Project description:Ab initio intermolecular potential energy surfaces (PES) of N2-NO have been constructed at the level of theory CCSD(T) with the augmented correlation-consistent basis sets aug-cc-pVmZ (with m = 2, 3, 4). The nitrogen in the closed-shell electronic configuration X1Σ+ and nitric oxide in the open-shell electronic configuration A2Σ+ were employed to calculate ab initio intermolecular interaction energies. The two new ab initio 5-site intermolecular pair potentials at the theoretical level CCSD(T)/aug-cc-pVmZ (with m = 4, 24) were developed appropriately and are suitable for N2-NO dimer by using the nonlinear least-squares fitting method combining MIO and Levenberg-Marquardt algorithms. The correlation quality of these two potentials was found to be very good with R 2 values in the range of 0.98372 to 0.99775. The cross second virial coefficients B 12(T) of the N2-NO dimer were calculated in the temperature range of 100 to 470 K using the two ab initio 5-site potentials. The discrepancies between the calculated results and the experimental data can be acceptable.
Project description:We use a new high-accuracy all-dimensional potential to compute the cross second virial coefficient B12(T) between molecular hydrogen and carbon monoxide. The path-integral method is used to fully account for quantum effects. Values are calculated from 10 K to 2000 K and the uncertainty of the potential is propagated into uncertainties of B12. Our calculated B12(T) are in excellent agreement with most of the limited experimental data available, but cover a much wider range of temperatures and have lower uncertainties. Similar to recently reported findings from scattering calculations, we find that the reduced-dimensionality potential obtained by averaging over the rovibrational motion of the monomers gives results that are a good approximation to those obtained when flexibility is fully taken into account. Also, the four-dimensional approximation with monomers taken at their vibrationally averaged bond lengths works well. This finding is important, since full-dimensional potentials are difficult to develop even for triatomic monomers and are not currently possible to obtain for larger molecules. Likewise, most types of accurate quantum mechanical calculations, e.g., spectral or scattering, are severely limited in the number of dimensions that can be handled.
Project description:The Huggins coefficient kH is a well-known metric for quantifying the increase in solution viscosity arising from intermolecular interactions in relatively dilute macromolecular solutions, and there has been much interest in this solution property in connection with developing improved antibody therapeutics. While numerous kH measurements have been reported for select monoclonal antibodies (mAbs) solutions, there has been limited study of kH in terms of the fundamental molecular interactions that determine this property. In this paper, we compare measurements of the osmotic second virial coefficient B22, a common metric of intermolecular and interparticle interaction strength, to measurements of kH for model antibody solutions. This comparison is motivated by the seminal work of Russel for hard sphere particles having a short-range "sticky" interparticle interaction, and we also compare our data with known results for uncharged flexible polymers having variable excluded volume interactions because proteins are polypeptide chains. Our observations indicate that neither the adhesive hard sphere model, a common colloidal model of globular proteins, nor the familiar uncharged flexible polymer model, an excellent model of intrinsically disordered proteins, describes the dependence of kH of these antibodies on B22. Clearly, an improved understanding of protein and ion solvation by water as well as dipole-dipole and charge-dipole effects is required to understand the significance of kH from the standpoint of fundamental protein-protein interactions. Despite shortcomings in our theoretical understanding of kH for antibody solutions, this quantity provides a useful practical measure of the strength of interprotein interactions at elevated protein concentrations that is of direct significance for the development of antibody formulations that minimize the solution viscosity.
Project description:The second virial coefficient, B2, measures a protein solution's deviation from ideal behavior. It is widely used to predict or explain solubility, crystallization condition, aggregation propensity, and critical temperature for liquid-liquid phase separation. B2 is determined by the interaction energy between two protein molecules and, specifically, by the integration of the Mayer f-function in the relative configurational space (translation and rotation) of the two molecules. Simple theoretical models, such as one attributed to Derjaguin, Landau, Verwey, and Overbeek (DLVO), can fit the dependence of B2 on salt concentrations. However, model parameters derived often are physically unrealistic and hardly transferable from protein to protein. Previous B2 calculations incorporating atomistic details were done with limited sampling in the configurational space, due to enormous computational cost. Our FMAP method, based on fast Fourier transform, can considerably accelerate such calculations, and here we adapt it to calculate B2 values for proteins represented at the atomic level in implicit solvent. After tuning of a single parameter in the energy function, FMAPB2 predicts well the B2 values for lysozyme and other proteins over wide ranges of solvent conditions (salt concentration, pH, and temperature). The method is available as a web server at http://pipe.rcc.fsu.edu/fmapb2 .
