Computational study of formamide–water complexes using the SAPT and AIM methods

In this work, the complexes formed between formamide and water were studied by means of the SAPT and AIM methods. Complexation leads to significant alterations in the geometries and electronic structure of formamide. Intermolecular interactions in the complexes are intense, especially in the cases where the solvent interacts with the carbonyl and amide groups simultaneously. In the transition states, the interaction between the water molecule and the lone pair on the amide nitrogen is also important. In all the complexes studied herein, the electrostatic interactions between formamide and water are the main attractive force, and their contribution may be five times as large as the corresponding contribution from dispersion, and twice as large as the contribution from induction. However, an increase in the resonance of planar formamide with the successive addition of water molecules may suggest that the hydrogen bonds taking place between formamide and water have some covalent character.     

The origin of sticking between a hydroperoxy radical and a water surface

An understanding of how gas-phase radicals in the earth's atmosphere become incorporated with liquid-phase cloud droplets is a vital part of understanding the chemical budgeting of these highly reactive species. Recent studies have suggested that hydroperoxy radicals (HO2) have an affinity for binding to a water surface. The calculations presented here are used to extricate the components of the attractive contribution of the intermolecular interactions that are responsible for the unusually strong binding between the hydroperoxy radical and a water surface. The analyses reveal that, for the binding of an HO2 radical to a water surface, the two water molecules nearest the radical are the most relevant to the bonding and the addition of other water molecules has little affect on the bonding between the radical and the two nearest waters. These results suggest that, once the HO2 is bound to the surface, the binding is a relatively local phenomenon. Identifying the properties responsible for the strong attraction is an important result that can be used to identify other radical systems whose chemistry might be impacted by the presence of water.     

Toward the de novo design of a catalytically active helix bundle: a substrate-accessible carboxylate-bridged dinuclear metal center.

De novo design of proteins provides an attractive approach to uncover the essential features required for their functions. Previously, we described the design and crystal structure determination of a di-Zn(II) complex of "due-ferri-1" (DF1), a protein patterned after the diiron-dimanganese class of redox-active proteins [Lombardi, A.; Summa, C.; Geremia, S.; Randaccio, L.; Pavone, V.; DeGrado, W. F. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 6298-6305]. The overall structure of DF1, which contains a carboxylate-bridged dinuclear metal site, agrees well with the intended design. However, access to this dimetal site is blocked by a pair of hydrophobic leucine residues (L13 and L13'), which prevent facile entry of metal ions and small molecules. We have now taken the next step in the eventual construction of a catalytically active metalloenzyme by engineering an active site cavity into DF1 through the replacement of these two leucine residues with smaller residues. The crystal structure of the dimanganous form of L13A-DF1 indeed shows a substrate access channel to the dimetal center. In the crystal structure, water molecules and a ligating dimethyl sulfoxide molecule, which forms a monatomic bridge between the metal ions, occupy the cavity. Furthermore, the diferric form of a derivative of L13A-DF1, DF2, is shown to bind azide, acetate, and small aromatic molecules.     

Fluctuating hydration structure around nanometer-size hydrophobic solutes. I. Caging and drying around C60 and C60H60 spheres

The hydration structure around nanometer-size hydrophobic solutes is studied with molecular dynamics simulation by taking aqueous solutions of C60 and C60H60 as examples. In the hydration shell around a single C60 or C60H60, dipoles of simulated water molecules tend to be aligned to form the vortexlike coherent pattern which lasts for 100 ps, while individual water molecules stay within the hydration shell for about 10 ps. This structural pattern organized by fluctuating and diffusively moving molecules should be called a "fluctuating cage". In the narrow region between a pair of C60 molecules or a pair of C60H60 molecules, water density strongly fluctuates and is correlated to the mean force between solutes. The fluctuating caging and drying between solutes affect the hydrophobic interaction and dynamical behaviors of solutes.     

The influence of molecular shape and charge distribution on the molecular approach in solution. NMR dipolar relaxation studies of the many-body effects

The paramagnetic dipolar spin-lattice relaxation of nuclear spins is expressed in terms of the geometrical and dynamical parameters of the molecules and used to analyze the intra- and intermolecular microdynamics. The possible conformational changes of a TEMPOL nitroxide-labelled sugar in deuterated chloroform are studied and then the intermolecular processes are considered. The influence of the discrete polar natures of acetonitrile, chloroform, and methanol on the TEMPOL solvation dynamics is recognized. The importance of the water structure on the collisional approach of two attractive ions is emphasized. Finally, the attractive effects of the dipole-dipole electrostatic forces are shown for the water/TEMPOL pair. Diffusion and jump analytical theories, integral equations of statistical mechanics, and Monte-Carlo simulations of the diffusion are combined to treat the anisotropic interactions and the many-body effects.     

