Computational characterization and prediction of metal-organic framework properties

In this introductory review, we give an overview of the computational chemistry methods commonly used in the field of metal-organic frameworks (MOFs), to describe or predict the structures themselves and characterize their various properties, either at the quantum chemical level or through classical molecular simulation. We discuss the methods for the prediction of crystal structures, geometrical properties and large-scale screening of hypothetical MOFs, as well as their thermal and mechanical properties. A separate section deals with the simulation of adsorption of fluids and fluid mixtures in MOFs

Information-theoretic approaches to atoms-in-molecules : Hirshfeld family of partitioning schemes

Many population analysis methods are based on the precept that molecules should be built from fragments (typically atoms) that maximally resemble the isolated fragment. The resulting molecular building blocks are intuitive (because they maximally resemble well-understood systems) and transferable (because if two molecular fragments both resemble an isolated fragment, they necessarily resemble each other). Information theory is one way to measure the deviation between molecular fragments and their isolated counterparts, and it is a way that lends itself to interpretation. For example, one can analyze the relative importance of electron transfer and polarization of the fragments. We present key features, advantages, and disadvantages of the information-theoretic approach. We also codify existing information-theoretic partitioning methods in a way, that clarifies the enormous freedom one has within the information-theoretic ansatz

Electrostatic Molecular Interaction from X-ray Diffraction Data. I. Development of the Method; Test on Pyrazine

Electrostatic interaction is often an important part of the total interaction between molecules. It depends on the electron density distribution in the participating molecules, which can, in principle, be determined by X-ray diffraction methods. A method is described to calculate the electrostatic interaction between two nonpenetrating molecules by adding the pair-wise interaction between the constituent atoms. The molecular electron density distribution is expressed in terms of the densities corresponding with spherical atoms and deformations according to Hirshfeld's method. The electrostatic interaction between the various deformation densities is replaced by the interaction between the atomic multipole moments corresponding with the deformation densities. Application of the method to pyrazine, C4H4N2, showed qualitative agreement with results based on quantum-chemical calculations

Charged dendrimers revisited: Effective charge and surface potential of dendritic polyglycerol sulfate

We investigate key electrostatic features of charged dendrimers at hand of the biomedically important dendritic polyglycerol sulfate (dPGS) macromolecule using multi-scale computer simulations and Zetasizer experiments. In our simulation study, we first develop an effective mesoscale Hamiltonian specific to dPGS based on input from all-atom, explicit-water simulations of dPGS of low generation. Employing this in coarse-grained, implicit-solvent/explicit-salt Langevin dynamics simulations, we then study dPGS structural and electrostatic properties up to the sixth generation. By systematically mapping then the calculated electrostatic potential onto the Debye-H\"uckel form -- that serves as a basic defining equation for the effective charge -- we determine well-defined effective net charges and corresponding radii, surface charge densities, and surface potentials of dPGS. The latter are found to be up to one order of magnitude smaller than the bare values and consistent with previously derived theories on charge renormalization and weak saturation for high dendrimer generations (charges). Finally, we find that the surface potential of the dendrimers estimated from the simulations compare very well with our new electrophoretic experiments

The Poisson-Boltzmann model for implicit solvation of electrolyte solutions: Quantum chemical implementation and assessment via Sechenov coefficients.

We present the theory and implementation of a Poisson-Boltzmann implicit solvation model for electrolyte solutions. This model can be combined with arbitrary electronic structure methods that provide an accurate charge density of the solute. A hierarchy of approximations for this model includes a linear approximation for weak electrostatic potentials, finite size of the mobile electrolyte ions, and a Stern-layer correction. Recasting the Poisson-Boltzmann equations into Euler-Lagrange equations then significantly simplifies the derivation of the free energy of solvation for these approximate models. The parameters of the model are either fit directly to experimental observables-e.g., the finite ion size-or optimized for agreement with experimental results. Experimental data for this optimization are available in the form of Sechenov coefficients that describe the linear dependence of the salting-out effect of solutes with respect to the electrolyte concentration. In the final part, we rationalize the qualitative disagreement of the finite ion size modification to the Poisson-Boltzmann model with experimental observations by taking into account the electrolyte concentration dependence of the Stern layer. A route toward a revised model that captures the experimental observations while including the finite ion size effects is then outlined. This implementation paves the way for the study of electrochemical and electrocatalytic processes of molecules and cluster models with accurate electronic structure methods

