Short-range Parameters Research Articles

Modulating charge patterning and ionic strength as a strategy to induce conformational changes in intrinsically disordered proteins.

We present an analytical theory to describe conformational changes as a function of salt for polymers with a given sequence of charges. We apply this model to describe Intrinsically Disordered Proteins (IDPs) by explicitly accounting for charged residues and their exact placement in the primary sequence while approximating the effect of non-electrostatic interactions at a mean-field level by effective short-range (two body and three-body) interaction parameters. The effect of ions is introduced by treating electrostatic interactions within Debye-Huckle approximation. Using typical values of the short-range mean-field parameters derived from all-atom Monte Carlo simulations (at zero salt), we predict the conformational changes as a function of salt concentration. We notice that conformational transitions in response to changes in ionic strength strongly depend on sequence specific charge patterning. For example, globule to coil transition can be observed upon increasing salt concentration, in stark contrast to uniformly charged polyelectrolyte theories based on net charge only. In addition, it is possible to observe non-monotonic behavior with salt as well. Drastic differences in salt-induced conformational transitions is also evident between two doubly phosphorylated sequences-derived from the same wild type sequence-that only differ in the site of phosphorylation. Similar effects are also predicted between two sequences derived from the same parent sequence differing by a single site mutation where a negative charge is replaced by a positive charge. These effects are purely a result of charge decoration and can only be understood in terms of metrics based on specific placement of charges, and cannot be explained by models based on charge composition alone. Identifying sequences and hot spots within sequences-for post translational modification or charge mutation-using our high-throughput theory will yield fundamental insights into design and biological regulation mediated by phosphorylation and/or local changes in salt concentration.

Coupling of Charge Regulation and Conformational Equilibria in Linear Weak Polyelectrolytes: Treatment of Long-Range Interactions via Effective Short-Ranged and pH-Dependent Interaction Parameters.

The classical Rotational Isomeric State (RIS) model, originally proposed by Flory, has been used to rationalize a wide range of physicochemical properties of neutral polymers. However, many weak polyelectrolytes of interest are able to regulate their charge depending on the conformational state of the bonds. Recently, it has been shown that the RIS model can be coupled with the Site Binding (SB) model, for which the ionizable sites can adopt two states: protonated or deprotonated. The resulting combined scheme, the SBRIS model, allows for analyzing ionization and conformational equilibria on the same foot. In the present work, this approach is extended to include pH-dependent electrostatic Long-Range (LR) interactions, ubiquitous in weak polyelectrolytes at moderate and low ionic strengths. With this aim, the original LR interactions are taken into account by defining effective Short-Range (SR) and pH-dependent parameters, such as effective microscopic protonation constants and rotational bond energies. The new parameters are systematically calculated using variational methods. The machinery of statistical mechanics for SR interactions, including the powerful and fast transfer matrix methods, can then be applied. The resulting technique, which we will refer to as the Local Effective Interaction Parameters (LEIP) method, is illustrated with a minimal model of a flexible linear polyelectrolyte containing only one type of rotating bond. LEIP reproduces very well the pH dependence of the degree of protonation and bond probabilities obtained by semi-grand canonical Monte Carlo simulations, where LR interactions are explicitly taken into account. The reduction in the computational time in several orders of magnitude suggests that the LEIP technique could be useful in a range of areas involving linear weak polyelectrolytes, allowing direct fitting of the relevant physical parameters to the experimental quantities.

Neutron Diffraction Study on the Structure of Hydrated Li+ in Dilute Aqueous Solutions.

Neutron diffraction measurements have been carried out for 6Li/7Li isotopically substituted aqueous 1.0 mol % (0.5 mol/kg) LiCl and 1.1 mol % (0.56 mol/kg) LiClO4 solutions in D2O to obtain structural insight concerning hydration structure of Li+ in more dilute electrolyte solutions. The first-order difference function, ΔLi(Q), was analyzed by means of the least squares fitting procedure to obtain short-range structural parameters around the Li+. It was revealed that the nearest neighbor Li+···O(D2O) distance, rLiO, and the coordination number, nLiO, for the aqueous 1.0 mol % LiCl solution are 2.01 ± 0.02 Å and 5.9 ± 0.1, respectively. The values, rLiO = 1.97 ± 0.02 Å and nLiO = 6.1 ± 0.1, are obtained for aqueous 1.1 mol % LiClO4 solution. These results indicate that the hydration number of Li+ in a dilute solution is close to 6, which is much larger than 4, which has long been believed. A possible explanation is that the hydration number of Li+ varies with the solute concentration.

