Inclusion Of Water Molecules Research Articles

A Comparative Ab Initio Study of the Primary Hydration and Proton Dissociation of Various Imide and Sulfonic Acid Ionomers

We compare the role of neighboring group substitutions on proton dissociation of hydrated acidic moieties suitable for proton exchange membranes through electronic structure calculations. Three pairs of ionomers containing similar electron withdrawing groups within the pair were chosen for the study: two fully fluorinated sulfonyl imides (CF(3)SO(2)NHSO(2)CF(3) and CF(3)CF(2)SO(2)NHSO(2)CF(3)), two partially fluorinated sulfonyl imides (CH(3)SO(2)NHSO(2)CF(3) and C(6)H(5)SO(2)NHSO(2)CF(2)CF(3)), and two aromatic sulfonic acid based materials (CH(3)C(6)H(4)SO(3)H and CH(3)OC(6)H(3)OCH(3)C(6)H(4)SO(3)H). Fully optimized counterpoise (CP) corrected geometries were obtained for each ionomer fragment with the inclusion of water molecules at the B3LYP/6-311G** level of density functional theory. Spontaneous proton dissociation was observed upon addition of three water molecules in each system, and the transition to a solvent-separated ion pair occurred when four water molecules were introduced. No considerable quantitative or qualitative differences in proton dissociation, hydrogen bond networks formed, or water binding energies were found between systems containing similar electron withdrawing groups. Each of the sulfonyl imide ionomers exhibited qualitatively similar results regarding proton dissociation and separation. The fully fluorinated sulfonyl imides, however, showed a greater propensity to exist in dissociated and ion-pair separated states at low degrees of hydration than the partially fluorinated sulfonyl imides. This effect is due to the additional electron withdrawing groups providing charge stabilization as the dissociated proton migrates away from the imide anion.

Fragrance release profile from sonochemically prepared protein microsphere containers

Protein microspheres have been prepared by sonicating a mixture of pure fragrant oil (amyl acetate (AA)) with an aqueous protein (bovine serum albumin) solution. The prepared protein spheres are nano- to micrometer sized with an encapsulation efficiency of approx. 97% for the AA present on the surface and inside the BSA capsule. Containers were found stable for more than 6months when stored sealed at 4°C and 20°C. For the release profile measurements, we used a simple, automated and direct method. We continuously weighed the encapsulated microspheres and measured the evaporation rates. The release profiles at 15°C and 25°C display two different evaporation rates. The higher rate is the sum of a few evaporation rates, including water molecules, while the slower rate is due to the evaporation of pure AA. The changes in the evaporation rates occur upon the collapse of the container. This event coincides with the full evaporation of water. For morphological characterization we dyed the AA with Nile red, and used SEM, ESEM, Cryo-SEM, light microscopy, and confocal laser scanning microscopy measurements.

The effect of methylation on the excited state dynamics of aminouracils

The excited state properties of two amino substituted uracils, 5-aminouracil (5AU) and 5-dimethylaminouracil (5DMAU) have been studied by steady-state and time-resolved fluorescence spectroscopy. In addition, the electronic transitions corresponding to photon absorption and emission were calculated using the TD-DFT/PCM method (with PBEO and CAM-B3LYP functionals), explicitly including water molecules of the first solvent shell. The fluorescence decays, recorded by fluorescence upconversion, reveal that the emitting states of both molecules are substantially longer-lived than that of uracil. However, while the 5AU fluorescence decays on a picosecond timescale, the 5DMAU fluorescence contains a weak, long-lived component, continuing beyond 100 ps. Calculations show that the excited state deactivation of 5AU is governed by the existence of a minimum on the pi pi* excited state potential energy surface. For 5DMAU, on the other hand, a very long-lived but weakly fluorescent intramolecular charge transfer (ICT) state, involving a significant charge transfer between the dimethylamino group and the pyrimidine ring, is found. This stable ICT state is characterized by a rotation of the dimethylamino group towards a quasi-perpendicular geometry

