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The MUlti-start optimization algorithm for Surface complexation Equilibrium (MUSE) algorithm has been developed to optimize the fitting of thermodynamic constants for surface complexation modeling (SCM). Although there is a plethora of software to perform data fitting and determine intrinsic equilibrium constants, the algorithms used are highly dependent on initial values and choice of parameters. This limits their transferability to model other systems, for example, reactive transport processes. With this in mind, a hybridized optimization approach, based on a multistart algorithm combined with a local optimizer, has been developed to allow the simultaneous optimization of SCM parameters and to assess the sensitivity of these parameters to changes in the model assumptions. In this study, the CD–MUSIC formalism with a Basic Stern electrostatic model is utilized to model chromate adsorption on ferrihydrite, although the MUSE algorithm can be applied to any adsorption data set and be implemented in any mode...

International audience; Noncovalent interactions play a key role in functional materials. Metal–organofluorine interactions are of special interest because they directly affect the structure and reactivity of hybrid fluorinated materials. In-depth understanding and modulating of these interactions would enable the rational design of functional materials from fundamental chemical principles. In this work, we propose a computational approach that enables a comprehensive and quantitative characterization of noncovalent interactions (NCIs) in hybrid fluorinated crystals. Our approach couples dispersion-corrected density functional theory to NCI analysis. Additionally, we determine electron densities at bond critical points and identify electrostatic interactions using a simple electrostatic model. The versatility of this approach to probe a wide range of NCIs is demonstrated for a series of four bimetallic fluorinated crystals incorporating alkali–manganese(II) pairs and trifluoroacetato ligands. Noncovalent interactions in these hybrid crystals include metal–oxygen, metal–fluorine, hydrogen bonds, and van der Waals forces. Using K2Mn2(tfa)6(tfaH)2·H2O as an example, we demonstrate that its two-dimensional layered structure stems from a unique balance between these four NCIs. The computational approach presented herein should have general applicability to the quantitative study of NCIs in hybrid crystals, thereby serving as a guide for crystal engineering of novel hybrid materials.

We extend the linearized Poisson-Boltzmann (LPB) continuum electrostatic model for molecular solvation to address charge-hydration asymmetry. Our new solvation-layer interface condition (SLIC)/LPB corrects for first-shell response by perturbing the traditional continuum-theory interface conditions at the protein-solvent and the Stern-layer interfaces. We also present a GPU-accelerated treecode implementation capable of simulating large proteins, and our results demonstrate that the new model exhibits significant accuracy improvements over traditional LPB models, while reducing the number of fitting parameters from dozens (atomic radii) to just five parameters, which have physical meanings related to first-shell water behavior at an uncharged interface. In particular, atom radii in the SLIC model are not optimized but uniformly scaled from their Lennard-Jones radii. Compared to explicit-solvent free-energy calculations of individual atoms in small molecules, SLIC/LPB is significantly more accurate than standard parametrizations (RMS error 0.55 kcal/mol for SLIC, compared to RMS error of 3.05 kcal/mol for standard LPB). On parametrizing the electrostatic model with a simple nonpolar component for total molecular solvation free energies, our model predicts octanol/water transfer free energies with an RMS error 1.07 kcal/mol. A more detailed assessment illustrates that standard continuum electrostatic models reproduce total charging free energies via a compensation of significant errors in atomic self-energies; this finding offers a window into improving the accuracy of Generalized-Born theories and other coarse-grained models. Most remarkably, the SLIC model also reproduces positive charging free energies for atoms in hydrophobic groups, whereas standard PB models are unable to generate positive charging free energies regardless of the parametrized radii. The GPU-accelerated solver is freely available online, as is a MATLAB implementation.

Our manuscript describes the implementation and performance of Ewald-based approaches for the calculation of Gaussian integrals in the pmemd.gem code as released in the AMBER18 suite, as well as a new parametrization of our density-based Gaussian Electrostatic Model* (GEM*) force field using CCSD(T)/CBS//SAPT2+3/aug-cc-pVTZ data for the fit.

A simple electrostatic model explains the enhanced stereoselectivity of N-oxide catalyzed allylations compared to propargylations, which in turn explicates the dearth of stereoselective N-oxide propargylation catalysts. These results suggest that N-oxide catalysts that are effective for both allylations and propargylations can be designed by targeting inherently stereoselective ligand configurations and through the manipulation of distortion effects in the operative transition states.