Physisorption of hydroxide ions from aqueous solution to a hydrophobic surface

We present results from detailed molecular dynamics simulations revealing a counterintuitive spontaneous physical adsorption of hydroxide ions at a water/hydrophobic interface. The driving force for the migration of the hydroxide ions from the aqueous phase is the preferential orientation of the water molecules in the first two water layers away from the hydrophobic surface. This ordering of the water molecules generates an electrical potential gradient that strongly and favorably interacts with the dipole moment of the hydroxide ion. These findings offer a physical mechanism that explains intriguing experimental reports indicating that the interface between water and a nonionic surface is negatively charged.     

Cooperativity in ordinary ice and breaking of hydrogen bonds

The total interaction energy between two H-bonded water molecules in a condensed phase is composed of a binding energy between them and an energy due to a cooperative effect. An approximate simple expression is suggested for the dependence of the interaction energy between two H-bonded water molecules on the number of neighboring water molecules with which they are H-bonded. Using this expression, the probabilities of breaking a H bond with various numbers of H-bonded neighbors are estimated. These probabilities are used in computer simulations of the breaking of specified fractions of H bonds in an ordinary (hexagonal) ice. A large "piece" of hexagonal ice (up to 8 millions molecules) is built up, and various percentages of H bonds are considered broken. It is shown that 62-63% of H bonds must be broken in order to disintegrate the "piece" of ice into disconnected clusters. This value is only a little larger than the percolation threshold (61%) predicted both by the percolation theory for tetrahedral ice and by simulations in which all H bonds were considered equally probable to be broken. When the percentage of broken bonds is smaller than 62-63%, there is a network of H-bonded molecules which contains the overwhelming majority of water molecules. This result contradicts some models of water which consider that water consists of a mixture of water clusters of various sizes. The distribution of water molecules with unequal probabilities for breaking is compared with the simulation involving equal probabilities for breaking. It was found that in the former case, there is an enhanced number of water monomers without H bonds, that the numbers of 2- and 3-bonded molecules are smaller, and the number of 4-bonded molecules is larger than in the latter case.     

Anthracene derivatives and the corresponding dimers with TEMPO radicals

Anthracene derivatives with several TEMPO radicals (2-4, 10) were prepared, and each photodimerization reaction was investigated. Although the photodimerization was unsuccessful in obtaining the dimers of anthracenes 2 and 3, which could be alternatively prepared in a stepwise manner, the photodimers of anthracenes 4 and 10 were available by the direct photoreaction. The dissociation reaction of the dimers proceeded well by heating them in solution to give the corresponding monomers in each case, and thus the reversible system could be constructed in the latter two systems. While no large difference was observed in their magnetic behaviors between the monomer/dimer pair of 4 and 8, an intriguing difference was found in the magnetic behaviors for the pair of 10 and 11 from ferromagnetic interactions in 10 to the variable magnetic interactions in 11 depending on the solvent molecules incorporated in the crystals.     

AcquaAlta: a directional approach to the solvation of ligand-protein complexes

Water molecules mediating polar interactions in ligand-protein complexes can substantially contribute to binding affinity and specificity. To account for such water molecules in computer-aided drug design, we performed an extensive search in the Cambridge Structural Database (CSD) to identify the geometrical criteria defining interactions of water molecules with ligand and protein. In addition, with ab initio calculations the propensity of ligand hydration was evaluated. Based on this information, we developed an algorithm (AcquaAlta) to reproduce water molecules bridging polar interactions between ligand and protein moieties. This approach was validated with 20 crystal structures and yielded a match of 76% between experimental and calculated water positions. When water molecules establishing only weak interactions with the protein were neglected, the match could be improved to 88%. Supported by a pharmacophore-based alignment tool, the solvation algorithm was then applied to the docking of oligopeptides to the periplasmic oligopeptide binding protein A (OppA). Calculated waters based on the crystal poses matched an average of 66% of the experimental waters. With water molecules calculated based on the docked ligands, the average match with the experimental waters dropped to 53%.     

