Protein interactions studied by SAXS: effect of ionic strength and protein concentration for BSA in aqueous solutions

We have studied a series of samples of bovine serum albumin (BSA) solutions with protein concentration, c, ranging from 2 to 500 mg/mL and ionic strength, I, from 0 to 2 M by small-angle X-ray scattering (SAXS). The scattering intensity distribution was compared to simulations using an oblate ellipsoid form factor with radii of 17 x 42 x 42 A, combined with either a screened Coulomb, repulsive structure factor, SSC(q), or an attractive square-well structure factor, SSW(q). At pH = 7, BSA is negatively charged. At low ionic strength, I < 0.3 M, the total interaction exhibits a decrease of the repulsive interaction when compared to the salt-free solution, as the net surface charge is screened, and the data can be fitted by assuming an ellipsoid form factor and screened Coulomb interaction. At moderate ionic strength (0.3-0.5 M), the interaction is rather weak, and a hard-sphere structure factor has been used to simulate the data with a higher volume fraction. Upon further increase of the ionic strength (I >or= 1.0 M), the overall interaction potential was dominated by an additional attractive potential, and the data could be successfully fitted by an ellipsoid form factor and a square-well potential model. The fit parameters, well depth and well width, indicate that the attractive potential caused by a high salt concentration is weak and long-ranged. Although the long-range, attractive potential dominated the protein interaction, no gelation or precipitation was observed in any of the samples. This is explained by the increase of a short-range, repulsive interaction between protein molecules by forming a hydration layer with increasing salt concentration. The competition between long-range, attractive and short-range, repulsive interactions accounted for the stability of concentrated BSA solution at high ionic strength.     

Cold collisions of an open-shell S-state atom with a 2Π molecule: N(4S) colliding with OH in a magnetic field

We present quantum-theoretical studies of collisions between an open-shell S-state atom and a (2)Π-state molecule in the presence of a magnetic field. We analyze the collisional Hamiltonian and discuss possible mechanisms for inelastic collisions in such systems. The theory is applied to the collisions of the nitrogen atom ((4)S) with the OH molecule, with both collision partners initially in fully spin-stretched (magnetically trappable) states, assuming that the interaction takes place exclusively on the two high-spin (quintet) potential energy surfaces. The surfaces for the quintet states are obtained from spin-unrestricted coupled-cluster calculations with single, double, and noniterative triple excitations. We find substantial inelasticity, arising from strong couplings due to the anisotropy of the interaction potential and the anisotropic spin-spin dipolar interaction. The mechanism involving the dipolar interaction dominates for small magnetic field strengths and ultralow collision energies, while the mechanism involving the potential anisotropy prevails when the field strength is larger (above 100 G) or the collision energy is higher (above 1 mK). The numerical results suggest that sympathetic cooling of magnetically trapped OH by collisions with ultracold N atoms will not be successful at higher temperatures.     

On the encapsulation of nickel clusters by molecular nitrogen

The structures and energetic effects of molecular nitrogen adsorbates on nickel clusters are investigated using an extended Huckel model coupled with two models of the adsorbate-nickel interaction. The potential parameters for the adsorbates are chosen to mimic experimental information about the binding strength of nitrogen on both cluster and bulk surface phases of nickel. The first model potential is a simple Lennard-Jones interaction that leads to binding sites in holes defined by sets of near-neighbor nickel atoms. The second model potential has a simple three-body form that forces the model nitrogen adsorbates to bind directly to single nickel atoms. Significant rearrangement of the core nickel structures are found in both models. A disconnectivity graph analysis of the potential energy surfaces implies that the rearrangements arise from low transition state barriers and the small differences between available isomers in the nickel core.     

Negative thermal expansion in single-component systems with isotropic interactions

We have devised an isotropic interaction potential that gives rise to negative thermal expansion (NTE) behavior in equilibrium many-particle systems in both two and three dimensions over a wide temperature and pressure range (including zero pressure). An optimization procedure is used in order to find a potential that yields a strong NTE effect. A key feature of the potential that gives rise to this behavior is the softened interior of its basin of attraction. Although such anomalous behavior is well-known in material systems with directional interactions (e.g., zirconium tungstate), to our knowledge, this is the first time that NTE behavior has been established to occur in single-component many-particle systems for isotropic interactions. Using constant-pressure Monte Carlo simulations, we show that as the temperature is increased, the system exhibits negative, zero, and then positive thermal expansion before melting (for both two- and three-dimensional systems). The behavior is explicitly compared to that of a Lennard-Jones system, which exhibits typical expansion upon heating for all temperatures and pressures.     

