Conditional reversible work method for molecular coarse graining applications

Systematically coarse grained models for complex fluids usually lack chemical and thermodynamic transferability. Efforts to improve transferability require the development of effective potentials with unequivocal physical significance. In this paper, we introduce conditional reversible work (CRW) potentials that describe nonbonded interactions in coarse grained models at the pair level. The method used to obtain these potentials is straightforward to implement, can be readily extended to compute hydration contributions in implicit-solvent potentials, and is easy to automize. As a first illustration of the method, we present CRW potentials for 3-site models of hexane and toluene. The temperature-transferability of the liquid phase density obtained with these potentials has been investigated, and a comparison has been made with effective potentials obtained by the iterative Boltzmann inversion method.     

Influence of the interaction potential on simulated sputtering and reflection data

The TRIM.SP program which is based on the binary collision approximation was changed to handle not only repulsive interaction potentials, but also potentials with an attractive part. Sputtering yields, average depth and reflection coefficients calculated with four different potentials are compared. Three purely repulsive potentials (Molière, Kr-C and ZBL) are used and an ab initio pair potential, which is especially calculated for silicon bombardment by silicon. The general trends in the calculated results are similar for all potentials applied, but differences between the repulsive potentials and the ab initio potential occur for the reflection coefficients and the sputtering yield at large angles of incidence.     

Nanosecond redox equilibrium method for determining oxidation potentials in organic media

A general, nanosecond equilibrium method is described for determining thermodynamically meaningful oxidation potentials in organic media for compounds that form highly reactive cation radicals upon one-electron oxidation. The method provides oxidation potentials with unusually high precision and accuracy. Redox ladders have been constructed of appropriate reference compounds in dichloromethane and in acetonitrile that can be used to set up electron-transfer equilibria with compounds with unknown oxidation potentials. The method has been successfully applied to determining equilibrium oxidation potentials for a series of aryl-alkylcyclopropanes, whose oxidation potentials were imprecisely known previously. Structure-property trends for oxidation potentials of the cyclopropanes are discussed.     

Efficient silicon surface and cluster modeling using quantum capping potentials

A one-electron, silicon quantum capping potential for use in capping the dangling bonds formed by artificially limiting silicon clusters or surfaces is developed. The quantum capping potentials are general and can be used directly in any computational package that can handle effective core potentials. For silicon clusters and silicon surface models, we compared the results of traditional hydrogen atom capping with those obtained from capping with quantum capping potentials. The results clearly show that cluster and surface models capped with quantum capping potentials have ionization potentials, electron affinities, and highest occupied molecular orbital-lowest unoccupied molecular orbital gaps that are in very good agreement with those of larger systems. The silicon quantum capping potentials should be applied in cases where one wishes to model processes involving charges or low-energy excitations in silicon clusters and surfaces consisting of more than ca. 150 atoms.     

Determination of zeta potentials of polymeric nanoparticles by the conductivity variation method

An easy method of measurement of the zeta potentials of sub-50-nm polymeric nanoparticles is suggested. Although zeta potential measurements of nanoparticles or emulsions above 50 nm have been successfully carried out, zeta potentials of emulsions or nanoparticles below 50 nm could not be precisely measured in the region of extremely low conductivity by conventional electrophoresis with a He-Ne laser. However, zeta potentials of sub-50-nm nanoparticles were measured in the region of thin electrical double layers by addition of sodium chloride and zeta potentials in the condition without sodium chloride could be predicted by extrapolation of the measured potentials. The electrophoretic mobility of 150-nm nanoparticles stabilized with sodium dodecylsulfate was the same as that calculated from extrapolation of the measured ones. The zeta potentials of sub-50-nm nanoparticles stabilized with sodium dodecylsulfate could be calculated by the same procedure.     

Interaction potentials for the halide ion-rare gas systems

The halide ion-rare gas interaction potentials are determined directly from gaseous ion transport data. The potentials are tested by calculating the transport coefficients from them and then comparing the calculated values with the available data. Similar tests are made of other potentials that have been proposed for these systems. These tests indicate that the present potentials are the most accurate ones presently available at intermediate and large separations. In favorable cases, these potentials are expected to be accurate within 10% over wide ranges of ion-atom separation.     

