Molecular dynamics simulation of cellobiose in water

The conformational behavior of cellobiose was studied by molecular dynamics simulation in a periodic box of waters. Several different initial conformations were used and the results compared with equivalent vacuum simulations. The average positions and rms fluctuations within single torsional conformations of cellobiose were affected only slightly by the solvent. However, water damped local torsional librations and transitions. The conformational energies of the solute and their fluctuations were also sensitive to the presence of solvent. Intramolecular hydrogen bonding was weakened relative to that observed in vacuo due to competition with solvating waters. All cellobiose hydroxyl groups participated in intermolecular hydrogen bonds with water, with approximately eight hydrogen bonds formed per glucose ring. The hydrogen bonding was predominantly between water hydrogens and solute hydroxyl oxygens. Intermolecular hydrogen bonding to ring and bridge oxygens was seldom present. The diffusion coefficients of both water and solute agree closely with experimental values. Water interchanged rapidly between the solvating first shell and the bulk on the picosecond time scale. © 1993 John Wiley & Sons, Inc.     

Cooperative effects at water-crystalline silica interfaces strengthen surface silanol hydrogen bonding. An ab initio molecular dynamics study

Silica and silica based materials are widely used in chemistry and materials science due to their importance in many technological fields. The properties of these materials, which are crucial for their applications, are mainly determined by the presence of hydrogen bonding between surface silanols. Here, we present ab initio molecular dynamics simulations (AIMD) on different surfaces derived from the crystallographic α-quartz (100) and the α-cristobalite (001) and (101) faces, both free and at the interface with liquid water. The focus was on studying whether water adsorption can disrupt the H-bond pattern at the pristine free silica surface and how deep the perturbation due to the contact with the surface affects the structure of the water multilayer. Results highlight that the water phase is over structured at the interface with silica, as compared to water bulk. Furthermore, an apparent counterintuitive behavior has been observed for quartz (100) and cristobalite (001) surfaces: the interaction with water does not cleave the pre-existent H-bonds between the surface silanol groups. On the contrary, in several cases, it is observed that SiOH···OHSi H-bonds are even strengthened, as the result of a mutual cooperative H-donor/H-acceptor enhancement between silanols and water molecules, which may alter the adsorption capability of these silica surfaces.     

Interaction of ester functional groups with aluminum oxide surfaces studied using infrared reflection absorption spectroscopy

The bonding of two types of ester group-containing molecules with a set of different oxide layers on aluminum has been investigated using infrared reflection absorption spectroscopy. The different oxide layers were made by giving typical surface treatments to the aluminum substrate. The purpose of the investigation was to find out what type of ester-oxide bond is formed and whether this is influenced by changes in the composition and chemistry of the oxide. The extent by which these bonded ester molecules resisted disbondment in water or substitution by molecules capable of chemisorption was also investigated. The ester groups were found to show hydrogen bonding with hydroxyls on the oxide surfaces through their carbonyl oxygens. For all oxides, the ester groups showed the same nu(C = O) carbonyl stretching vibration after adsorption, indicating very similar bonding occurs. However, the oxides showed differences in the amount of molecules bonded to the oxide surface, and a clear relation was observed with the hydroxyl concentration present on the oxide surface, which was determined from XPS measurements. The two compounds showed differences in the free to bonded nu(C = O) infrared peak shift, indicating differences in bonding strength with the oxide surface between the two types of molecules. The bonding of the ester groups with the oxide surfaces was found to be not stable in the presence of water and also not in the presence of a compound capable of chemisorption with the aluminum oxide surface.     

