Structure and dynamics of methanol in water: a quantum mechanical charge field molecular dynamics study

An ab initio quantum mechanical charge field molecular dynamics simulation was carried out for one methanol molecule in water to analyze the structure and dynamics of hydrophobic and hydrophilic groups. It is found that water molecules around the methyl group form a cage-like structure whereas the hydroxyl group acts as both hydrogen bond donor and acceptor, thus forming several hydrogen bonds with water molecules. The dynamic analyses correlate well with the structural data, evaluated by means of radial distribution functions, angular distribution functions, and coordination number distributions. The overall ligand mean residence time, τ identifies the methanol molecule as structure maker. The relative dynamics data of hydrogen bonds between hydroxyl of methanol and water molecules prove the existence of both strong and weak hydrogen bonds. The results obtained from the simulation are in excellent agreement with the experimental results for dilute solution of CH(3)OH in water. The overall hydration shell of methanol consists in average of 18 water molecules out of which three are hydrogen bonded.     

When is a molecule properly solvated by a continuum model or in a cluster ansatz? A first-principles simulation of alanine hydration

In order to test the validity of the cluster ansatz approach as well as of the continuum model approach and to learn about the solvation shell, we carried out first-principles molecular dynamics simulations of the alanine hydration. Our calculations contained one alanine molecule dissolved in 60 water molecules. Dipole moments of individual molecules were derived by means of maximally localized Wannier functions. We observed an average dipole moment of about 16.0 D for alanine and of about 3.3 D for water. In particular, the average water dipole moment in proximity of alanine's COO(-) group decayed continously with increasing distance, while, surprisingly, close to the CH3 and NH3+ group, the dipole moment first rose before its value dropped. In a cluster ansatz approach, we considered snapshots of alanine surrounded by different water molecule shells. The dipole moments from the cluster approaches utilizing both maximally localized Wannier functions as well as natural population analysis served to approximate the dipole moments of the total trajectory. Sufficient convergence of the cluster ansatz approach is found for either of the two solvent shells around the polar groups and one solvent shell around the apolar groups or two solvent shells around the polar groups surrounded by a dieletric continuum.     

Hydration shell exchange dynamics during ion transfer across the liquid/liquid interface

We examine using molecular dynamics simulations the rate and mechanism of water molecules exchange around the Li(+) and Na(+) ions during ion transfer across the interface between water and nitrobenzene. As the ions are transferred from the water to the organic phase, they keep their first hydration shell and an incomplete second shell. The rate of water exchange between the first shell and the rest of the interfacial water molecule decreases during the transfer, which is consistent with an increase in the barrier along the ion-water potential of mean force. While in bulk water the exchange of water molecules around the Li(+) follows an associative (A) or associative interchange (I(a)) type mechanism, the fraction of exchange events of type A increases at the interface. In contrast, while in bulk water the exchange of water molecules around the six coordinated Na(+) hydrated species mainly follows a dissociative mechanism, the situation at the interface involves an equilibrium interchange between the four- and five-coordinated hydrated ion. Simulation of the reversed process, in which the hydrated Li(+) ion is transferred to the aqueous phase, shows the same general behavior as a function of location from the interface.     

Molecular dynamics simulation of glycine zwitterion in aqueous solution

A classical molecular dynamics method was used to study the modifications of the solution structure and the properties of glycine zwitterion in aqueous solution due to the increase of glycine zwitterion concentration and the incorporation of Na(+) and Cl(-) ions to the solution. The glycine zwitterion had fundamentally a hydrophilic behavior at infinite dilution, establishing around six hydrogen bonds with the water molecules that surrounded it, which formed a strong hydration layer. Because of the increase of glycine zwitterion concentration, the hydration structure became more compact and the quantity of water molecules bound to this molecule decreased. The Na(+) ion bound to the CO(2) group of glycine, while the Cl(-) ion bound mainly to the NH(3) group of this molecule. The integration of the ions to the hydration layer of the glycine zwitterion produced modifications in the orientational correlation between atoms of glycine zwitterion and water that surrounded them and an increase of the approaches between the glycine zwitterion molecules. The incorporation of ions to the solution also produced changes in the water-water orientational correlation. Decreases of the water-water hydrogen bonds and diffusion coefficient of all molecules were observed when the glycine zwitterion concentration increased and when the ions were incorporated to the solution.     

