Temperature dependence of the distribution of the first passage time: results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G

More than 22 000 folding kinetic simulations were performed to study the temperature dependence of the distribution of first passage time (FPT) for the folding of an all-atom Gō-like model of the second beta-hairpin fragment of protein G. We find that the mean FPT (MFPT) for folding has a U (or V)-shaped dependence on the temperature with a minimum at a characteristic optimal folding temperature T(opt). The optimal folding temperature T(opt) is located between the thermodynamic folding transition temperature and the solidification temperature based on the Lindemann criterion for the solid. Both the T(opt) and the MFPT decrease when the energy bias gap against nonnative contacts increases. The high-order moments are nearly constant when the temperature is higher than T(opt) and start to diverge when the temperature is lower than T(opt). The distribution of FPT is close to a log-normal-like distribution at T > or = T(opt). At even lower temperatures, the distribution starts to develop long power-law-like tails, indicating the non-self-averaging intermittent behavior of the folding dynamics. It is demonstrated that the distribution of FPT can also be calculated reliably from the derivative of the fraction not folded (or fraction folded), a measurable quantity by routine ensemble-averaged experimental techniques at dilute protein concentrations.     

Magnetic field-induced reactions on the surface of chloroaluminum phthalocyanine thin films

The μ-(oxo)bis[phthalocyaninato] aluminum(III) (AlPc)(2)O films, with the crystallites oriented preferably in one direction, were obtained via chemical transformation of chloroaluminum(III) phthalocyanine AlClPc film upon its annealing in magnetic field. A comparative analysis of the influence of postdeposition annealing without and under applied magnetic field of 1 T on composition and morphology of AlClPc films has been carried out. The chemical transformation of AlClPc to (AlPc)(2)O on the substrate surface is studied by the methods of UV-vis and infrared spectroscopies, Raman, x-ray photoelectron spectroscopy as well as atomic force microscopy. Two interesting effects were observed upon heating the AlClPc films in magnetic field of 1 T. First, the temperature of the chemical transformation of AlClPc to (AlPc)(2)O decreased from 300 °C to 200 °C when magnetic field was applied during postdeposition annealing. Second, the formation of (AlPc)(2)O films with elongated crystallites with a preferential orientation was observed. The heating of (AlPc)(2)O films in a magnetic field at the same conditions did not demonstrate any effect on the structure and morphology of these films.     

Low-temperature preparation of highly conductive thin films from acrylic acid-stabilized silver nanoparticles prepared through ligand exchange

The preparation of AcA-stabilized Ag nanoparticles and its application to make highly conductive thin films are reported. The AcA-stabilized Ag nanoparticles were prepared through a ligand exchange of original oleylamine (OLA)-coated Ag nanoparticles with acrylic acid (AcA), which acted as both an antisolvent and a modifying ligand during the ligand exchange process. Efficiencies of the ligand exchange as well as the properties of Ag nanoparticles were analyzed using various techniques including TEM, FT-IR, XPS, TGA, and UV-vis methods. The thin films were fabricated by annealing spin-coated AcA-stabilized Ag nanoparticles. Further, the effects of annealing temperature, time, and film thickness on both the film morphology and electrical conductivity have been investigated. In this work, due to the low boiling temperature of stabilizer (AcA) and adjustment of annealing conditions, high electrical conductivity was obtained for the Ag thin films. For example, when annealing at 175 °C for 30 min, a 70 nm thick film showed a maximum electrical conductivity of 1.12 × 10(5) S cm(-1). A conductive layer on a flexible polymer substrate (e.g., PET) sheet has been successfully prepared by annealing a spin-coated film at 140 °C for 30 min. The combined advantages of long-term stability of the AcA-stabilized Ag nanoparticles, low annealing temperature, and high conductivity of the prepared thin films make this relatively simple method attractive for applications in flexible electronics.     