Entropy and enthalpy convergence of hydrophobic solvation beyond the hard-sphere limit

The experimentally well-known convergence of solvation entropies and enthalpies of different small hydrophobic solutes at universal temperatures seems to indicate that hydrophobic solvation is dominated by universal water features and not so much by solute specifics. The reported convergence of the denaturing entropy of a group of different proteins at roughly the same temperature as hydrophobic solutes was consequently argued to indicate that the denaturing entropy of proteins is dominated by the hydrophobic effect and used to estimate the hydrophobic contribution to protein stability. However, this appealing picture was subsequently questioned since the initially claimed universal convergence of denaturing entropies holds only for a small subset of proteins; for a larger data collection no convergence is seen. We report extensive simulation results for the solvation of small spherical solutes in explicit water with varying solute-water potentials. We show that convergence of solvation properties for solutes of different radii exists but that the convergence temperatures depend sensitively on solute-water potential features such as stiffness of the repulsive part and attraction strength, not so much on the attraction range. Accordingly, convergence of solvation properties is only expected for solutes of a homologous series that differ in the number of one species of subunits (which attests to the additivity of solvation properties) or solutes that are characterized by similar solute-water interaction potentials. In contrast, for peptides that arguably consist of multiple groups with widely disperse interactions with water, it means that thermodynamic convergence at a universal temperature cannot be expected, in general, in agreement with experimental results.     

Modeling the nonradiative decay rate of electronically excited thioflavin T

A computational model of nonradiative decay is developed and applied to explain the time-dependent emission spectrum of thioflavin T (ThT). The computational model is based on a previous model developed by Glasbeek and co-workers (van der Meer, M. J.; Zhang, H.; Glasbeek, M. J. Chem. Phys. 2000, 112, 2878) for auramine O, a molecule that, like ThT, exhibits a high nonradiative rate. The nonradiative rates of both auramine O and ThT are inversely proportional to the solvent viscosity. The Glasbeek model assumes that the excited state consists of an adiabatic potential surface constructed by adiabatic coupling of emissive and dark states. For ThT, the twist angle between the benzothiazole and the aniline is responsible for the extensive mixing of the two excited states. At a twist angle of 90°, the S(1) state assumes a charge-transfer-state character with very small oscillator strength, which causes the emission intensity to be very small as well. In the ground state, the twist angle of ThT is rather small. The photoexcitation leads first to a strongly emissive state (small twist angle). As time progresses, the twist angle increases and the oscillator strength decreases. The fit of the experimental results by the model calculations is good for times longer than 3 ps. When a two-coordinate model is invoked or a solvation spectral-shift component is added, the fit to the experimental results is good at all times.     

Polymer-induced phase separation and crystallization in immunoglobulin G solutions

We study the effects of the size of polymer additives and ionic strength on the phase behavior of a nonglobular protein-immunoglobulin G (IgG)-by using a simple four-site model to mimic the shape of IgG. The interaction potential between the protein molecules consists of a Derjaguin-Landau-Verwey-Overbeek-type colloidal potential and an Asakura-Oosawa depletion potential arising from the addition of polymer. Liquid-liquid equilibria and fluid-solid equilibria are calculated by using the Gibbs ensemble Monte Carlo technique and the Gibbs-Duhem integration (GDI) method, respectively. Absolute Helmholtz energy is also calculated to get an initial coexisting point as required by GDI. The results reveal a nonmonotonic dependence of the critical polymer concentration rho(PEG) (*) (i.e., the minimum polymer concentration needed to induce liquid-liquid phase separation) on the polymer-to-protein size ratio q (equivalently, the range of the polymer-induced depletion interaction potential). We have developed a simple equation for estimating the minimum amount of polymer needed to induce the liquid-liquid phase separation and show that rho(PEG) (*) approximately [q(1+q)(3)]. The results also show that the liquid-liquid phase separation is metastable for low-molecular weight polymers (q=0.2) but stable at large molecular weights (q=1.0), thereby indicating that small sizes of polymer are required for protein crystallization. The simulation results provide practical guidelines for the selection of polymer size and ionic strength for protein phase separation and crystallization.     

