Water Transport through Nanotubes with Varying Interaction Strength between Tube Wall and Water.
ABSTRACT: We present the results from extensive molecular dynamics simulations to study the effect of varying interaction strength, ?NT-OW, between the nanotube atoms and water's oxygen atom. We find the existence of a narrow transition region (?NT-OW ? 0.05 - 0.075 kcal/mol) in which water occupancy within a nanotube and flux through it increases dramatically with increasing ?NT-OW, with the exact location defined by nanotube diameter and length. This transition region narrows with increasing nanotube diameter to nearly a step-change in water transport from no flow to high water flux between ?NT-OW= 0.05 kcal/mol to 0.055 kcal/mol for tube diameter 1.6 nm. Interestingly, this transition region (?NT-OW= 0.05 - 0.075 kcal/mol) also coincides with water contact angles close to 90° on an unrolled nanotube surface hinting at a fundamental link between nanotube wetting characteristics and water transport through it. Finally, we find that the observed water flux is proportional to the average water occupancy divided by the average residence time within the nanotube, with a proportionality constant found to be 0.36, independent of the nanotube diameter and length.
Project description:We study the conformational equilibrium between B-to-A forms of ds-DNA adsorbed onto a single-walled carbon nanotube (SWNT) using free energy profile calculations based on all-atom molecular dynamics simulations. The potential of mean force (PMF) of the B-to-A transition of ds-DNA in the presence of an uncharged (10,0) carbon nanotube for two dodecamers with poly-AT or poly-GC sequences is calculated as a function of a root-mean-square-distance (ΔRMSD) difference metric for the B-to-A transition. The calculations reveal that in the presence of a SWNT DNA favors B-form DNA significantly in both poly-GC and poly-AT sequences. Furthermore, the poly-AT DNA:SWNT complex shows a higher energy penalty for adopting an A-like conformation than poly-GC DNA:SWNT by several kcal/mol. The presence of a SWNT on either poly-AT or poly-GC DNA affects the PMF of the transition such that the B form is favored by as much as 10 kcal/mol. In agreement with published data, we find a potential energy minimum between A and B-form DNA at ΔRMSD ≈ -1.5 Å and that the presence of the SWNT moves this minimum by as much as ΔRMSD = 3 Å.
Project description:In the title compound, C(12)H(12)N(6)·4H(2)O, the two triazole rings adopt a cis configuration with a crystallographic twofold axis passing through the central benzene group. The benzene and triazole rings are almost coplanar with a dihedral angle of 5.5?(1)°. In the crystal, water mol-ecules are joined together by OW-H?OW hydrogen bonds to form a one-dimensional zigzag chain. These water chains are further connected to the organic mol-ecule, forming a three-dimensional network by inter-molecular OW-H?N and N-H?OW hydrogen bonds. Moreover, ?-? stacking inter-actions between triazole rings [centroid-centroid distances = 3.667?(1)-3.731?(1)?Å] are observed. One of the water mol-ecules shows one of the H atoms to be disordered over two positions.
Project description:Possible transition between two phases of supercooled liquid water, namely the low- and high-density liquid water, has been only predicted to occur below 230 K from molecular dynamics (MD) simulation. However, such a phase transition cannot be detected in the laboratory because of the so-called "no-man's land" under deeply supercooled condition, where only crystalline ices have been observed. Here, we show MD simulation evidence that, inside an isolated carbon nanotube (CNT) with a diameter of 1.25 nm, both low- and high-density liquid water states can be detected near ambient temperature and above ambient pressure. In the temperature-pressure phase diagram, the low- and high-density liquid water phases are separated by the hexagonal ice nanotube (hINT) phase, and the melting line terminates at the isochore end point near 292 K because of the retracting melting line from 292 to 278 K. Beyond the isochore end point (292 K), low- and high-density liquid becomes indistinguishable. When the pressure is increased from 10 to 600 MPa along the 280-K isotherm, we observe that water inside the 1.25-nm-diameter CNT can undergo low-density liquid to hINT to high-density liquid reentrant first-order transitions.