Room temperature water splitting at the surface of magnetite

An array of surface science measurements has revealed novel water adsorption behavior at the Fe(3)O(4)(001) surface. Following room temperature exposure to water, a low coverage of hydrogen atoms is observed, with no associated water hydroxyl group. Mild annealing of the hydrogenated surface leads to desorption of water via abstraction of surface oxygen atoms, leading to a reduction of the surface. These results point to an irreversible splitting of the water molecule. The observed phenomena are discussed in the context of recent DFT calculations (Mulakaluri, N.; Pentcheva, R.; Scheffler, M. J. Phys. Chem. C 2010, 114, 11148), which show that the Jahn-Teller distorted surface isolates adsorbed H in a geometry that could kinetically hinder recombinative desorption. In contrast, the adsorption geometry facilitates interaction between water hydroxyl species, which are concluded to leave the surface following a reactive desorption process, possibly via the creation of O(2).     

Spectroscopic evidence for the partial dissociation of H2O on ZnO(1010)

The interaction of water with the non-polar ZnO(1010) surface has been studied by high resolution electron energy loss spectroscopy (HREELS) and thermal desorption spectroscopy (TDS). Adsorption of water at room temperature leads to the partial dissociation of water molecules giving rise to a well defined (2x1) superstructure. This observation was confirmed by the HREELS data which show the water-induced O-H stretching modes at 396 and 460 meV (3193 and 3709 cm-1) as well as the peak at 456 meV (3677 cm-1) arising from the OH species. The large red shift of the loss at 396 meV indicates unusually strong hydrogen bonding interactions of water to both neighbouring adsorbate molecules and the surface O atoms which are responsible for the partial dissociation of water molecules on the perfect ZnO(1010) surface.     

Surface protonation at the rutile (110) interface: explicit incorporation of solvation structure within the refined MUSIC model framework

The detailed solvation structure at the (110) surface of rutile (alpha-TiO2) in contact with bulk liquid water has been obtained primarily from experimentally verified classical molecular dynamics (CMD) simulations of the ab initio-optimized surface in contact with SPC/E water. The results are used to explicitly quantify H-bonding interactions, which are then used within the refined MUSIC model framework to predict surface oxygen protonation constants. Quantum mechanical molecular dynamics (QMD) simulations in the presence of freely dissociable water molecules produced H-bond distributions around deprotonated surface oxygens very similar to those obtained by CMD with nondissociable SPC/E water, thereby confirming that the less computationally intensive CMD simulations provide accurate H-bond information. Utilizing this H-bond information within the refined MUSIC model, along with manually adjusted Ti-O surface bond lengths that are nonetheless within 0.05 A of those obtained from static density functional theory (DFT) calculations and measured in X-ray reflectivity experiments (as well as bulk crystal values), give surface protonation constants that result in a calculated zero net proton charge pH value (pHznpc) at 25 degrees C that agrees quantitatively with the experimentally determined value (5.4+/-0.2) for a specific rutile powder dominated by the (110) crystal face. Moreover, the predicted pHznpc values agree to within 0.1 pH unit with those measured at all temperatures between 10 and 250 degrees C. A slightly smaller manual adjustment of the DFT-derived Ti-O surface bond lengths was sufficient to bring the predicted pHznpcvalue of the rutile (110) surface at 25 degrees C into quantitative agreement with the experimental value (4.8+/-0.3) obtained from a polished and annealed rutile (110) single crystal surface in contact with dilute sodium nitrate solutions using second harmonic generation (SHG) intensity measurements as a function of ionic strength. Additionally, the H-bond interactions between protolyzable surface oxygen groups and water were found to be stronger than those between bulk water molecules at all temperatures investigated in our CMD simulations (25, 150 and 250 degrees C). Comparison with the protonation scheme previously determined for the (110) surface of isostructural cassiterite (alpha-SnO2) reveals that the greater extent of H-bonding on the latter surface, and in particular between water and the terminal hydroxyl group (Sn-OH) results in the predicted protonation constant for that group being lower than for the bridged oxygen (Sn-O-Sn), while the reverse is true for the rutile (110) surface. These results demonstrate the importance of H-bond structure in dictating surface protonation behavior, and that explicit use of this solvation structure within the refined MUSIC model framework results in predicted surface protonation constants that are also consistent with a variety of other experimental and computational data.     