A thermodynamic perspective of the metastability of holey sheets: the role of curvature

Producing nanostructures with high surface area that are stable is important to accomplish sustained use of catalytic materials in practical settings. Avoiding the processes of ripening and sintering that typically hinder stability has long been recognized as a significant challenge and much research is focused on addressing these issues. In this article, we investigate a Pt nanostructure-a holey nanosheet-that exhibits high surface area and stability. The findings from lattice gas simulations produce a stability diagram that relates a critical hole diameter to sheet thickness. The stability is now addressed from a thermodynamic point of view, and, in particular, the crucial role of curvature is considered. We find that the stability of certain sized holes is due to the near zero mean curvature of the surface of the holes and of the surrounding flat sheet. Molecular dynamics simulations of Pt (using an embedded atom potential) are reported for small nanoclusters and model holes in sheets to illustrate the strong effects of curvature on thermodynamic properties such as the lowering of melting and surface melting temperatures.     

Chemical kinetics of reactions in the unfrozen solution of ice

Some reactions are accelerated in ice compared to aqueous solution at higher temperatures. Accelerated reactions in ice take place mainly due to the freeze-concentration effect of solutes in an unfrozen solution at temperatures higher than the eutectic point of the solution. Pincock was the first to report an acceleration model for reactions in ice,1 which successfully simulated experimental results. We propose here a modified version of the model for reactions in ice. The new model includes the total molar change involved in reactions in ice. Furthermore, we explain why many reactions are not accelerated in ice. The acceleration of reactions can be observed in the cases of (i) second- or higher-order reactions, (ii) low concentrations, and (iii) reactions with a small activation energy. Reactions with a buffer solution or additives in order to adjust ion strength, zero- or first-order reactions, or reactions containing high reactant concentrations are not accelerated by freezing. We conclude that the acceleration of reactions in the unfrozen solution of ice is not an abnormal phenomenon.     

Chain conformations and phase separation in polymer solutions with varying solvent quality

Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength between the polymer and solvent is varied. Results show that when the polymer-solvent interaction is unfavorable, the chain collapses as one would expect in a poor solvent. For more attractive polymer-solvent interactions, the solvent quality improves and the chain is increasingly solvated and exhibits ideal and then swollen conformations. However, as the polymer-solvent interaction strength is increased further to be more than about twice the strength of the polymer-polymer and solvent-solvent interactions, the chain exhibits an unexpected collapsing behavior. Correspondingly, for strong polymer-solvent attractions, phase separation is observed in the solutions of multiple chains. These results indicate that the solvent becomes effectively poor again at very attractive polymer-solvent interactions. Nonetheless, the mechanism of chain collapsing and phase separation in this limit differs from the case with a poor solvent rendered by unfavorable polymer-solvent interactions. In the latter, the solvent is excluded from the domain of the collapsed chains while in the former, the solvent is still present in the pervaded volume of a collapsed chain or in the polymer-rich domain that phase separates from the pure solvent. In the limit of strong polymer-solvent attractions, the solvent behaves as a glue to stick monomers together, causing a single chain to collapse and multiple chains to aggregate and phase separate.     