Water hydrogen bond analysis on hydrophilic and hydrophobic biomolecule sites

Elastic and quasielastic neutron scattering experiments have been used to investigate the hydrogen bonding network dynamics of hydration water on hydrophilic and hydrophobic sites. To this end the evolution of hydration water dynamics of a prototypical hydrophobic amino acid with polar backbone, N-acetyl-leucine-methylamide (NALMA), and hydrophilic amino acid, N-acetyl-glycine-methylamide (NAGMA), has been investigated as a function of the molecular ratio water : peptide. The results suggest that the dynamical contribution of the intrinsic and low hydration molecules of water is characteristic of pure librational/rotational movement. The water molecule remains attached to the hydrophilic site with only the possibility of hindered rotations that eventually break the bond with the peptide and reform it immediately after. A gradual evolution from librational motions to hindered rotations is observed as a function of temperature. When the hydration increases, we observe (together with the hindered rotations of hydrogen bonds) a slow diffusion of water molecules on the surface of the peptides.     

The trehalose coating effect on the internal protein dynamics

(15)N and (13)C NMR experiments were applied to conduct a comparative study of a cold shock protein (Csp) in two states-lyophilized powder and a protein embedded in a glassy trehalose matrix. Both samples were studied at various levels of rehydration. The experiments used (measuring relaxation rates R(1) and R(1ρ), motionally averaged dipolar couplings and solid state exchange method detecting reorientation of the chemical shift anisotropy tensor) allow obtaining abundant information on the protein structural features and internal motions in a range of correlation times from nanoseconds to seconds. The main results are: (a) the trehalose coating makes the protein structure more native in comparison with the dehydrated lyophilized powder, however, trehalose still cannot remove all non-native hydrogen bonds which are present in a dehydrated protein; (b) trehalose has an appreciable effect on the internal dynamics: the motion of the backbone N-H groups in the nanosecond and microsecond time scales becomes slower while the motional amplitude remains constant; (c) upon adding water to the Csp-trehalose mixture, water molecules accumulate around proteins forming a layer between the protein surface and the trehalose matrix. The protein dynamics become faster, however, not as fast as in the fully hydrated state; (d) the hydration response of dynamics of the NH and CH(CH(2)) groups in a protein is qualitatively different: upon increasing protein hydration, the correlation times of the N-H motions become shorter and the amplitude remains stable, and for CH(CH(2)) groups the motional amplitude increases and the correlation times do not change. This can be explained by a different ability of the NH and CH(CH(2)) groups to form hydrogen bonds.     

The infrared spectrum of solid L-alanine: influence of pH-induced structural changes

The influence of the pH on the infrared spectrum of L-alanine has been analyzed by diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy. The amino acid was precipitated from aqueous solutions and dried at 36.5 degrees C, in order to stabilize cationic L-alanine or alaninium [CH3CH(NH3(+))COOH] at pH 1, the zwitterionic form [CH3CH(NH3(+))COO(-)] at pH 6, and anionic L-alanine or alaninate [CH3CH(NH2)COO(-)] at pH 13. New insight on the specific inter and intramolecular interactions in the different forms of L-alanine was reached by a novel methodological approach: an infrared technique not used before to analyze solid amino acid samples (DRIFTS), in combination with a detailed analysis based on spectral deconvolution. The frequency ranges of interest include the carbonyl/carboxyl stretching and amine deformation modes and the OH/NH stretching modes. It was shown that intermolecular hydrogen bonds between the NH3(+) and COO(-) groups are predominant in the zwitterionic form, whereas in cationic L-alanine, H bonds between the COOH groups are responsible for the formation of dimers. In anionic L-alanine, only strong electrostatic interactions between the COO(-) groups and Na(+) ions are proposed, evidencing the relevant role of the counterion.     

