Effect of polystyrene on di-butyl phthalate (DBP) bioavailability and DBP-induced phytotoxicity in lettuce

Hydrophobic microplastics with a relatively large surface area can act as carriers for pollutants and exert a series of indirect effects on crop plants. This study investigated the toxic effects of small polystyrene (SPS, 100-1000 nm) and large polystyrene (LPS, >10,000 nm) microplastics, on lettuce under di-butyl phthalate (DBP) stress. The results indicated that single SPS, LPS, and DBP treatments significantly decreased lettuce biomass, and induced oxidative stress and damaged lettuce leaves and roots. According to Gaussian analysis, SPS or LPS could interact with DBP through van der Waals force, thereby reducing lettuce biomass and DBP enrichment in roots and leaves under combined treatments, increasing antioxidant enzyme activities and exacerbating oxidative stress and subcellular damage, compared to single DBP treatments. Observation using scanning electron microscopy demonstrated that polystyrene (PS) adhered to the root surfaces, which, in turn, caused physical blockage of the root pores. Cell membrane and wall damage was observed during PS and/or DBP exposures, as identified by transmission electron microscopy. Molecular docking illustrated that DBP and monobutyl phthalate could interact with superoxide dismutase residues through hydrogen bonding, π-π stacking, alkyl conjugation, and van der Waals forces. Interestingly, there were no statistical differences between the phytotoxicity of nano- and microplastics to lettuce. These findings showed that PS aggravated DBP-induced phytotoxicity.

A switchable self-assembling and disassembling chiral system based on a porphyrin-substituted phenylalanine-phenylalanine motif

Artificial light-harvesting systems have until now not been able to self-assemble into structures with a large photon capture cross-section that upon a stimulus reversibly can switch into an inactive state. Here we describe a simple and robust FLFL-dipeptide construct to which a meso-tetraphenylporphyrin has been appended and which self-assembles to fibrils, platelets or nanospheres depending on the solvent composition. The fibrils, functioning as quenched antennas, give intense excitonic couplets in the electronic circular dichroism spectra which are mirror imaged if the unnatural FDFD-analogue is used. By slightly increasing the solvent polarity, these light-harvesting fibres disassemble to spherical structures with silent electronic circular dichroism spectra but which fluoresce. Upon further dilution with the nonpolar solvent, the intense Cotton effects are recovered, thus proving a reversible switching. A single crystal X-ray structure shows a head-to-head arrangement of porphyrins that explains both their excitonic coupling and quenched fluorescence.

Free energy of binding of coiled-coil complexes with different electrostatic environments: the influence of force field polarisation and capping

Coiled-coils are well known protein-protein interaction motifs, with the leucine zipper region of activator protein-1 (AP-1) consisting of the c-Jun and c-Fos proteins being a typical example. Molecular dynamics (MD) simulations using the MM/GBSA method have been used to predict the free energy of interaction of these proteins. The influence of force field polarisation and capping on the predicted free energy of binding of complexes with different electrostatic environments (net charge) were investigated. Although both force field polarisation and peptide capping are important for the prediction of the absolute free energy of binding, peptide capping has the largest influence on the predicted free energy of binding. Polarisable simulations appear better suited to determine structural properties of the complexes of these proteins while non-polarisable simulations seem to give better predictions of the associated free energies of binding.

Distributed polarizability models for imidazolium-based ionic liquids

Quantum chemical calculations are used to derive distributed polarizability models sufficiently accurate and compact to be used in classical molecular dynamics simulations of imidazolium-based room temperature ionic liquids. Two distributed polarizability models are fitted to reproduce the induction energy of three imidazolium cations (1,3-dimethyl-, 1-ethyl-3-methyl-, and 1-butyl-3-methylimidazolium) and four anions (tetrafluoroborate, hexafluorophosphate, nitrate, and thiocyanate) polarized by a point charge located successively on a grid of surrounding points. The first model includes charge-flow polarizabilities between first-neighbor atoms and isotropic dipolar polarizability on all atoms (except H), while the second model includes anisotropic dipolar polarizabilities on all atoms (except H). For the imidazolium cations, particular attention is given to the transferability of the distributed polarizability sets. The molecular polarizability and its anisotropy rebuilt by the distributed models are found to be in good agreement with the exact ab initio values for the three cations and 23 additional conformers of 1-ethyl-3-methyl-, 1-butyl-3-methyl-, 1-pentyl-3-methyl-, and 1-hexyl-3-methylimidazolium cations.

