Towards a force field based on density fitting

Total intermolecular interaction energies are determined with a first version of the Gaussian electrostatic model (GEM-0), a force field based on a density fitting approach using s-type Gaussian functions. The total interaction energy is computed in the spirit of the sum of interacting fragment ab initio (SIBFA) force field by separately evaluating each one of its components: electrostatic (Coulomb), exchange repulsion, polarization, and charge transfer intermolecular interaction energies, in order to reproduce reference constrained space orbital variation (CSOV) energy decomposition calculations at the B3LYP/aug-cc-pVTZ level. The use of an auxiliary basis set restricted to spherical Gaussian functions facilitates the rotation of the fitted densities of rigid fragments and enables a fast and accurate density fitting evaluation of Coulomb and exchange-repulsion energy, the latter using the overlap model introduced by Wheatley and Price [Mol. Phys. 69, 50718 (1990)]. The SIBFA energy scheme for polarization and charge transfer has been implemented using the electric fields and electrostatic potentials generated by the fitted densities. GEM-0 has been tested on ten stationary points of the water dimer potential energy surface and on three water clusters (n = 16,20,64). The results show very good agreement with density functional theory calculations, reproducing the individual CSOV energy contributions for a given interaction as well as the B3LYP total interaction energies with errors below kBT at room temperature. Preliminary results for Coulomb and exchange-repulsion energies of metal cation complexes and coupled cluster singles doubles electron densities are discussed.     

Binding of 5-phospho-D-arabinonohydroxamate and 5-phospho-D-arabinonate inhibitors to zinc phosphomannose isomerase from Candida albicans studied by polarizable molecular mechanics and quantum mechanics

Type I phosphomannose isomerase (PMI) is a Zn-dependent metalloenzyme involved in the isomerization of D-fructose 6-phosphate to D-mannose 6-phosphate. One of our laboratories has recently designed and synthesized 5-phospho-D-arabinonohydroxamate (5PAH), an inhibitor endowed with a nanomolar affinity for PMI (Roux et al., Biochemistry 2004, 43, 2926). By contrast, the 5-phospho-D-arabinonate (5PAA), in which the hydroxamate moiety is replaced by a carboxylate one, is devoid of inhibitory potency. Subsequent biochemical studies showed that in its PMI complex, 5PAH binds Zn(II) through its hydroxamate moiety rather than through its phosphate. These results have stimulated the present theoretical investigation in which we resort to the SIBFA polarizable molecular mechanics procedure to unravel the structural and energetical aspects of 5PAH and 5PAA binding to a 164-residue model of PMI. Consistent with the experimental results, our theoretical studies indicate that the complexation of PMI by 5PAH is much more favorable than by 5PAA, and that in the 5PAH complex, Zn(II) ligation by hydroxamate is much more favorable than by phosphate. Validations by parallel quantum-chemical computations on model of the recognition site extracted from the PMI-inhibitor complexes, and totaling up to 140 atoms, showed the values of the SIBFA intermolecular interaction energies in such models to be able to reproduce the quantum-chemistry ones with relative errors < 3%. On the basis of the PMI-5PAH SIBFA energy-minimized structure, we report the first hypothesis of a detailed view of the active site of the zinc PMI complexed to the high-energy intermediate analogue inhibitor, which allows us to identify active site residues likely involved in the proton transfer between the two adjacent carbons of the substrates.     

Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy

We present an overview of the SIBFA polarizable molecular mechanics procedure, which is formulated and calibrated on the basis of quantum chemistry (QC). It embodies nonclassical effects such as electrostatic penetration, exchange-polarization, and charge transfer. We address the issues of anisotropy, nonadditivity, and transferability by performing parallel QC computations on multimolecular complexes. These encompass multiply H-bonded complexes and polycoordinated complexes of divalent cations. Recent applications to the docking of inhibitors to Zn-metalloproteins are presented next, namely metallo-beta-lactamase, phosphomannoisomerase, and the nucleocapsid of the HIV-1 retrovirus. Finally, toward third-generation intermolecular potentials based on density fitting, we present the development of a novel methodology, the Gaussian electrostatic model (GEM), which relies on ab initio-derived fragment electron densities to compute the components of the total interaction energy. As GEM offers the possibility of a continuous electrostatic model going from distributed multipoles to densities, it allows an inclusion of short-range quantum effects in the molecular mechanics energies. The perspectives of an integrated SIBFA/GEM/QM procedure are discussed.     

Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-beta-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry

Using the polarizable molecular mechanics method SIBFA, we have performed a search for the most stable binding modes of D- and L-thiomandelate to a 104-residue model of the metallo-beta-lactamase from B. fragilis, an enzyme involved in the acquired resistance of bacteria to antibiotics. Energy balances taking into account solvation effects computed with a continuum reaction field procedure indicated the D-isomer to be more stably bound than the L-one, conform to the experimental result. The most stably bound complex has the S(-) ligand bridging monodentately the two Zn(II) cations and one carboxylate O(-) H-bonded to the Asn193 side chain. We have validated the SIBFA energy results by performing additional SIBFA as well as quantum chemical (QC) calculations on small (88 atoms) model complexes extracted from the 104-residue complexes, which include the residues involved in inhibitor binding. Computations were done in parallel using uncorrelated (HF) as well as correlated (DFT, LMP2, MP2) computations, and the comparisons extended to corresponding captopril complexes (Antony et al., J Comput Chem 2002, 23, 1281). The magnitudes of the SIBFA intermolecular interaction energies were found to correctly reproduce their QC counterparts and their trends for a total of twenty complexes.     

Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations

We present refinements of the SIBFA molecular mechanics procedure to represent the intermolecular interaction energies of Zn(II). The two first-order contributions, electrostatic (E(MTP)), and short-range repulsion (E(rep)), are refined following the recent developments due to Piquemal et al. (Piquemal et al. J Phys Chem A 2003, 107, 9800; and Piquemal et al., submitted). Thus, E(MTP) is augmented with a penetration component, E(pen), which accounts for the effects of reduction in electronic density of a given molecular fragment sensed by another interacting fragment upon mutual overlap. E(pen) is fit in a limited number of selected Zn(II)-mono-ligated complexes so that the sum of E(MTP) and E(pen) reproduces the Coulomb contribution E(c) from an ab initio Hartree-Fock energy decomposition procedure. Denoting by S, the overlap matrix between localized orbitals on the interacting monomers, and by R, the distance between their centroids, E(rep) is expressed by a S(2)/R term now augmented with an S(2)/R(2) one. It is calibrated in selected monoligated Zn(II) complexes to fit the corresponding exchange repulsion E(exch) from ab initio energy decomposition, and no longer as previously the difference between (E(c) + E(exch)) and E(MTP). Along with the reformulation of the first-order contributions, a limited recalibration of the second-order contributions was carried out. As in our original formulation (Gresh, J Comput Chem 1995, 16, 856), the Zn(II) parameters for each energy contribution were calibrated to reproduce the radial behavior of its ab initio HF counterpart in monoligated complexes with N, O, and S ligands. The SIBFA procedure was subsequently validated by comparisons with parallel ab initio computations on several Zn(II) polyligated complexes, including binuclear Zn(II) complexes as in models for the Gal4 and beta-lactamase metalloproteins. The largest relative error with respect to the RVS computations is 3%, and the ordering in relative energies of competing structures reproduced even though the absolute numerical values of the ab initio interaction energies can be as large as 1220 kcal/mol. A term-to-term identification of the SIBFA contributions to their ab initio counterparts remained possible even for the largest sized complexes.     