Long-time correlations and hydrophobe-modified hydrogen-bonding dynamics in hydrophobic hydration

The physical mechanisms behind hydrophobic hydration have been debated for over 65 years. Spectroscopic techniques have the ability to probe the dynamics of water in increasing detail, but many fundamental issues remain controversial. We have performed systematic first-principles ab initio Car-Parrinello molecular dynamics simulations over a broad temperature range and provide a detailed microscopic view on the dynamics of hydration water around a hydrophobic molecule, tetramethylurea. Our simulations provide a unifying view and resolve some of the controversies concerning femtosecond-infrared, THz-GHz dielectric relaxation, and nuclear magnetic resonance experiments and classical molecular dynamics simulations. Our computational results are in good quantitative agreement with experiments, and we provide a physical picture of the long-debated "iceberg" model; we show that the slow, long-time component is present within the hydration shell and that molecular jumps and over-coordination play important roles. We show that the structure and dynamics of hydration water around an organic molecule are non-uniform.     

Isotope labeling and theoretical study of the formation of a3* ions from protonated tetraglycine

Extensive 13C, 15N, and 2H labeling of tetraglycine was used to investigate the b3+ --> a3* reaction during low-energy collision-induced dissociation (CID) in a quadrupole ion-trap mass spectrometer. The patterns observed with respect to the retention or elimination of the isotope labels demonstrate that the reaction pathway involves elimination of CO and NH3. The ammonia molecule includes 2 H atoms from amide or amino positions, and one from an alpha-carbon position. The loss of NH3 does not involve elimination of the N-terminal amino group but, instead, the N atom of the presumed oxazolone ring in the b3+ ion. The CO molecule eliminated is the carbonyl group of the same oxazolone ring, and the alpha-carbon H atom is transferred from the amino acid adjacent to the oxazolone ring. Quantum chemical calculations indicate a multistep reaction cascade involving CO loss on the b3 --> a3 pathway and loss of NH=CH2 from the a3 ion to form b2. In the postreaction complex of b2 and NH=CH2, the latter can be attacked by the N-terminal amino group of the former. The product of this attack, an isomerized a3 ion, can eliminate NH3 from its N-terminus to form a3*. Calculations suggest that the ammonia and a3* species can form various ion-molecule complexes, and NH3 can initiate relay-type mobilization of the oxazolone H atoms from alpha-carbon positions to form a new oxazolone isomer. This multiple-step reaction scheme clearly explains the isotope labeling results, including unexpected scrambling of H atoms from alpha-carbon positions.     

Revisiting the structure and dynamics of hydrated Cd2+ in aqueous solutions: Insights from the RI-SCS-MP2/MM molecular dynamics simulation

The spin component scale MP2/molecular mechanics molecular dynamics simulation investigated the hydration shell formation and hydrated Cd²⁺ dynamics in the water environment. At the first hydration shell, six water molecules with 2.27 Å for the average distance between water and Cd²⁺. Dynamical properties were analyzed by computing the water molecule's mean residence time (MRT) in its first and second hydration shells. The MRT of each shell was determined to be 31.8 and 1.92 ps, suggesting the strong influence of Cd²⁺ in the first hydration shell. The second shell was labile, with an average number of water molecules being 18. Despite the strong interaction between Cd²⁺ and water molecules in the first shell, the influence of ions in the second hydration shell remained weak.     

Controlled self-assembly of filled micelles on nanotubes

We have used coarse-grained molecular dynamics simulations to show that hydrated lipid micelles of preferred sizes and amounts of filling with hydrophobic molecules can be self-assembled on the surfaces of carbon nanotubes. We simulated micelle formation on a hydrated (40,0) carbon nanotube with an open end that was covered with amphiphilic double-headed CH(3)(CH(2))(14)CH(((CH(2)OCH(2)CH(2))(2)(CH(2)COCH(2)))(2)H)(2) or single-headed CH(3)(CH(2))(14)CH(2)((CH(2)OCH(2)CH(2))(2)(CH(2)COCH(2)))(4)H lipids and filled with hexadecane molecules. Once the hexadecane molecules inside the nanotube were pressurized and the lipids on its surface were dragged by the water flowing around it, kinetically stable micelles filled with hexadecane molecules were sequentially formed at the nanotube tip. We investigated the stability of the thus-formed kinetically stable filled micelles and compared them with thermodynamically stable filled micelles that were self-assembled in the solution.     