Communication: Quantum polarized fluctuating charge model: a practical method to include ligand polarizability in biomolecular simulations

We present a simple and practical method to include ligand electronic polarization in molecular dynamics (MD) simulation of biomolecular systems. The method involves periodically spawning quantum mechanical (QM) electrostatic potential (ESP) calculations on an extra set of computer processors using molecular coordinate snapshots from a running parallel MD simulation. The QM ESPs are evaluated for the small-molecule ligand in the presence of the electric field induced by the protein, solvent, and ion charges within the MD snapshot. Partial charges on ligand atom centers are fit through the multi-conformer restrained electrostatic potential (RESP) fit method on several successive ESPs. The RESP method was selected since it produces charges consistent with the AMBER/GAFF force-field used in the simulations. The updated charges are introduced back into the running simulation when the next snapshot is saved. The result is a simulation whose ligand partial charges continuously respond in real-time to the short-term mean electrostatic field of the evolving environment without incurring additional wall-clock time. We show that (1) by incorporating the cost of polarization back into the potential energy of the MD simulation, the algorithm conserves energy when run in the microcanonical ensemble and (2) the mean solvation free energies for 15 neutral amino acid side chains calculated with the quantum polarized fluctuating charge method and thermodynamic integration agree better with experiment relative to the Amber fixed charge force-field.

A new method for induced fit docking (GENIUS) and its application to virtual screening of novel HCV NS3-4A protease inhibitors

Hepatitis C virus (HCV) is an etiologic agent of chronic liver disease, and approximately 170 million people worldwide are infected with the virus. HCV NS3-4A serine protease is essential for the replication of this virus, and thus has been investigated as an attractive target for anti-HCV drugs. In this study, we developed our new induced-fit docking program (genius), and applied it to the discovery of a new class of NS3-4A protease inhibitors (IC(50)=1-10 μM including high selectivity index). The new inhibitors thus identified were modified, based on the docking models, and revealed preliminary structure-activity relationships. Moreover, the genius in silico screening performance was validated by using an enrichment factor. We believe our designed scaffold could contribute to the improvement of HCV chemotherapy.

Polarizable empirical force field for sulfur-containing compounds based on the classical Drude oscillator model

Condensed-phase computational studies of molecules using molecular mechanics approaches require the use of force fields to describe the energetics of the systems as a function of structure. The advantage of polarizable force fields over nonpolarizable (or additive) models lies in their ability to vary their electronic distribution as a function of the environment. Toward development of a polarizable force field for biological molecules, parameters for a series of sulfur-containing molecules are presented. Parameter optimization was performed to reproduce quantum mechanical and experimental data for gas phase properties including geometries, conformational energies, vibrational spectra, and dipole moments as well as for condensed phase properties such as heats of vaporization, molecular volumes, and free energies of hydration. Compounds in the training set include methanethiol, ethanethiol, propanethiol, ethyl methyl sulfide, and dimethyl disulfide. The molecular volumes and heats of vaporization are in good accordance with experimental values, with the polarizable model performing better than the CHARMM22 nonpolarizable force field. Improvements with the polarizable model were also obtained for molecular dipole moments and in the treatment of intermolecular interactions as a function of orientation, in part due to the presence of lone pairs and anisotropic atomic polarizability on the sulfur atoms. Significant advantage of the polarizable model was reflected in calculation of the dielectric constants, a property that CHARMM22 systematically underestimates. The ability of this polarizable model to accurately describe a range of gas and condensed phase properties paves the way for more accurate simulation studies of sulfur-containing molecules including cysteine and methionine residues in proteins.

Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field

Lennard-Jones (LJ) parameters for a variety of model compounds have previously been optimized within the CHARMM Drude polarizable force field to reproduce accurately pure liquid phase thermodynamic properties as well as additional target data. While the polarizable force field resulting from this optimization procedure has been shown to satisfactorily reproduce a wide range of experimental reference data across numerous series of small molecules, a slight but systematic overestimate of the hydration free energies has also been noted. Here, the reproduction of experimental hydration free energies is greatly improved by the introduction of pair-specific LJ parameters between solute heavy atoms and water oxygen atoms that override the standard LJ parameters obtained from combining rules. The changes are small and a systematic protocol is developed for the optimization of pair-specific LJ parameters and applied to the development of pair-specific LJ parameters for alkanes, alcohols and ethers. The resulting parameters not only yield hydration free energies in good agreement with experimental values, but also provide a framework upon which other pair-specific LJ parameters can be added as new compounds are parametrized within the CHARMM Drude polarizable force field. Detailed analysis of the contributions to the hydration free energies reveals that the dispersion interaction is the main source of the systematic errors in the hydration free energies. This information suggests that the systematic error may result from problems with the LJ combining rules and is combined with analysis of the pair-specific LJ parameters obtained in this work to identify a preliminary improved combining rule.

Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications

A current emphasis in empirical force fields is on the development of potential functions that explicitly treat electronic polarizability. In the present article, the commonly used methodologies for modelling electronic polarization are presented along with an overview of selected application studies. Models presented include induced point-dipoles, classical Drude oscillators, and fluctuating charge methods. The theoretical background of each method is followed by an introduction to extended Langrangian integrators required for computationally tractable molecular dynamics simulations using polarizable force fields. The remainder of the review focuses on application studies using these methods. Emphasis is placed on water models, for which numerous examples exist, with a more thorough discussion presented on the recently published models associated with the Drude-based CHARMM and the AMOEBA force fields. The utility of polarizable models for the study of ion solvation is then presented followed by an overview of studies of small molecules (e.g. CCl(4), alkanes, etc) and macromolecule (proteins, nucleic acids and lipid bilayers) application studies. The review is written with the goal of providing a general overview of the current status of the field and to facilitate future application and developments.

Dynamics of molecular self-ordering in tetraphenyl porphyrin monolayers on metallic substrates

A molecular model system of tetraphenyl porphyrins (TPP) adsorbed on metallic substrates is systematically investigated within a joint scanning tunnelling microscopy/molecular modelling approach. The molecular conformation of TPP molecules, their adsorption on a gold surface and the growth of highly ordered TPP islands are modelled with a combination of density functional theory and dynamic force field methods. The results indicate a subtle interplay between different contributions. The molecule-substrate interaction causes a bending of the porphyrin core which also determines the relative orientations of phenyl legs attached to the core. A major consequence of this is a characteristic (and energetically most favourable) arrangement of molecules within self-assembled molecular clusters; the phenyl legs of adjacent molecules are not aligned parallel to each other (often denoted as pi-pi stacking) but perpendicularly in a T-shaped arrangement. The results of the simulations are fully consistent with the scanning tunnelling microscopy observations, in terms of the symmetries of individual molecules, orientation and relative alignment of molecules in the self-assembled clusters.