Joint quantum chemical and polarizable molecular mechanics investigation of formate complexes with penta- and hexahydrated Zn2+: Comparison between energetics of model bidentate,monodentate, and through-water Zn2+ binding modes and evaluation of nonadditivity effects

In order to gain an understanding of the energetics of polycoordinated Zn²⁺ binding to the formate anion (the end side chain of the Asp and Glu residues of proteins), we compare three competing binding modes in the presence of five and six water molecules: a, bidentate binding of Zn²⁺ to both formate oxygens; b, monodentate binding of Zn²⁺ to one formate oxygen; and c, through-water binding of Zn²⁺ to formate, in which the cation remains bound to its first-hydration shell waters and interacts with both formate oxygens through three water molecules. We also investigate a complex d, which is similar to c, in which formate is protonated into formic acid and one water molecule is deprotonated. The computations are carried out using the ab initio self-consistent field/MP2 with three basis sets of increasing size density functional theory, semiempirical AM1 and PM3, and the sum of interactions between fragments ab initio computed (SIBFA) molecular mechanics procedures. The summed energies of the isolated molecules making up the complexes disfavor tautomer d compared to a–c. On the other hand, the ab initio computations give the ordering of intermolecular interaction energies as d formic acid tautomer >b monodentate >a bidentate >c through-water. Whereas the first-order energy E₁ favors both inner-shell Zn²⁺ complexes with formate over the outer-shell complex, the polarization and the charge-transfer components of the second-order energy E₂ both favor the outer-shell complex over the inner-shell one, despite the increased separation between the cation and the highly polarizable formate ion. Energy balances including continuum solvation enthalpies produce an equilibration of complexes a–d. The preference favoring the monodentate complex over the bidentate one is consistent with other ab initio results for formate binding by a fully coordinated Zn²⁺ cation and with structural results from X-ray crystallography. The SIBFA results are consistent with the ab initio results, and the computed interaction energy values match the ab initio ones to within 3%. The effects of nonadditivity are analyzed in the ab initio, SIBFA, and semiempirical computations. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1379–1390, 1999     

Cation–ligand interactions: Reproduction of extended basis set Ab initio SCF computations by the SIBFA 2 additive procedure

In the framework of the additive SIBFA 2 procedure, the intermolecular interaction energy is computed as a sum of five terms: ΔE = E_MTP + E_rep + E_pol + E_CT + E_disp. In order to assess the accuracy of the procedure to compute cation–ligand interactions, the interaction of alkali (Na⁺, K⁺) and alkaline-earth (Mg²⁺, Ca²⁺) cations with two representative ligands H₂O and HCOO^? has been studied and the results compared with those of ab initio SCF extended basis set computations. The additive procedure reproduces very satisfactorily the results of ab initio computations as concerns the numerical values of the interaction energies and the equilibrium cation–ligand distances, as well as the evolution of the energy components. A detailed study of these components at different distances helps, in particular, to delineate the relative weights of the charge-transfer and polarization contributions within the second-order energy.     

Microelectrode Sensing of Adenosine/Adenosine‐5′‐triphosphate with Fast‐Scan Cyclic Voltammetry

Adenosine and adenosine‐5′‐triphosphate (ATP) are important extracellular signaling molecules. Here, we studied adenosine and ATP using fast‐scan cyclic voltammetry at carbon‐fiber microelectrodes. Although ATP and adenosine have similar oxidation potentials, ATP oxidation current was highly dependent on buffer pH and divalent cation concentrations but adenosine current was not. Therefore, they can be distinguished by adding a divalent cation chelator or calibrating electrodes at different pH values. The enzymatic degradation of adenosine by adenosine deaminase was monitored in a mixture of adenosine and ATP in presence of EDTA (ethylenediaminetetraacetate). This sensing method is promising for enzyme kinetics or in vitro studies.     