The utilization of classical spin Monte Carlo methods to simulate the magnetic behavior of extended three-dimensional cubic networks incorporating M(II) ions with an S = 5/2 ground state spin

The numerical simulations of the magnetic properties of extended three-dimensional networks containing M(II) ions with an S = 5/2 ground-state spin have been carried out within the framework of the isotropic Heisenberg model. Analytical expressions fitting the numerical simulations for the primitive cubic, diamond, together with (10-3) cubic networks have all been derived. With these empirical formulas in hands, we can now extract the interaction between the magnetic ions from the experimental data for these networks. In the case of the primitive cubic network, these expressions are directly compared with those from the high-temperature expansions of the partition function. A fit of the experimental data for three complexes, namely [(N(CH(3))(4)][Mn(N(3))] 1, [Mn(CN(4))](n)() 2, and [Fe(II)(bipy)(3)][Mn(II)(2)(ox)(3)] 3, has been carried out. The best fits were those obtained using the following parameters, J = -3.5 cm(-)(1), g = 2.01 (1); J = -8.3 cm(-)(1), g = 1.95 (2); and J = -2.0 cm(-)(1), g = 1.95 (3).     

Electrolyte distribution around two like-charged rods: their effective attractive interaction and angular dependent charge reversal

A simple model for two like-charged parallel rods immersed in an electrolyte solution is considered. We derived the three point extension (TPE) of the hypernetted chain/mean spherical approximation (TPE-HNC/MSA) and Poisson-Boltzmann (TPE-PB) integral equations. We numerically solve these equations and compare them to our results of Monte Carlo (MC) simulations. The effective interaction force, F(T), the charge distribution profiles, rho(el)(x,y), and the angular dependent integrated charge function, P(theta), are calculated for this system. The analysis of F(T) is carried out in terms of the electrostatic and entropic (depletion) contributions, F(E) and F(C). We studied several cases of monovalent and divalent electrolytes, for which the ionic size and concentration are varied. We find good qualitative agreement between TPE-HNC/MSA and MC in all the cases studied. The rod-rod force is found to be attractive when immersed in large size, monovalent or divalent electrolytes. In general, the TPE-PB has poor agreement with the MC. For large monovalent and divalent electrolytes, we find angular dependent charge reversal charge inversion and polarizability. We discuss the intimate relationship between this angular dependent charge reversal and rod-rod attraction.     

Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations

We have used molecular dynamics simulations to study the physical properties of modified TIP3P water model included in the CHARMM program, using four different methods-the Ewald summation technique, and three different spherical truncation methods-for the treatment of the long-range interactions. Both the structure and dynamics of the liquid water model were affected by the methods used to truncate the long-range interactions. For some of the methods artificial structuring of the model liquid was observed around the cutoff radius. The model liquid properties were also affected by the commonly applied temperature control methods. Four different methods for controlling the temperature of the system were studied, and the effects of these methods on the bulk properties for liquid water were analyzed. The system size was also found to change the dynamics of the model liquid water. Two control simulations with the SPC/E water model were carried out. The self-diffusion coefficient (D), the radial distribution function (g(OO)), the distance dependent Kirkwood G-factor [G(k)(r)] and the intermolecular potential energy (E(pot)) were determined from the different trajectories and compared with the experimental data.     

Development and application of a ReaxFF reactive force field for hydrogen combustion

To investigate the reaction kinetics of hydrogen combustion at high-pressure and high-temperature conditions, we constructed a ReaxFF training set to include reaction energies and transition states relevant to hydrogen combustion and optimized the ReaxFF force field parameters against training data obtained from quantum mechanical calculations and experimental values. The optimized ReaxFF potential functions were used to run NVT MD (i.e., molecular dynamics simulation with fixed number of atoms, volume, and temperature) simulations for various H(2)/O(2) mixtures. We observed that the hydroperoxyl (HO(2)) radical plays a key role in the reaction kinetics at our input conditions (T ≥ 3000 K, P > 400 atm). The reaction mechanism observed is in good agreement with predictions of existing continuum-scale kinetic models for hydrogen combustion, and a transition of reaction mechanism is observed as we move from high pressure, low temperature to low pressure, high temperature. Since ReaxFF derives its parameters from quantum mechanical data and can simulate reaction pathways without any preconditioning, we believe that atomistic simulations through ReaxFF could be a useful tool in enhancing existing continuum-scale kinetic models for prediction of hydrogen combustion kinetics at high-pressure and high-temperature conditions, which otherwise is difficult to attain through experiments.     

