No / Various host-guest peptide series are used by experimentalists as reference conformational states. One such use is as a baseline for random-coil NMR chemical shifts. Comparison to this random-coil baseline, through secondary chemical shifts, is used to infer protein secondary structure. The use of these random-coil data sets rests on the perception that the reference chemical shifts arise from states where there is little or no conformational bias. However, there is growing evidence that the conformational composition of natively and nonnatively unfolded proteins fail to approach anything that can be construed as random coil. Here, we use molecular dynamics simulations of an alanine-based host-guest peptide series (AAXAA) as a model of unfolded and denatured states to examine the intrinsic propensities of the amino acids. We produced ensembles that are in good agreement with the experimental NMR chemical shifts and confirm that the sampling of the 20 natural amino acids in this peptide series is be far from random. Preferences toward certain regions of conformational space were both present and dependent upon the environment when compared under conditions typically used to denature proteins, i.e., thermal and chemical denaturation. Moreover, the simulations allowed us to examine the conformational makeup of the underlying ensembles giving rise to the ensemble-averaged chemical shifts. We present these data as an intrinsic backbone propensity library that forms part of our Structural Library of Intrinsic Residue Propensities to inform model building, to aid in interpretation of experiment, and for structure prediction of natively and nonnatively unfolded states. / NIH GM 50789, Ministry of Education, Youth and Sports (MSMT) of the Czech Republic LH11020

No description available.

We employ molecular dynamics simulations to investigate the evaporation process of nanosized droplets adsorbed on a substrate. Beads interacting with each other via Lennard-Jones (LJ) potentials are used to construct the simulation systems. The solid substrate contains 6 layers of beads forming a face-centered-cubic lattice. The bottom 3 layers are held rigid while the rest is kept at a constant temperature with a Langevin thermostat. A liquid droplet, consisting of LJ beads as well, is placed on top of the substrate. An appropriate amount of vapor beads are also supplied to the simulation box to help establish liquid-vapor equilibrium. To ensure adsorption, a stronger attraction is rendered between the droplet and a circular patch of 3 layers of beads at the center of the substrate surface while the rest of the substrate is made non-sticky for the fluid beads. During equilibration, the droplet and vapor are maintained at the same temperature as the thermalized substrate. After relaxation, the droplet adheres to the attractive patch as expected. Then a deletion zone is introduced into the top part of the vapor region. Fluid beads in this zone are removed at a given rate. To ensure that the evaporation dynamics and kinetics are properly captured, only the thermalized substrate is kept at the constant temperature during droplet evaporation. To carry out steady-state evaporation, the removed beads are reintroduced into a channel through the substrate and right below the droplet's center. These beads are then supplied to the droplet, compensating for the evaporation loss at the droplet surface. When the evaporation rate and the insertion rate are balanced, the system enters a steady state with the droplet undergoing continuous evaporation and its contact line pinned at the boundary of the attractive patch on the substrate. A one-to-one correspondence is found between the evaporation rate and the total number of fluid beads in the simulation box, as well as the contact angle of the droplet. Using this steady nonequilibrium system, we have mapped out the flow, temperature, and density fields inside and around the evaporating droplet as well as the local evaporation flux along the droplet surface with unprecedented resolutions. The results are used to test the existing theories on sessile droplet evaporation. / Master of Science / Droplet evaporation is a widespread natural phenomenon with numerous applications across various fields. While there has been extensive research on droplet evaporation, it remains a challenge to characterize the interior of the droplet and the local evaporation behavior on the droplet surface. Here we employ molecular dynamics (MD) simulation to model a nanosized droplet adsorbed on a substrate, which evaporates continuously while maintains a constant shape. This is realized by supplying the evaporated fluid back to the bottom of the droplet through an in-silico approach. Such a steady-evaporation system allows us to accurately map out the internal capillary flow of the evaporating droplet with a pinned contact line, where the droplet, vapor, and substrate meet. We find that local evaporation occurs faster near the contact line than at the apex of the droplet.

