Influence Of Solvent Molecules Research Articles

Intramolecular interaction between sidechains in intact Trp-cage miniprotein(TC5b)

Intramolecular interaction energies of sidechains in the intact TC5b are individually computed using density fitted 2nd order Moller-Plesset perturbation theory with aug-cc-pVTZ basis set. Large intramolecular interaction energies are observed in between residue lysine(8), aspartate(9), and arginine(16). Strong attractive interaction is also observed between terminal residues. In general, the interaction energies between sidechains without the influence of solvent molecules are relatively small if the pair does not have charges. The sum of 2-body interactions between sidechains in residues1-10 and residues 11–20 are found to be attractive, consistent with the fact TC5b is known to fold at physiological pH. This is largely due to attractive interactions between the charged residues arginine(16) and aspartate(9).

Solvent-Driven Transformation of Zn/Cd2+-Deoxycholate Assemblies.

Deoxycholic acid (DOC) is a unique, biologically derived surfactant with facial amphiphilicity that has been exploited, albeit minimally, in supramolecular assembly of materials. Here, we present the synthesis and structural characterization of three hybrid metal (Zn2+ and Cd2+)-DOC compounds. Analysis by single-crystal X-ray diffraction reveals the many interactions that are possible between these facial surfactants and the influence of solvent molecules that drive the assembly of materials. These structures are the first metal-DOC complexes besides those obtained from alkali and alkaline earth metals. We isolated polymeric chains of both Cd and Zn (Znpoly-DOC and Cdpoly-DOC) from water. Major interactions between DOC molecules in these phases are hydrophobic in nature. Cdpoly-DOC exhibits unique P1 symmetry, with complete interdigitation of the amphiphiles between neighboring polymeric chains. Zn4-DOC, obtained from methanol dissolution of Znpoly-DOC, features the OZn4 tetrahedron, widely known in basic zinc acetate and MOF-5 (metal organic framework). We document a solvent-driven, room-temperature transition between Znpoly-DOC and Zn4-DOC (in both directions) by scanning and transmission electron microscopies in addition to small-angle X-ray scattering, powder X-ray diffraction, and infrared spectroscopy. These studies show the methanol-driven transition of Znpoly-DOC to Zn4-DOC occurs via an intermediate with no long-range order of the Zn4 clusters, indicating the strongest interactions driving assembly are intramolecular. On the contrary, water-driven solid-to-solid transformation from Zn4-DOC to Znpoly-DOC exhibits crystal-to-crystal transformation. Znpoly-DOC is robust, easy to synthesize, and comprised of biologically benign components, so we demonstrate dye absorption as a proxy for water treatment applications. It favors absorption of positively charged dyes. These studies advance molecular level knowledge of the supramolecular assembly of facial surfactants that can be exploited in the design of organic-inorganic hybrid materials. This work also highlights the potential of solvent for tuning supramolecular assembly processes, leading to new hybrid materials featuring facial surfactants.

Neutron Scattering Techniques for Studying Metal Complexes in Aqueous Solution.

Neutron scattering combined with ab initio calculations provides a powerful tool for studying metal complexes in different solvents and, particularly, in water. The majority of traditional characterization techniques in catalysis provide only limited information on homogeneous catalytic processes. Neutron scattering, on the other hand, thanks to its sensitivity to hydrogen atoms, and therefore water molecules, can be used to build detailed models of reaction paths and to observe, at a molecular level, the influence of solvent molecules on a catalytic process. In this Mini-Review we describe several examples on how neutron scattering combined with ab initio calculations can be used to examine the nature of the interaction of water molecules with catalytically active metal complexes in solution.

Catenated Cages Mediated by Enthalpic Reaction Intermediates

Catenated cages are generally considered thermodynamically more stable than their constituent monomeric cages. However, the catenation mechanism is yet to be elucidated; it would require systematic...

Characterization of the interaction forces in a drug carrier complex of doxorubicin with a drug-binding peptide.

Polypeptide-based materials are used as building blocks for drug delivery systems aimed at toxicity decrease in chemotherapeutics. A molecular-level approach is adopted for investigating the non-covalent interactions between doxorubicin and a recently synthesized drug-binging peptide as a key part of a system for delivery to neoplastic cells. Molecular dynamics simulations in aqueous solution at room and body temperature are applied to investigate the structure and the binding modes within the drug-peptide complex. The tryptophans are outlined as the main chemotherapeutic adsorption sites, and the importance of their placement in the peptide sequence is highlighted. The drug-peptide binging energy is evaluated by density functional theory calculations. Principal component analysis reveals comparable importance of several types of interaction for the binding strength. π-Stacking is dominant, but other factors are also significant: intercalation, peptide backbone stacking, electrostatics, dispersion, and solvation. Intra- and intermolecular H-bonding also stabilizes the complexes. The influence of solvent molecules on the binding energy is mild. The obtained data characterize the drug-to-peptide attachment as a mainly attractive collective process with interactions spanning a broad range of values. These results explain with atomistic detail the experimentally registered doxorubicin-binging ability of the peptide and outline the complex as a prospective carrying unit that can be employed in design of drug delivery systems.