A consistent set of atomic electronegativities of main block and d-block transition elements has been obtained from the position and value of the molecular electrostatic potential bond critical point of the C-E bond of a methyl-element-hydride system, H(3)C-EH(n) (E is an element and n = 0, 1, 2, 3, 4, and 5 depending on the position of E in the periodic table). The new scale shows very good agreement with the popular electronegativity scales such as Pauling, Allen, Allred-Rochow, Mulliken, and Sanderson scales of electronegativity, especially for the main block elements. The present scale of electronegativity for transition elements is expected to be more accurate than the previously derived values because of a more consistent approach. Further, the same approach has led to the evaluation of group electronegativities when the hydrogens of E are replaced by other substituent groups. These group electronegativity values are found to correlate well with Inamoto and Mullay scales.

A series of nonempirical intermolecular potentials has been developed for the cyanuric chloride dimer, using the overlap model to determine the anisotropy of the repulsive wall around each atom. Calibration against intermolecular perturbation theory calculations enables the penetration and charge-transfer energy to be explicitly included with the exchange-repulsion to give a simple repulsion model in an anisotropic atom−atom form. These model repulsion potentials are used in conjunction with an atomic multipole electrostatic model and an atom−atom dispersion model to give nonempirical potential models, which are tested for their ability to reproduce the crystal structure of cyanuric chloride. The best nonempirical potential is successfully used to construct a simpler transferable model for closely related azaaromatic chlorides. The nonempirical potential reproduces the experimental space group of cyanuric chloride, unlike some empirically fitted repulsion−dispersion potentials. This first nonempirical rep...

Calculations of pK values of individual titratable groups in one structure of Bacillus circulans xylanase and two similar structures of Bacillus agaradhaerens xylanase were performed by combination of molecular dynamics simulation and a continuum electrostatic model. The influence of the starting structure and the simulation length was investigated. The results agree well with the observations of other authors that calculations using an ensemble of structures describe titration properties of proteins more accurately than calculations based on a single structure. This study emphasizes the features of the collected ensemble rather than the precision of the finally obtained values. The evolution along the trajectory of individual averaged pKa values and their components, such as contribution of desolvation penalty and interactions with protein permanent charges, were analyzed. For the majority of titratable sites, it was shown that simulation time shorter than 500 ps is insufficient to represent their ioniza...

Electrostatic potential in the vicinity of the surface of a cation-exchange resin has been evaluated by modeling chromatographic retention. Binary mixtures of K + and its crown ether complex in methanol are used as mobile phases, and two types of solutes, that is, cationic and crown ether probes, have been examined. The cationic probes show the sigmoidal retention changes with increasing concentration of a crown ether incorporated into the mobile phase, whereas crown ether probes give retention maximums. The model derived from the Poisson-Boltzmann theory well explains these specific changes in probe retention and gives the electrostatic potential at the closest approach of each probe molecule. The closest approaches for probe molecules correlate well with their molecular sizes. In addition, changes in retention of cationic probes also correlate well with the electrostatic potential changes at the closest approaches of probe molecules, indicating that simple sensing of the electrostatic potential is feasible using probe retention. The reduction of crown ether complexation occurs in the vicinity of the cation-exchange resin surface and causes the specific retention behaviors of crown ether probes in the mobile-phase systems composed of K + and its complex with a modifier crown ether.

This study analyzes the impact of phosphorothioate substitutions on the thermodynamic stability of a 12-nt RNA hairpin containing a (5')GAAA(3') tetraloop. The thermodynamic consequences of stereospecific phosphorothioate substitutions 5' to each adenosine in the loop region are measured using optical melting and calorimetry experiments. Surprisingly, a single stereospecific phosphorothioate substitution 5' to the second adenosine of the tetraloop, R(p)-A7, results in a stabilization corresponding to a Delta(DeltaG(37)(degrees)(C)) of approximately -2.9 kcal mol(-1) (0.1 M NaCl) when compared with that of an unmodified sample. Five other phosphorothioate-substituted samples did not show significant thermodynamic differences in comparison with the unsubstituted samples. Addition of Mg(2+) to all of the hairpins studied results in increased t(m's) that are fit with a general electrostatic model to a dissociation constant of K(d)(Mg(2+)) approximately 2-3 mM (0.1 M NaCl). The R(p)-A7 phosphorothioate-substituted hairpin showed an unusual decrease in t(m) and apparent increase in enthalpy of unfolding upon addition of Cd(2+). These results may impact the interpretation of interference mapping experiments that use phosphorothioate substitutions to characterize RNAs in solution.