A multivalent hexapod: conformational dynamics of six-legged molecules in self-assembled monolayers at a solid-liquid interface

A molecular hexapod having a benzene core and six oligo(p-phenylene vinylene) (OPV) legs is an ideal system to probe various types of (intramolecular) dynamics of individual molecules in physisorbed self-assembled monolayers at a solid-liquid interface. Scanning tunneling microscopy reveals that molecules adsorb in 2D crystalline as well as disordered domains. Strikingly, not all molecules have the six OPV units in contact with the graphite substrate: 4% of the molecules in the 2D crystalline domains and up to 80% of the molecules in the disordered domains have one or two OPV units desorbed. In addition, the presence of such a defect promotes the coexistence of another defect adjacent to it. Time-dependent STM experiments and molecular dynamics simulations reveal in detail the different dynamics involved and the multivalent nature of the interactions between hexapod and surface.

The important role of lone-pairs in force field (MM4) calculations on hydrogen bonding in alcohols

An expanded treatment of hydrogen bonding has been developed for MM4 force field calculations, which is an extension from the traditional van der Waals-electrostatic model. It adds explicit hydrogen-bond angularity by the inclusion of lone-pair directionality. The vectors that account for this directionality are placed along the hydrogen acceptor and its chemically intuitive electron pairs. No physical lone-pairs are used in the calculations. Instead, an H-bond angularity function, and a lone-pair directionality function, are incorporated into the hydrogen-bond term. The inclusion of the lone-pair directionality results in improved accuracy in hydrogen-bonded geometries and interaction energies. In this work is described hydrogen bonding in alcohols, and also in water and hydrogen fluoride dimer. The extension to other compounds such as aldehydes, ketones, amides, and so on is straightforward and will be discussed in future work. The conformational energies of ethylene glycol are discussed.

Chiral expression at the solid-liquid interface: a joint experimental and theoretical study of the self-assembly of chiral porphyrins on graphite

The chiral organization of an enantiopure functional molecule on an achiral surface has been studied with the aim of understanding the influence of stereogenic centers on the self-assembly in two dimensions. A chiral tetra meso-amidophenyl-substituted porphyrin containing long hydrophobic tails at the periphery of the conjugated pi-electron system was prepared for this purpose. Scanning tunneling microscopy (STM) images of the compound at the graphite-heptanol interface reveal a chiral arrangement of the molecules, with the porphyrin rows tilted by 13 degrees with respect to the normal to the graphite axes. In terms of molecular modeling, a combination of molecular dynamics simulations on systems constrained by periodic boundary conditions and on unconstrained large molecular aggregates has been applied to reach a quantitative interpretation on both the density of the layer and its orientation with respect to the graphite surface. The results show clearly that (i) the methyl groups of the stereogenic point toward the graphite surface and (ii) the porphyrin molecules self-assemble into an interdigitated structure where the alkyl chains align along one of the graphite axes and the porphyrin cores are slightly shifted with respect to one another. The direction of this shift, which defines the chirality of the monolayer, is set by the chirality of the stereogenic centers. Such an arrangement results in the formation of a dense chiral monolayer that is further stabilized by hydrogen bonding with protic solvents.

Structure and dynamics of a bisurea-based supramolecular polymer in n-dodecane

The structure and dynamics of a supramolecular polymer formed by a bisurea-type compound, 2,4-bis(2-ethylhexylureido)toluene (EHUT), in an apolar solvent, n-dodecane (C12), were examined in detail. The EHUT/C12 organo-gel system forms long, dynamic chain-like supramolecular polymers, which lead to an entangled network showing remarkable viscoelastic behavior with two major relaxation modes. A slow relaxation mode with an approximately constant relaxation time, tauS, was observed in a flow region and the other, fast, relaxation mode with a time tauF1 (<tauS) was observed in a high-frequency range. Because no dielectric relaxation behavior was observed over a frequency region including the mechanical tauS and tauF1 relaxation modes, the formed supramolecular polymer does not possess any total dipole moment due to antiparallel intermolecular hydrogen bonding of the two ureido groups of each EHUT unit. A structural model for the supramolecular polymer formed in EHUT/C12 is proposed based on force-field simulations. This proposed model is consistent with all the experimental data concerning this system: flow birefringence measurements, dielectric spectroscopy, SANS, and FTIR.