Parallel ab initio and molecular mechanics investigation of polycoordinated Zn(II) complexes with model hard and soft ligands: Variations of binding energy and of its components with number and charges of ligands

In this study we compare the binding energies of polycoordinated complexes of Zn²⁺ within cavities composed of model “hard” (H₂O, OH⁻) or “soft” (CH₃SH, CH₃S⁻) ligands. Ab initio supermolecule computations are performed at the HF and MP2 levels using extended basis sets to determine the binding energies and their components as a function of: the number of ligands, ranging from three to six; the net charge of the cavity; and the “hard” versus “soft” character of the ligands. These ab initio computations are used to test the reliability of the SIBFA molecular mechanics procedure, originally formulated and calibrated on the basis of ab initio computations, for such charged systems. The SIBFA intermolecular interaction energies match the corresponding ab initio values using a coreless effective potential split‐valence basis set with a relative error of ≤3%. Extensions to binuclear Zn²⁺ complexes, such as those that occur in the Zn‐binding sites of Gal4 and β‐lactamase proteins, are performed to test the applicability of the methodology for such systems. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1011–1039, 2000     

Aptamer-oligonucleotide binding studied by capillary electrophoresis: cation effect and separation efficiency

Novel features of DNA structure, recognition and discrimination have been recently elucidated through the solution structural characterization of DNA aptamers that bind cofactors, amino acids and peptides with high affinity and specificity. Multidimensional nuclear magnetic resonance methodologies have been successfully applied to solve the solution structures. In this work, it was demonstrated that capillary electrophoresis was a powerful tool allowing the fundamental study of the binding mechanism between a DNA aptamer and three ligands, adenosine and adenylate compounds, i.e., adenosine diphosphate (ADP) and adenosine triphosphate (ATP). In order to gain further insight into this binding, thermodynamic measurements under different values of parameters (such as salt nature and its concentration (x) in the run buffer) were carried out. The results showed that dehydration at the binding interface, van der Waals interactions, H-bonding and adjustment of the aptamer recognition surface were implied in the aptamer-ligand association. As well, it was demonstrated that the addition in the medium of the sodium monovalent cation Na(+) or the nickel divalent cation Ni(2+) decreased the complex formation. Separation efficiency and peak shape can also be improved by Mg(2+) divalent cation, which increased the mass transfer kinetics during the ligand-aptamer binding process. A significant separation for the worst separated pair of peaks on the electropherogram ((ADP, ATP) peak pair) was thus achieved.     

Interaction of neutral and zwitterionic glycine with Zn2+ in gas phase: ab initio and SIBFA molecular mechanics calculations

The interaction of Zn²⁺ with glycine (Gly) in the gas phase is studied by a combination of ab initio and molecular mechanics techniques. The structures and energetics of the various isomers of the Gly–Zn²⁺ complex are first established via high‐level ab initio calculations. Two low‐energy isomers are characterized: one in which the metal ion interacts with the carboxylate end of zwitterionic glycine, and another in which it chelates the amino nitrogen and the carbonyl oygen of neutral glycine. These calculations lead to the first accurate value of the gas‐phase affinity of glycine for Zn²⁺. Ab initio calculations were also used to evaluate the performance of various implementations of the SIBFA force field. To assess the extent of transferability of the distributed multipoles and polarizabilities used in the SIBFA computations, two approaches are followed. In the first, approach (a), these quantities are extracted from the ab initio Hartree–Fock wave functions of glycine or its zwitterion in its entirety, and for each individual Zn²⁺‐binding conformation. In the second, approach (b), they are assembled from the appropriate constitutive fragments, namely methylamine and formic acid for neutral glycine, and protonated methylamine and formate for the zwitterion; they undergo the appropriate vector or matrix rotation to be assembled in the conformation studied. The values of the Zn²⁺–glycine interaction energies are compared to those resulting from ab initio SCF and MP2 computations using both the all‐electron 6‐311+G(2d,2p) basis set and an effective core potential together with the valence CEP 4‐31G(2d) basis set. Approach (a) values closely reproduce the ab initio ones, both in terms of the total interaction energies and of the individual components. Approach (b) can provide a similar match to ab initio interaction energies as does approach (a), provided that the two constitutive Gly building blocks are considered as separate entities having mutual interactions that are computed simultaneously with those occurring with Zn²⁺. Thus, the supermolecule is treated as a three‐body rather than a two‐body system. These results indicate that the current implementation of the SIBFA force field should be adequate to undertake accurate studies on zinc metallopeptides. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 963–973, 2000     