The analytic generalized Born approximation is an efficient electrostatic model that describes molecules in solution. Here it is modified to permit a more accurate description of large macromolecul...

We have investigated different models for parameterizing the frequency-dependent molecular polarizability. The parameterization is based on an electrostatic model for interacting atoms and includes atomic polarizabilities, atom-type parameters describing the damping of the electric fields and the frequency dependence. One set of parameters has been used for each element. The investigation has been carried out for 115 molecules with the elements H, C, N, O, F, and Cl, for which the frequency-dependent polarizability tensor has been calculated with ab initio methods. We find that the static polarizability of aliphatic and aromatic compounds can be described with the same set of parameters. The conclusion is that a simple electrostatic model to a good degree can model the essential behavior of the frequency-dependent molecular polarizability.

Ab initio quantum chemical methods as well as simulation/dynamics programs have been conventionally used for probing the hydration of molecules, an important problem in chemistry and biology. However, very few attempts have as yet been reported for understanding the stepwise patterns in hydration processes at the molecular level. The present work investigates the problem of hydration of the 18-crown-6 (18C6) molecule based on rigorous topography mapping of molecular electrostatic potential (MESP) followed by an application of a simple electrostatic model (electrostatic potential for intermolecular complexation) for obtaining trends in energetics. Structures and energies of the hydrated species, 18C6·nH2O (n = 1, 2, 3, 4, 6) have been studied by the EPIC model followed by ab initio HF/6-31G** investigations. The remarkable agreement between the model and ab initio results highlights the utility of MESP topography for exploring the lock-and-key features in a hydration process via cooperative electrostatic e...

The electronic absorption line shape of a model chromophore at liquid interfaces is numerically evaluated using electrostatic continuum theory. The interface is described as a sharp boundary separa...

The generalized Born (GB) approximation is a reasonable electrostatic model that is fast enough for use with extensive conformational sampling. This study combines the GB model with a torsion-space...

We studied an electrostatic model of ice adhesion based on the existence of the surface states of protonic charge carriers on the surface of ice. At distances greater than one intermolecular distan...

The structures and electrochemical behavior of a series of symmetric dinuclear complexes in which two iron centers are bridged by three bis[4-(4'-methyl-2,2'-bipyridinyl)]alkane ligands are presented. Square wave voltammetry was used to characterize the extent of interaction between the metal-centered halves. Because the saturated linkages preclude significant electron delocalization, the observed interaction is concluded to be almost purely Coulombic in nature. Furthermore, molecular modeling and X-ray crystallographic data confirm that the iron-iron separation in the complex containing three methylenes in the linkages is nearly identical to the ironiron separation in the complex containing two methylenes in the linkages. Using a simple electrostatic model and employing structural parameters obtained from X-ray data and molecular modeling, the electrochemical trends within the series are interpreted.

Calcul des parametres d'intensite de transitions 4f-4f d'especes a coordination comme en solutions aqueuses basiques, a rapport Ln 3+ : coordinat=1:3 les coordinats organiques tridentes etant l'oxydiacetate, le dipicolinate, l'iminodiacetate ou le methylimino-diacetate, en considerant les couplages statique (champ cristallin de charges ponctuelles) et dynamique (polarisation du coordinat)

En presence d'ions divalents, la conformation helice de carraghenanes peut etre stabilisee ou destabilisee par l'addition d'electrolyte 1:1 selon la concentration en sel de la solution et selon les densites de charge des conformations helice et pelote. Ces effets sont expliques par le modele theorique utilise; dans ce modele, la contribution electrostatique a la constante de propagation de la transition est calculee a partir de l'equation de Boltzmann-Poisson: les effets des interactions polyion-polyion sont donc traites implicitement

Free energy and enthalpy of single ion solvation in water and propylene carbonate, using electrostatic model