Fitting electron density as a physically sound basis for the development of interatomic potentials of complex alloys

The development of new interatomic potentials to model metallic systems is a difficult task, due in part to the dependence between the parameters that describe the electron density and the short-range interactions. Parameter search methods are prone to false convergence. To solve this problem, we have developed a methodology for obtaining the electron density parameters independently of the short-range interactions, so that physically sound parameters can be obtained to describe the electron density, after which the short-range parameters can be fitted, thus reducing the complexity of the process and yielding better interatomic potentials. With the new method we can develop self-consistent, accurate force fields, using solely calculations, without the need to fit to experimental data. Density functional theory calculations are used to compute the observables with which the potential is fit. We applied the method to a Ni-based Inconel 625 superalloy (IN625), modelled here as Ni, Cr, Mo and Fe solid solution alloys. The capability of the force fields developed using this new method is validated, by comparing the structural and thermo-elastic properties predicted with the force fields, with the corresponding experimental data, both for single crystals and polycrystalline alloys.

A convenient and accurate wide-range parameter relationship between Buckingham and Morse potential energy functions

ABSTRACTThis study explores the close-range, short-range and long-range relationships between the parameters of the Morse and Buckingham potential energy functions. The results show that the close-range and short-range relationships are valid for bond compression and for very small changes in bond length, respectively, while the long-range relationship is valid for bond stretching. A wide-range relationship is proposed to combine the comparative advantages of the close-range, short-range and long-range parameter relationships. The wide-range relationship is useful for replacing the close-range, short-range and long-range parameter relationships, thereby preventing the undesired effects of potential energy jumps resulting from functional switching between the close-range, short-range and long-range interaction energies.

DSD-PBEP86-NL and DOD-PBEP86-NL functionals for noncovalent interactions: Basis set effects and tentative applications to large noncovalent systems

Basis set effects on the DSD-PBEP86-NL and DOD-PBEP86-NL functionals for noncovalent interactions have been extensively studied in this work. The cc-pVXZ (X = D, T, Q, 5, 6) and augmented aug-cc-pVXZ (X = D, T, Q) basis sets are systematically tested without counterpoise (CP) corrections against the well-known S66 database. Additionally, the basis sets of def2-TZVPP and def2-TZVPPD are also examined. Based on our computations, the performances of the aug-cc-pVQZ, cc-pV5Z, and cc-pV6Z basis sets are very approximate to those obtained with the def2-QZVP basis set for both the DSD-PBEP86-NL and DOD-PBEP86-NL functionals. Note that the short-range attenuation parameters for these two functionals were directly optimized using the def2-QZVP basis set without CP corrections against the S66 database. Generally speaking, the cc-pVXZ (X = D, T, Q), aug-cc-pVXZ (X = D, T, Q), def2-TZVPP, and def2-TZVPPD basis sets favor half CP correction for these two functionals. Nevertheless, the aug-cc-pVQZ basis set already performs well without any CP correction, especially for the DOD-PBEP86-NL functional. With respect to accuracy and computational cost, the cc-pVTZ and def2-TZVPP basis sets with half CP corrections are recommended for these two functionals to evaluate interaction energies of large noncovalent complexes.

Chemical ordering beyond the superstructure in long-range ordered systems

To describe chemical ordering in solid solutions systems Warren–Cowley short-range parameters are ordinarily used. However, they are not directly suited for application to long-range ordered systems, as they do not converge to zero for large separations. In this paper, the theory is generalized to long-range ordered systems and chemical short-range order beyond the superstructure arrangements is discussed quantitatively on the example of a non-stoichiometric B2-ordered intermetallic alloy. Parameters of interatomic potentials are taken from an embedded atom method calculations and the degree of order is simulated by the Monte Carlo method. Both on-lattice and off-lattice methods, where the latter allows individual atoms to deviate from their regular lattice sites, were used, and the resulting effects are discussed.

Ab Initio Atom-Atom Potentials Using CamCASP: Theory and Application to Many-Body Models for the Pyridine Dimer.