Solvent Effect on the Fluorescence Spectra of Coumarin 120 in Water: A Combined Quantum Mechanical and Molecular Mechanical Study

The solvent effect on the steady-state and time-resolved fluorescence spectra of coumarin 120 in water was studied utilizing a molecular dynamics simulation with combined quantum mechanical/molecular mechanical method. The constructed steady-state fluorescence spectra reproduced the Stokes shift of the experimental data. The solvent effects on the spectra were examined by constructing three different spectra: spectra using the entire system, spectra including water molecules only in the first solvent shell, and spectra excluding all water molecules. We found that the variation in C–C bond length makes the largest contribution to the solvent shift in the fluorescence spectrum, which indicates the importance of the electronic structure variation.

A combined quantum mechanics/molecular mechanics study of the one- and two-photon absorption in the green fluorescent protein

We present for the first time a QM/MM study of the one- and two-photon absorption spectra of the GFP chromophore embedded in the full protein environment described by an advanced quantum mechanically derived polarizable force field. The calculations are performed on a crystal structure of the green fluorescent protein (GFP) using the polarizable embedding density functional theory (PE-DFT) scheme. The importance of treating the protein environment explicitly with a polarizable force field and higher-order multipoles is demonstrated, as well as the importance of including water molecules close to the chromophore in the protein barrel. For the most advanced description we achieve good agreement with experimental findings, with a peak at 405 nm for the neutral and a peak at 475 nm for the anionic form of the GFP chromophore. The presence of a dark OPA state, as suggested by other studies to explain the discrepancies between OPA and TPA spectra, is not supported by our calculations.

U-Shaped Aromatic Ureadicarboxylic Acids as Versatile Building Blocks: Construction of Ladder and Zigzag Networks and Channels

In order to examine versatility of ureadicarboxylic acids as U-shaped building blocks for crystal engineering, their crystal structures and cocrystals with pyridine derivatives were investigated. H-bonding networks created by a sequential linking of H-bonded carboxylic acid dimers resulted in the formation of ladder-type networks in the crystals of N,N′-diethyl-N,N′-diphenylureadicarboxylic acid (2) and N,N′-diallyl-N,N′-diphenylureadicarboxylic acid (3). A zigzag type H-bonding network with wedging of water molecules into carboxy–carboxy H-bonding was observed for N,N′-dibenzyl-N,N′-diphenylureadicarboxylic acid (4). Cocrystals of N,N′-dimethyl-N,N′-diphenylureadicarboxylic acid (1) with 2,5-di(pyridine-4-yl)thiazolo[5,4-d]thiazole (5) and 2 with 4,4′-dipyridyl (6) afforded zigzag-type assembled structures. Two types of channel structures were created in the cocrystals of 1 and dipyridylurea (7) by inclusion of water molecules together with either methanol or ethanol. The former afforded a straight-type ...

A new kind of intermolecular stacking interaction between copper (II) mixed chelate complex (Casiopeína III-ia) and adenine

Casiopeínas® are Cu (II) mixed chelate complexes that have shown cytotoxic, genotoxic and antineoplastic activity. In order to understand the interaction of these complexes with biomolecules, we have studied in this work the interaction of Casiopeína III-ia [CAS 223930-33-4] with adenine, cytosine, thymine and guanine. X-ray diffraction analysis shown the molecular structure of an adduct {[Cu(dmbipy)(acac)(H 2O)]NO 3(adenine) 2·2H 2O} where dmbipy = 4,4′-dimethyl-2,2′-bipyridyne and acac = acetylacetonate, which is an example of intermolecular interaction between a ternary Cu (II) compound and adenine. Adduct is stabilized by hydrogen bonds, which include water molecules and adenines, and by π–π and C–H⋯π interactions between the ligands attached to the copper ion and the adenines. DFT calculations shown charge transfer between complex ligands and adenines being the former the acceptor and the latter the donor; these results reproduce very well the weak interactions found in the crystalline structure. DFT results shown the same behavior for thymine and guanine, meanwhile, cytosine has shown a direct coordination to metal center.