Molecular mechanics (MM4) study of amines

The MM4 force field has been extended to include aliphatic amines. About 20 amines have been examined to obtain a set of useful molecular mechanics parameters for this class. The vibrational spectra of seven amines (172 frequencies) calculated by MM4 have an overall rms error of 27 cm(-1), compared with corresponding MM4 value of 24 cm(-1) for alkanes. The rms and signed average errors of the moments of inertia of nine simple amines compared with the experimental data were 0.18% and -0.004%, respectively. The heats of formation of 30 amines were also studied. The MM4 weighted standard deviation is 0.41 kcal/mol, compared with experiment. Electronegativity effects occur in the hydrocarbon portion of an amine from the nitrogen, and are accounted for by including electronegativity induced changes in bond lengths and angles, and induced dipole-dipole interactions in the molecule. Negative hyperconjugation results from the presence of the lone pair of electrons on nitrogen, and leads to the Bohlmann bands in the infrared, and also to strong and unusual geometric changes in the molecules (Bohlmann effect), all of which are fairly well accounted for. The conformational energies in amines appear to be less straightforward than those for most other classes of molecules, apparently because of the Bohlmann effect, and these are probably not yet completely understood. In general, the agreement between the MM4 calculated results and the available data is reasonably good.

Harmonic and Anharmonic Features of IR and NIR Absorption and VCD Spectra of Chiral 4-X-[2.2]Paracyclophanes

The vibrational absorption spectra and vibrational circular dichroism (VCD) spectra of both enantiomers of 4-X-[2.2]paracyclophanes (X = COOCD3, Cl, I) have been recorded for a few regions in the range of 900-12000 cm(-1). The analysis of the VCD spectra for the two IR regions, 900-1600 cm(-1) and 2800-3200 cm(-1), is conducted by comparing with DFT calculations of the corresponding spectra; the latter region reveals common motifs of vibrational modes for the three molecules for aliphatic CH stretching fundamentals, whereas in the mid-IR region, one is able to identify specific signatures arising from the substituent groups X. In the CH stretching region between 2900 and 2800 cm(-1), we identify and interpret a group of three IR VCD bands due to HCH bending overtone transitions in Fermi resonance with CH stretching fundamental transitions. The analysis of the NIR region between approximately 8000 and approximately 9000 cm(-1) for X = COOCD3 reveals important features of the aromatic CH stretching overtones that are of value since the aromatic CH stretching fundamentals are almost silent. The intensifying of such overtones is attributed to electrical anharmonicity terms, which are evaluated here by ab initio methods and compared with literature data.

Solvent type affects the number, distribution, and relative quantities of volatile compounds found in sweet whey powder

This study compares the performance of diethyl ether, methylene chloride, methyl formate, and pentane in the analysis of volatile flavor components in sweet whey powder. Extracts were prepared from sweet whey powder using each solvent. Volatile components were isolated by solvent extraction followed by solvent-assisted flavor evaporation. Gas chromatography-mass spectroscopy, coelution with known standards, and retention indices were used to identify the volatile compounds. Sixty total compounds were either positively or tentatively identified across all 4 solvents, but the number, distribution between the molecular classes, and relative quantities detected depended on solvent type. The highest number, widest distribution, and greatest relative quantities were found using methylene chloride and methyl formate, whereas diethyl ether and especially pentane were noticeably less effective. Results are characterized using molecular-based characteristics of solvents and solutes including dipole moment, dielectric constant, Log P (octanol-water partition coefficient), polarizability, water solubility, and Lewis acidity/basicity. Polarity and acidity/basicity were the primary factors that determined solvent performance. This work establishes a molecular-level basis for the selection of solvents in the analysis of sweet whey powder flavors.