On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations

We have implemented the accelerated molecular dynamics approach (Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. 2004, 120 (24), 11919) in the framework of ab initio MD (AIMD). Using three simple examples, we demonstrate that accelerated AIMD (A-AIMD) can be used to accelerate solvent relaxation in AIMD simulations and facilitate the detection of reaction coordinates: (i) We show, for one cyclohexane molecule in the gas phase, that the method can be used to accelerate the rate of the chair-to-chair interconversion by a factor of ～1 × 10(5), while allowing for the reconstruction of the correct canonical distribution of low-energy states; (ii) We then show, for a water box of 64 H(2)O molecules, that A-AIMD can also be used in the condensed phase to accelerate the sampling of water conformations, without affecting the structural properties of the solvent; and (iii) The method is then used to compute the potential of mean force (PMF) for the dissociation of Na-Cl in water, accelerating the convergence by a factor of ～3-4 compared to conventional AIMD simulations.(2) These results suggest that A-AIMD is a useful addition to existing methods for enhanced conformational and phase-space sampling in solution. While the method does not make the use of collective variables superfluous, it also does not require the user to define a set of collective variables that can capture all the low-energy minima on the potential energy surface. This property may prove very useful when dealing with highly complex multidimensional systems that require a quantum mechanical treatment.     

On the hydration of the phosphocholine headgroup in aqueous solution

The hydration of the phosphocholine headgroup in 1,2-dipropionyl-sn-glycero-3-phosphocholine (C(3)-PC) in solution has been determined by using neutron diffraction enhanced with isotopic substitution in combination with computer simulation techniques. The atomic scale hydration structure around this head group shows that both the -N(CH(3))(3) and -CH(2) portions of the choline headgroup are strongly associated with water, through a unique hydrogen bonding regime, where specifically a hydrogen bond from the C-H group to water and a strong association between the water oxygen and N(+) atom in solution have both been observed. In addition, both PO(4) oxygens (P=O) and C=O oxygens are oversaturated when compared to bulk water in that the average number of hydrogen bonds from water to both X=O oxygens is about 2.5 for each group. That water binds strongly to the glycerol groups and is suggestive that water may bind to these groups when phosophotidylcholine is embedded in a membrane bilayer.     

Adsorption of atomic hydrogen on ZnO(1010): STM study

The adsorption of atomic hydrogen on a single crystal ZnO(1010) surface has been studied by scanning tunneling microscopy (STM) under ultrahigh vacuum conditions at room temperature and at elevated temperatures. High resolution STM images indicate that a well-ordered (1x1) H adlayer is formed on the ZnO(1010) surface. The STM data strongly indicate that the hydrogen adsorbs on top of the oxygen atoms forming hydroxyl species. Scanning tunneling spectroscopy (STS) studies reveal a H atom induced metallization at room temperature. In contrast to the clean surface for the hydrogen-covered surface distinct defects structures consisting of missing O and Zn atoms could be identified.     

Effect of intermolecular hydrogen bonding on low-surface-energy material of poly(vinylphenol)

We discovered that poly(vinylphenol) (PVPh) possesses an extremely low surface energy (15.7 mJ/m2) after a simple thermal treatment procedure, even lower than that of poly(tetrafluoroethylene) (22.0 mJ/m2) calculated on the basis of the two-liquid geometric method. Infrared analyses indicate that the intermolecular hydrogen bonding of PVPh decreases by converting the hydroxyl group into a free hydroxyl and increasing intramolecular hydrogen bonding after thermal treatment. PVPh results in a lower surface energy because of the decrease of intermolecular hydrogen bonding between hydroxyl groups. In addition, we also compared surface energies of PVPh-co-PS (polystyrene) copolymers (random and block) and their corresponding blends. Again, these random copolymers possess a lower fraction of intermolecular hydrogen bonding and surface energy than the corresponding block copolymers or blends after similar thermal treatment. This finding provides a unique and easy method to prepare a low-surface-energy material through a simple thermal treatment procedure without using fluoro polymers or silicones.     