Elementary supramolecular strings in solutions of chiral trifluoroacetylated amino alcohols

IR spectroscopy is applied to studying the effect of nonpolar and low-polar solvents on the molecular structure of solid-state quasi-one-dimensional strings formed through the chiral self-assembly from solutions of trifluoroacetylated homochiral amino alcohols (TFAAA). It is experimentally confirmed that in stable two-phase string/solvent gels and respective xerogels, solid-phase strings contain no solvent molecules as a structural element, experiencing, however, a weak disturbing influence of solvent molecules. It is shown that the process of spontaneous self-assembly of chiral strings in solutions is accompanied by the formation of a complex system of hydrogen bonds involving the C=O, N–H, and O–H functional groups of dissolved TFAAA molecules and by the displacement of solvent molecules to the periphery of the resulting quasi-one-dimensional strings. The results of the present work, together with data obtained by other experimental methods, indicate that TFAAA-based elementary strings have diameters of 1–2 nm, being crystalline, molecularly thin, quasi-one-dimensional objects. The amplitude of the thermally activated bending vibrations (transverse phonons) of elementary strings is sufficient to cause the entanglement of elementary strings, which leads to the formation of larger diameter supercoiled strings.

Prediction of the 1H and 13C NMR Spectra of α-d-Glucose in Water by DFT Methods and MD Simulations

We have applied computational protocols based on DFT and molecular dynamics simulations to the prediction of the alkyl 1H and 13C chemical shifts of alpha-d-glucose in water. Computed data have been compared with accurate experimental chemical shifts obtained in our laboratory. 13C chemical shifts do not show a marked solvent effect. In contrast, the results for 1H chemical shifts provided by structures optimized in the gas phase are only fair and point out that it is necessary to take into account both the flexibility of the glucose structure and the strong effect exerted by solvent water thereupon. Thus, molecular dynamics simulations were carried out to model both the internal geometry as well as the influence of solvent molecules on the conformational distribution of the solute. Snapshots from the simulation were used as input to DFT NMR calculations with varying degrees of sophistication. The most important factor that affects the accuracy of computed 1H chemical shifts is the solute geometry; the effect of the solvent on the shielding constants can be reasonably accounted for by self-consistent reaction field models without the need of explicitly including solvent molecules in the NMR property calculation.

Diels−Alder Adduct of Pentacene and Maleimide: Crystal Growth and the Influence of Solvent Molecules on Structure and Hydrogen Bonding

Crystals of the soluble Diels−Alder adduct of pentacene and maleimide, C26H17NO2, as well as of the corresponding 1:1 inclusion compounds with 1,2-dichlorobenzene and toluene and the 2:3 compound with pyridine, have been grown by either solution growth techniques (1, C26H17NO2·C6H4Cl2; 2, C26H17NO2·C6H5CH3; and 3, 2C26H17NO2·3C5H5N) or by vacuum sublimation (4, C26H17NO2). Each of the crystal structures are comprised of discrete C26H17NO2 molecules, with the maleimide moiety adding to the third (central) ring of the original pentacene molecule. The structures present several distinct hydrogen-bonding patterns, depending upon the character of the solvent used. Whereas the C26H17NO2 molecules in 4 (no solvent) are arranged in extended hydrogen-bonded (N−H···O) chains, in 1 and 2, the C26H17NO2 molecules form hydrogen-bonded (N−H···O) dimers, alternating with the included solvent molecules. In 3, the N−H···O bonds are replaced with N−H···N and weak C−H···O interactions between C26H17NO2 and pyridine molecules, leading to hydrogen-bonded C26H17NO2···C5H5N pairs. The inclusion compounds thermally decompose in the temperature range 125−160 °C, losing the solvent molecules and leaving behind C26H17NO2, which principally sublimes rather than undergoing the retro-Diels−Alder decomposition in the temperature range 275−340 °C.