Gauge invariant shielding constants calculations of ?H, ?C, and ??N were calculated for acetonitrile in the gas and liquid phases. Dierent basis sets as well as dierent ab initio and DFT methods were tested to select a time-ecient level of theory with reasonable accuracy. The eect of nuclear motion on the shielding constants was also explored. To investigate solvent eects on the shielding constants of acetonitrile, dierent clusters were extracted from molecular dynamics simulations. Convergence to the experimental values varied for the dierent clusters. The geometry of the central molecule in a cluster played an important factor in reaching convergence. / Master of Science

Doctor of Philosophy / Department of Chemistry / Paul E. Smith / Molecular Dynamics (MD) simulations have played an important role in providing detailed atomic information for the study of biological systems. The quality of an MD simulation depends on both the degree of sampling and the accuracy of force field. Kirkwood-Buff (KB) theory provides a relationship between species distributions from simulation results and thermodynamic properties from experiments. Recently, it has been used to develop new, hopefully improved, force fields and to study preferential interactions. Here we combine KB theory and MD simulations to study a variety of intermolecular interactions in solution. Firstly, we present a force field for neutral amines and carboxylic acids. The parameters were developed to reproduce the composition dependent KB integrals obtained from an analysis of the experimental data, allowing for accurate descriptions of activities involved with uncharged N-terminus and lysine residues, as well as the protonated states for the C-terminus and both aspartic and glutamic acids. Secondly, the KB force fields and KB theory are used to investigate the urea cosolvent effect on peptide aggregation behavior by molecular dynamics simulation. Neo-pentane, benzene, glycine and methanol are selected to represent different characteristics of proteins. The chemical potential derivatives with respect to the cosolvent concentrations are calculated and analyzed, and the four solutes exhibit large differences. Finally, the contributions from the vibrational partition function to the total free energy and enthalpy changes are investigated for several systems and processes including: the enthalpy of evaporation, the free energy of solvation, the activity of a solute in solution, protein folding, and the enthalpy of mixing. The vibrational frequencies of N-methylacetamide, acetone and water are calculated using density functional theory and MD simulations. We argue that the contributions from the vibrational partition function are large and in classical force fields these contributions should be implicitly included by the use of effective intermolecular interactions.

Most drugs undergo passive transport during absorption and distribution in the body. It is desirable to predict passive permeation of future drug candidates in order to increase the productivity of the drug discovery process. Unlike drug-receptor interactions, there is no receptor map for passive permeability because the process of transport across the lipid bilayer involves multiple mechanisms. This work intends to increase the understanding of permeation of drug-like molecules through lipid bilayers. Drug molecules in solution typically form various species due to ionization, complexation, etc. Therefore, species specific properties must be obtained to bridge the experiment and simulations. Due to the volume contrast between intra- and extravesicular compartments of liposomes, minor perturbations in ionic and binding equilibria become significant contributors to transport rates. Using tyramine as a model amine, quantitative numerical models were developed to determine intrinsic permeability coefficients. The microscopic ionization and binding constants needed for this were independently measured. The partition coefficient in 1,9-decadiene was measured for a series of compounds as a quantitative surrogate for the partitioning into the hydrocarbon region of the bilayer. These studies uncovered an apparent long-range interaction between the two polar substituents that caused deviations in the microscopic pKa values and partition coefficient of tyramine from the expected values. Additionally the partition coefficients in the preferred binding region of the bilayer were also measured by equilibrium uptake into liposomes. All-atom molecular dynamics simulations of lipid bilayers containing tyramine, 4- ethylphenol, or phenylethylamine provided free energies of transfer of these solutes from water to various locations on the transport path. The experimentally measured partition coefficients were consistent with the free energy profiles in showing the barrier in the hydrocarbon region and preferred binding region near the interface. The substituent contributions to these free energies were also quantitatively consistent between the experiments and simulations. Specific interactions between solutes and the bilayer suggest that amphiphiles are likely to show preferred binding in the head group region and that the most of hydrogen bonds involving solutes located inside the bilayer are with water molecules. Solute re-orientation inside the bilayer lowers the partitioning barrier by allowing favorable interactions.