Generation and solid state characterization of tetrapyridinium perchlorate salts derived from tetrapyridyl tetraphenylethylenes

Two tetraarylethylene derivatives symmetrically functionalized at the 4, 4′, 4″, and 4 ‴ positions with either 4-pyridyl or 3-pyridyl groups were converted to their corresponding tetrapyridinium perchlorate salts upon exposure to Fe(ClO 4) 3· xH 2O. These tetra-perchlorates were isolated as single crystals and their structures were determined by X-ray diffractometry. In both cases extensive hydrogen bonding networks were observed involving pyridinium N–H groups, perchlorate anions, and included water molecules. Additionally, both structures feature hydrophobic crystalline regions formed from stacking of tetraarylethylene cations in helical fashion. Polar pyridinium N–H groups are directed outward from these stacks into hydrophilic crystalline regions containing perchlorate anions and water molecules of hydration. Information obtained regarding the solid state structures of these functionalized tetraarylethylene derivatives should prove useful in design of more elaborate supramolecular architectures.

Modeling of Chemical Reactions in Micelle: Water-Mediated Keto–Enol Interconversion As a Case Study

The effect of a zwitterionic micelle environment on the efficiency of the keto-enol interconversion of 2-phenylacetylthiophene has been investigated by means of a joint application of experimental and theoretical/computational approaches. Results have revealed a reduction of the reaction rate constant if compared with bulk water essentially because of the different solvation conditions experienced by the reactant species, including water molecules, in the micelle environment. The slight inhibiting effect due to the application of a static electric field has also been theoretically investigated and presented.

Interstitial water and the formation of low barrier hydrogen bonds: A computational model study

The B3LYP/D95+(d,p) analysis of the uncharged low barrier hydrogen bond (LBHB) between 4-methyl-1H-imidazole (Mim) and acetic acid (HAc) shows that uncharged LBHBs can be formed either by adding three water molecules around the cluster or by placing the Mim–HAc pair in a dielectric environment created by a polarizable continuum model with a permittivity larger than 20.7. The permittivity of environment around uncharged LBHB can be lowered significantly by including water molecules into the system. A Mim–HAc LBHB stabilized with one water molecule observed in diethyl ether (ε = 4.34), with two water molecules in toluene (ε = 2.38), and with three water molecules in vacuo (ε = 1). Solvation models with different numbers of water molecules predict average differences in the proton affinities of the hydrogen bonded bases (ΔPA) for stable uncharged LBHB systems in vacuo to be 91.5 kcal/mol being different from the ΔPA values close to zero in charge-assisted LBHB systems. The results clearly indicate that small amounts of interstitial water molecules at the active site of enzymes do not preclude the existence of LBHBs in biological catalysis. Our results also show that interstitial water molecules provide a useful clue in the search for uncharged LBHBs in an enzymatic environment and the number of water molecules can be used as a relative measure for the polarity around the direct environment of LBHBs. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

Poly[di-μ-aqua-diaqua-di-μ6-malonato-cobalt(II)dipotassium(I)

In the title complex, [CoK2(C3H2O4)2(H2O)4]n, the Co atom is located on a position with site symmetry 2/m, the K atom and one water mol­ecule are located on a mirror plane, and the malonate and one water mol­ecule are located on a twofold rotation axis. The KI atom is seven-coordinated by four carboxyl­ate O atoms from four malonate ligands and by three water O atoms, forming a distorted polyhedron. The CoII atom is in an almost octa­hedral environment formed by four carboxyl­ate O atoms from two malonate ligands and two water O atoms. The structure consists of layers parallel to (20) built up from edge-sharing KO7 and CoO6 polyhedra, which are connected by O—H⋯O hydrogen bonding including water mol­ecules into a three-dimensional network.