Correction to DFT interaction energies by an empirical dispersion term valid for a range of intermolecular distances

The computation of intermolecular interaction energies via commonly used density functionals is hindered by their inaccurate inclusion of medium and long range dispersion interactions. Practical computation of inter- and intra-macrobiomolecule interaction energies, in particular, requires a fairly accurate yet not overly expensive methodology. It is also desirable to compute intermolecular energies not only at their equilibrium (lowest energy) configurations but also over a range of biophysically relevant distances. We present a method to compute intermolecular interaction energies by including an empirical correction for dispersion which is valid over a range of intermolecular distances. This is achieved by optimizing parameters that moderate the empirical correction by explicit comparison of density functional (B3LYP) energies with distance-dependent (DD) reference values obtained at the CCSD(T)/CBS limit. The resulting method, hereafter referred to as B3LYP-DD, yields interaction energies with an accuracy generally better than 1 kcal mol(-1) for different types of noncovalent complexes, over a range of intermolecular distances and interaction strengths, relative to the expensive CCSD(T)/CBS standard. For a training set of dispersion interacting complexes, B3LYP-DD interaction energies in combination with diffuse functions display absolute errors equal to or smaller than 0.68 kcal mol(-1). The empirical correction does not significantly increase the computational cost as compared to standard density functional calculations. Applications relevant to biomolecular energy and structure, such as prediction of DNA base-pair interactions, are also presented.     

Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds?

Halogenated compounds are gaining an increasing importance in medicinal chemistry and materials science. Ab initio quantum chemistry (QC) has unraveled the existence of a “sigma hole” along the C? X (X = F, Cl, Br, I) bond, namely, a depletion of electronic density prolonging the bond, concomitant with a build‐up on its sides, both of which are enhanced along the F < Cl < Br < I series. We have evaluated whether these features were intrinsically built‐in in an anisotropic, polarizable molecular mechanics (APMM) procedure such as SIBFA (sum of interactions between fragments ab initio computed). For that purpose, we have computed the interaction energies of fluoro‐, chloro‐, and bromobenzene with two probes: a divalent cation, Mg(II), and water approaching X through either one H or its O atom. This was done by parallel QC energy‐decomposition analyses (EDA) and SIBFA computations. With both probes, the leading QC contribution responsible for the existence of the sigma hole is the Coulomb contribution E_c. For all three halogenated compounds, and with both probes, the in‐ and out‐of‐plane angular features of E_c were closely mirrored by the SIBFA electrostatic multipolar contribution (E_MTP). Resorting to such a contribution thus dispenses with empirically‐fitted “extra”, off‐centered partial atomic charges as in classical molecular mechanics/dynamics. © 2013 Wiley Periodicals, Inc.     

Energetics of Zn2+ binding to a series of biologically relevant ligands: A molecular mechanics investigation grounded on ab initio self-consistent field supermolecular computations

