No description available.

No description available.

No description available.

Molecular dynamic simulation is utilized to investigate the adsorption mechanism of water molecules surrounding Au nanoparticle of different sizes. We selected 13, 55, 147 atoms icosahedral gold nanopartilce in our model and their diameter are 7.92Å, 13.2Å, 18.5Å, respectively. We calculated density profile of water molecules and found that there were two adsorption layers out of the surface of gold nanoparticles. We also calculated average number of hydrogen bonds per water . It is higer in the adsorption layer than in bulk water region and we found that the direction of hydrogen bonds are numerously parallel with gold surface in the adsorption layer. We also claculated orientational order parameter for water molecules and explore the difference of the tetrahedral structure of the water molecules between the adsorption layer and bulk water region. Besides, we compared of cases of different gold sizes.

In recent years, the characteristic of Nano fluid channel has important contribute in bio-technology and nano-machine. Gold atoms in all materials have significant effects on human bodies, which have attracted considerable academic interests when applied to biotechnology. Especially the Au nanotubes has combine an excellent bio-compatible not only using in chemical analyzed and chemical inspect, but also has function on transport fluid molecule in micro channel. This study utilizes molecular dynamics to the behavior of water molecules inside Au nanotubes. We used the potential of Spohr, F3C and Tight-binding in different water density and temperature to investigate the adsorption mechanism and dynamic behavior of water molecules inside Au nanotubes. We discuss the numbers of absorbed water molecule near the inner tube wall all achieve to saturation at three different densities, temperature and size of Au nanotubes. This work we compared water density, the percentage profiles of hydrogen bond, orientational order and flux for water molecules inside the Au nanotubes.

Thesis (Ph.D.) in Physics--University of Maine, 2004. / Includes vita. Includes bibliographical references (leaves 100-104).

<p>In silico ligand docking is a versatile and common technique when predicting ligands and inhibitors for protein binding sites. The various docking programmes aim to calculate binding energies and to predict interactions, thus identifying potential ligands.The currently available programmes lack satisfying means by which to account for structural water molecules which can either mediate protein-ligand contacts or be displaced upon ligand binding. The present project aims to generate data to facilitate the global work of developing scoring functions in docking programmes to account for structural water molecules contribution to ligand binding to fill the said void. This is done by validating the performance of docking using a simple model system (cytochrome C peroxidase (CCP) W191G) containing four well ordered, deeply buried structural water molecules which are known to either interact with a ligand or to be displaced upon ligand binding.Known ligands were docked into eight (crystallographically determined) receptor set-ups comprising the receptor and no, one or two of the water molecules. The performance was validated by comparison of the binding modes of the docked ligands and the crystal structures, comparison of docking scores of the ligands in the different set-ups, enrichment of the ligands from a database of decoys and finally by predicting new ligands from the decoy database. In addition a high resolution crystal structure of CCP W191G in complex with 3-aminopyridine (3AP) was determined in order to resolve ambiguities in the binding mode of this ligand.</p>