Interactions of L-alanine with alumina as studied by vibrational spectroscopy

The interactions of L-alanine with gamma- and alpha-alumina have been investigated by diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS). L-alanine/alumina samples were dried from aqueous suspensions, at 36.5 degrees C, with two amino acid concentrations (0.4 and 0.8 mmol g-1) and at different pH values (1, 6, and 13). The vibrational spectra proved that the nature of L-alanine interactions with both aluminas is the same (hydrogen bonding), although the groups involved depend on the L-alanine form and on alumina surface groups, both controlled by the pH. For samples prepared at pH 1, cationic L-alanine [CH3CH(NH3+)COOH] displaces physisorbed water from alumina, and strong hydrogen bonds are established between the carbonyl groups of alanine, as electron donors, and the surface Al-OH2+ groups of alumina. This occurs at the expense of alanine dimer dissociation and breaking of intramolecular bonds. When samples are prepared at pH 6, the interacting groups are Al-OH2+ and the carboxylate groups of zwitterionic L-alanine [CH3CH(NH3+)COO-]. The affinity of L-alanine toward alumina decreases, as the strong NH3+...-OOC intermolecular hydrogen bonds prevail over the interactions with alumina. Thus, for a load of 0.8 mmol g-1, phase segregation is observed. On alpha-alumina, crystal deposition is even observed for a load of 0.4 mmol g-1. At pH 13, the carboxylate groups of anionic L-alanine [CH3CH(NH2)COO-] are not affected by alumina. Instead, hydrogen bond interactions occur between NH2 and the Al-OH surface groups of the substrate. Complementary N2 adsorption-desorption isotherms showed that adsorption of L-alanine occurs onto the alumina pore network for samples prepared at pH 1 and 13, whereas at pH 6 the amino acid/alumina interactions are not strong enough to promote adsorption. The mesoporous structure and the high specific surface area of gamma-alumina make it a more efficient substrate for adsorption of L-alanine. For each alumina, however, it is the nature of the specific interactions and not the porosity of the substrate that determines the adsorption process.     

Molecular modeling of interactions between L-lysine and functionalized quartz surfaces

Molecular modeling techniques have been used to investigate the interaction of L-lysine in aqueous medium with silanol and methyl sites onto quartz substrates. The substrate effect has been studied for partially hydrophilic surfaces formed by silanol and methyl groups with a ratio of 1:5 and hydrophobic fully methylated surfaces. Molecular dynamics and static calculations indicate that L-lysine does not show any significant interaction with fully methylated surfaces, while its interaction with hydroxylated/methylated surfaces is dominated by electrostatic and H-bond terms. Accordingly, on fully methylated surfaces there is no preferential orientation of L-lysine with respect to the surface, while for hydroxylated/methylated surfaces the L-lysine-surface interaction mainly depends on the molecular orientation, with a preferred geometry involving the ammonium group pointing toward the silanol site. The structure of water shells around L-lysine molecules was shown to be strongly affected by the relative hydrophilic/hydrophobic character of the surfaces. In particular, the order is almost completely lost for partially hydrophilic surfaces, while well-defined hydration shells around L-lysine are obtained for hydrophobic surfaces.     

Influence of concentration and temperature on the dynamics of water in the hydrophobic hydration shell of tetramethylurea

We study the influence of the amphipilic compound tetramethylurea (TMU) on the dynamical properties of water, using dielectric relaxation spectroscopy in the regime between 0.2 GHz and 2 THz. This technique is capable of resolving different water species, their relative fractions, and their corresponding reorientation dynamics. We find that the reorientation dynamics of water molecules in the hydration shell of the hydrophobic groups of TMU is between 3 (at low concentrations) and 10 (at higher concentrations) times slower than the dynamics of bulk water. The data indicate that the effect of hydrophobic groups on water is strong but relatively short-ranged. With increasing temperature, the fraction of water contained in the hydrophobic hydration shell decreases, which implies that the overall effect of hydrophobic groups on water becomes smaller.     