Interaction potentials for Li+—rare-gas systems

The accuracies of proposed interaction potentials for the Li⁺—rare-gas systems are tested by comparing the transport coefficients calculated from the potentials with the experimental values. The agreement is generally good for theoretical potentials that take electron correlation into account and for potentials inferred from ion-beam measurements of high accuracy, except where the transport data are primarily influenced by the long-range tail of the potential. The transport data are also used to directly determine the Li⁺—rare-gas interaction potentials, with an estimated accuracy of 10% over wide ranges of ion—atom separation.     

Theoretical determination of one-electron redox potentials for DNA bases, base pairs, and stacks

Electron affinities, ionization potentials, and redox potentials for DNA bases, base pairs, and N-methylated derivatives are computed at the DFT/M06-2X/6-31++G(d,p) level of theory. Redox properties of a guanine-guanine stack model are explored as well. Reduction and oxidation potentials are in good agreement with the experimental ones. Electron affinities of base pairs were found to be negative. Methylation of canonical bases affects the ionization potentials the most. Base pair formation and base stacking lower ionization potentials by 0.3 eV. Pairing of guanine with the 5-methylcytosine does not seem to influence the redox properties of this base pair much.     

One-electron oxidation and reduction potentials of nitroxide antioxidants: a theoretical study

High-level ab initio calculations have been used to determine the oxidation and reduction potentials of a large number of nitroxides including derivatives of piperidine, pyrrolidine, isoindoline, and azaphenalene, substituted with COOH, NH2, NH3+, OCH3, OH, and NO2 groups, with a view to (a) identifying a low-cost theoretical procedures for the determination of electrode potentials of nitroxides and (b) studying the effect of substituents on these systems. Accurate oxidation and reduction potentials to within 40 mV (3.9 kJ mol(-1)) of experimental values were found using G3(MP2)-RAD//B3-LYP/6-31G(d) gas-phase energies and PCM solvation calculations at the B3-LYP/6-31G(d) level. For larger systems, an ONIOM method in which G3(MP2)-RAD calculations for the core are combined with lower-cost RMP2/6-311+G(3df,2p) calculations for the full system, was able to approximate G3(MP2)-RAD values (to within 1.6 kJ mol(-1)) at a fraction of the computational cost. The overall ring structure has more effect on the electrode potentials than the inclusion of substituents. Azaphenalene derivatives display the lowest oxidation potentials and least negative reduction potentials and are thus the most promising target to function as antioxidants in biological systems. Piperidine and pyrrolidine derivatives have intermediate oxidation potentials but on average pyrrolidine derivatives display more negative reduction potentials. Isoindoline derivatives show higher oxidation potentials and more negative reduction potentials. Within a ring, the substituents have a relatively small effect with electron donating groups such as amino and hydroxy groups stabilizing the oxidized species and electron withdrawing groups such as carboxy groups stabilizing the reduced species, as expected.     

Correlation potentials for the He atom and the hydrogen molecule: A comparison between the correlation factor approach and DFT correlation energy functionals

Two points about correlation potentials have been dealt with in this article. The first one is related to the shape of some of the most representative correlation potentials applied to the ground state of the He atom. It is shown here that both LDA and two-body density correlation potentials compare well with that obtained through the quantum chemistry definition of correlation energy. This is an interesting result because, in previous works, it had been shown that none of the correlation potentials compared well with the Kohn–Sham one. The gradient-corrected correlation potentials exhibit a very different behavior to that of both exact potentials (quantum chemistry and Kohn–Sham ones). The other question posed here refers to how a reference to the two-body density must modify DFT functionals for the correlation energy, when a multideterminant wave function is needed. This question has been addressed by analyzing the variation of correlation potentials as the bond length of the H₂ molecule increases. The results show that an external reference to the two-body density qualitatively improves DFT correlation potentials and also that only those functionals explicitly depending on two-body density can give the quantitative correct trends. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 67: 143–156, 1998     

Kinetic determinations of accurate relative oxidation potentials of amines with reactive radical cations

Accurate oxidation potentials for organic compounds are critical for the evaluation of thermodynamic and kinetic properties of their radical cations. Except when using a specialized apparatus, electrochemical oxidation of molecules with reactive radical cations is usually an irreversible process, providing peak potentials, E(p), rather than thermodynamically meaningful oxidation potentials, E(ox). In a previous study on amines with radical cations that underwent rapid decarboxylation, we estimated E(ox) by correcting the E(p) from cyclic voltammetry with rate constants for decarboxylation obtained using laser flash photolysis. Here we use redox equilibration experiments to determine accurate relative oxidation potentials for the same amines. We also describe an extension of these experiments to show how relative oxidation potentials can be obtained in the absence of equilibrium, from a complete kinetic analysis of the reversible redox kinetics. The results provide support for the previous cyclic voltammetry/laser flash photolysis method for determining oxidation potentials.     

