The reorganization energies in one-electron oxidation of ferrous complexes in aqueous solution

The photoelectron emission method was used to determine the reorganization free energy of nuclear coordinates in one-electron oxidation reactions. The experimental results for eight ferrous complexes, some of which have large organic ligands, in aqueous solution are in excellent agreement with the theoretical ones.     

Anomalous reorganization free energies in optical electron transfer in solution

Autoionization bands are observed in the photoelectron emission spectroscopy of aqueous solutions of cyanometalate complexes (Mn, Fe, W, Mo), anions (NO₃, CIO⁻₄ and cations (Ag⁺ TI⁺. Reorganization free energies for autoionization bands are anomalously low in absolute value (by≈1 eV) in comparison with direct transitions to the continuum. Interpretation is based on potential energy profiles and model calculations for the reorganization free energy.     

A theoretical description of charge reorganization energies in molecular organic P‐type semiconductors

Charge transport properties of materials composed of small organic molecules are important for numerous optoelectronic applications. A material's ability to transport charges is considerably influenced by the charge reorganization energies of the composing molecules. Hence, predictions about charge‐transport properties of organic materials deserve reliable statements about these charge reorganization energies. However, using density functional theory which is mostly used for the predictions, the computed reorganization energies depend strongly on the chosen functional. To gain insight, a benchmark of various density functionals for the accurate calculation of charge reorganization energies is presented. A correlation between the charge reorganization energies and the ionization potentials is found which suggests applying IP‐tuning to obtain reliable values for charge reorganization energies. According to benchmark investigations with IP‐EOM‐CCSD single‐point calculations, the tuned functionals provide indeed more reliable charge reorganization energies. Among the standard functionals, ωB97X‐D and SOGGA11X yield accurate charge reorganization energies in comparison with IP‐EOM‐CCSD values. © 2016 Wiley Periodicals, Inc.     

A quasichemical approach for protein-cluster free energies in dilute solution

Reversible formation of protein oligomers or small clusters is a key step in processes such as protein polymerization, fibril formation, and protein phase separation from dilute solution. A straightforward, statistical mechanical approach to accurately calculate cluster free energies in solution is presented using a cell-based, quasichemical (QC) approximation for the partition function of proteins in an implicit solvent. The inputs to the model are the protein potential of mean force (PMF) and the corresponding subcell degeneracies up to relatively low particle densities. The approach is tested using simple two and three dimensional lattice models in which proteins interact with either isotropic or anisotropic nearest-neighbor attractions. Comparison with direct Monte Carlo simulation shows that cluster probabilities and free energies of oligomer formation (DeltaG(i) (0)) are quantitatively predicted by the QC approach for protein volume fractions approximately 10(-2) (weight/volume concentration approximately 10 g l(-1)) and below. For small clusters, DeltaG(i) (0) depends weakly on the strength of short-ranged attractive interactions for most experimentally relevant values of the normalized osmotic second virial coefficient (b(2) (*)). For larger clusters (i"2), there is a small but non-negligible b(2) (*) dependence. The results suggest that nonspecific, hydrophobic attractions may not significantly stabilize prenuclei in processes such as non-native aggregation. Biased Monte Carlo methods are shown to accurately provide subcell degeneracies that are intractable to obtain analytically or by direct enumeration, and so offer a means to generalize the approach to mixtures and proteins with more complex PMFs.     

Local measures of intermolecular free energies in solution

Proton spin-lattice relaxation rate changes induced by freely diffusing oxygen in aqueous and mixed solvents are reported for representative amino acids and glucose. The local oxygen concentration at each spectrally resolved proton was deduced from the paramagnetic contribution to the relaxation rate. The measured relaxation increment is compared to that of the force-free diffusion relaxation model, and the differences are related to a free energy for the oxygen association with different portions of the solute molecules. The free energy differences are small, on the order of -800 to -2000 J/mol, but are uniformly negative for all proton positions measured on the amino acids in water and reflect the energetic benefit of weak association of hydrophobic cosolutes. For glucose, CH proton positions report negative free energies for oxygen association, the magnitude of which depends on the solvent; however, the hydroxyl positions report positive free energy differences relative to the force-free diffusion model, which is consistent with partial occupancy in the OH region by a solvent hydrogen bond.     