"Like-charge attraction" between anionic polyelectrolytes: molecular dynamics simulations

"Like-charge attraction" is a phenomenon found in many biological systems containing DNA or proteins, as well as in polyelectrolyte systems of industrial importance. "Like-charge attraction" between polyanions is observed in the presence of mobile multivalent cations. At a certain limiting concentration of cations, the negatively charged macroions cease to repel each other and even an attractive force between the anions is found. With classical molecular dynamics simulations it is possible to elucidate the processes that govern the attractive behavior with atomistic resolution. As an industrially relevant example we study the interaction of negatively charged carboxylate groups of sodium polyacrylate molecules with divalent cationic Ca2+ counterions. Here we show that Ca2+ ions initially associate with single chains of polyacrylates and strongly influence sodium ion distribution; shielded polyanions approach each other and eventually "stick" together (precipitate), contrary to the assumption that precipitation is initially induced by intermolecular Ca2+ bridging.     

Hydrophilicity and the viscosity of interfacial water

We measure the viscosity of nanometer-thick water films at the interface with an amorphous silica surface. We obtain viscosity values from three different measurements: friction force in a water meniscus formed between an oxide-terminated W tip and the silica surface under ambient conditions; similar measurements for these interfaces under water; and the repulsive "drainage" force as the two surfaces approach at various speeds in water. In all three cases, we obtain effective viscosities that are approximately 10(6) times greater than that of bulk water for nanometer-scale interfacial separations. This enhanced viscosity is not observed when we degrade the hydrophilicity of the surface by terminating it with -H or -CH3. In view of recent results from other interfaces, we conclude that the criterion for the formation of a viscous interphase is the degree of hydrophilicity of the interfacial pair.     

Adsorption at the air/water interface in dodecylammonium chloride/sodium dodecyl sulfate mixtures

The composition and properties of the adsorption films of dodecylammonium chloride/sodium dodecyl sulfate at the air/water interface depend on interactions between the film molecules and equilibria in the bulk phase (monomer-micelle and/or monomerprecipitate equilibria).The negative value of surface molecular interaction parameter ^mon calculated using the regular solution theory indicates strong attractive interactions between adsorbed molecules. Electrostatic interactions between oppositely charged ionic head groups enhance the adsorption of surfactants and decrease the minimum molar area of surfactant molecules at the air/water interface. The addition of an oppositely charged surfactant enhances packing at the air/water interface and transition from a liquid expanded to a liquid condensed state. Surface potential measurements reveal positive values for the mixtures investigated, implying the cationic surfactant ions are closer to the surface than the anionic ones.     

Role of attractive methane-water interactions in the potential of mean force between methane molecules in water

On the basis of a Gaussian quasichemical model of hydration, a model of non-van der Waals character, we explore the role of attractive methane-water interactions in the hydration of methane and in the potential of mean force between two methane molecules in water. We find that the hydration of methane is dominated by packing and a mean-field energetic contribution. Contributions beyond the mean-field term are unimportant in the hydration phenomena for a hydrophobic solute such as methane. Attractive solute-water interactions make a net repulsive contribution to these pair potentials of mean force. With no conditioning, the observed distributions of binding energies are super-Gaussian and can be effectively modeled by a Gumbel (extreme value) distribution. This further supports the view that the characteristic form of the unconditioned distribution in the high-epsilon tail is due to energetic interactions with a small number of molecules. Generalized extreme value distributions also effectively model the results with minimal conditioning, but in those cases the distributions are sufficiently narrow that the details of their shape are not significant.     

Directed Synthesis and Chemistry of Unsymmetric Dicationic Diboranes and Their Use in Frustrated Lewis Pair-like Chemistry

The chemistry of dicationic diboranes with two B^II atoms that are engaged in direct B−B bonding is by enlarge unexplored, although these molecules have intriguing properties due to their combined Lewis acidic and electron-donor properties. Unsymmetric dicationic diboranes are extremely rare, but especially attractive due to their polarized B−B bond. In this work we report the directed synthesis of several stable unsymmetric dicationic diboranes by reaction between the electron-rich ditriflato-diborane B₂(hpp)₂(OTf)₂ (hpp=1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-α]pyrimidinate) and phosphino-pyridines, establishing B−N and B−P bonds with the diborane concomitant with triflate elimination. In the case of 2-((ditertbutylphosphino)methyl)pyridine, the B−N bond is formed instantly, but the B−P bond formation requires (due to steric constraints) several days at ambient conditions for completion, creating an intermediate that could be used for frustrated Lewis pair (FLP)-like chemistry. Here we test its reaction with an aldehyde, and propose a new type of FLP-like chemistry.     