Concurrent dual-resolution Monte Carlo simulation of liquid methane

We conduct molecular simulations of liquid methane in a system where molecular resolution fluctuates between atomically explicit and spherically symmetric united atoms. An appropriate dual-resolution canonical ensemble is constructed using (a) effective united atom pair potentials and (b) resolution-control potentials that confine explicit and united atoms chiefly to different slabs in the simulation domain. A Monte Carlo simulation is developed to sample this ensemble. We show that compatibility of the united-atom potentials with the explicit potentials in a concurrent simulation can be tuned by adjusting the width of the interface between the two resolution regions and by direct modification of the united-atom pair potentials. Our results lay the groundwork for treatment of larger atomically specific molecules with similar concurrent multiresolution techniques.     

The surface potential of solvent and the intraphase pre-existing potential

Using own and literature data, the differences of real solvation energy for ferricenium and ferrocene in six solvents are found. These quantities are confronted with the calculated difference of the dielectric response energies plus nonelectrostatic energies for the redox couple. Such a comparison allows determining the sum of the surface and intraphase potentials. The comparison of these sums with the experimental values of the surface potential differences obtained by the measuring of Volta potentials allowed determining the differences of pre-existing intraphase potentials formed by solvent molecules on the ferrocene molecule. Thus, the intraphase potentials are evaluated for the first time, using an approach not based on the molecular-dynamic modeling. Using some approximations, the surface potentials of the studied solvents are found.     

Experimental and computed absolute redox potentials of polycyclic aromatic hydrocarbons are highly linearly correlated over a wide range of structures and potentials

A more rigorous theoretical treatment of methods previously used to correlate computed energy values with experimental redox potentials, combined with the availability of well-developed computational solvation methods, results in a shift away from computing ionization potentials/electron affinities in favor of computing absolute reduction potentials. Seventy-nine literature redox potentials measured under comparable conditions from 51 alternant and nonalternant polycyclic aromatic hydrocarbons are linearly correlated with their absolute reduction potentials computed by density functional theory (B3LYP/6-31+G(d)) with SMD/IEF-PCM solvation. The resulting correlation is very strong (R(2) = 0.9981, MAD = 0.056 eV). When extrapolated to the x-intercept, the correlation results in an estimate of 5.17 ± 0.01 eV for the absolute potential of the ferrocene-ferrocenium redox couple in acetonitrile at 25 °C, indicating that this simple method can be used reliably for both calculating absolute redox potentials and for predicting relative redox potentials. When oxidation and reduction data are evaluated separately, the overall MAD value is improved by 50% to 0.028 eV, which improves relative potential predictions, but the computed values do not extrapolate to a reasonable estimate of the absolute potential of the ferrocene-ferrocenium ion reference.     

Systematic implicit solvent coarse graining of dimyristoylphosphatidylcholine lipids

We have used systematic structure‐based coarse graining to derive effective site–site potentials for a 10‐site coarse‐grained dimyristoylphosphatidylcholine (DMPC) lipid model and investigated their state point dependence. The potentials provide for the coarse‐grained model the same site–site radial distribution functions, bond and angle distributions as those computed in atomistic simulations carried out at four different lipid–water molar ratios. It was shown that there is a non‐negligible dependence of the effective potentials on the concentration at which they were generated, which is also manifested in the properties of the lipid bilayers simulated using these potentials. Thus, effective potentials computed at low lipid concentration favor to more condensed and ordered structure of the bilayer with lower average area per lipid, while potentials obtained at higher lipid concentrations provide more fluid‐like structure. The best agreement with the reference data and experiment was achieved using the set of potentials derived from atomistic simulations at 1:30 lipid:water molar ratio providing fully saturated hydration of DMPC lipids. Despite theoretical limitations of pairwise coarse‐grained potentials expressed in their state point dependence, all the resulting potentials provide a stable bilayer structure with correct partitioning of different lipid groups across the bilayer as well as acceptable values of the average lipid area, compressibility and orientational ordering. In addition to bilayer simulations, the model has proven its robustness in modeling of self‐aggregation of lipids from randomly dispersed solution to ordered bilayer structures, bicelles, and vesicles. © 2014 Wiley Periodicals, Inc.     