L'alternance de deux groupes de polarités très différentes, CH2 et CF2, permet au poly fluorure de vinylidène (PVDF) d’être un polymère industriellement très intéressant. Cependant, cette spécificité mène aussi à d’importantes inversions du monomère lors de la polymérisation vinylique. Pendant la polymérisation, en complément de la propagation tête-queue, CH2CF2CH2CF2, les monomères inversés conduisent à l’addition en queue-queue, CF2CH2CH2CF2, et tête-tête, CH2CF2CF2CH2. Le taux de transformation de polymère se trouve expérimentalement entre 3 et 7%. Ce pourcentage élevé entraine sans aucun doute la modification de propriétés macroscopiques. En utilisant la dynamique moléculaire, cette thèse a pour but de montrer l'effet de ces défauts sur la température de transition vitreuse (Tg), la dynamique locale et sur la température de fusion (Tm) du PVDF. En phase amorphe, le PVDF avec différents pourcentages de régio-défauts a été étudié : 3.6, 4.1, 9.3 et 23%. Cette étude permet de prédire le comportement de polymères qui ne sont pas synthétisés. Étant donné que les Tg simulées et expérimentales concordent avec précision, les motifs moléculaires qui donnent lieu à l'effet plastifiant de l'inversion de monomères peuvent être envisagés. En plus d'accentuer leur effet de plastifiant, la conclusion significative est que la relaxation de la chaîne peut être révélée en abordant explicitement des mouvements locaux. Car cette procédure ne peut pas être déduite de la connaissance du Tg, nous avons basé notre analyse sur le fait cela : 1) Nous avons démontré que des relations linéaires directes entre Tg et l'énergie d'activation conformationnelle de transition (Ea) extraite à partir d'un graphe d'Arrhenius, existent. Ce diagramme correspond au logarithme naturel des taux de transition entre les états rotameriques contre l'inverse de la température. La pente de cette courbe rapporte directement à cet Ea efficace. Un tel lien a été seulement spéculé dans la littérature. 2) Nous avons calculé des relations d'Arrhenius pour différents genres de torsions le long de la chaîne d'épine dorsale. En conséquence, une barrière d'énergie potentielle, ea, est associée à la rotation d'un lien dans un environnement spécifique. L'addition de ces énergies pesées par le pourcentage de chaque lien le long de l'épine dorsale, donne un ea moyen qui est équivalent à l'ea efficace. À l'aide de cette procédure, nous avons maintenant accès au mouvement local de la chaîne entière. 3) Nous avons vérifié cette procédure pour calculer une valeur pour le Tg du copolymère alternatif du l'éthylène-tétrafluoroéthylène (E-TFE), qui possède les segments qui sont présents le PVDF changé. L'ambiguïté concernant la valeur de la Tg du copolymère E_TFE peut être résolue grâce à cette approche, puisque le PVDF avec 50% de défauts régio-isomériques conduit à l'E_TFE. D'ailleurs, nous avons étudié les temps de relaxation pour la fonction d'autocorrélation de torsion au-dessus d'un large éventail de température. La dynamique locale est alors spécifiquement étudiée. L'équation Vogel-Fulcher-Tammann (VFT) est utilisée pour décrire le processus de relaxation associée aux mouvements coopératifs des segments le long de la chaîne. Nous avons également étudié le possibilité d'utiliser le Kohlrausch-Williams-Watts (KWW), fonction exponentielle étirée, afin de décrire la dépendance temporelle du processus de relaxation, ce travail a été effectué à différentes températures. Les résultats concordent bien avec les données expérimentales. L'objectif principal de cette section est d'étudier conjointement la fréquence des transitions conformationnelles et le temps de relaxation obtenu par la fonction d’autocorrelation de torsion, sur une plage importante de température, afin d’établir un entre les fréquences des transitions conformationnelles et le comportement de type VFT. Nous montrons pour la première fois qu’une relation linéaire peut être établie entre la barrière de transition conformationnelle et l’énergie d’activation effective. Nous montrons pour la première fois qu'une relation linéaire peut être établie entre la barrière de transition conformationnelle, Ea et l'énergie d'activation effective, B, responsables de la dynamique locale. Parmi les cinq phases cristallines que présente le PVDF, les cristaux α et ß présentent des propriétés particulières intéressantes et ont fait l'objet d'une attention significative. Ces deux structures cristallines sont celles que l’on rencontre le plus souvent, la phase α est la plus thermodynamiquement stable le cristal β possède des propriétés ferroélectriques. Toutefois, le comportement lors de la fusion de ces deux phases cristallines n’est pas encore totalement compris. Certains chercheurs pensent que la température de fusion de la phase β est supérieure à la phase alpha . D'autres affirment que le pic endothermique vu sur le thermogramme obtenue par calorimétrie différentielle à balayage (DSC) a été attribué par erreur à la phase β, cela à cause d’une confusion dans les références . À cet égard, le comportement de la Tm des cristaux α et β par rapport à leur épaisseur est obtenu par la dynamique moléculaire. Différents types de nanocristaux composés de chaînes de PVDF, sans ou avec 10% de régio-défauts, ayant des longueurs différentes ont