Detailed investigations are performed of the binding energetics of Zn²⁺ to a series of neutral and anionic ligands making up the sidechains of amino acid residues of proteins, as well as ligands which can be involved in Zn²⁺ binding during enzymatic activation: imidazole, formamide, methanethiol, methanethiolate, methoxy, and hydroxy. The computations are performed using the SIBFA molecular mechanics procedure (SMM), which expresses the interaction energy under the form of four separate contributions related to the corresponding ab initio supermolecular ones: electrostatic, short-range repulsion, polarization, and charge transfer. Recent refinements to this procedure are first exposed. To test the reliability of this procedure in large-scale simulations of inhibitor binding to metalloenzyme cavities, we undertake systematic comparisons of the SMM results with those of recent large basis set ab initio self-consistent field (SCF) supermolecule computations, in which a decomposition of the total ΔE into its four corresponding components is done (N. Gresh, W. Stevens, and M. Krauss, J. Comp. Chem., 16 , 843, 1995). For each complex, the evolution of each individual SMM energy component as a function of radial and in- and out-of-plane angular variations of the Zn²⁺ position reproduces with good accuracy the behavior of the corresponding SCF term. Computations performed subsequently on di- and oligoligated complexes of Zn²⁺ show that the SIBFA molecular mechanics (SMM) functionals, E_pol and E_ct, closely account for the nonadditive behaviors of the corresponding second-order energy contributions determined from the ab initio SCF calculations on these complexes and their nonlinear dependence on the number of ligands. Thus, the total intermolecular interaction energies computed with this procedure reproduce, with good accuracy, the corresponding SCF ones without the need for additional, extraneous terms in the intermolecular potential of polyligated complexes of divalent cations. © 1995 by John Wiley & Sons, Inc.     

Theoretical studies of molecular conformation. Derivation of an additive procedure for the computation of intramolecular interaction energies. Comparison withab initio SCF computations

An additive procedure (SIBFA) is developed for the rapid computation of conformational energy variations in very large molecules. The macromolecule is built out of constitutive molecular fragments and the intramolecular energy is computed as a sum of interaction energies between the fragments. The electrostatic and the polarization components are calculated using multicenter multipole expansions of theab initio SCF electron density of the fragments. The repulsion component is obtained as a sum of bond and lone pair interactions.Tests of the procedure on a series of model compounds containing ether oxygens and pyridine-like nitrogens are reported and compared with the results of correspondingab initio SCF calculations. The resulting methodology is compatible with the simultaneous computation of intermolecular interactions.     

Comparative binding energetics of Mg2+, Ca2+, Zn2+, and Cd2+ to biologically relevant ligands: Combined ab initio SCF supermolecule and molecular mechanics investigation

A combined ab initio SCF supermolecule and molecular mechanics investigation is carried out on the binding energetics of the divalent cations Mg²⁺, Ca²⁺, Zn²⁺, and Cd²⁺ to a series of the most common ligand functional groups found in biomolecules. The SCF binding energy components are resolved using the restricted variational space method.¹ The results show that the SIBFA molecular mechanics (SMM) procedure² reproduces the ab initio binding energies and total energy variations as a function of intermolecular variables. The model also reproduces the selectivity energetics for exchange reactions. Thus, the SMM procedure can be used without reparametrization to describe the coordination energetics of complex molecules including those subject to coordination changes. The energetic properties of divalent cation-hexahydrate complexes are compared as examples of a complete, realistic coordination system. The hexahydrates exhibit strong nonadditive effects typical of dication coordination. Nevertheless, these energetics are satisfactorily reproduced by the SMM procedure. © 1996 John Wiley & Sons, Inc.     

Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short‐range penetration correction up to quadrupoles

We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short‐range charge penetration correction modifying the charge‐charge, charge‐dipole and charge‐quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry‐Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono‐ and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER‐HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration‐corrected polarizable force fields highlighting the mandatory need of non‐spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short‐range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio‐ or bioinorganic systems in periodic boundary conditions. © 2016 Wiley Periodicals, Inc.     

Theory Studies on the Intermolecular Interactions of Urea Nitrate with RDX

Six fully optimized geometries of urea nitrate cation and RDX complexes have been obtained with DFT-B3LYP and MP2 methods at the 6-311++G** level. The intermolecular interaction energies have been calculated with basis set superposition error (BSSE) and zero point energy (ZPE) correction. The nature of intermolecular interaction has been revealed by the analysis of AIM and NBO. The results indicate that the greatest binding energy of urea nitrate with RDX is –82.47kJ/mol. The O–H…O and N–H…O hydrogen bonds are important intermolecular interactions of urea nitrate cation with RDX, and the origin of hydrogen bonds is the oxygen atom offering its lone-pair electrons to the σ(O-H)* or σ(O-H)* antibonding orbital. The intermolecular interactions strengthen the N–NO2 bond, leading to the reduced sensitivity of urea nitrate and RDX mixture explosive.     