Orientadores: Edvaldo Sabadini, Fred Yukio Fujiwara / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-05T11:17:03Z (GMT). No. of bitstreams: 1 Egidio_FernandadoCarmo_M.pdf: 997650 bytes, checksum: 3662c5dade756ee697c267ad8996aa15 (MD5) Previous issue date: 2005 / Resumo: Ciclodextrinas (CD) são oligossacarídeos cíclicos produzidos pela ação enzimática microbiológica sobre o amido. As três ciclodextrinas naturais disponíveis comercialmente são a-CD, b-CD e g-CD, constituídas por 6, 7 e 8 unidades glicosídicas, respectivamente. Possuem estrutura rígida representada como um cone truncado oco com cavidade hidrofóbica, formada pelos grupos CH2 e éter, e exterior hidrofílico, contendo os grupos hidroxila. Esses oligossacarídeos interagem com uma ampla variedade de moléculas, formando complexos de inclusão, e a interação com polímeros pode levar à formação de estruturas supramoleculares. As ciclodextrinas apresentam uma solubilidade anômala em água, com uma tendência irregular, sendo a b-CD aproximadamente dez vezes menos solúvel que as outras duas ciclodextrinas da série homóloga. O mesmo comportamento é observado quando D2O é o solvente, mas, neste caso, a solubilidade é ainda menor para as três ciclodextrinas. Pode-se explicar esse comportamento em termos do efeito causado pelas ciclodextrinas na estrutura do solvente e pela solvatação destas moléculas. A solvatação pode ser estudada por Ressonância Magnética Nuclear, RMN, através de medidas do tempo de relaxação transversal T2 do solvente. Os valores de T2 são diferentes para moléculas de solvente livres e ligadas à superfície do soluto, devido à processos dinâmicos, como a rotação molecular. O T2 é muito sensível à interação do solvente com o soluto, de forma que a presença de um soluto diminui o T2 das moléculas do solvente diretamente ligadas ao soluto. Este trabalho fez o estudo da solubilidade e solvatação das ciclodextrinas considerando também o equilíbrio entre o estado sólido e a solução saturada. Os cristais de ciclodextrinas foram estudados por Difração de Raios-X e Análise Termogravimétrica. A estrutura molecular dos oligômeros afetam sua flexibilidade, solvatação e acomodação no meio líquido, resultando na anomalia na solubilidade em H2O e D2O. / Abstract: Cyclodextrins (CD) are cyclic oligomers produced by the action of certain microbial enzymes on starch. The commercially available members of this series are a-CD, b-CD and g-CD, having 6, 7 and 8 glucose units, respectively. They have a rigid structure pictorially represented as a truncated cone with a hydrophobic cavity, which are formed by CH2 and ether groups, and a hydrophilic exterior with hydroxyl groups at the rims. The cyclodextrins are known to interact with different types of molecules, including polymers, forming supramolecular inclusion compounds. The cyclodextrins molecules present an anomalous solubility in water and an irregular trend is observed in the series. b-CD is almost ten times less soluble than the others two cyclodextrins. The same behavior is observed when D2O is the solvent, however, in this solvent the solubility of three cyclodextrins is much lower. This behavior is explained in terms of the effect caused by cyclodextrins on the water lattice structure and by the solvation of these molecules. The cyclodextrins solvation was studied using transversal relaxation time (T2) of water in Nuclear Magnetic Resonance experiments. The T2 of free water and the water bounded on the surface of a solute are different due to the differences in their molecular dynamics (mainly the rotation). Hence, T2 of the solvent is very sensitive to interaction between solute and solvent and becomes lower as the solute concentration increases. In this work, not only the solubility and solvation of cyclodextrins were studied, but also the solid phase in equilibrium with the concentrated solution. The solid phase was studied by X-Ray Diffraction and Thermogravimetric Analysis. The molecular structures of cyclodextrins influence their flexibility and solvation, which leads to the anomalous solubility of the three cyclic oligomers in H2O and D2O. / Mestrado / Físico-Química / Mestre em Química

In silico ligand docking is a versatile and common technique when predicting ligands and inhibitors for protein binding sites. The various docking programmes aim to calculate binding energies and to predict interactions, thus identifying potential ligands.The currently available programmes lack satisfying means by which to account for structural water molecules which can either mediate protein-ligand contacts or be displaced upon ligand binding. The present project aims to generate data to facilitate the global work of developing scoring functions in docking programmes to account for structural water molecules contribution to ligand binding to fill the said void. This is done by validating the performance of docking using a simple model system (cytochrome C peroxidase (CCP) W191G) containing four well ordered, deeply buried structural water molecules which are known to either interact with a ligand or to be displaced upon ligand binding.Known ligands were docked into eight (crystallographically determined) receptor set-ups comprising the receptor and no, one or two of the water molecules. The performance was validated by comparison of the binding modes of the docked ligands and the crystal structures, comparison of docking scores of the ligands in the different set-ups, enrichment of the ligands from a database of decoys and finally by predicting new ligands from the decoy database. In addition a high resolution crystal structure of CCP W191G in complex with 3-aminopyridine (3AP) was determined in order to resolve ambiguities in the binding mode of this ligand.

