Three different dissolved silane molecules adsorbed at a polar ZnO surface (000&1macr;) are studied by means of constant temperature molecular dynamics simulations. The adsorbed single silane molecules exhibit a different behavior depending on the chemical nature of their tail. For octyltrihydroxysilane molecules with their rather unpolar tail an orthogonal orientation at the polar metal oxide surface is statistically favored with all three polar hydroxide groups of the head being in contact with the polar ZnO surface and the unpolar tail remaining in the isopropanol phase. On the contrary, due to their highly polar tail, aminopropyltrihydroxysilane molecules show a more or less parallel orientation at the surface. Apart from some minor fluctuations two hydroxide groups as well as the amino group of the tail are in contact with the surface. The behavior of the thiolpropyltrihydroxysilane molecules is somehow located in between resulting in parallel as well as orthogonal orientations of the molecule at the surface. Though many of the results obtained for single adsorbed silane molecules can also be transferred to adsorbed silane molecules within whole layers a remarkable difference appears: Now even for aminopropyltrihydroxysilane molecules a mixture of parallel and orthogonal alignment of the molecules can be observed whereas some of the octyltrihydroxysilane molecules also show a parallel orientation. 相似文献
The conformational properties of Met-enkephalin (Tyr-Gly-Gly-Phe-Met) were investigated by high temperature quenched molecular dynamics simulations in vapor. Each of these selected structures were then analyzed according to their backbone(φ,Ψ) conformational distributions and sorted into 13 families by computing the rms difference between the Cα-C backbone fragments of each residue over all the structures. Selected lowest energy conformations from each of 13 families were thoroughly energy minimized. The results of simulations show that Met-enkephalin is a flexible molecule. It shows a type Ⅰβ-turn, with the Gly2 carbonyl forming a hydrogen bond with the Met5 amino proton and a type Ⅱβ turn, with the Tyr1 amino proton forming a hydrogen bond with the Phe4 carbonyl. The multiple fit were carried out for all of the 13 conformers with morphine(9 atoms on the pharmacophore groups). F2 and F6 were the most similar to morphine. The rms were 0.0504 nm and 0.0726 nm. The results of simulations also show that Tyr amino N corresponds to N on piperidine ring in morphine, Tyr phenol corresponds to the phenol in morphine, the aromatic ring of Phe corresponds to the cyclohexene ring in morphine. The distances between the three pharmacophores, d1 (Tyr N to Tyr OH), d2 (Tyr N to Tyr du1), d3(Tyr N to Phe du2) and d4(Tyr N to Phe du2) were found to be about 0.8, 0.5, 0.7-0.9 and 0.5 nm, respectively, the corresponding, distances of morphine were found to be 0.7697(N18 to O6),0.5143(N18 to du25), 0.3962(N18 to du24)和0.5566(N18 to O15)nm. Therefore, they may be acted on the same receptor. This model should aid in pharmaceutical design of peptide and nonpeptide ligands with opioid. 相似文献
The interactions between konjac glucomannan and carrageenan were studied with the method of molecular dynamics simulation. Part representative structure segments of KGM and two unit structures of κ-carrageenan （Fig. 2） were used as mode, and the force-field was AMBER2. The stability and sites of konjac glucomannan/carrageenan interactions in water were researched at 373 K with the following results： the potential energy （EPOT） of the mixed gel was dropped, while those of single-konjac glucomannan gel and single carrageenan were increased. The surface area （SA） of KGM in the mixed system was decreased to 1002.2A^°^2, and that of carrageenan to 800.9 A^°^2. The variations of two parameters showed that the stability of compound gel konjac glucomannan/carrageenan was improved, which is consistent with the previous studies. The sites of interactions in the mixed gel were the -OH groups on C（2）, C（4） and C（6）, the acetyl group in KGM mannose, and the -OH group on C（6） in carrageenan. The hydrogen bond was formed directly or indirectly by the bridge of waters. 相似文献
The influence of the density and the type of surface oxygen on the adsorption of berberine alkaloid onto activated carbon was investigated using the molecular dynamics simulation method in vacuum. The carbon surface consisted of a basal plane of graphite and surface oxygen groups which were bonded on the graphite plane in a regular square array with various densities. Two types of surface oxygen groups, =O and —OH, were employed. The simulation results showed that the berberine alkaloids were favorable to be adsorbed on the negative charged carbon surfaces. It was indicated that the vdw attraction of the carbon surface to the alkaloid molecule dominates the adsorption only at the lower surface density of oxygen. It is also indicated that a good adsorptive selectivity for a certain berberine alkaloid can be obtained by controlling the density of surface oxygen.The adsorption simulation of berberine alkaloids onto activated carbon in the presence of water was also carried out by using a dome-shape molecular model for presenting the alkaloid/water/carbon system. It was found that the adsorption of berberine alkaloids on the activated carbon which has a higher density of surface oxygen was strongly inhibited by the presence of water. 相似文献
Summary: We describe molecular dynamics simulations of α‐tetrathiophene molecules deposited on a flat graphite substrate, at two different temperatures (300 K and 400 K) and several degrees of coverage (from approximately one to three molecular layers). The simulations employ a modified version of the CFF91 force field, with the torsion parameters tailored on high‐level ab initio calculations on 2,2′‐bithiophene. We found that the molecules in the first layer were relatively planar and packed against the underlying surface, while those outside it were not arranged in well‐defined layers and were more conformationally disordered. On the time scale of the simulation, the molecules did not crystallize but rather achieved a liquid crystalline‐like state with their average director parallel to the surface.
Side view of the final configuration in the simulation of 24 tetrathiophenes at 300 K. Molecules are depicted with different shades of gray according to their z coordinate (first, second or third layer). 相似文献