Theoretical study of adsorption of sarin and soman on tetrahedral edge clay mineral fragments

This study provides details of the structure and interactions of Sarin and Soman with edge tetrahedral fragments of clay minerals. The adsorption mechanism of Sarin and Soman on these mineral fragments containing the Si(4+) and Al(3+) central cations was investigated. The calculations were performed using the B3LYP and MP2 levels of theory in conjunction with the 6-31G(d) basis set. The studied systems were fully optimized. Optimized geometries, adsorption energies, and Gibbs free energies of Sarin and Soman adsorption complexes were computed. The number and strength of formed intermolecular interactions have been analyzed using the AIM theory. The charge of the systems and a termination of the mineral fragment are the main contributing factors on the formation of intermolecular interactions in the studied systems. In the neutral complexes, Sarin and Soman is physisorbed on these mineral fragments due to the formation of C-H...O, and O-H...O hydrogen bonds. The chemical bond is formed between a phosphorus atom of Sarin and Soman and an oxygen atom of the -2 charged clusters containing an Al(3+) central cation and -1 charged complex containing a Si(4+) central cation (chemisorption). Sarin and Soman interact mostly in the same way with the same terminated edge mineral fragments containing different central cations. However, the interaction energies of the complexes with an Al(3+) central cation are larger than these values for the Si(4+) complexes. The interaction enthalpies of all studied systems corrected for the basis set superposition error were found to be negative. However, on the basis of the Gibbs free energy values, only strongly interacting complexes containing a charged edge mineral fragment with an Al(3+) central cation are stable at room temperature. We can conclude that Sarin and Soman will be adsorbed preferably on this type of edge mineral surfaces. Moreover, on the basis of the character of these edge surfaces, a tetrahedral edge mineral fragment can provide effective centers for the dissociation.     

Donor-acceptor (electronic) coupling in the precursor complex to organic electron transfer: intermolecular and intramolecular self-exchange between phenothiazine redox centers

Intermolecular electron transfer (ET) between the free phenothiazine donor (PH) and its cation radical (PH*+) proceeds via the [1:1] precursor complex (PH)(2)*+ which is transiently observed for the first time by its diagnostic (charge-resonance) absorption band in the near-IR region. Similar intervalence (optical) transitions are also observed in mixed-valence cation radicals with the generic representation: P(br)P*+, in which two phenothiazine redox centers are interlinked by p-phenylene, o-xylylene, and o-phenylene (br) bridges. Mulliken-Hush analysis of the intervalence (charge-resonance) bands afford reliable values of the electronic coupling element H(IV) based on the separation parameters for (P/P*+) centers estimated from some X-ray structures of the intermolecular (PH)(2)*+ and the intramolecular P(br)P*+ systems. The values of H(IV), together with the reorganization energies lambda derived from the intervalence transitions, yield activation barriers DeltaG(ET)() and first-order rate constants k(ET) for electron-transfer based on the Marcus-Hush (two-state) formalism. Such theoretically based values of the intrinsic barrier and ET rate constants agree with the experimental activation barrier (E(a)) and the self-exchange rate constant (k(SE)) independently determined by ESR line broadening measurements. This convergence validates the use of the two-state model to adequately evaluate the critical electronic coupling elements between (P/P*+) redox centers in both (a) intermolecular ET via the precursor complex and (b) intramolecular ET within bridged mixed-valence cation radicals. Important to intermolecular ET mechanism is the intervention of the strongly coupled precursor complex since it leads to electron-transfer rates of self-exchange that are 2 orders of magnitude faster (and activation barrier that is substantially lower) than otherwise predicted solely on the basis of Marcus reorganization energy.