A model study of the intermolecular interactions of amino acids in aqueous solution: The glycine-water system

We have performed calculations of the glycine zwitterion surrounded by water molecules with the help of the mutually consistent field (MCF) method and perturbation theoretical expressions. Two different models for the hydration shell have been chosen, the glycine·6H₂O and glycine·12H₂O complexes, representing the most probable first and second solvation shell, respectively. To calculate the exchange and charge transfer energy contributions we have applied approximative expressions derived from perturbation theory for weakly overlapping subunits. For the sake of comparison we also calculated the interaction energy in the supermolecule approach for the smaller of the two solvation complexes. Furthermore, we have investigated the part of the potential energy surface which is determined by varying the lengths of the hydrogen bonds between glycine and water in the complex glycine·12H₂O using the electrostatic approach. The exchange energy contribution to the interaction energy for different points on the surface was approximated with the help of an analytical expression fitted to three directly calculated points. For the charge transfer energy a polynomial expansion of second order was established on the basis of five values, computed with the aid of the perturbation theoretical expression. To get a more detailed insight in the relatively strong hydrogen bonds between the water molecules and the ionic hydrophilic parts of glycineab initio model studies on NH ₄ ⁺ ·3H₂O and HCOO⁻·3H₂O systems are reported.     

Net charge changes in the calculation of relative ligand‐binding free energies via classical atomistic molecular dynamics simulation

The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio‐)chemical thermodynamics. Many important endogenous receptor‐binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice‐summation scheme or a cutoff‐truncation scheme with Barker–Watts reaction‐field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest‐host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free‐energy calculation studies if changes in the net charge are involved. © 2013 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Viscometric and conductometric study of polyelectrolytes of low charge density in salt free aqueous solutions

Viscometric and conductometric measurements have been performed on dilute, salt free solutions of poly(vinyl alcohol) (PVA) and poly(vinyl alcohol, vinyl sulphate ester) copolymer salts in order to get information on transition from a neutral to charged macromolecules. With increasing linear charge density from a very low value to a moderate one a non linear dependence of polyelectrolyte effect on copolymer composition was observed. A comparison has shown that there is a close analogy between the expansion of polyanions and swelling of polyelectrolyte networks at comparable linear charge density range. Due to the intra- and inter-molecular mobile ionic bridges a considerable contraction was pointed out by viscometry for barium, magnesium and copper salts. However, the differences in properties of counterions of higher charge number indicates that in addition to the valency, there is a definite chemical effect, too. It has been revealed by the electric conductance measurements that the transition from a neutral to charged macromolecules could be a very complex one calling for a new and more detailed theoretical consideration of polyelectrolyte solutions.     

The effect of substitution on reorganization energy and charge mobility in metal free phthalocyanine

To gain insight into how the electronic properties of discotic organic materials may be modified through substitution, the reorganization energy and the charge mobility of metal free phthalocyanine, and of several mono-substituted derivatives, are studied by electronic structure methods. It is found that the reorganization energy of phthalocyanine is not significantly changed by substitution on an outer phenyl ring, but is more strongly influenced when the inner crown amine ring is substituted. The relationship between reorganization energy and substituent is studied through the use of; substituent constant, HOMO energy, and geometry relaxation. The computed charge mobility shows stronger relationship to coupling matrix element than reorganization energy. A hybrid computational screening method in which the reorganization energy is calculated at the DFT level and the coupling matrix element is calculated at the AM1 level shows good predicting power for trends in charge mobility at reduced computational expense.     

AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution

Summary Two new continuum solvation models have been presented recently, and in this paper they are explained and reviewed in detail with further examples. Solvation Model 2 (AM1-SM2) is based on the Austin Model 1 and Solvation Model 3 (PM3-SM3) on the Parameterized Model 3 semiempirical Hamiltonian. In addition to the incorporation of phosphorus parameters, both of these new models address specific deficiencies in the original Solvation Model 1 (AM1-SM1), viz., (1) more accurate account is taken of the hydrophobic effect of hydrocarbons, (2) assignment of heavy-atom surface tensions is based on the presence or absence of bonded hydrogen atoms, and (3) the treatment of specific hydration-shell water molecules is more consistent. The new models offer considerably improved performance compared to AM1-SM1 for neutral molecules and essentially equivalent performance for ions. The solute charges within the Parameterized Model 3 Hamiltonian limit the utility of PM3-SM3 for compounds containing nitrogen and possibly phosphorus. For other systems both AM1-SM2 and PM3-SM3 give realistic results, but AM1-SM2 in general outperforms PM3-SM3. Key features of the models are discussed with respect to alternative approaches.     

Radical mechanism of pectin oxidation in aqueous solution

The kinetic features of functionalization of natural polysacharide, pectin, by liquid-phase oxidation were studied.     

Influence of size,ellipticity and charge separation on the free energy of some aqueous bolaform electrolyte models

The free energy of some models of aqueous bolaform electrolytes have been calculated at the Debye-Hückel limiting law plus B ₂ level of approximation. The repulsive forces are modeled by hard spheres or hard ellipsoids. The charges are placed either at the center of the sphere or at the foci of the ellipsoid. Parameters were chosen to approximate the size and shape of sodium and calcium p-benzenedisufonate and sodium 4,4-biphenyldisulfonate. The results show that contrary to the standard explanations for the unusual properties of bolaform electrolytes, separating the charges has little effect on the excess free energy. It is also shown that changing from a sphere to an ellipse has little effect on the excess free energy. The most important determinates of the properties of these salts are the sizes of the ions. Agreement of the model calculations with experimental results is reasonable considering the simplicity of the models.     

Heterogeneously catalyzed oxidation of butanediols in base free aqueous media

The oxidation of four butanediols under base-free conditions has been investigated using a set of Au, Pd and Pt catalysts prepared using sol-immobilization. The supported nanoparticles are found to be active with bimetallic alloys having much higher activity when compared with the monometallic counterparts. In general the AuPt catalysts are the most active and in all cases the corresponding C4 oxidation products were observed with high selectivity; sequential reaction of these products leads to the formation of acetic acid as an undesired by-product.     

Calorimetry of model biomolecules in aqueous solution

A survey of the thermodynamic properties of aqueous solutions of model compounds is presented. The review is focused on the analysis of the thermal data obtained from dilution and mixing experiments monitoring weak interactions occurring between solvated solute species. The treatment of experimental results in the form of a virial-like expansion and the factorization analysis known as “group-contribution approach” is discussed in order to gain insight into the phenomenological process at molecular level.Examples are chosen in three dominating classes of biomolecular interactions: purine-like, peptide and carbohydrate molecules.     

Analysis of charge-transfer absorption and emission spectra on an absolute scale: evaluation of free energies, matrix elements, and reorganization energies

The relationship between the absorption and emission spectra of the charge-transfer complexes formed between a series of methyl-substituted benzene donors with 1,2,4,5-tetracyanobenzene as acceptor in 1,2-dichloroethane was examined in detail. The association constants for charge-transfer complex formation and the emission quantum yields for these complexes were used to place the experimental absorption and emission spectra on absolute scales. The simultaneous analysis of these spectra is valid only when the Mulliken two-state model is justified. For several of the complexes included in this study the electron-transfer parameters, including the electronic coupling matrix elements, obtained from the analysis of the individual absorption and emission spectra are in close agreement. The simultaneous analysis of the combined absorption and emission spectra leads to a well-defined set of electron-transfer parameters for these complexes. In other complexes, where the two-state model does not apply because of the influence of localized excited states on the absorption spectrum, analysis of the absorption and emission spectra led to significantly different sets of electron-transfer parameters. It is demonstrated that the electronic coupling matrix elements are a very sensitive indicator of the influence of localized excited states on these spectra.