Density dependent potentials: structure and thermodynamics

Local density dependent potentials constitute a family of many body potentials which have been recently introduced in mesoscopic modeling of simple and complex fluids. We construct a field theory for these potentials and calculate the structure factor of the fluid through a saddle point expansion. We propose also an integral equation for local density potentials which shows quantitative agreement both for the correlation functions and thermodynamic properties of such potentials, even close to binodals where the simpler saddle point approximation fails. Contrary to the limitations of global density dependent potentials, there is no ambiguity in the expression of thermodynamics quantities such as the pressure.     

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.     

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.     

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.     

Ionization and appearance potentials in organic chemistry. II—Appearance potentials and enthalpy differences for the stereoisomers of methylbicyclo[4.4.0]decanes

The ionization potentials for the stereoisomers of trans-fused 2- and 3-methylbicyclo[4.4.0]decanes and the appearance potentials for the ions at m/e 137 [M–CH₃]⁺, 109, 96, 95 and 82 were measured by the electron impact method. The ionization potentials and appearance potentials of the [M–CH₃]⁺ ions appeared to be equal for each of the epimers. Appearance potentials of the other ions were always lower for the less stable epimer. No quantitative correlation was observed between the difference in the appearance potentials for any ions and the differences in enthalpies of the ground states.     

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.     

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.     

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.     

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.     

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     

Calculations of partial cross sections for photofragmentation processes using complex absorbing potentials

We investigate the use of complex absorbing potentials for the calculation of partial cross sections in multichannel photofragmentation processes. An exactly solvable, coupled-two-channel problem involving square-well potentials is used to compare the performance of various types of absorbing potentials. Special emphasis is given to the near-threshold regions and the conditions under which the numerical results are able to reproduce the Wigner threshold laws. It was found that singular, transmission-free absorbing potentials perform better than those of power or polynomial form.     

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.     

Volta potential at metal-solid salt interface and real potentials of ions in solid electrolytes

Experimental conditions and results of investigations of Volta potentials of metal-solidelectrolyte and solid electrolyte-aqueous electrolyte solution by means of the dynamic condenser method are presented. These investigations were made for silver-silver halides and silver-silver nitrate as well as for cadmium-cadmium halide systems. On the basis of measured Volta potentials the real potentials of ions in these solid electrolytes are calculated. These real potentials are the ionic components of the crystalline lattice energy in the sense of the Gibbs energy.     

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.     

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.     

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.     

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.     

Generalized potentials: Free particle,harmonic, and Morse partner potentials

In this work, we propose a very simple procedure to find the partner to specific potentials. According to our method, partner potentials are those obtained in the generalization of standard potentials, for which they are generalized potentials whose Hamiltonian match the so‐called isospectral Hamiltonian. The proposed approach is straightforward and basically takes into consideration the use of three well‐established relationships: The first one is used to identify the particular potential; the second, to find the adjoint or modified potential; and the third, to obtain the corresponding generalized or partner potential. As a useful application of the proposed procedure, we give explicitly the generalized and modified free‐particle, harmonic oscillator, and Morse one‐dimensional potentials. As expected, it is shown that the adjoint and partner potentials are isospectral with respect to the particular or former potential. This procedure can be easily applied to the generalization of any other known potential, as well as to obtain new potentials that can be advantageously used for modeling important quantum interactions. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 71: 465–472, 1999     

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.