Combined Monte Carlo and molecular dynamics simulation of hydrated 18:0 sphingomyelin-cholesterol lipid bilayers

We have carried out atomic level molecular dynamics and Monte Carlo simulations of hydrated 18:0 sphingomyelin (SM)-cholesterol (CHOL) bilayers at temperatures of 20 and 50 degrees C. The simulated systems each contained 266 SM, 122 CHOL, and 11861 water molecules. Each simulation was run for 10 ns under semi-isotropic pressure boundary conditions. The particle-mesh Ewald method was used for long-range electrostatic interactions. Properties of the systems were calculated over the final 3 ns. We compare the properties of 20 and 50 degrees C bilayer systems with each other, with experimental data, and with experimental and simulated properties of pure SM bilayers and dipalmitoyl phospatidyl choline (DPPC)-CHOL bilayers. The simulations reveal an overall similarity of both systems, despite the 30 degrees C temperature difference which brackets the pure SM main phase transition. The area per molecule, lipid chain order parameter profiles, atom distributions, and electron density profiles are all very similar for the two simulated systems. Consistent with simulations from our lab and others, we find strong intramolecular hydrogen bonding in SM molecules between the phosphate ester oxygen and the hydroxyl hydrogen atoms. We also find that cholesterol hydroxyl groups tend to form hydrogen bonds primarily with SM carbonyl, methyl, and amide moieties and to a lesser extent methyl and hydroxyl oxygens.     

Ab initio molecular dynamics with discrete variable representation basis sets: techniques and application to liquid water

Finite temperature ab initio molecular dynamics (AIMD), in which forces are obtained from "on-the-fly" electronic structure calculations, is a widely used technique for studying structural and dynamical properties of chemically active systems. Recently, we introduced an AIMD scheme based on discrete variable representation (DVR) basis sets, which was shown to have improved convergence properties over the conventional plane wave (PW) basis set [Liu,Y.; et al. Phys. Rev. B 2003, 68, 125110]. In the present work, the numerical algorithms for the DVR based AIMD scheme (DVR/AIMD) are provided in detail, and the latest developments of the approach are presented. The accuracy and stability of the current implementation of the DVR/AIMD scheme are tested by performing a simulation of liquid water at ambient conditions. The structural information obtained from the present work is in good agreement with the result of recent AIMD simulations with a PW basis set (PW/AIMD). Advantages of using the DVR/AIMD scheme over the PW/AIMD method are discussed. In particular, it is shown that a DVR/AIMD simulation of liquid water in the complete basis set limit is possible with a relatively small number of grid points.     

Hydration shell structure and dynamics of curium(III) in aqueous solution: first principles and empirical studies