Glass transition temperature of glucose, sucrose, and trehalose: an experimental and in silico study

Isothermal-isobaric molecular dynamics simulations are used to calculate the specific volume of models of different amorphous carbohydrates (glucose, sucrose, and trehalose) as a function of temperature. Plots of specific volume vs temperature exhibit a characteristic change in slope when the amorphous systems change from the glassy to the rubbery state. The intersection of the regression lines of data below (glassy state) and above (rubbery state) the change in slope provides the glass transition temperature (T(g)). These predicted glass transition temperatures are compared to experimental T(g) values as obtained from differential scanning calorimetry measurements. As expected, the predicted values are systematically higher than the experimental ones (about 12-34 K) as the cooling rates of the modeling methods are about a factor of 10(12) faster. Nevertheless, the calculated trend of T(g) values agrees exactly with the experimental trend: T(g)(glucose) < T(g)(sucrose) < T(g)(trehalose). Furthermore, the relative differences between the glass transition temperatures were also computed precisely, implying that atomistic molecular dynamics simulations can reproduce trends of T(g) values in amorphous carbohydrates with high quality.     

An efficient molecular docking using conformational space annealing

Molecular docking falls into the general category of global optimization problems because its main purpose is to find the most stable complex consisting of a receptor and its ligand. Conformational space annealing (CSA), a powerful global optimization method, is incorporated with the Tinker molecular modeling package to perform molecular docking simulations of six receptor-ligand complexes (3PTB, 1ULB, 2CPP, 1STP, 3CPA, and 1PPH) from the Protein Data Bank. In parallel, Monte Carlo with the minimization (MCM) method is also incorporated into the Tinker package for comparison. The energy function, consisting of electrostatic interactions, van der Waals interactions, and torsional energy terms, is calculated using the AMBER94 all-atom empirical force field. Rigid docking simulations for all six complexes and flexible docking simulations for three complexes (1STP, 3CPA, and 1PPH) are carried out using the CSA and the MCM methods. The simulation results show that the docking procedures using the CSA method generally find the most stable complexes as well as the native-like complexes more efficiently and accurately than those using the MCM, demonstrating that CSA is a promising search method for molecular docking problems.     

Evaporation of a sub-micrometer droplet

Evaporation of a spherically symmetric sub-micrometer size liquid droplet is studied using a diffuse interface hydrodynamic model supplemented by the van der Waals equation of state with parameters characteristic for argon. The droplet, surrounded by saturated vapor, is held in a container with the temperature of the walls kept fixed. The evaporation is triggered by a sudden rise of the temperature of the walls. Time and space evolution of the basic thermodynamic quantities is presented. The time and space scales studied range from picoseconds to microseconds and from nanometers to micrometers, respectively. We find that the temperature and chemical potential are both continuous at the interface on the scale larger than the interfacial width. We find that at long times the radius R of the droplet changes with time t as R(2)(t) = R(2)(0) - 2tkappa(v)(T(w) - T(l))/ln(l), where kappa(v) is the heat conductivity of the vapor, n(l) and T(l) are the density and the temperature of liquid inside the droplet, respectively, l is the latent heat of transition per molecule, and T(w) is the temperature of the ambient vapor.     

Do anions influence the polarity of protic ionic liquids?

Polarity studies in two classes of imidazolium-based protic ionic liquids (PILs) possessing [HSO(4)](-), [HCOO](-), [CH(3)COO](-) and [CH(3)CH(2)COO](-) anions were carried out using a solvatochromic method from 298.15 to 353.15 K. For 1-methylimidazolium class of PILs, E(T)(30) was found to be independent over the entire range of temperature, while E(T)(30) was noted to decrease with a rise in temperature in the case of 1-butylimidazolium class of PILs containing [CH(3)COO](-) and [CH(3)CH(2)COO](-) anions. The E(T)(30) value decreases in both the classes upon varying the anions ([HSO(4)](-), [HCOO](-), [CH(3)COO](-) and [CH(3)CH(2)COO](-)). The E(T)(30) value is controlled by hydrogen bond acceptor basicity, β, and dipolarity/polarizability, π*. The E(T)(30) value for PILs varies inversely to the strength of the coulombic interaction between ions in PILs. Strong interactions between ions lead to lower E(T)(30) values. Unlike the poor thermal effect on E(T)(30), the Kamlet-Taft parameters i.e. α, β and π* have pronounced thermal effect in the imidazolium-based PILs. Variation in the Kamlet-Taft parameters is controlled by the stabilization of ions and the degree of proton transfer from Br?nsted acid to Br?nsted base.     