This thesis deals with several aspects of the structure and dynamics of water molecules confined in nanoscopic pores. Water molecules confined in hydrophobic nanocavities exhibit unusual structural and dynamic properties. Confining walls of single-wall carbon nanotubes (SWCNTs) promote strong inter-water hydrogen bonding which in turn leads to several novel structural, dynamic and thermodynamic features not found in bulk water. Confined water molecules form ordered hydrogen-bonded networks, exhibit exceptionally high flow rates as compared to conventional flow in pipes, allow fast proton conduction and exhibit various other anomalous properties. Proteins are known to exploit some of the properties of confined water to perform certain physiological functions. Various properties of confined water can also be exploited in the design of nanofludic devices such as those for desalination and flow sensors. In addition, water molecules confined in SWCNTs and near graphene sheets serve as model systems to study various effects of confinement on the properties of liquids. In this thesis, we present the results of detailed molecular dynamics simulation studies of confined water molecules. In chapter 1, we summarize the findings of existing simulations and experimental studies of bulk and confined water molecules. We also highlight the significance of studying the structure and dynamics of confined water molecules in biological and biotechnological applications. Chapter 2 provides a brief ac-count of the methods and techniques used to perform the simulations described in subsequent chapters of the thesis. We also present a brief overview of the methods used to extract physical properties of water molecules from simulation data, with emphasis on the Two Phase Thermodynamics (2PT) method which we have used to compute the entropy of confined and bulk water molecules. In chapter 3, we discuss the thermodynamics of water entry in SWCNTs of various diameters. Experiments and computer simulations demonstrate that water spontaneously fills the interior of a carbon nanotube. Given the hydrophobic nature of the interior of carbon nanotubes and the strong confinement produced by narrow nanotubes, the spontaneous entry of water molecules in the pores of such nanotubes is surprising. To gain a quantitative thermodynamic understanding of this phenomenon, we use the recently developed Two Phase Thermodynamics (2PT) method to compute translational and rotational entropies of water molecules confined in SWCNTs and show that the increase in energy of a water molecule inside the nanotube is compensated by the gain in its rotational entropy. The confined water is in equilibrium with the bulk water and the Helmholtz free energy per water molecule of confined water is the same as that in the bulk within the accuracy of the simulation results. A comparison of translational and rotational spectra of water molecules confined in carbon nanotubes with those of bulk water shows significant shifts in the positions of spectral peaks that are directly related to the tube radius. These peaks are experimentally accessible and can be used to characterize water dynamics from spectroscopy experiments. We have also computed the free-energy transfer when a bulk water molecule enters a SWCNT for various temperatures and carbon-water interactions. We show that for reduced carbon-oxygen interaction, the free energy transfer is unfavourable and the SWCNT remains unoccupied for significant periods of time. As the temperature is increased, the free energy of confined water becomes unfavourable and reduced occupancy of water is observed. Bulk water exhibits many anomalous properties. No single water model is able to reproduce all properties of bulk water. Different empirical water models have been developed to reproduce different properties of water. In chapter 4, a comparative study of the structure, dynamics and thermodynamic proper-ties of water molecules confined in narrow SWCNTs, obtained from simulations using several water models including polarizable ones, is presented. We show that the inclusion of polarizability quantitatively affects the nature of hydro-gen bonding which governs different properties of water molecules. The SPC/E water model is shown to reproduce results in close agreement with those from polarizable water models with much less computational cost. In chapter 5, we report results obtained from simulations of the properties of water confined in the space between two planar surfaces. We consider three cases: two graphene surfaces, two Boron Nitride (BN) surfaces and one graphene and one BN surface. This is the first detailed study of the behaviour of water near extended BN surfaces. We show that the hydrophilic nature of the BN surface leads to several interesting effects on the dynamics of water molecules near it. We have observed a change in the activation energy, extracted from the temperature dependence of the translational and rotational dynamics, near 280K. This change in activation energy coincides with a change in the structure of the confined sheet of water, indicated by a sudden change in energy. We have also found signatures of glassy dynamics at low temperatures for all three cases, the glassy effects being the strongest for water molecules confined between two BN sheets. These results are similar to those of earlier studies in which novel phases of water have been found for water molecules confined between other surfaces at high pressure. In chapter 6, we have described our observation of a novel phenomenon exhibited by water molecules flowing through a SWCNT under a pressure gradient. We have shown that the flow induces changes in the orientation of the water molecules flowing through the nanotube. In particular, the dipole moments of the water molecules inside the nanotube get aligned along the axis of the nanotube under the effect of the flow. With increasing flow velocities, the net dipole moment first increases and eventually saturates to a constant value. This behaviour is similar to the Langevin theory of paramagnetism with the flow velocity acting as an effective aligning field. Preferential entry of water molecules with dipole moments pointing inward is shown to be the main cause of this effect. This observation provides a way to control the dipolar alignment of water molecules inside nano-channels, with possible applications in nanofluidic devices. Chapter 7 contains a summary of our main results and a few concluding re-marks.