Searching for Stable, Five-Coordinate Aquated Al(III) Species. Water Exchange Mechanism and Effect of pH

Density functional theory calculations have been performed for the water exchange mechanism of aquated Al(III). The effect of pH was considered by studying the exchange processes for [Al(H2O)6]3+ and its conjugated base, [Al(H2O)5OH]2+. Both complexes were found to exchange water in a dissociative way with activation energies (EA) of 15.9 and 10.2 kcal/mol, respectively. The influence of solvent molecules on the gas-phase cluster model was considered by the addition of up to four water molecules to the model system. The stabilizing effect of the solvent on the transition state decreases EA to 8.6 (hexa-aqua complex) and 7.6 (monohydroxo complex) kcal/mol, whereas EA for all hydroxo species is consistently significantly lower than those for the related aqua systems, which indicates a much faster water exchange rate. For the hydroxo complex, all calculated five-coordinate intermediates, nH2O.[Al(H2O)4(OH)]2+ (n = 1, 2, 3, 4, 5), are more stable than the corresponding six-coordinate reactants. Our results therefore suggest the presence of a stable five-coordinate species of aquated Al(III), namely, the [Al(H2O)4(OH)]2+ complex.

The influence of solvent molecules on NMR spectrum of barbituric acid in the DMSO solution

AbstractThis work shows the modification of barbituric acid (BA) chemical shifts by dimethylsulphoxide (DMSO) molecules. The discussed changes are caused by creation of the H-bonded associates formed by barbituric acid with DMSO in solution. Free molecule of barbituric acid, the cluster of BA with two DMSO molecules and two different clusters of BA with four DMSO units are taken into consideration. The chemical shifts of these systems have been calculated and the obtained results have been compared with experimental data. Theoretical calculations predict a significant downfield shift for imino protons of barbituric acid involved in intermolecular-N-H...DMSO hydrogen bonds. The influence of the solvent molecules on other nuclei chemical shifts, especially protons of barbituric acid methylene group, is also reported.The calculations have involved Hartree-Fock and several Density Functional Theory methods. All methods correctly describe experimental 1H and 13C NMR spectra of barbituric acid. The best consistence between experiment and theory is observed for the BLYP functional. Four approximations of magnetic properties calculations embedded in the Gaussian’98 package have been tested. The results of the performed calculations indicate that from a practical point of view the GIAO method should be preferred.

Universal consequences of the presence of excluded volume interactions in dilute polymer solutions undergoing shear flow.

The role of solvent quality in determining the universal material properties of dilute polymer solutions undergoing steady simple shear flow is examined. A bead-spring chain representation of the polymer molecule is used, and the influence of solvent molecules on polymer conformations is modelled by a narrow Gaussian excluded volume potential that acts pairwise between the beads of the chain. Brownian dynamics simulations data, acquired for chains of finite length, and extrapolated to the limit of infinite chain length, are shown to be model independent. This feature of the narrow Gaussian potential, which leads to results identical to a delta-function repulsive potential, enables the prediction of both universal crossover scaling functions and asymptotic behavior in the excluded volume limit. Universal viscometric functions, obtained by this procedure, are found to exhibit increased shear thinning with increasing solvent quality. In the excluded volume limit, they are found to obey power law scaling with the characteristic shear rate beta, in close agreement with previously obtained renormalization group results. The presence of excluded volume interactions is also shown to lead to a weakening of the alignment of the polymer chain with the flow direction.

Influence of solvent molecules on the stereochemical code of glycyl residues in proteins.

The Ramachandran steric map and energy diagrams of the glycyl residue are symmetric. A plot of (phi,psi) angles of glycyl residues in 250 nonhomologous and high-resolution protein structures is also largely symmetric. However, there is a clear aberration in the symmetry. Although there is a cluster of points corresponding to the right-handed alpha-helical region, the "equivalent" cluster is clearly shifted to in and around the (phi,psi) values of (90 degrees, 0 degrees ) instead of being centered at the left-handed alpha-helical region of (60 degrees, 40 degrees ). This lack of symmetry exists even in the (phi,psi) distribution of residues from non-alpha-helical regions in proteins. Here we provide an explanation for this observation. An analysis of glycyl conformations in small peptide structures and in "coil" proteins, which are largely devoid of helical and sheet regions, shows that glycyl residues prefer to adopt conformations around (+/-90 degrees, 0 degrees ) instead of right- and left-handed alpha-helical regions. By using theoretical calculations, such conformations are shown to have highest solvent accessibility in a system of two-linked peptide units with glycyl residue at the central C(alpha) atom. This finding is consistent with the observations from 250 nonhomologous protein structures where glycyl residues with conformations close to (+/-90 degrees, 0 degrees ) are seen to have high solvent accessibility. Analysis of a subset of nonhomologous structures with very high resolution (1.5 A or better) shows that water molecules are indeed present at distances suitable for hydrogen bond interaction with glycyl residues possessing conformations close to (+/-90 degrees, 0 degrees ). It is suggested that water molecules play a key role in determining and stabilizing these conformations of glycyl residues and explain the aberration in the symmetry of glycyl conformations in proteins.