N-heterocyclic carbene stabilized copper- and silver-phenylchalcogenolate ring complexes

The ligation of a N-heterocyclic carbene (NHC) to group 11 metal salts (Cu, Ag) was explored as an alternative to PR(3) ligands for the formation of copper- and silver-chalcogenolate cluster complexes. AgOAc and CuCl salts ligate with the NHC 1,3-di-isopropylbenzimidazole-2-ylidene ((i)Pr(2)-bimy) forming [Ag(OAc)((i)Pr(2)-bimy)] 1, [Ag(OAc)((i)Pr(2)-bimy)(2)] 2, [CuCl((i)Pr(2)-bimy)](2)3 and [CuCl((i)Pr(2)-bimy)(2)] 4 depending on the ratio of ligand to metal used. These have been characterized via spectroscopic and crystallographic methods. Complexes 1 and 3 were reacted with S(Ph)SiMe(3) and Se(Ph)SiMe(3) to form the polynuclear metal-chalcogenolates [Ag(4)(μ-EPh)(4)((i)Pr(2)-bimy)(4)] (5, E = S; 6, E = Se) and [Cu(3)(μ-EPh)(3)((i)Pr(2)-bimy)(3)] (7, E = S; 8, E = Se) in good yields. The structures of 5-8, as determined by single crystal X-ray crystallography, are described.     

Effect of temperature on the morphology and kinetics of surface pattern formation in thin block copolymer films

Hole formation and growth on the top layer of thin symmetric diblock copolymer films, forming an ordered lamellar structure parallel to the solid substrate (silicon wafer) within these films, is investigated as a function of time (t), temperature (T), and film thickness (l), using a high-throughput experimental technique. The kinetics of this surface pattern formation process is interpreted in terms of a first-order reaction model with a time-dependent rate constant determined uniquely by the short-time diffusive growth kinetics characteristic of this type of ordering process. On the basis of this model, we conclude that the average hole size, lambda(h), approaches a steady-state value, lambda(h)(t-->infinity) identical with lambda(h,infinity)(T), after long annealing times. The observed change in lambda(h,infinity)(T) with temperature is consistent with a reduction of the surface elasticity (Helfrich elastic constant) of the outer block copolymer layer with increasing temperature. We also find that the time constant, tau(T), characterizing the rate at which lambda(h)(t) approaches lambda(h,infinity)(T), first decreases and then increases with increasing temperature. This temperature variation of tau(T) is attributed to two basic competing effects that influence the rate of ordering in block copolymer materials: the reduction in molecular mobility at low temperatures associated with glass formation and a slowing of the rate of ordering due to fluctuation effects associated with an approach to the block copolymer film disordering temperature (T(d)) from below.     

Optimized explicit-solvent replica exchange molecular dynamics from scratch

Replica exchange molecular dynamics (REMD) simulations have become an important tool to study proteins and other biological molecules in silico. However, such investigations require considerable, and often prohibitive, numerical effort when the molecules are simulated in explicit solvents. In this communication we show that in this case the cost can be minimized by choosing the number of replicas as N(opt) approximately 1+0.594 radical C ln(Tmax/Tmin), where C is the specific heat, and the temperatures distributed according to Ti(opt) approximately T min(Tmax/Tmin)(i-1)/(N-1).     