Self-organized transient facilitated atomic transport in Pt/Al(111)

During the course of atomic transport in a host material, impurity atoms need to surmount an energy barrier driven by thermodynamic bias or at ultralow temperatures by quantum tunneling. In the present article, we demonstrate using atomistic simulations that at ultralow temperature, transient interlayer atomic transport is also possible without tunneling when the Pt/Al(111) impurity/host system self-organizes itself spontaneously into an intermixed configuration. No such extremely fast athermal concerted process has been reported before at ultralow temperatures. The outlined novel transient atomic exchange mechanism could be of general validity. We find that the source of ultralow temperature heavy particle barrier crossing is intrinsic and no external bias is necessary for atomic intermixing and surface alloying in Pt/Al, although the dynamic barrier height is a few eV. The mechanism is driven by the local thermalization of the Al(111) surface in a self-organized manner arranged spontaneously by the system without any external stimulus. The core of the short lived thermalized region reaches the local temperature of approximately 1000 K (including a few tens of Al atoms), while the average temperature of the simulation cell is approximately 3 K. The transient facilitated intermixing process also takes place with repulsive impurity-host interaction potential leading to negative atomic mobility; hence, the atomic injection is largely independent of the strength of the impurity-surface interaction. We predict that similar exotic behavior is possible in other materials as well.     

Extension of the Steele 10-4-3 potential for adsorption calculations in cylindrical, spherical, and other pore geometries

Simplified fluid-substrate interaction models derived from the Lennard-Jones potential are widely used in the simulation of gas physisorption phenomena. In this paper, we reinterpret the well known Steele 10-4-3 potential for a gas molecule interacting with a planar surface, and use the resultant scheme to derive new potentials for cylindrical and spherical pore geometries. These new potentials correctly recover the Steele result in the limit of infinite pore radius, a useful improvement over existing models. We demonstrate the new cylindrical Steele 10-4-3 potential in calculations of argon adsorption via fluid density functional theory. This potential yields markedly different adsorption behavior than existing cylindrical potentials, which follow from small but significant differences in both the strength and the shape of the fluid-surface interaction. These differences cannot be fully reconciled simply by reparameterizing (scaling) the existing models; the new potential is more realistic in design, and is especially to be preferred in studies where comparison with planar substrates is made. Finally, we discuss extensions of this approach to more complicated pore geometries, yielding a family of Steele-like potentials that all satisfy the correct planar limit.     

Molecular solvation in water-methanol and water-sorbitol mixtures: the roles of preferential hydration, hydrophobicity, and the equation of state

Molecular dynamics simulations of aqueous mixtures of methanol and sorbitol were performed over a wide range of binary composition, density (pressure), and temperature to study the equation of state and solvation of small apolar solutes. Experimentally, methanol is a canonical solubilizing agent for apolar solutes and a protein denaturant in mixed-aqueous solvents; sorbitol represents a canonical "salting-out" or protein-stabilizing cosolvent. The results reported here show increasing sorbitol concentration under isothermal, isobaric conditions results in monotonic increases in apolar solute excess chemical potential (mu2ex) over the range of experimentally relevant temperatures. For methanol at elevated temperatures, increasing cosolvent composition results in monotonically decreasing mu2ex. However, at lower temperatures mu2ex exhibits a maximum versus cosolvent concentration, as seen experimentally for Ar in ethanol-water solutions. Both density anomalies and hydrophobic effects--characterized by temperatures of density maxima and apolar solute solubility minima, respectively--are suppressed upon addition of either sorbitol or methanol at all temperatures and compositions simulated here. Thus, the contrasting effects of sorbitol and methanol on solute chemical potential cannot be explained by qualitative differences in their ability to enhance or suppress hydrophobic effects. Rather, we find mu2ex values across a broad range of temperatures and cosolvent composition can be quantitatively explained in terms of isobaric changes in solvent density--i.e., the equation of state--along with the corresponding packing fraction of the solvent. Analysis in terms of truncated preferential interaction parameters highlights that care must be taken in interpreting cosolvent effects on solvation in terms of local preferential hydration.     

Exploring artificial neural networks to model interatomic and intermolecular potential energy surfaces

We demonstrate how a back-propagation artificial neural network can be trained to represent a potential energy surface (PES) in a formless manner with limited data points and exploited to predict interaction energies for configurations not included in the training set. A similar exercise is undertaken for predicting the eigenvalues and eigenvectors of a model Hamiltonian matrix that delicately depends on parameters and exhibits crossing of eigen values.     

