₂–NHCO)CH₃ the computed energy profile for the acylation step shows too high activation energy barriers. The energetics of this rate-limiting step is considerably improved, if more realistic model for the substrate is considered, following the motifs of the ThrI11–GlyI12–ProI13-–CysI14–LysI15–AlaI16–ArgI17–IleI18–IleI19 sequence of the bovine pancreatic trypsin inhibitor.     

Molecular caps for full quantum mechanical computation of peptide-water interaction energy

We present a systematic study of numerical accuracy of various forms of molecular caps that are employed in a recently developed molecular fractionation scheme for full quantum mechanical computation of protein-molecule interaction energy. A previously studied pentapeptide (Gly-Ser-Ala-Asp-Val) or P5 interacting with a water molecule is used as a benchmark system for numerical testing. One-dimensional potential energy curves are generated for a number of peptide-water interaction pathways. Our study shows that various forms of caps all give consistently accurate energies compared to the corresponding full system calculation with only small deviations. We also tested the accuracy of cutting peptide backbone at different positions and comparisons of results are presented.     

STUDY ON FLUORESCENCE BEHAVIOUR OF EU~(3+) CONTAINING POLY(METHYL METHACRYLATE)

Fluorimetry has been used to characterize ionomers synthesized by copolymerization ofmethyl mehacrylate, methacrylic acid and europium methacrylate (EMA). Under excita-tion of UV light at 375 nm no seif-quenching was found in fluorescence of EMA containingionomers at 615nm within the concentration range of 1.6×10~(-2) to 11.49×10~(-2) mol%.This means that the distance between two Eu~(3+) ions is larger than 5nm. In the sameconcentration range seif-quenching took place in europium octanoate (EOA) containingpoly(methyl methacrylate) in which EOA was doped as an additive.     

Mechanical,thermal and morphological properties of poly(ε‐caprolactone)/zein blends

Blends of poly(ε‐caprolactone) (PCL) with zein (PCL/zein) in different proportions (100/0, 75/25, 50/50, 25/75 and 0/100 wt% containing 5 wt% glycerol) were compared based on their mechanical properties (tensile strength, elongation at break, and Young's modulus), and on their thermal properties, the latter determined by thermogravimetric analysis (TGA) and dynamic mechanical thermal analysis (DMTA). The morphology of the materials was studied by scanning electron microscopy (SEM). Blends of PCL/zein showed reduced tensile strength and elongation at break, but increased Young's modulus compared to the pure polymers, in agreement with the DMTA and SEM results. These findings indicated that PCL and zein were incompatible. TGA showed that the thermal stability was enhanced by the addition of zein to PCL, whereas SEM showed a poor interfacial interaction between the polymers. Copyright © 2004 John Wiley & Sons, Ltd.     

Mechanical properties of clay‐reinforced polyamide

Intercalated and exfoliated nanocomposites were prepared by extrusion and injection of polyamide‐6 and highly swollen or slightly swollen montmorillonite, respectively. The microstructure of the nanocomposites has been studied previously. In this article, we investigated the influence of the preferential orientation of the montmorillonite sheets on the mechanical properties of the nanocomposites. Dynamic mechanical analysis and tensile tests showed that the elastic modulus depends mainly on the filler loading. A parallel coupling could well account for the behavior of the nanocomposites. The calculated elastic and storage moduli of montmorillonite were set to 140 and 40 GPa, respectively. Compression tests were performed to study the anisotropy of the mechanical properties. The elastic modulus and flow strain were sensitive to the filler orientation. A Tandon–Weng approach was applied to consider the geometry of the filler. In all low‐deformation tests, no significant difference between intercalated and exfoliated systems was observed. Finally, the influence of the dispersion and exfoliation state of the filler on the ultimate properties of the nanocomposites (tensile tests) is discussed. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 40: 272–283, 2002     

Crosslinked polystyrene with improved mechanical properties

The synthesis of some divinyl monomers—bis(vinylphenyl)ethane ( 2 ), bis(vinylbenzyloxy)hexane ( 3a ), and bis(vinylbenzyloxy)dodecane ( 3b ) is reported. Copolymers of the new monomers and styrene were evaluated as an alternative to divinylbenzene-crosslinked polymers for use as matrices and absorbents. The mechanical properties and the amount of residual double bonds in the copolymers were compared. It was found that the new copolymers, unlike the divinylbenzene-crosslinked polymers, retained their mechanical strength even at high crosslinking degrees. Stress at break values of 79, 68, and 18 N/mm² were found for the polymers crosslinked with 20 mol % of 3a, 2 , and divinylbenzene; 5, 25 and 45% of the divinyl units in these polymers were left as pendant double bonds. Porous styrene– 2 copolymers were synthesized and shown to have lower surface areas than the corresponding divinylbenzene-crosslinked polymers. The pore size distribution showed that this was due to the absence of the smallest pores which are found in the divinylbenzene-crosslinked polymers in between heavily crosslinked nodules. © 1993 John Wiley & Sons, Inc.     

Laser field induced charge transfer: Para-nitroaniline coupled to a quantum mechanical radiation field

Summary We present a preliminary model for describing a solvated intramolecular charge transfer reaction coupled to a quantum mechanical radiation field. Actual calculations of energies and couplings were performed with a recently developed self-consistent reaction field response method. The representation of dressed molecular states is used for calculating state populations for various laser fields. The state populations are sensitive to the properties of the laser field.     

The effect of grass fiber filler on curing characteristics and mechanical properties of natural rubber

Natural rubber is reinforced with a novel type of grass fiber (Cyperus Tegetum Rox b). The effects of fiber loading of different mesh sizes on curing characteristics and mechanical properties of grass fiber filled natural rubber composite are studied. Since 400 mesh grass fiber loaded natural rubber composite shows superior mechanical properties, therefore the effect of silane coupling agent was studied for this particular composite. Here composites were prepared by using water leached grass fiber. Optimum cure time increases with the increase in fiber loading but the change in scorch time is less. The same trend of increase in optimum cure time is observed in the presence of Si69. But the value is higher compared to that of rubber composite without Si69. With increase in the fiber loading, modulus and hardness of the composite increases but tensile strength decreases. The mechanical properties of the composite, namely moduli at 200 and 300% elongation and hardness increase in the presence of Si69 but tensile strength is less compared to that of the composite without Si69. Elongation at break is not much affected due to the presence of Si69. Copyright © 2004 John Wiley & Sons, Ltd.     

Preparation and properties of composites made from rice straw and poly(vinyl chloride) (PVC)

Rice straw was employed for the preparation of lignocellulosic‐poly(vinyl chloride) (PVC) composites. The effect of pretreatment of rice straw, concentration of PVC, pressure as well as pressing temperature on the mechanical properties and water absorption was studied. Also, the effect of lignin as coupling agent on the mechanical properties and water absorption of composite was studied. Composites of rice straw comprising both PVC and a coupling agent offer superior properties compared to those made from only rice straw and PVC. The extent of improvement in the mechanical properties and dimensional stability of composites depended not only on the pretreatment of rice straw, concentration of PVC and lignin but also on pressure and pressing temperature. Copyright © 2004 John Wiley & Sons, Ltd.