A generalization of the charge equilibration method for nonmetallic materials

Assigning effective atomic charges that properly reproduce the electrostatic fields of molecules is a crucial step in the construction of accurate interatomic potentials. We propose a new approach to calculate these charges, which as previous approaches are, is based on the idea of charge equilibration. However, we only allow charge to flow between covalently bonded neighbors by using the concept of so-called split charges. The semiempirical fit parameters in our approach do not only reflect atomic properties (electronegativity and atomic hardness) but also bond-dependent properties. The new method contains two popular but hitherto disjunct approaches as limiting cases. We apply our methodology to a set of molecules containing the elements silicon, carbon, oxygen, and hydrogen. Effective charges derived from electrostatic potential surfaces can be predicted more than twice as accurately as with previous works, at the expense of one additional fit parameter per bond type controlling the polarizability between two bonded atoms. Additional bond-type parameters can be introduced, but barely improve the results. An increase in accuracy of only 30% over existing techniques is achieved when predicting Mulliken charges. However, this could be improved with additional bond-type parameters.

A Hirshfeld partitioning of polarizabilities of water clusters

A new Hirshfeld partitioning of cluster polarizability into intrinsic polarizabilities and charge delocalization contributions is presented. For water clusters, density-functional theory calculations demonstrate that the total polarizability of a water molecule in a cluster depends upon the number and type of hydrogen bonds the molecule makes with its neighbors. The intrinsic contribution to the molecular polarizability is transferable between water molecules displaying the same H-bond scheme in clusters of different sizes, and geometries, while the charge delocalization contribution also depends on the cluster size. These results could be used to improve the existing force fields.

The hydrogen perturbation in molecular connectivity computations

A new algorithm for the delta(v) number, the basic parameter of molecular connectivity indices, is proposed. The new algorithm, which is centered on graph concepts like complete graphs and general graphs, encodes the information of the bonded hydrogen on different atoms through a perturbation parameter that makes use of no new graph concepts. The model quality of the new algorithm is tested with 13 properties of seven different classes of compounds, as well as with composite classes of compounds with the same property and with composite properties of the same class of compounds. Chosen properties and classes of compounds display different percentage of bonded hydrogen atoms, which allow a checking of the importance of this parameter. A comparison is drawn with previous results with zero contribution for the hydrogen perturbation as well as among results obtained by changing the number of compounds of a property but keeping constant the percentage of hydrogen atoms. Results underline the importance of the property as well as the importance of the number of compounds in determining the level of the hydrogen perturbation. Molecular connectivity terms are in some cases more critical than the combination of indices in detecting the perturbation introduced by the hydrogen atoms.

Potential functions for hydrogen bonds in protein structure prediction and design

Hydrogen bonds are an important contributor to free energies of biological macromolecules and macromolecular complexes, and hence an accurate description of these interactions is important for progress in biomolecular modeling. A simple description of the hydrogen bond is based on an electrostatic dipole-dipole interaction involving hydrogen-donor and acceptor-acceptor base dipoles, but the physical nature of hydrogen bond formation is more complex. At the most fundamental level, hydrogen bonding is a quantum mechanical phenomenon with contributions from covalent effects, polarization, and charge transfer. Recent experiments and theoretical calculations suggest that both electrostatic and covalent components determine the properties of hydrogen bonds. Likely, the level of rigor required to describe hydrogen bonding will depend on the problem posed. Current approaches to modeling hydrogen bonds include knowledge-based descriptions based on surveys of hydrogen bond geometries in structural databases of proteins and small molecules, empirical molecular mechanics models, and quantum mechanics-based electronic structure calculations. Ab initio calculations of hydrogen bonding energies and geometries accurately reproduce energy landscapes obtained from the distributions of hydrogen bond geometries observed in protein structures. Orientation-dependent hydrogen bonding potentials were found to improve the quality of protein structure prediction and refinement, protein-protein docking, and protein design.