Molecular recognition in cyclodextrin complexes of amino acid derivatives. 2. A new perturbation: the room-temperature crystallographic structure determination for the N-acetyl-p-methoxy-L-phenylalanine methyl ester/beta-cyclodextrin complex

Cyclodextrins (CDs) are cyclic oligosaccharides that encapsulate various small organic molecules, forming inclusion complexes. Because CD complexes are held together purely by noncovalent interactions, they function as excellent models for the study of chiral and molecular recognition mechanisms. Recently, room-temperature crystallographic studies of both the 2:2 N-acetyl-L-phenylalanine methyl ester/beta-CD and 2:2 N-acetyl-L-phenylalanine amide/beta-CD complexes were reported. The effect of changes in carboxyl backbone functional group on molecular recognition by the host CD molecule was examined for the nearly isomorphous supramolecular complexes. A new perturbation of the system is now examined, specifically perturbation of the aromatic side chain. We report a room-temperature crystal structure determination for the 2:2 N-acetyl-p-methoxy-L-phenylalanine methyl ester/beta-CD inclusion complex. The complex crystallizes isomorphously with the two previously reported examples in space group P1; the asymmetric unit consists of a hydrated head-to-head host dimer with two included guest molecules. The crystal packing provides both a nonconstraining extended hydrophobic pocket and an adjacent hydrophilic region, where hydrogen-bonding interactions can potentially occur with primary hydroxyl groups of neighboring CD molecules and waters of hydration. The rigid host molecules show no sign of conformational disorder, and water of hydration molecules exhibit the same type of disorder observed for the other two complexes, with a few significant differences in locations of water molecules in the hydrophilic region near guest molecules. There is evidence for modest disorder in the guest region of an electron density map. In comparing this system with the two previously reported complexes of phenylalanine derivatives, it is found that the packing of the guest molecules inside the torus of the CD changes upon substitution of a methoxy group at the para position of the aromatic phenyl ring. Backbone hydrogen-bonding interactions for the guest molecules with the CD primary hydroxyls and waters also change. This structure determination is a new and revealing addition to a small but growing database of amino acid and peptidomimetic interactions with carbohydrates.     

Ion-molecule reactions of several ions with ethylene oxide and propenal in a selected ion flow tube

The selected ion flow tube (SIFT) technique has been used to investigate the ion-molecule reactions of several ions with the neutral molecules ethylene oxide, CH(2)OCH(2)-c, and propenal, CH(2)CHCHO. Both molecules have been identified in hot-core star forming regions [] and have significance to astrochemical models of the interstellar (ISM) and circumstellar medium (CSM). Moreover, the molecules contain functional groups, such as the epoxide group (ethylene oxide) and an aldehyde group, which are part of a conjugated pi-electron system (propenal) whose reactivities have not been studied in detail in gas-phase ion-molecule reactions. The larger recombination energy ions, Ar(+) and N(2)(+), were reacted with the neutrals to give insight into general fragmentation tendencies. These reactions proceeded via dissociative charge-transfer yielding major fragmentation products of CH(3)(+) and HCO(+) for ethylene oxide and CH(2)CH(+) and HCO(+) for propenal. The amino acids glycine and alanine are of particular interest to astrobiology, especially if they can be synthesized in the gas phase. In an attempt to synthesize amino acid precursors, ethylene oxide and propenal were reacted with NH(n)(+) (n = 1-4) and HCNH(+). As might be expected from the proton detachment energies, NH(+), NH(2)(+), and HCNH(+) reacted via proton transfer. NH(3)(+) reacted with each molecule via H-atom abstraction to produce NH(4)(+), and NH(4)(+) reacted via a ternary association. All binary reactions proceeded near the gas kinetic rate. Several associated molecule switching reactions were performed and implications of these reactions to the structures of the association products are discussed Ikeda et al. and Hollis et al.     

Molecular dynamics study of the solvation of calcium carbonate in water

We performed molecular dynamics simulations of diluted solutions of calcium carbonate in water. To this end, we combined and tested previous polarizable models. The carbonate anion forms long-living hydrogen bonds with water and shows an amphiphilic character, in which the water molecules are expelled in a region close to its C(3) symmetry axis. The calcium cation forms a strongly bound ion pair with the carbonate. The first hydration shell around the CaCO(3) pair is found to be very similar to the location of the water molecules surrounding CaCO(3) in ikaite, the hydrated mineral.     