Project description:Human 5'-methylthioadenosine phosphorylase (MTAP) links the polyamine biosynthetic and S-adenosyl-l-methionine salvage pathways and is a target for anticancer drugs. p-Cl-PhT-DADMe-ImmA is a 10 pM, slow-onset tight-binding transition state analogue inhibitor of the enzyme. Titration of homotrimeric MTAP with this inhibitor established equivalent binding and independent catalytic function of the three catalytic sites. Thermodynamic analysis of MTAP with tight-binding inhibitors revealed entropic-driven interactions with small enthalpic penalties. A large negative heat capacity change of -600 cal/(mol K) upon inhibitor binding to MTAP is consistent with altered hydrophobic interactions and release of water. Crystal structures of apo MTAP and MTAP in complex with p-Cl-PhT-DADMe-ImmA were determined at 1.9 and 2.0 Å resolution, respectively. Inhibitor binding caused condensation of the enzyme active site, reorganization at the trimer interfaces, the release of water from the active sites and subunit interfaces, and compaction of the trimeric structure. These structural changes cause the entropy-favored binding of transition state analogues. Homotrimeric human MTAP is contrasted to the structurally related homotrimeric human purine nucleoside phosphorylase. p-Cl-PhT-DADMe-ImmA binding to MTAP involves a favorable entropy term of -17.6 kcal/mol with unfavorable enthalpy of 2.6 kcal/mol. In contrast, binding of an 8.5 pM transition state analogue to human PNP has been shown to exhibit the opposite behavior, with an unfavorable entropy term of 3.5 kcal/mol and a favorable enthalpy of -18.6 kcal/mol. Transition state analogue interactions reflect protein architecture near the transition state, and the profound thermodynamic differences for MTAP and PNP suggest dramatic differences in contributions to catalysis from protein architecture.
Project description:Research shows a positive relationship between dietary energy density (ED) and body mass index (BMI), but dietary ED of weight loss maintainers is unknown. This preliminary investigation was a secondary data analysis that compared self-reported dietary ED and food group servings consumed in overweight adults (OW: BMI=27-45kg/m(2)), normal weight adults (NW: BMI=19-24.9 kg/m(2)), and weight loss maintainers (WLM: current BMI=19-24.9kg/m(2) [lost?10% of maximum body weight and maintained loss for ?5years]) participating in 2 studies, with data collected from July 2006 to March 2007. Three 24-h phone dietary recalls from 287 participants (OW=97, NW=85, WLM=105) assessed self-reported dietary intake. ED (kcal/g) was calculated by three methods (food+all beverages except water [F+AB], food+caloric beverages [F+CB], and food only [FO]). Differences in self-reported consumption of dietary ED, food group servings, energy, grams of food/beverages, fat, and fiber were assessed using one-way MANCOVA, adjusting for age, sex, and weekly energy expenditure from self-reported physical activity. ED, calculated by all three methods, was significantly lower in WLM than in NW or OW (FO: WLM=1.39±0.45kcal/g; NW=1.60±0.43 kcal/g; OW=1.83±0.42 kcal/g). Self-reported daily servings of vegetables and whole grains consumed were significantly higher in WLM compared to NW and OW (vegetables: WLM=4.9±3.1 servings/day; NW=3.9±2.0 servings/day; OW=3.4±1.7 servings/day; whole grains: WLM=2.2±1.8 servings/day; NW=1.4±1.2 servings/day; OW=1.3±1.3 servings/day). WLM self-reported consuming significantly less energy from fat and more fiber than the other two groups. Self-reported energy intake per day was significantly lower in WLM than OW, and WLM self-reported consuming significantly more grams of food/beverages per day than OW. These preliminary findings suggest that consuming a diet lower in ED, characterized by greater intake of vegetables and whole grains, may aid with weight loss maintenance and should be further tested in prospective randomized controlled trials.
Project description:In the title compound, C15H23N3O3S·H2O, the piperidine ring has a chair conformation. In the crystal, the sulfonamide mol-ecules are linked by N-H?O hydrogen bonds, forming a layer parallel to (10-1). The layers are inter-connected via N-H?Ow, Ow-H?N and Ow-H?O (w = water) hydrogen bonds, forming a three-dimensional network.