Density Functional Theory/Molecular Mechanics Approach for Electronic g-Tensors of Solvated Molecules

A general density functional theory/molecular mechanics approach for computation of electronic g-tensors of solvated molecules is presented. We apply the theory to the commonly studied di-tert-butyl nitroxide molecule, the simplest model compound for nitroxide spin labels, and explore the role of an aqueous environment and of various approximations for its treatment. It is found that successive improvements of the solvent shift of the g-tensor are obtained by going from the polarizable continuum model to discrete solvent models of various levels of sophistication. The study shows that an accurate parametrization of the electrostatic potential and polarizability of the solvent molecules in terms of distributed multipole expansions and anisotropic polarizabilities to a large degree relieves the need to explicitly include water molecules in the quantum region, which is the common case in density functional/continuum model approaches. It is also shown that the local dynamics of the solvent around the solute significantly influences the electronic g-tensor and should be included in benchmarking of exchange-correlation functionals for evaluation of solvent shifts of g-tensors. These findings can have important ramifications for the use of advanced hybrid density functional theory/molecular mechanics approaches for modeling spin labels in solvents, proteins, and membrane environments.

Structural and Electric Field Effects of Ions in Aqueous Nanodrops

Ensemble infrared photodissociation (IRPD) spectra in the hydrogen stretch region (∼2950-3800 cm(-1)) are reported for M(H(2)O)(35-37), with M = I(-), Cl(-), HCO(3)(-), OH(-), tetrabutyl-, tetrapropyl-, and tetramethylammonium, Cs(+), Na(+), Li(+), H(+), Ba(2+), Ca(2+), Co(2+), Mg(2+), La(3+), and Tm(3+), at 133 K. A single, broad feature is observed in the bonded-OH region of the spectra that indicates that the water network in these clusters is bulk-like and likely resembles liquid water more strongly than ice. The free-OH region for all of these clusters is dominated by peaks corresponding to water molecules that accept two and donate one hydrogen bond (AAD water molecules), indicating that AAD water molecules are more abundant at the surface of these ions than AD water molecules. A-only water molecules are present in significant abundance only for the trivalent metal cations. The frequency of the AAD free-OH stretch band shifts nearly linearly with the charge state of the ion, consistent with a Stark shift attributable to the ion's electric field. From these data, a frequency range of 3704.9-3709.7 cm(-1) is extrapolated for the free-OH of AAD water molecules at the (uncharged) bulk liquid water surface, consistent with sum-frequency generation spectroscopy experiments. Differences in both the bonded- and the free-OH regions of the spectra for these ions are attributable to ion-induced patterning of the water network that extends to the surface of the clusters, which includes water molecules in the third and fourth solvation shells; that is, these ions pattern water molecules at long distance to various extents. These spectra are simulated using two different electrostatic models previously used to calculate OH-stretch spectra of bulk water and aqueous solutions and parametrized for bonded-OH frequencies. These models qualitatively reproduce a number of features in the experimental spectra, although it is evident that more sophisticated treatment of water molecule and ion polarizability and vibrational coupling is necessary for more quantitative comparisons.

Understanding CO2 Capture Mechanisms in Aqueous Monoethanolamine via First Principles Simulations

CO2 absorption mechanisms in 30 wt % monoethanolamine aqueous solution were explored at both low and high CO2 pressures via ab initio molecular dynamics simulations. Detailed reaction processes were analyzed using both implicit and explicit solvent models. The results demonstrate that explicitly including water molecules in the simulation model is critical to achieve quantitative agreement between the calculated heats of absorption and the reported experimental values.