Project description:The thermodynamic properties of protein solutions are determined by the molecular interactions involving both solvent and solute molecules. A quantitative understanding of the relationship would facilitate more systematic procedures for manipulating the properties in a process environment. In this work the molecular basis for the osmotic second virial coefficient, B22, is studied; osmotic effects are critical in membrane transport, and the value of B22 has also been shown to correlate with protein crystallization behavior. The calculations here account for steric, electrostatic, and short-range interactions, with the structural and functional anisotropy of the protein molecules explicitly accounted for. The orientational dependence of the protein interactions is seen to have a pronounced effect on the calculations; in particular, the relatively few protein-protein configurations in which the apposing surfaces display geometric complementarity contribute disproportionately strongly to B22. The importance of electrostatic interactions is also amplified in these high-complementarity configurations. The significance of molecular recognition in determining B22 can explain the correlation with crystallization behavior, and it suggests that alteration of local molecular geometry can help in manipulating protein solution behavior. The results also have implications for the role of protein interactions in biological self-organization.
Project description:The development of future generations of Ni-base superalloys will depend on a systematic understanding of how each alloying element affects the fundamental properties of Ni-base superalloys, particularly with respect to their creep behavior. First, this article presents the temperature-dependent data of all factors entering into dilute impurity diffusion for 26 Ni-X alloy systems, including atomic jump frequencies, thermodynamic parameters, and diffusivity plots. Second, this article presents the data used to calculate the relative creep rate ratios showing the effect of each of the 26 alloying elements, X, on the dilute Ni-X alloy. The dataset refers to "A comprehensive first-principles study of solute elements in dilute Ni alloys: Diffusion coefficients and their implications to tailor creep rate" by Hargather et al. [1].
Project description:Virial coefficients are predicted over a large range of both temperatures and model parameter values (i.e., alchemical transformation) from an individual Mayer-sampling Monte Carlo simulation by statistical mechanical extrapolation with minimal increase in computational cost. With this extrapolation method, a Mayer-sampling Monte Carlo simulation of the SPC/E (extended simple point charge) water model quantitatively predicted the second virial coefficient as a continuous function spanning over four orders of magnitude in value and over three orders of magnitude in temperature with less than a 2% deviation. In addition, the same simulation predicted the second virial coefficient if the site charges were scaled by a constant factor, from an increase of 40% down to zero charge. This method is also shown to perform well for the third virial coefficient and the exponential parameter for a Lennard-Jones fluid.
Project description:We investigate the thermodynamic properties of various super-critical model adsorptive systems with different fluid-solid attractive strengths using the confined-density virial expansion, with coefficients calculated using the Mayer-sampling Monte Carlo method up to fifth order. We find that the virial expansion converges for adsorptive systems over a density range corresponding approximately to the film-formation regime. Beyond this regime, higher order effects become increasingly important. The virial expansion of the density profile is also investigated. It is determined that this expansion gives insight into the structure associated with adsorption. We also find that weakly attractive systems have a more negative second virial coefficient than strongly attractive systems. This runs counter to the usual interpretation of bulk fluid virial coefficients. This is due to the infinite-dilution limit being very different for adsorbed fluids compared to bulk fluids.
Project description:This article begins by highlighting some of the ground-based studies emanating from NASA's Microgravity Protein Crystal Growth (PCG) program. This is followed by a more detailed discussion of the history of and the progress made in one of the NASA-funded PCG investigations involving the use of measured second virial coefficients (B values) as a diagnostic indicator of solution conditions conducive to protein crystallization. A second application of measured B values involves the determination of solution conditions that improve or maximize the solubility of aqueous and membrane proteins. These two important applications have led to several technological improvements that simplify the experimental expertise required, enable the measurement of membrane proteins and improve the diagnostic capability and measurement throughput.
Project description:Diffusion coefficients of alloying elements in Mg are critical for the development of new Mg alloys for lightweight applications. Here we present the data set of the temperature-dependent dilute tracer diffusion coefficients for 47 substitutional alloying elements in hexagonal closed packed (hcp) Mg calculated from first-principles calculations based on density functional theory (DFT) by combining transition state theory and an 8-frequency model. Benchmark for the DFT calculations and systematic comparison with experimental diffusion data are also presented. The data set refers to "Diffusion coefficients of alloying elements in dilute Mg alloys: A comprehensive first-principles study" by Zhou et al. [1].