Project description:In the title compound, C13H10BrN3O2·H2O, the conformation about the azomethine double bond is E. The mol-ecule exists in the amido form with a C=O bond length of 1.229?(2)?Å. There is an intra-molecular O-H?N hydrogen bond forming an S(6) ring motif. The whole mol-ecule is almost planar, with an r.m.s. deviation of 0.021?Å for all non-H atoms, and the dihedral angle between the planes of the pyridine and benzene rings is 0.74?(12)°. In the crystal, the water mol-ecule of crystallization links the organic mol-ecules via Ow-H?O, Ow-H?N and N-H?Ow hydrogen bonds and short C-H?Ow contacts, forming sheets lying parallel to (100). Within the sheets there is a weak ?-? inter-action involving the pyridine and benzene rings [centroid-to-centroid distance = 3.8473?(15)?Å]. The sheets are linked via C-H?Br inter-actions, forming a three-dimensional network.
Project description:The hydrolysis rates of the dianions of phosphate and phosphorothioate esters are substantially accelerated by the addition of polar aprotic solvents such as DMSO and acetonitrile. The activation barrier DeltaG is smaller due to a lower enthalpy of activation. The enthalpy of transfer of p-nitrophenyl phosphate (pNPP) and p-nitrophenyl phosphorothioate (pNPPT), from water to 0.6 (mol) aq DMSO (60 mol % water in DMSO) were measured calorimetrically. The enthalpies of activation for the hydrolysis reactions in the two solvents permitted the calculation of the enthalpy of transfer of the transition states. This transfer is thermodynamically favorable for both the reactants and the transition states but is more favorable for the transition states. In the case of pNPP, the enthalpy of transfer of the reactant is -23.9 kcal/mol, compared to -28.3 for the transition state. The difference is greater for pNPPT, where the enthalpy of transfer of the reactant is -23.2 kcal/mol and that for the transition state is -35.3. The results show that the reduced enthalpies of activation in both hydrolysis reactions arise not from a destabilization of the reactants in the mixed solvent, but from the fact that the enthalpy of transfer of the transition states to the mixed solvent is significantly more negative than the enthalpy of transfer of the reactants.
Project description:The asymmetric unit of the title hydrated mol-ecular salt, C6H16N2 (2+)·2ClO4 (-)·2H2O, contains a half dication (completed by inversion symmetry), a perchlorate anion and a water mol-ecule. The extended structure consists of infinite chains of formula [(ClO4)H2O] n (n) (-) ions extending along the b axis linked by Ow-H?O (w = water) hydrogen bonds. These chains are cross-linked by the dications via N-H?Ow and weak C-H?O hydrogen bonds, thus forming a three-dimensional supra-molecular network. Three-dimensional Hirshfeld surface analysis and two-dimensional fingerprint maps reveal that the structure is dominated by H?O/O?H and H?H contacts.
Project description:A study of the Thermus thermophilus chorismate mutase (TtCM) is described by using quantum mechanics (self-consistent-charge density-functional tight binding)/molecular mechanics, umbrella sampling, and the weighted histogram analysis method. The computed free energies of activation for the reactions in water and TtCM are comparable to the experimental values. The free energies for formation of near attack conformer have been determined to be 8.06 and 0.05 kcal/mol in water and TtCM, respectively. The near attack conformer stabilization contributes approximately 90% to the proficiency of the enzymatic reaction compared with the reaction in water. The transition state (TS) structures and partial atom charges are much the same in the enzymatic and water reactions. The difference in the electrostatic interactions of Arg-89 with O13 in the enzyme-substrate complex and enzyme-TS complex provides the latter with but 0.55 kcal/mol of 1.92 kcal/mol total TS stabilization. Differences in electrostatic interactions between components at the active site in the enzyme-substrate complex and enzyme-TS complex are barely significant, such that TS stabilization is of minor importance and the enzymatic catalysis is through an entropic advantage.