Creating accurate, analytic atom-atom potentials for small organic molecules from first principles can be a time-consuming and computationally intensive task, particularly if we also require them to include explicit polarization terms, which are essential in many systems. We describe how the CamCASP suite of programs can be used to generate such potentials using some of the most accurate electronic structure methods currently applicable. We derive the long-range terms from monomer properties and determine the short-range anisotropy parameters by a novel and robust method based on the iterated stockholder atom approach. Using these techniques, we develop distributed multipole models for the electrostatic, polarization, and dispersion interactions in the pyridine dimer and develop a series of many-body potentials for the pyridine system. Even the simplest of these potentials exhibits root mean square errors of only about 0.6 kJ mol(-1) for the low-energy pyridine dimers, significantly surpassing the best empirical potentials. Our best model is shown to support eight stable minima, four of which have not been reported before in the literature. Further, the functional form can be made systematically more elaborate so as to improve the accuracy without a significant increase in the human-time spent in their generation. We investigate the effects of anisotropy, rank of multipoles, and choice of polarizability and dispersion models.

Assessing Local and Long-Range Structural Disorder in Aggregate-Free Lime Binders

For aggregate-free, calcite-containing lime binders, we correlate long-range crystallinity parameters from X-ray diffraction measurements (lattice constants, crystalline domain sizes, and microstrain fluctuation values) with short-range structural parameters from extended X-ray absorption fine structure data (coordination environments, attenuation factors, and fit stabilities). In doing so, we reveal a correlation between unit cell contraction and a more ideal local calcite structure. Using Fourier transform infrared spectroscopy and X-ray absorption near edge spectroscopy, we rule out the possibility of contributions from amorphous calcium carbonate and show that the structural disorder is likely related to localized regions of incomplete carbonation. Thus, by using data from this judicious combination of structural characterization tools, we demonstrate that short-range structural distortions occur in calcitic lime binders and that these distortions can be detected even in multiphase mixtures.

Nonlocal gravity in the solar system

The implications of the recent classical nonlocal generalization of Einstein’s theory of gravitation for gravitational physics in the solar system are investigated. In this theory, the nonlocal character of gravity appears to simulate dark matter. Nonlocal gravity in the Newtonian regime involves a reciprocal kernel with three spatial parameters, of which two have already been determined from the rotation curves of spiral galaxies and the internal dynamics of clusters of galaxies. However, the short-range parameter a0 remains to be determined. In this connection, the nonlocal contribution to the perihelion precession of a planetary orbit is estimated and a preliminary lower limit on a0 is determined.

Experimental measurement and thermodynamic modeling of CO2 solubility in aqueous solutions of morpholine

In the present work, new experimental data of CO2 solubility in aqueous solutions of 2, 3 and 4.5M (17.5, 26.1 and 39.16wt.%) morpholine (MOR) at two different temperatures (313.15 and 333.15K) is obtained by static method. The Deshmukh–Mather thermodynamic model is performed to calculate CO2 solubility in aqueous MOR solutions. The short-range interaction parameters between ion–ion and ion–molecule species in the activity coefficient model are considered to be function of temperature and are adjusted to experimental data. The model shows good results for the solubility calculations. The overall average absolute relative percent deviation (AAD%) for all the data points of CO2 partial pressure is 9.86%.

Analytic Expression for Three-Body Recombination Rates into Deep Dimers

We investigate three-body recombination rates into deep dimers in cold atomic gases with large scattering length within hyper-spherical adiabatic zero-range approach. We derive closed analytic expressions for the rates for one- and two-species gases. Although the deep dimers are beyond the zero-range theory the latter can still describe the recombination into deep dimers by use of one additional short-range absorption parameter. The recombination rate, as function of the scattering length, retains the known universal behavior—the fourth power trend with characteristic log-periodic peaks—however increasing the short-range absorption broadens the peaks until they are eventually completely smeared out. Increasing the heavy-to-light mass ratio in a two-species system with two identical bosons and a third particle decreases the distance between the peaks and increases the overall scale of the recombination rate.

Classical Description of the Vibrational Spectroscopy, Structure, and Electrostatics of the Halide Solvation Shell with the POLIR Potential.

POLIR (POLarizable for IR) (J. Chem. Phys. 2008, 129, 034504) is a polarizable, flexible, and transferable water potential which describes the IR spectrum in the O-H stretch region via the classical dipole correlation function with simple quantum corrections. POLIR also reproduces experimental spectral shifts in solutions of Ca(2+), Mg(2+), and Cu(2+) (J. Am. Chem. Soc. 2011, 133, 9441-9450). Here we present an extended investigation of POLIR water in the solvation shell of the halides F(-), Cl(-), Br(-), and I(-) using various interaction potentials, polarizabilities, and short-range electrostatic damping parameters. Our results indicate that the correlation of the first solvation shell dipoles produces IR spectra that are in agreement with experiment; that is, vibrational spectral shifts may be obtained with classical mechanics and simple corrections. Calculated ion induced dipoles agree with quantum simulations. Further analysis shows that ion-dependent shifts in the spectra may be attributed to the hydrogen bond O···O-H angle distribution within the first solvation shell, decomposed into ion-water and water-water contributions.