ainsi été simulées dans les phases α et β. On applique l'équation de Gibbs-Thomson (G-T) afin de déterminer l'énergie de surface et l’enthalpie de fusion des nanocristaux. Les valeurs déterminées sont en accord avec les données expérimentales. Nous avons montré que le PVDF en phase β pur a une température de fusion inférieure à celle du PVDF en phase α pur. Cependant, en insérant des défauts à l'intérieur du cristal, la phase α modifiée présente une température de fusion inférieure à celle de la phase β modifiée. / Abstract : Alternating two groups, CH2 and CF2, of very different polarities along the backbone chain of polyvinylidene fluoride (PVDF) leads to very interesting properties, such as ferroelectricity. However, these properties are affected by the presence of regioisomerism defects (monomer inversion) that appear during the synthesis. During the polymerization, in addition to the Head-to-Tail (HT) sequences, CH2CF2CH2CF2, the reversed monomer units lead to formation of Tail-to-Tail (TT), CF2CH2CH2CF2, and Head-to-Head (HH), CH2CF2CF2CH2, links. The rate of this chain alteration experimentally lies between 3 and 7 %. This percentage undoubtedly brings changes in macroscopic properties. The aim of this thesis is to reveal the impact of these defects on the glass transition temperature (Tg), local dynamics and melting temperature (Tm) of PVDF by using Molecular Dynamics (MD) simulation. In amorphous phase, PVDF chains with different percentages of regiodefects were investigated: 0, 3.6, 4.1, 9.3, and 23 %. This study makes it possible to predict the experimental behavior of polymers which have not yet been synthesized. Once Tg is acquired, the relaxation of the chain can be investigated through the calculation of the activation energy (Ea) of the conformational transition. The significant conclusion is that the relaxation of the chain can be revealed by addressing the local motions. More specifically: a) We demonstrate a direct linear relationship between Tg and Ea extracted from an Arrhenius plot. This diagram corresponds to the natural logarithm of transition rates between rotameric states versus the inverse of the temperature. The slope of this curve yields directly Ea. Such a link was only speculated in the literature. b) A significant finding of this work is that the mobility of the chain can be associated with different types of bonds in PVDF with regiodefects. c) Based on the analysis of Ea for the different bond contributions, we proposed a value for the Tg of ethylene-tetrafluoroethylene (E-TFE), an isomeric polymer of PVDF with 50% regiodefects. Experimentally, the available data for the Tg of E-TFE are limited and highly variable. For example, it has been reported as varying from -108 °C to 145 °C. The ambiguity of Tg for this copolymer can be resolved with this approach. Furthermore, we studied the relaxation time associated with the torsional autocorrelation function (TACF) over a wide temperature range. The Vogel-Fulcher-Tammann (VFT) equation was used to describe the temperature dependence of the relaxation time. The Kohlrausch Williams Watts (KWW) stretched exponential function is then applied to fit the time dependence of the relaxation process at various temperatures. The results obtained from this work were found to be in good agreement with the experimental data. A particular interest in this study is the question of how the non-Arrhenius VFT of relaxation process is related to the Arrhenius behavior of conformational jump rates near the glass transition. In both cases, the energies (the conformational transition energy (Ea) and the effective activation energy (B) in VFT equation), were very close to the value of a single torsional barrier. However, in contrast to the relaxation time associated with TACF, the rates of conformational jumps show the activation energy higher than the single barrier value. We have shown that a linear relationship can be established between the conformational transition energy and the effective activation energy. In crystalline PVDF, among the five typical phases, the α and β crystals are of particular interest. The α phase is the most thermodynamically stable form and the β crystal possesses ferroelectric properties. The melting behaviour of these two crystal phases is not so clear. Some researchers believe that the melting temperature of the β phase is higher than that of the α phase. Others have claimed that the higher melting temperature of the peak in Differential Scanning Calorimetry (DSC) has been mistakenly attributed to β phase melting, due to confusion in the referencing of literature sources. In this regard, the melting temperatures of α and β crystals (with and without regiodefects) with respect to their thickness are captured by MD simulation. We then applied the Gibbs-Thomson (G-T) equation to determine the melting temperature, as well as the surface energy and enthalpy of fusion, for α and β nanocrystals. We have shown that pure β phase PVDF has a lower melting temperature than pure α phase PVDF. However, by inserting regiodefects randomly inside the crystal, the α phase with regiodefects shows a lower melting temperature than that of the β phase with regiodefects. We attributed this behaviour to the different structures of the two phases.