Development of novel statistical potentials describing cation-pi interactions in proteins and comparison with semiempirical and quantum chemistry approaches

Novel statistical potentials derived from known protein structures are presented. They are designed to describe cation-pi and amino-pi interactions between a positively charged amino acid or an amino acid carrying a partially charged amino group and an aromatic moiety. These potentials are based on the propensity of residue types to be separated by a certain spatial distance or to have a given relative orientation. Several such potentials, describing different kinds of correlations between residue types, distances, and orientations, are derived and combined in a way that maximizes their information content and minimizes their redundancy. To test the ability of these potentials to describe cation-pi and amino-pi systems, we compare their energies with those computed with the CHARMM molecular mechanics force field and with quantum chemistry calculations at the Hartree-Fock level (HF) and at the second order of the M?ller-Plesset perturbation theory (MP2). The latter calculations are performed in the gas phase and in acetone, in order to mimic the average dielectric constant of protein environments. The energies computed with the best of our statistical potentials and with gas-phase HF or MP2 show correlation coefficients up to 0.96 when considering one side-chain degree of freedom in the statistical potentials and up to 0.94 when using a totally simplified model excluding all side-chain degrees of freedom. These potentials perform as well as, or better than, the CHARMM molecular mechanics force field that uses a much more detailed protein representation. The good performance of our cation-pi statistical potentials suggests their utility in protein structure and stability prediction and in protein design.     

Thermodynamic and kinetic theory of ionic micellar systems: 2. Statistical-thermodynamic relations

The role of electrochemical potentials in the grand canonical ensemble of ionic micellar systems is characterized. The notion of relative electrochemical potentials is introduced with allowance for the electroneutrality condition. Fundamental relations and primary statistical-thermodynamic relations are derived for ideal and real ionic micellar systems with participation of electrochemical potentials, in which inaccuracies observed in published literature, are eliminated. A differential equation for the osmotic pressure of ionic aggregated system is obtained. Relations that link the work of the aggregation of ionic micelle with chemical and electrochemical potentials and aggregation numbers are established. Separate contributions to the work of aggregation are commented on.     

DSX: a knowledge-based scoring function for the assessment of protein-ligand complexes

We introduce the new knowledge-based scoring function DSX that consists of distance-dependent pair potentials, novel torsion angle potentials, and newly defined solvent accessible surface-dependent potentials. DSX pair potentials are based on the statistical formalism of DrugScore, extended by a much more specialized set of atom types. The original DrugScore-like reference state is rather unstable with respect to modifications in the used atom types. Therefore, an important method to overcome this problem and to allow for robust results when deriving pair potentials for arbitrary sets of atom types is presented. A validation based on a carefully prepared test set is shown, enabling direct comparison to the majority of other popular scoring functions. Here, DSX features superior performance with respect to docking- and ranking power and runtime requirements. Furthermore, the beneficial combination with torsion angle-dependent and desolvation-dependent potentials is demonstrated. DSX is robust, flexible, and capable of working together with special features of popular docking engines, e.g., flexible protein residues in AutoDock or GOLD. The program is freely available to the scientific community and can be downloaded from our Web site www.agklebe.de .     

Interaction potentials for the alkali ion—rare-gas systems

The alkali ion—rare-gas interaction potentials are determined directly from gaseous ion transport data. The potentials are tested by calculating the transport coefficients from them and then comparing the calculated values with the many sets of measured values. Similar tests are made of other potentials that have been proposed, especially those inferred from alkali ion—beam-scattering measurements in the rare gases. These tests indicate that the present potentials are generally accurate within 10% over wide ranges of ion—rare-gas separation.     

Modelling of repulsive potentials from atom charge density distributions: interactions of inert gas atoms

Using electron charge density overlap integrals, a correlation procedure for estimating short-range repulsive intermolecular potentials has been investigated. It is found that the repulsive potentials correlate well with the density overlap integral divided by the square of the distance. A simple combining rule for inert gas atoms is obtained and compared with an accurate determination of repulsive potentials for all the mixed rare gases and with other combining rules.