Genetic Algorithm Optimization of Point Charges in Force Field Development: Challenges and Insights

Evolutionary methods, such as genetic algorithms (GAs), provide powerful tools for optimization of the force field parameters, especially in the case of simultaneous fitting of the force field terms against extensive reference data. However, GA fitting of the nonbonded interaction parameters that includes point charges has not been explored in the literature, likely due to numerous difficulties with even a simpler problem of the least-squares fitting of the atomic point charges against a reference molecular electrostatic potential (MEP), which often demonstrates an unusually high variation of the fitted charges on buried atoms. Here, we examine the performance of the GA approach for the least-squares MEP point charge fitting, and show that the GA optimizations suffer from a magnified version of the classical buried atom effect, producing highly scattered yet correlated solutions. This effect can be understood in terms of the linearly independent, natural coordinates of the MEP fitting problem defined by the eigenvectors of the least-squares sum Hessian matrix, which are also equivalent to the eigenvectors of the covariance matrix evaluated for the scattered GA solutions. GAs quickly converge with respect to the high-curvature coordinates defined by the eigenvectors related to the leading terms of the multipole expansion, but have difficulty converging with respect to the low-curvature coordinates that mostly depend on the buried atom charges. The performance of the evolutionary techniques dramatically improves when the point charge optimization is performed using the Hessian or covariance matrix eigenvectors, an approach with a significant potential for the evolutionary optimization of the fixed-charge biomolecular force fields

Interaction of proteins in solution from small angle scattering: a perturbative approach

In this work, an improved methodology for studying interactions of proteins in solution by small-angle scattering, is presented. Unlike the most common approach, where the protein-protein correlation functions $g_{ij}(r)$ are approximated by their zero-density limit (i.e. the Boltzmann factor), we propose a more accurate representation of $g_{ij}(r)$ which takes into account terms up to the first order in the density expansion of the mean-force potential. This improvement is expected to be particulary effective in the case of strong protein-protein interactions at intermediate concentrations. The method is applied to analyse small angle X-ray scattering data obtained as a function of the ionic strength (from 7 to 507 mM) from acidic solutions of $\beta$-Lactoglobuline at the fixed concentration of 10 $\rm g L^{-1}$. The results are compared with those obtained using the zero-density approximation and show a significant improvement particularly in the more demanding case of low ionic strength.Comment: 12 pages, 3 figures, to appear in Biophysical Journal (April 2002) Due to an unfortunate name mismatch, the original submission contained an incorrect sourc

Inhibition of DNA ejection from bacteriophage by Mg+2 counterions

The problem of inhibiting viral DNA ejection from bacteriophages by multivalent counterions, specifically Mg$^{+2}$ counterions, is studied. Experimentally, it is known that MgSO$_4$ salt has a strong and non-monotonic effect on the amount of DNA ejected. There exists an optimal concentration at which the minimum amount of DNA is ejected from the virus. At lower or higher concentrations, more DNA is ejected from the capsid. We propose that this phenomenon is the result of DNA overcharging by Mg$^{+2}$ multivalent counterions. As Mg$^{+2}$ concentration increases from zero, the net charge of DNA changes from negative to positive. The optimal inhibition corresponds to the Mg$^{+2}$ concentration where DNA is neutral. At lower/higher concentrations, DNA genome is charged. It prefers to be in solution to lower its electrostatic self-energy, which consequently leads to an increase in DNA ejection. By fitting our theory to available experimental data, the strength of DNA$-$DNA short range attraction energies, mediated by Mg$^{+2}$, is found to be $-$0.004 $k_BT$ per nucleotide base. This and other fitted parameters agree well with known values from other experiments and computer simulations. The parameters are also in aggreement qualitatively with values for tri- and tetra-valent counterions.Comment: 17 pages, 4 figures, improved manuscript. Submitted to J. Chem. Phys (2010

Electrostatic charging and discharging models and analysis for ranger spacecraft during launch

Electrostatic charging and discharging models and analysis for Ranger spacecraft during launc