Information theory-based scoring function for the structure-based prediction of protein-ligand binding affinity

The development and validation of a new knowledge based scoring function (SIScoreJE) to predict binding energy between proteins and ligands is presented. SIScoreJE efficiently predicts the binding energy between a small molecule and its protein receptor. Protein-ligand atomic contact information was derived from a Non-Redundant Data set (NRD) of over 3000 X-ray crystal structures of protein-ligand complexes. This information was classified for individual "atom contact pairs" (ACP) which is used to calculate the atomic contact preferences. In addition to the two schemes generated in this study we have assessed a number of other common atom-type classification schemes. The preferences were calculated using an information theoretic relationship of joint entropy. Among 18 different atom-type classification schemes "ScoreJE Atom Type set2" (SATs2) was found to be the most suitable for our approach. To test the sensitivity of the method to the inclusion of solvent, Single-body Solvation Potentials (SSP) were also derived from the atomic contacts between the protein atom types and water molecules modeled using AQUARIUS2. Validation was carried out using an evaluation data set of 100 protein-ligand complexes with known binding energies to test the ability of the scoring functions to reproduce known binding affinities. In summary, it was found that a combined SSP/ScoreJE (SIScoreJE) performed significantly better than ScoreJE alone, and SIScoreJE and ScoreJE performed better than GOLD::GoldScore, GOLD::ChemScore, and XScore.     

Hydration scheme of the purine and pyrimidine bases and base-pairs of the nucleic acids

The hydration scheme of the bases of the nucleic acids, leading to a representation of their first hydration shell, was computed using the overlap multipole procedure. The shell involves five, four, four and three bound water molecules in G, A, C and T respectively. The formation of the base pairs displaces one water molecule in the A-T pair and four water molecules in the G-C pair from the hydration shell. The hydration produces a destabilization of the pairing energy in comparison to the binding in vacuo, greater for the G-C pair than for the A-T pair. There remains nevertheless an appreciable residual affinity for inter-base hydrogen bonding in water.     

Molecular dynamics simulation of nanocolloidal amorphous silica particles: Part I

Explicit molecular dynamics simulations were applied to a pair of amorphous silica nanoparticles in aqueous solution, with diameter of 4.4 nm and with four different background electrolyte concentrations, to extract the mean force acting between the two silica nanoparticles. Dependences of the interparticle forces on the separation and the background electrolyte concentration were demonstrated. The nature of the interaction of the counterions with charged silica surface sites (deprotonated silanols) was investigated. A "patchy" double layer of adsorbed sodium counterions was observed. Dependences of the interparticle potential of mean force on the separation and the background electrolyte concentration were demonstrated. Direct evidence of the solvation forces is presented in terms of changes of the water ordering at the surfaces of the isolated and double nanoparticles. The nature of the interaction of the counterions with charged silica surface sites (deprotonated silanols) was investigated in terms of quantifying the effects of the number of water molecules separately inside each pair of nanoparticles by defining an impermeability measure. A direct correlation was found between the impermeability (related to the silica surface "hairiness") and the disruption of water ordering. Differences in the impermeability between the two nanoparticles are attributed to differences in the calculated electric dipole moment.     

Molecular dynamics investigation of the effects of a water surface on the aggregation of bent-core molecules

Molecular dynamics simulations are used to determine how the presence of a water surface affects the way that bent-core surfactant molecules interact with one another. The simulations are carried out for isolated pairs of bent-core molecules, and for pairs of bent-core molecules on a water surface. The results show that the water surface fundamentally alters the nature of the interaction between the bent-core molecules: a stable complex is formed when the two molecules are on the water surface, but not for an isolated pair of molecules. This difference occurs because the water surface constrains the internal structure and orientation of the molecules, which makes the packing of the molecules into a stable complex more thermodynamically favorable.     

Enthalpies of solution and solvation of amides in N,N-dimethylformamide: Application of the random contact point approach

Calorimetrically determined molar enthalpies of solution at infinite dilution in N,N-dimethylformamide and densities of several amides at 25°C are reported. Some of the enthalpies are combined with literature data for enthalpies of vaporization to obtain molar enthalpies of solvation. Relations are found between the enthalpies of solution and the size, and between these enthalpies and the enthalpic pair interaction coefficients of the solute molecules. These relations are quantified by an extension of the random contact point approach. This additivity scheme is also applied to enthalpies of solvation, vaporization and cavity formation. With this approach thermodynamic quantities of solution, solvation, vaporization, and pair interaction of different solutes and solvents are correlated with a single consistent set of group interaction parameters. In addition, the random contact point model provides a simple method to calculate thermodynamics of cavity formation which appear to be as reliable as those of the much more complicated scaled particle theory.