Comparative study of cluster Ag17Cu2 by instantaneous normal mode analysis and by isothermal Brownian-type molecular dynamics simulation

We perform isothermal Brownian-type molecular dynamics simulations to obtain the velocity autocorrelation function and its time Fourier-transformed power spectral density for the metallic cluster Ag(17)Cu(2). The temperature dependences of these dynamical quantities from T = 0 to 1500 K were examined and across this temperature range the cluster melting temperature T(m), which we define to be the principal maximum position of the specific heat is determined. The instantaneous normal mode analysis is then used to dissect the cluster dynamics by calculating the vibrational instantaneous normal mode density of states and hence its frequency integrated value I(j) which is an ensemble average of all vibrational projection operators for the jth atom in the cluster. In addition to comparing the results with simulation data, we look more closely at the entities I(j) of all atoms using the point group symmetry and diagnose their temperature variations. We find that I(j) exhibit features that may be used to deduce T(m), which turns out to agree very well with those inferred from the power spectral density and specific heat.     

First-principles investigation of transition metal atom M (M = Cu, Ag, Au) adsorption on CeO2(110)

Transition metal atom M (M = Cu, Ag, Au) adsorption on CeO(2)(110), a technologically important catalytic support surface, is investigated with density-functional theory within the DFT+U formalism. A set of model configurations was generated by placing M at three surface sites, viz., on top of an O, an O bridge site, and a Ce bridge site. Prior to DFT optimization, small distortions in selected Ce-O distances were imposed to explore the energetics associated with reduction of Ce(4+) to Ce(3+) due to charge transfer to Ce during M adsorption. Charge redistribution is confirmed with spin density isosurfaces and site projected density of states. We demonstrate that Cu and Au atoms can be oxidized to Cu(2+) and Au(2+), although the adsorption energy, E(ads), of Au(2+) is less favorable and, unlike Cu(2+), it has not been experimentally observed. Oxidation of Ag always results in Ag(+). For M adsorption at an O bridge site, E(ads)(2NN) > E(ads)(3NN) > E(ads)(1NN) where NN denotes the nearest neighbor Ce(3+) site relative to M. Alternatively, for M adsorption at a Ce bridge site, E(ads)(3NN) > E(ads)(2NN) > E(ads)(1NN). The adsorption behavior of M on CeO(2) (110) is compared with M adsorption on CeO(2)(111).     

High temperature nucleation and growth of glutathione protected ~Ag75 clusters

We report the first high temperature solution state synthesis of glutathione (-SG) protected atomically precise silver clusters. Noble metal cluster synthesis from metal ions generally requires ice cold temperatures as they are extremely sensitive and high temperature routes are used only for core reduction methods, starting from nanoparticles. The clusters formed by the new route have distinct features in their absorption profile and they exhibit red luminescence. They are characterised by other spectroscopic and microscopic techniques and a tentative formula of Ag(75)(SG)(40) has been assigned.     

Highly luminescent gold(I)-silver(I) and gold(I)-copper(I) chalcogenide clusters

The reactions of [AuClL] with Ag(2)O, where L represents the heterofunctional ligands PPh(2)py and PPh(2)CH(2)CH(2)py, give the trigoldoxonium complexes [O(AuL)(3)]BF(4). Treatment of these compounds with thio- or selenourea affords the triply bridging sulfide or selenide derivatives [E(AuL)(3)]BF(4) (E=S, Se). These trinuclear species react with Ag(OTf) or [Cu(NCMe)(4)]PF(6) to give different results, depending on the phosphine and the metal. The reactions of [E(AuPPh(2)py)(3)]BF(4) with silver or copper salts give [E(AuPPh(2)py)(3)M](2+) (E=O, S, Se; M=Ag, Cu) clusters that are highly luminescent. The silver complexes consist of tetrahedral Au(3)Ag clusters further bonded to another unit through aurophilic interactions, whereas in the copper species two coordination isomers with different metallophilic interactions were found. The first is analogous to the silver complexes and in the second, two [S(AuPPh(2)py)(3)](+) units bridge two copper atoms through one pyridine group in each unit. The reactions of [E(AuPPh(2)CH(2)CH(2)py)(3)]BF(4) with silver and copper salts give complexes with [E(AuPPh(2)CH(2)CH(2)py)(3)M](2+) stoichiometry (E=O, S, Se; M=Ag, Cu) with the metal bonded to the three nitrogen atoms in the absence of AuM interactions. The luminescence of these clusters has been studied by varying the chalcogenide, the heterofunctional ligand, and the metal.     