Results of ab initio molecular dynamics (AIMD), quantum mechanics/molecular mechanics (QM/MM), and classical molecular dynamics (CMD) simulations of Cm(3+) in liquid water at a temperature of 300 K are reported. The AIMD simulation was based on the Car-Parrinello MD scheme and GGA-PBE formulation of density functional theory. Two QM/MM simulations were performed by treating Cm(3+) and the water molecules in the first shell quantum mechanically using the PBE (QM/MM-PBE) and the hybrid PBE0 density functionals (QM/MM-PBE0). Two CMD simulations were carried out using ab initio derived pair plus three-body potentials (CMD-3B) and empirical Lennard-Jones pair potential (CMD-LJ). The AIMD and QM/MM-PBE simulations predict average first shell hydration numbers of 8, both of which disagree with recent experimental EXAFS and TRLFS value of 9. On the other hand, the average first shell hydration numbers obtained in the QM/MM-PBE0 and CMD simulations was 9, which agrees with experiment. All the simulations predicted an average first shell and second shell Cm-O bond distance of 2.49-2.53 ? and 4.67-4.75 ? respectively, both of which are in fair agreement with corresponding experimental values of 2.45-2.48 and 4.65 ?. The geometric arrangement of the 8-fold and 9-fold coordinated first shell structures corresponded to the square antiprism and tricapped trigonal prisms, respectively. The second shell hydration number for AIMD QM/MM-PBE, QM/MM-PBE0, CMD-3B, and CMD-LJ, were 15.8, 17.2, 17.7, 17.4, and 16.4 respectively, which indicates second hydration shell overcoordination compared to a recent EXAFS experimental value of 13. Save the EXAFS spectra CMD-LJ simulation, all the computed EXAFS spectra agree fairly well with experiment and a clear distinction could not be made between configurations with 8-fold and 9-fold coordinated first shells. The mechanisms responsible for the first shell associative and dissociative ligand exchange in the classical simulations have been analyzed. The first shell mean residence time was predicted to be on the nanosecond time scale. The computed diffusion constants of Cm(3+) and water are in good agreement with experimental data.     

Fractional surface termination of diamond by electrochemical oxidation

The crystalline form of sp(3)-hybridized carbon, diamond, offers various electrolyte-stable surface terminations. The H-termination-selective attachment of nitrophenyl diazonium, imaged by AFM, shows that electrochemical oxidation can control the fractional hydrogen/oxygen surface termination of diamond on the nanometer scale. This is of particular interest for all applications relying on interfacial electrochemistry, especially for biointerfaces.     

Surface structure of (10(-)10) and (11(-)20) surfaces of ZnO with density functional theory and atomistic simulation

We have calculated the stability of two of the low-index surfaces known to dominate the morphology of ZnO as a function of stoichiometry. These two surfaces are (10(-)10) and (11(-)20). In each case, two terminations only are stable for a significant range of oxygen and hydrogen chemical potential: the pure stoichiometric surface and a surface covered in a monolayer of water. The mode by which the water adsorbs is however different for the two surfaces considered. On the (10(-)10) surface the close proximity of the water molecules means hydrogen bonding can occur between adjacent chemiabsorbed water molecules and hence there is little difference in the stability of the hydrated and hydroxylated surface, and in fact the most stable surface occurs with a combination of dissociated and undissociated water adsorption. In the case of the (11(-)20) surface, it is only when full dissociation has occurred that a hydrogen-bonding network can form. Our results also show good agreement between DFT and atomistic simulations, suggesting that potential based methods can usefully be applied to ZnO.     

Hydrogen bonding interactions between ethylene glycol and water: density,excess molar volume,and spectral study

Studies of the density and the excess molar volume of ethylene glycol (EG)-water mixtures were carried out to illustrate the hydrogen bonding interactions of EG with water at different temperatures. The re-sults suggest that a likely complex of 3 ethylene glycol molecules bonding with 4 water molecules in an ethylene glycol-water mixture (EGW) is formed at the maximal excess molar volume,which displays stronger absorption capabilities for SO2 when the concentration of SO2 reaches 400×10?6 (volume ratio) in the gas phase. Meanwhile,FTIR and UV spectra of EGWs were recorded at various EG concentra-tions to display the hydrogen bonding interactions of EG with water. The FTIR spectra show that the stretching vibrational band of hydroxyl in the EGWs shifts to a lower frequency and the bending vibra-tional band of water shifts to a higher frequency with increasing the EG concentration,respectively. Furthermore,the UV spectra show that the electron transferring band of the hydroxyl oxygen in EG shows red shift with increasing the EG concentration. The frequency shifts in FTIR spectra and the shifts of absorption bands in UV absorption spectra of EGWs are interpreted as the strong hydrogen bonding interactions of the hydrogen atoms in water with the hydroxyl oxygen atoms of EG.     