Tridymite-like host clathrate [K(H2O)n][CuZn(CN)4]: crystal structure, guest molecular motion and properties

A new clathrate [K(H(2)O)(n)][CuZn(CN)(4)] has been synthesized and its host structure has been determined by the single-crystal X-ray diffraction method. It has a [CuZn(CN)(4)](-) tridymite-like 3D framework host, formed with tetrahedral Cu(I) and Zn(II) ions and cyanide bridges and includes water molecules as guests, together with K(+). This tridymite-like structure is the first structural variation of the [CuZn(CN)(4)](-) 3D framework, whose only known structure has been a cristobalite-like structure. The new host shows properties never seen in the previous cristobalite-like structure host. It absorbs and desorbs water as a guest and the water content (n) varies between 1.2 and 11.2 at room temperature, by adjusting the conditions where the clathrate is placed. The desorption of the water causes deformation of the host structure and this deformation is recovered by the absorption of water. The water can be replaced with methanol and acetonitrile by their absorption instead of water. Solid-state (2)H-NMR spectra revealed the molecular motion of the water, methanol and acetonitrile guests in a temperature range between 123 K and 300 K.

IR absorption and Raman spectra of silicon dioxide nanoparticles in the presence of water: Computer experiment

Interactions of (SiO2)50 clusters with 10, 20, 30, or 40 water molecules are studied by molecular dynamics method. Flat SiO2 nanoparticle covered with a water layer is formed after the inclusion of water molecules into the cluster. As a rule, the integral intensity of IR and Raman spectra lowers after the absorption of H2O molecules by the cluster. The power of IR radiation emitted by the cluster increases nonmonotonically with the addition of water molecules to the cluster. The absorption of water molecules by the cluster leads to a significant increase in the absorption coefficient and only a slight increase in the refractive index. The number of electrons participating in the interaction with electromagnetic radiation increases with the addition of water molecules to the cluster.

Evidence from FTIR Difference Spectroscopy of an Extensive Network of Hydrogen Bonds near the Oxygen-Evolving Mn4Ca Cluster of Photosystem II Involving D1-Glu65, D2-Glu312, and D1-Glu329

Analyses of the refined X-ray crystallographic structures of photosystem II (PSII) at 2.9-3.5 A have revealed the presence of possible channels for the removal of protons from the catalytic Mn(4)Ca cluster during the water-splitting reaction. As an initial attempt to verify these channels experimentally, the presence of a network of hydrogen bonds near the Mn(4)Ca cluster was probed with FTIR difference spectroscopy in a spectral region sensitive to the protonation states of carboxylate residues and, in particular, with a negative band at 1747 cm(-1) that is often observed in the S(2)-minus-S(1) FTIR difference spectrum of PSII from the cyanobacterium Synechocystis sp. PCC 6803. On the basis of its 4 cm(-1) downshift in D(2)O, this band was assigned to the carbonyl stretching vibration (C horizontal lineO) of a protonated carboxylate group whose pK(a) decreases during the S(1) to S(2) transition. The positive charge that forms on the Mn(4)Ca cluster during the S(1) to S(2) transition presumably causes structural perturbations that are transmitted to this carboxylate group via electrostatic interactions and/or an extended network of hydrogen bonds. In an attempt to identify the carboxylate group that gives rise to this band, the FTIR difference spectra of PSII core complexes from the mutants D1-Asp61Ala, D1-Glu65Ala, D1-Glu329Gln, and D2-Glu312Ala were examined. In the X-ray crystallographic models, these are the closest carboxylate residues to the Mn(4)Ca cluster that do not ligate Mn or Ca and all are highly conserved. The 1747 cm(-1) band is present in the S(2)-minus-S(1) FTIR difference spectrum of D1-Asp61Ala but absent from the corresponding spectra of D1-Glu65Ala, D2-Glu312Ala, and D1-Glu329Gln. The band is also sharply diminished in magnitude in the wild type when samples are maintained at a relative humidity of </=85%. It is proposed that D1-Glu65, D2-Glu312, and D1-Glu329 participate in a common network of hydrogen bonds that includes water molecules and the carboxylate group that gives rise to the 1747 cm(-1) band. It is further proposed that the mutation of any of these three residues, or partial dehydration caused by maintaining samples at a relative humidity of <or=85%, disrupts the network sufficiently that the structural perturbations associated with the S(1) to S(2) transition are no longer transmitted to the carboxylate group that gives rise to the 1747 cm(-1) band. Because D1-Glu329 is located approximately 20 A from D1-Glu65 and D2-Glu312, the postulated network of hydrogen bonds must extend for at least 20 A across the lumenal face of the Mn(4)Ca cluster. The D1-Asp61Ala, D1-Glu65Ala, and D2-Glu312Ala mutations also appear to substantially decrease the fraction of PSII reaction centers that undergo the S(3) to S(0) transition in response to a saturating flash. This behavior is consistent with D1-Asp61, D1-Glu65, and D2-Glu312 participating in a dominant proton egress channel that links the Mn(4)Ca cluster with the thylakoid lumen.