Effects of cross-links, pressure and temperature on the thermal properties and glass transition behaviour of polybutadiene

The thermal conductivity κ, heat capacity per unit volume ρc(p) and glass transition behaviour under pressure have been established for medium and high vinyl content polybutadiene PB with molecular weights 2600 and 100,000 and their highly cross-linked (ebonite) states obtained purely by high-pressure high-temperature treatments. Cross-linking eliminates the glass transitions and increases κ by as much as 50% at 295 K and 1 atm, and decreases ρc(p) to a limiting level close to that of the glassy state of PB, which is reached before the ultimate cross-link density is achieved. The pressure and temperature behaviours of κ are strongly changed by cross-links, which increases the effect of temperature but decreases the effect of pressure. We attribute these changes to a cross-linked induced permanent densification and consequential increase of phonon velocity simultaneously as conduction along polymer chains is disrupted. The glass transition temperatures for a time scale of 1 s are described to within 0.5 K by: T(g)(p) = 202.5 (1 + 2.94 p)(0.286) and T(g)(p) = 272.3 (1 + 2.57 p)(0.233) (p in GPa and T in K) up to 1 GPa, for PB2600 and PB100000, respectively, and can be estimated for medium and high vinyl content PBs with molecular weights in between by a constant, pressure independent, shift in temperature.     

Dynamic processes in a silicate liquid from above melting to below the glass transition

We collect and critically analyze extensive literature data, including our own, on three important kinetic processes--viscous flow, crystal nucleation, and growth--in lithium disilicate (Li(2)O·2SiO(2)) over a wide temperature range, from above T(m) to 0.98T(g) where T(g) ≈ 727 K is the calorimetric glass transition temperature and T(m) = 1307 K, which is the melting point. We found that crystal growth mediated by screw dislocations is the most likely growth mechanism in this system. We then calculated the diffusion coefficients controlling crystal growth, D(eff)(U), and completed the analyses by looking at the ionic diffusion coefficients of Li(+1), O(2-), and Si(4+) estimated from experiments and molecular dynamic simulations. These values were then employed to estimate the effective volume diffusion coefficients, D(eff)(V), resulting from their combination within a hypothetical Li(2)Si(2)O(5) "molecule". The similarity of the temperature dependencies of 1/η, where η is shear viscosity, and D(eff)(V) corroborates the validity of the Stokes-Einstein/Eyring equation (SEE) at high temperatures around T(m). Using the equality of D(eff)(V) and D(eff)(η), we estimated the jump distance λ ~ 2.70 ? from the SEE equation and showed that the values of D(eff)(U) have the same temperature dependence but exceed D(eff)(η) by about eightfold. The difference between D(eff)(η) and D(eff)(U) indicates that the former determines the process of mass transport in the bulk whereas the latter relates to the mobility of the structural units on the crystal/liquid interface. We then employed the values of η(T) reduced by eightfold to calculate the growth rates U(T). The resultant U(T) curve is consistent with experimental data until the temperature decreases to a decoupling temperature T(d)(U) ≈ 1.1-1.2T(g), when D(eff)(η) begins decrease with decreasing temperature faster than D(eff)(U). A similar decoupling occurs between D(eff)(η) and D(eff)(τ) (estimated from nucleation time-lags) but at a lower temperatureT(d)(τ) ≈ T(g). For T > T(g) the values of D(eff)(τ) exceed D(eff)(η) only by twofold. The different behaviors of D(eff)(τ)(T) and D(eff)(U)(T) are likely caused by differences in the mechanisms of critical nuclei formation. Therefore, we have shown that at low undercoolings, viscosity data can be employed for quantitative analyses of crystal growth rates, but in the deeply supercooled liquid state, mass transport for crystal nucleation and growth are not controlled by viscosity. The origin of decoupling is assigned to spatially dynamic heterogeneity in glass-forming melts.