Theoretical insights into the effect of surface structure and anion ordering on the properties of SrTaO2N for photocatalytic water splitting

As one of the representative perovskite-type oxynitride photocatalysts, SrTaO₂N has the ability to split water in the visible-light region. It was found that the surface modification and interfacial design of SrTaO₂N-based materials are closely related to the photocatalytic activity, but the microscopic mechanisms of these experimental phenomena are not well understood. In this work, we have utilized density functional theory (DFT) calculations to investigate the effect of anion ordering and exposed terminations on the electronic structures, optical absorption, water adsorption and the mechanisms of water oxidation and reduction reactions of SrTaO₂N. Our results indicate that cis configurations are more stable than trans configurations. The anion ordering has an important effect on the band gap and optical absorption coefficient. The terminations with exposed Ta atoms are more stable and have bigger work functions than those with exposed Sr atoms possibly due to the bonding ionicity and surface dipoles. The dissociative adsorption of water is energetically more favorable than the molecular adsorption on most surfaces. The highly active sites of hydrogen evolution reaction (HER) are the exposed nonmetal atoms. Terminations with exposed Sr and N atoms have lower overpotentials (0.70–0.77 V) of oxygen evolution reaction (OER) than others. They are comparable to the calculated results of common photocatalysts, such as Co₃O₄ and TiO₂. This study sheds light on the relationship between the termination structure with different anion orders and the photocatalysis-related properties of SrTaO₂N at a molecular level, which provides guidance for constructing highly active photocatalytic materials.     

Ab initio QM/MM molecular dynamics study on the excited-state hydrogen transfer of 7-azaindole in water solution

Ab initio molecular dynamics (AIMD) simulations for the excited-state hydrogen transfer (ESHT) reaction of 7-azaindole (7AI-(H2O)n; n = 1, 2) clusters in the gas phase and in water are presented. The effective fragment potential (EFP) is employed to model the surrounding water molecules. The AIMD simulations for 7AI-H2O and 7AI-(H2O)2 clusters show an asynchronous hydrogen transfer at t approximately 50 fs after the photoexcitation. While the ESHT mechanism for 7AI-H2O in water does not change appreciably compared with that in the gas phase, the AIMD simulations on 7AI-(H2O)2 in water solution exhibit two different mechanisms. Since the tautomer form is lower in energy compared to the normal form in the S1 state, 7AI and (H2O) n fragments separate from each other after the ESHT. With the use of the results of the AIMD trajectories, the minimum energy conical intersection point in the tautomer region has also been located.     

Comparison of polyethylene glycol adsorption to nanocellulose versus fumed silica in water

The recent intensification of industrially produced cellulose nanocrystals (CNCs) and cellulose nanofibrils has positioned nanocelluloses as promising materials for many water-based products and applications. However, for nanocelluloses to move beyond solely an academic interest, a thorough understanding of their interaction with water-soluble polymers is needed. In this work, we address a conflicting trend in literature that suggests polyethylene glycol (PEG) adsorbs to CNC surfaces by comparing the adsorption behaviour of PEG with CNCs versus fumed silica. While PEG is known to have strong hydrogen bonding tendencies and holds water tightly, it is sometimes (we believe erroneously) presumed that PEG binds to cellulose through hydrogen bonding in aqueous media. To test this assumption, the adsorption of PEG to CNCs and fumed silica (both in the form of particle films and in aqueous dispersions) was examined using quartz crystal microbalance with dissipation, isothermal titration calorimetry, rheology and dynamic light scattering. For all PEG molecular weights (300–10,000 g/mol) and concentrations (100–10,000 ppm) tested, strong rapid adsorption was found with fumed silica, whereas no adsorption to CNCs was observed. We conclude that unlike silanols, the hydroxyl groups on the surface of CNCs do not readily hydrogen bond with the ether oxygen in the PEG backbone. As such, this work along with previous papermaking literature supports the opinion that PEG does not adsorb to cellulose surfaces.