Ligand−Protein Cross-Docking with Water Molecules

The accuracy of ligand-protein docking may be affected by the presence of water molecules on the surface of the protein. Cross-docking simulations have been performed on a number of ligand-protein complexes for various proteins whose crystal structures contain water molecules in their binding sites. Only common sets of water molecules found in the binding site of the proteins were considered. A statistically significant overall increase in accuracy was observed when water molecules were included in cross-docking simulations. These results confirm the importance of including water molecules whenever possible in ligand-protein docking simulations.

Role of Water in Molecular Docking Simulations of Cytochrome P450 2D6

Active-site water molecules form an important component in biological systems, facilitating promiscuous binding or an increase in specificity and affinity. Taking water molecules into account in computational approaches to drug design or site-of-metabolism predictions is currently far from straightforward. In this study, the effects of including water molecules in molecular docking simulations of the important metabolic enzyme cytochrome P450 2D6 are investigated. The structure and dynamics of water molecules that are present in the active site simultaneously with a selected substrate are described, and based on this description, water molecules are selected to be included in docking experiments into multiple protein conformations. Apart from the parent substrate, 11 similar and 53 dissimilar substrates are included to investigate the transferability of active-site hydration sites between substrates. The role of water molecules appears to be highly dependent on the protein conformation and the substrate.

Theoretical studies of UO2(OH)(H2O)n+, UO2(OH)2(H2O)n, NpO2(OH)(H2O)n, and PuO2(OH)(H2O)n+ (n≤21) complexes in aqueous solution

Extensive ab initio calculations have been carried out to study equilibrium structures, vibrational frequencies, and the nature of chemical bonds of hydrated UO(2)(OH)(+), UO(2)(OH)(2), NpO(2)(OH), and PuO(2)(OH)(+) complexes that contain up to 21 water molecules both in first and second hydration spheres in both aqueous solution and the gas phase. The structures have been further optimized by considering long-range solvent effects through a polarizable continuum dielectric model. The hydrolysis reaction Gibbs free energy of UO(2)(H(2)O)(5) (2+) is computed to be 8.11 kcal/mol at the MP2 level in good agreement with experiments. Our results reveal that it is necessary to include water molecules bound to the complex in the first hydration sphere for proper treatment of the hydrated complex and the dielectric cavity although water molecules in the second hydration sphere do not change the coordination complex. Structural reoptimization of the complex in a dielectric cavity seems inevitable to seek subtle structural variations in the solvent and to correlate with the observed spectra and thermodynamic properties in the aqueous environment. Our computations reveal dramatically different equilibrium structures in the gas phase and solution and also confirm the observed facile exchanges between the complex and bulk solvent. Complete active space multiconfiguration self-consistent field followed by multireference singles+doubles CI (MRSDCI) computations on smaller complexes confirm predominantly single-configurational nature of these species and the validity of B3LYP and MP2 techniques for these complexes in their ground states.