Spin-Component-Scaled Double-Hybrid Density Functionals with Nonlocal van der Waals Correlations for Noncovalent Interactions.

Nonlocal (NL) van der Waals correlation has been incorporated into the spin-component and spin-opposite scaled double-hybrid density functionals (DHDFs) for noncovalent interactions. The short-range attenuation parameters for the tested DHDFs with the NL correlations are optimized by minimizing the mean absolute deviations (MADs) against the S66 database. And consequently, the obtained DHDFs with the NL correlations are denoted as PWPB95-NL, DSD-BLYP-NL, DSD-PBEP86-NL, and DOD-PBEP86-NL. These four DHDFs with the NL correlations are further assessed with the S22B, NCCE31, and ADIM6 databases. On the basis of our benchmark computations, the cooperation of the NL correlation and the spin-component and spin-opposite scaled DHDFs is successful for noncovalent interactions. However, the performances of the four aforementioned DHDFs with the NL correlations on the charge transfer interactions are less than satisfactory.

Segregation in Fe-Pd melt at 1873 K

The thermodynamic and structural properties of Fe-Pd liquid alloys at 1873 K have been computed using regular associated solution model. To compute these functions we have estimated the mole fractions of the complex assuming the existence of FePd3 complex in the melt. The thermodynamic properties such as free energy of mixing (GM), heat of mixing (HM), entropy of mixing (SM) and activity (a) of the melt have been estimated. To understand the microscopic structural properties, we have estimated the concentration fluctuation in long wavelength limit (Scc(0)) and the Warren-Cowley short range parameter (α1). The free energy of mixing was found to be negative at all compositions. But the heat of mixing and the entropy of mixing are found to be positive at all compositions. The equilibrium constant (K) is found be less than negative. The interaction energy parameters (w12, w13 and w23) are all found to be positive and temperature dependent. The theoretical estimation of the concentration fluctuation in long wavelength limit (SCC (0)) is found to be greater than the ideal values throughout the whole range. The theoretical analysis suggests that the Fe-Pd liquid alloy at 1873 K near the melting point is segregating (homo-coordinating) system. The Warren-Cowley short range order parameter is found to be positive which too suggest the homocoordinating (segregating) nature of the system at all compositions. The theoretical analysis also suggests that the Fe-Pd liquid alloy near melting point is weakly interacting system. DOI: http://dx.doi.org/10.3126/bibechana.v11i0.10386 BIBECHANA 11(1) (2014) 86-93

Nonlocal van der Waals Approach Merged with Double-Hybrid Density Functionals: Toward the Accurate Treatment of Noncovalent Interactions.

Noncovalent interactions drive the self-assembly of weakly interacting molecular systems to form supramolecular aggregates, which play a major role in nanotechnology and biochemistry. In this work, we present a thorough assessment of the performance of different double-hybrid density functionals (PBE0-DH-NL, revPBE0-DH-NL, B2PLYP-NL, and TPSS0-DH-NL), as well as their parent hybrid and (meta)GGA functionals, in combination with the most modern version of the nonlocal (NL) van der Waals correction. It is shown that this nonlocal correction can be successfully coupled with double-hybrid density functionals thanks to the short-range attenuation parameter b, which has been optimized against reference interaction energies of benchmarking molecular complexes (S22 and S66 databases). Among all the double-hybrid functionals evaluated, revPBE0-DH-NL and B2PLYP-NL behave remarkably accurate with mean unsigned errors (MUE) as small as 0.20 kcal/mol for the training sets and in the 0.25-0.42 kcal/mol range for an independent database (NCCE31). They can be thus seen as appropriate functionals to use in a broad number of applications where noncovalent interactions play an important role. Overall, the nonlocal van der Waals approach combined with last-generation density functionals is confirmed as an accurate and affordable computational tool for the modeling of weakly bonded molecular systems.