Alcohols, ethers, carbohydrates, and related compounds. I. The MM4 force field for simple compounds

Simple alcohols and ethers have been studied with the MM4 force field. The structures of 13 molecules have been well fit using the MM4 force field. Moments of inertia have been fit with rms percentage errors as indicated: 18 moments for ethers, 0.28%; 21 moments for alcohols, 0.22%. Rotational barriers and conformational equilibria have also been examined, and the experimental and ab initio results are reproduced substantially better with MM4 than they were with MM3. Much of the improvement comes from the use of additional interaction terms in the force constant matrix, of which the torsion-bend and torsion-torsion are particularly important. Induced dipoles are included in the calculation, and dipole moments are reasonably well fit. It has been possible for the first time to fit conformational energetic data for both open chain and cyclic alcohols (e.g., propanol and cyclohexanol) with the same parameter set. For vibrational spectra, over a total of 82 frequencies, the rms error is 27 cm(-1), as opposed to 38 cm(-1) with MM3. Both the alpha and beta bond shortening resulting from the presence of the electronegative oxygen atom in the molecule are well reproduced. The electronegativity of the oxygen is sufficient that one must also include not only the alpha and beta electronegativity effects on bond lengths, but also on angle distortions, if structures are to be well reproduced. The heats of formation of 32 alcohols and ethers were fit overall to within experimental error (weighted standard deviation error 0.26 kcal/mol).

Complete graph conjecture for inner-core electrons: homogeneous index case

The complete graph conjecture that encodes the inner-core electrons of atoms with principal quantum number n >or= 2 with complete graphs, and especially with odd complete graphs, is discussed. This conjecture is used to derive new values for the molecular connectivity and pseudoconnectivity basis indices of hydrogen-suppressed chemical pseudographs. For atoms with n = 2 the new values derived with this conjecture are coincident with the old ones. The modeling ability of the new homogeneous basis indices, and of the higher-order terms, is tested and compared with previous modeling studies, which are centered on basis indices that are either based on quantum concepts or partially based on this new conjecture for the inner-core electrons. Two similar algorithms have been proposed with this conjecture, and they parallel the two "quantum" algorithms put forward by molecular connectivity for atoms with n > 2. Nine properties of five classes of compounds have been tested: the molecular polarizabilities of a class of organic compounds, the dipole moment, molar refraction, boiling points, ionization energies, and parachor of a series of halomethanes, the lattice enthalpy of metal halides, the rates of hydrogen abstraction of chlorofluorocarbons, and the pED(50) of phenylalkylamines. The two tested algorithms based on the odd complete graph conjecture give rise to a highly interesting model of the nine properties, and three of them can even be modeled by the same set of basis indices. Interesting is the role of some basis indices all along the model.

Use of U-shaped donor-bridge-acceptor molecules to study electron tunneling through nonbonded contacts

A systematic determination of electronic coupling matrix elements in U-shaped molecules is demonstrated. The unique architecture of these systems allows for the determination of the electronic coupling through a pendant molecular moiety that resides between the donor and acceptor groups; this moiety quantifies the efficiency of electron tunneling through nonbonded contacts. Experimental electron-transfer rate constants and reaction free energies are used to calibrate a molecular-based model that describes the solvation energy. This approach makes it possible to experimentally determine electronic couplings and compare them with computational values.

Ab initio and molecular mechanics (MM3) calculations of protonated-neutral diamine hydrogen bonds

Ab initio calculations of cation-neutral diamine complexes have been carried out at the MP2/6-311+G** level. The geometry and energetics of the charge-reinforced hydrogen bond are analyzed with respect to the alkyl substitution of both the protonated and neutral nitrogen atoms, and these results have been used to improve the quality of the MM3(2000) force field. In addition, specialized hydrogen bond parameters optimized for MM3(2000) are presented. These parameters allow very accurate gas-phase modeling of the charge-neutral diamine environment. Molecular mechanics calculations can model effectively protonated amine-neutral amine hydrogen bonds in the gas phase and solution (continuum dielectric) through a combination of charge-dipole interactions and explicit hydrogen-bonding terms.