A potential model for methane in water describing correctly the solubility of the gas and the properties of the methane hydrate

We have obtained the excess chemical potential of methane in water, over a broad range of temperatures, from computer simulation. The methane molecules are described as simple Lennard-Jones interaction sites, while water is modeled by the recently proposed TIP4P/2005 model. We have observed that the experimental values of the chemical potential are not reproduced when using the Lorentz-Berthelot combining rules. However, we also noticed that the deviation is systematic, suggesting that this may be corrected. In fact, by introducing positive deviations from the energetic Lorentz-Berthelot rule to account indirectly for the polarization methane-water energy, we are able to describe accurately the excess chemical potential of methane in water. Thus, by using a model capable of describing accurately the density of pure water in a wide range of temperatures and by deviating from the Lorentz-Berthelot combining rules, it is possible to reproduce the properties of methane in water at infinite dilution. In addition, we have applied this methane-water potential to the study of the solid methane hydrate structure, commonly denoted as sI, and find that the model describes the experimental value of the unit cell of the hydrate with an error of about 0.2%. Moreover, we have considered the effect of the amount of methane contained in the hydrate. In doing so, we determine that the presence of methane increases slightly the value of the unit cell and decreases slightly the compressibility of the structure. We also note that the presence of methane increases greatly the range of pressures where the sI hydrate is mechanically stable.     

Dynamical and energetic properties of hydrogen and hydrogen-tetrahydrofuran clathrate hydrates

Classical equilibrium molecular dynamics (MD) simulations have been performed to investigate the dynamical and energetic properties in hydrogen and mixed hydrogen-tetrahydrofuran sII hydrates at 30 and 200 K and 0.05 kbar, and also at intermediate temperatures, using SPC/E and TIP4P-2005 water models. The potential model is found to have a large impact on overall density, with the TIP4P-2005 systems being on average 1% more dense than their SPC/E counterparts, due to the greater guest-host interaction energy. For the lightly-filled mixed H(2)-THF system, in which there is single H(2) occupation of the small cage (1s1l), we find that the largest contribution to the interaction energy of both types of guest is the van der Waals component with the surrounding water molecules in the constituent cavities. For the more densely-filled mixed H(2)-THF system, in which there is double H(2) occupation in the small cage (2s1l), we find that there is no dominant component (i.e., van der Waals or Coulombic) in the H(2) interaction energy with the rest of the system, but for the THF molecules, the dominant contribution is again the van der Waals interaction with the surrounding cage-water molecules; again, the Coulombic component increases in importance with increasing temperature. The lightly-filled pure H(2) hydrate (1s4l) system exhibits a similar pattern vis-à-vis the H(2) interaction energy as for the lightly-filled mixed H(2)-THF system, and for the more densely-filled pure H(2) system (2s4l), there is no dominant component of interaction energy, due to the multiple occupancy of the cavities. By consideration of Kubic harmonics, there is some evidence of preferential alignment of the THF molecules, particularly at 200 K; this was found to arise at higher temperatures due to transient hydrogen bonding of the oxygen atom in THF molecules with the surrounding cage-water molecules.     

Hydrated arrays of acidic surface groups as model systems for interfacial structure and mechanisms in PEMs

We utilize ab initio quantum mechanical calculations in order to explore structural conformations and cooperative mechanisms at a minimally hydrated 2D array of flexible acidic surface groups. This system serves as a model for rationalizing interactions and correlations of protons and water with ionized side chains that are affixed to hydrophobic polymer aggregates in polymer electrolyte membranes (PEMs). The model exhibits two basic minimum energy configurations upon varying the separation of surface groups from 5 to 12 A. In the "upright" structure at small separation, surface groups are fully dissociated and oriented perpendicular to the basal plane. Together with hydronium ions (H3O+) they form a highly ordered network with long-range correlations. At larger separations we found the transition to a "tilted" structure with cluster-like conformation of surface groups. This structure retains only short-range correlations. Moreover, we investigated the strength of water binding to the minimally hydrated structures. At small separations between surface groups, an additional water molecule interacts only weakly with the minimally hydrated array (binding energy < 0.1 eV) while the energy needed to remove one water molecule exceeds 1 eV. This shows that the minimally hydrated systems are very stable. Ideally, these studies would expedite the design of cheap, highly performing PEMs for fuel cells, with a major focus on membranes that could operate stably at minimal hydration and elevated temperatures (>120 degrees C).