Temperature Dependence of Magnetic Parameters in FePt Nanoparticles

Here, particular focus is placed on the atomic alignment and the order–disorder phase transition of the FePt alloy with the aid of a model that can describe realistic phenomena. Here, we present a method to study the order–disorder phenomena of FePt alloys. We will discuss the increase in the coercivity of FePt nanoparticles by an increasing annealing temperature for annealed FePt nanoparticles. According to the experimental evidence, we will present a model for explaining spin-glass-like behavior of these particles during the annealing procedure. In the phase transition from disordered FCC to ordered FCT in FePt nano-particles can be treated by first-order phase transitions. So, the mean field approach can be used in order to model this kind of phase transition. In nanoparticles, which are synthetized by sol–gel methods, the short range parameter is predominant because in these kinds of preparations, the long range order takes a lot of time to happen. By using a short range parameter, we are able to use the mean field approach, which considers the diffusion of atoms to the near neighborhood sites. The effects of random exchange and random magnetocrystalline anisotropy are known as the main results of coercivity reduction in magnetic nanoparticles. These effects are strongly dependent to the annealing temperature of nanoparticles. During disorder–order transition, these two effects are max. As transition continues, these effects vanish and coercivity of nanoparticles increases. Here, we will add these two effects to the Hamiltonian of the FePt system. With increasing the annealing temperature, the fraction of the FePt nanoparticles with a FCC disordered phase vanishes, which leads to decrease in the amount of 〈j〉. During the annealing process, the $\frac{c}{a}$ ratio varies as a function of the annealing temperature. The relation between the $\frac{c}{a}$ ratio and the annealing temperature is derived. The derived $\frac{c}{a}$ ratio and coercivity formulas are compared with experimental results. The results are in a good agreement with experimental data.

Refining classical force fields for ionic liquids: theory and application to [MMIM][Cl

Most of the force fields for ionic liquids cannot properly describe statics and dynamics. In this context, we propose an efficient method to adapt force fields, the basis of any classical molecular dynamics simulation. In the parameterisation process, a target function is minimized by a conjugate gradient based approach that vastly accelerates the tuning of the force field parameters through parallelization. As the description of the dynamics is captured in the parameterisation of the partial charges, we fit the short range parameters using only static properties, thus avoiding long simulations for the force field refinement. In the validation of the final parameterisation, the force field gives a good description of the dynamics in terms of the conductivity, especially in the temperature regime where the reference properties are matched very accurately. This method is sufficiently general and easily altered to fit an arbitrary set of reference properties, such that it can be considered for the construction of a versatile, transferable force field for ionic liquids.

Computational study of short-range interactions in bacteriochlorophyll aggregates

Chlorosomes are light harvesting complexes, interior of which is composed of bacteriochlorophylls that are assembled into lamellar aggregates. In this work, short-range structural parameters of aggregated bacteriochlorophyll-c were explored. The knowledge of bonds involved in aggregation together with other experimental results provides constraints which are satisfied by eight possible structural motifs. Each motif is based on a dimer unit with esterifying alcohols extending to opposite sides of the lamellar layer. The possible models include two of the previously proposed structural models, so-called antiparallel piggy-back dimer [1,2] and a parallel syn-anti model [3]. Structural models of aggregates were built as a single layer consisting of 8×10 monomers and were optimized by Amber program using modified General Amber Force Field. From the optimized models the central tetramer unit was selected for single-point energy analyses. Three electronic methods: RI-MP2/SVP, B97-D/TZVP, and PM6-DH2 were chosen for revealing energy relations in the structural models. Calculations disclose that the most preferable structure is the antiparallel chain model corresponding to the antiparallel piggy-back dimer, followed by one of antiparallel sheet models and one of parallel sheet arrangements. All simulations showed that due to the crystal packing a large deformation of monomeric building block occurred. The deformation energies (the difference between the energy of optimized isolated monomer and that of the monomer in assembled structures) are about 15kcal/mol for all considered computational methods. From energy decomposition, contributions of individual interactions to the overall stabilization energy were estimated. In addition, powder diffraction and optical spectra were calculated for all models and compared with experimental results.

Theoretical Study of the Structural and Thermodynamic Properties of Amorphous SiO2 and Amorphous SiO2 with an Oxygen Defect Center

Structural properties and thermodynamic properties of amorphous SiO2(a-SiO2) and amorphous SiO2 with an oxygen defect center (a-SiO2-ODC) are investigated by using interatomic pair potentials. Amorphous configurations of SiO2 glass are constructed by quenching using the molecular-dynamics method and subsequent relaxation using the first-principles method. The numerical result demonstrates that the calculated short-range structural parameters coincide well with the previous experimental and theoretical results reported. The thermodynamic properties including specific heat, Debye temperature, vibrational entropy, and so on are analyzed by calculating the phonon density. Furthermore, mechanical properties of both structures are obtained.