Spatial hydration structures and dynamics of phenol in sub- and supercritical water

The hydration structures and dynamics of phenol in aqueous solution at infinite dilution are investigated using molecular-dynamics simulation technique. The simulations are performed at several temperatures along the coexistence curve of water up to the critical point, and above the critical point with density fixed at 0.3 g/cm3. The hydration structures of phenol are characterized using the radial, cylindrical, and spatial distribution functions. In particular, full spatial maps of local atomic (solvent) density around a solute molecule are presented. It is demonstrated that in addition to normal H bonds with hydroxyl group of phenol, water forms pi-type complexes with the center of the benzene ring, in which H2O molecules act as H-bond donor. At ambient conditions phenol is solvated by 38 water molecules, which make up a large hydrophobic cavity, and forms on average 2.39 H bonds (1.55 of which are due to the hydroxyl group-water interactions and 0.84 are due to the pi complex) with its hydration shell. As temperature increases, the hydration structure of phenol undergoes significant changes. The disappearance of the pi-type H bonding is observed near the critical point. Self-diffusion coefficients of water and phenol are also calculated. Dramatic increase in the diffusivity of phenol in aqueous solution is observed near the critical point of simple point-charge-extended water and is related to the changes in water structure at these conditions.     

One water molecule stabilizes the cationized arginine zwitterion

Singly hydrated clusters of lithiated arginine, sodiated arginine, and lithiated arginine methyl ester are investigated using infrared action spectroscopy and computational chemistry. Whereas unsolvated lithiated arginine is nonzwitterionic, these results provide compelling evidence that attachment of a single water molecule to this ion makes the zwitterionic form of arginine, in which the side chain is protonated, more stable. The experimental spectra of lithiated and sodiated arginine with one water molecule are very similar and contain spectral signatures for protonated side chains, whereas those of lithiated arginine and singly hydrated lithiated arginine methyl ester are different and contain spectral signatures for neutral side chains. Calculations at the B3LYP/6-31++G** level of theory indicate that solvating lithiated arginine with a single water molecule preferentially stabilizes the zwitterionic forms of this ion by 25-32 kJ/mol and two essentially isoenergetic zwitterionic structure are most stable. In these structures, the metal ion either coordinates with the N-terminal amino group and an oxygen atom of the carboxylate group (NO coordinated) or with both oxygen atoms of the carboxylate group (OO coordinated). In contrast, the OO-coordinated zwitterionic structure of sodiated arginine, both with and without a water molecule, is clearly lowest in energy for both ions. Hydration of the metal ion in these clusters weakens the interactions between the metal ion and the amino acid, whereas hydrogen-bond strengths are largely unaffected. Thus, hydration preferentially stabilizes the zwitterionic structures, all of which contain strong hydrogen bonds. Metal ion size strongly affects the relative propensity for these ions to form NO or OO coordinated structures and results in different zwitterionic structures for lithiated and sodiated arginine clusters containing one water molecule.     

On the structure and dynamics of the hydrated sulfite ion in aqueous solution--an ab initio QMCF MD simulation and large angle X-ray scattering study

Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism has been applied in conjunction to experimental large angle X-ray scattering to study the structure and dynamics of the hydrated sulfite ion in aqueous solution. The results show that there is a considerable effect of the lone electron-pair on sulfur concerning structure and dynamics in comparison with the sulfate ion with higher oxidation number and symmetry of the hydration shell. The S-O bond distance in the hydrated sulfite ion has been determined to 1.53(1) ? by both methods. The hydrogen bonds between the three water molecules bound to each sulfite oxygen are only slightly stronger than those in bulk water. The sulfite ion can therefore be regarded as a weak structure maker. The water exchange rate is somewhat slower for the sulfite ion than for the sulfate ion, τ(0.5) = 3.2 and 2.6 ps, respectively. An even more striking observation in the angular radial distribution (ARD) functions is that the for sulfite ion the water exchange takes place in close vicinity of the lone electron-pair directed at its sides, while in principle no water exchange did take place of the water molecules hydrogen bound to sulfite oxygens during the simulation time. This is also confirmed when detailed pathway analysis is conducted. The simulation showed that the water molecules hydrogen bound to the sulfite oxygens can move inside the hydration shell to the area outside the lone electron-pair and there be exchanged. On the other hand, for the hydrated sulfate ion in aqueous solution one can clearly see from the ARD that the distribution of exchange events is symmetrical around the entire hydration sphere.