No description available.

CONTACT ANGLE OF A NANO-DROP ON A HETEROGENEOUS SURFACE By John Andre Ritchie, Master of Science A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science at Virginia Commonwealth University Virginia Commonwealth University, 2010 Major Director: Dr. Alenka Luzar, Professor of Chemistry We examine the relation between contact angle of a nanodrop of water and the location of surface-water interaction energy at the perimeter and beneath the drop. Young’s equations gives the relationship between surface tension, at the three phase solid liquid vapor interface, and contact angle on a homogeneous surface. Cassie and Baxter generalized this equation to heterogeneous surfaces implying that contact angle corresponds to the average properties of the surface under the drop. McCarthy and coworkers pointed out it is the nature of the substrate at droplet perimeter that controls contact angle. And more recently, McHale in his theoretical derivation applies the Cassie-Baxter equation to the area at the drop’s perimeter. For a nanodrop, the situation is further complicated by the finite range of water-substrate interactions making the definition of the perimeter region somewhat arbitrary. We simulate nanodroplets of water on graphene-like surfaces having hydrophobic and hydrophilic interaction energy at the perimeter and beneath the drop using molecular dynamics. The microscopic analogue of the contact angle was extracted from simulation trajectory data. We confirm the contact angle is exclusively related to the surface interaction energy in the region of the drop’s perimeter. We test the role of finite range of substrate-water interaction when the area of a circular hydrophilic patch beneath the drop’s core is incrementally expanded until the contact angle is equivalent to that on the pure hydrophilic surface. We identify a range of interaction corresponding to a considerable drop in θ when plotting contact angle as a function of patch size. We show the observed contact angle dependence on the size of the patch can be predicted by the Cassie-Baxter mixing relation when limited to the area within the interaction range from the drop’s perimeter.

<p></p><p>Flexible electronics involve electronic circuits fabricated on flexible substrates. They have promising applications in wearable devices and flexible sensors etc. and have thus attracted much research interest in recent years. The working environment of flexible electronic devices may require them to go through repeating deformations, during which cracks may generate and grow in the metallic components of the devices, reducing service life of these devices. To address such challenges, it is desirable to investigate methods to improve the reliability of flexible electronics in these working conditions. </p> <p>This research reported here will focus on topics related to laser-based fabrication of carbon nanotube-metal composites on flexible substrates: </p> <p>Experimental studies were carried out to investigate the structures and properties of carbon nanotube – metal composites produced by a laser-based fabrication process on flexible substrates. Extensive characterizations and testes were carried out, including measurements of electrical resistivity of laser-sintered material, characterizations with SEM, TEM, EDS and XPS, and mechanical performance tests (bending fatigue test, static tensile test and adhesion test). The experimental study suggests that the laser-fabricated metal composites have promising potentials to help enhancing reliability and durability of metal components in flexible electronic devices. </p> <p>A molecular dynamics model was also developed to study the coalescence of metal nanoparticles (gold NPs in this study) around the end of a multi-walled carbon nanotube (MWCNT) and their interaction with the CNT at elevated temperatures. The MD model was first tested by comparing the MD-predicted NP melting points with experiment-deduced results from the literature. Then the coalescence of five 3-nm Au NPs around the end of a MWCNT and their interactions with the CNT were studied with MD simulations. The molecular system was studied under different elevated temperatures and for different carbon nanotube diameters, and the simulation results were analyzed and discussed. </p><br><p></p>