Peptide/TiO2 surface interaction: a theoretical and experimental study on the structure of adsorbed ALA-GLU and ALA-LYS

The adsorption on the TiO(2) surface of two dipeptides AE (L-alanine-L-glutamic acid) and AK (L-alanine-L-lysine), that are "building blocks" of the more complex oligopeptide EAK16, has been investigated both theoretically and experimentally. Classical molecular dynamics simulations have been used to study the adsorption of H-Ala-Glu-NH(2) and H-Ala-Lys-NH(2) dipeptides onto a rutile TiO(2) (110) surface in water solution. Several peptide conformers have been considered simultaneously upon the surface. The most probable contact points between the molecules and the surface have been identified. Carbonyl oxygens as well as nitrogen atoms are possible Ti coordination points. Local effects are responsible for adsorption and desorption events. Self-interaction effects can induce molecular reorientations giving less strongly adsorbed species. The chemical structure and composition of thin films of the two dipeptides AE and AK on TiO(2) were investigated by XPS (X-ray photoelectron spectroscopy) measurements at both O and N K-edges. Theoretical ab initio calculations (DeltaSCF) were also performed to simulate the spectra, allowing for a direct comparison between experiment and theory.     

Multilayer adsorption of water at a rutile TiO2)(110) surface: towards a realistic modeling by molecular dynamics

We present a model combining ab initio concepts and molecular dynamics simulations for a more realistic treatment of complex adsorption processes. The energy, distance, and orientation of water molecules adsorbed on stoichiometric and reduced rutile TiO(2)(110) surfaces at 140 K are studied via constant temperature molecular dynamics simulations. From ab initio calculations relaxed atomic geometries for the surface and the most probable adsorption sites were derived. The study comprises (i) large two-dimensional surface supercells, providing a realistically low concentration of surface oxygen defects, and (ii) a water coverage sufficiently large to model the onset of the growth of a bulk phase of water on the surface. By our combined approach the influence of both, the metal oxide surface, below, and the bulk water phase, above, on the water molecules forming the interface between the TiO(2) surface and the water bulk layer is taken into account. The good agreement of calculated adsorption energies with experimental temperature programmed desorption spectra demonstrates the validity of our model.     

Adsorption, diffusion and desorption of chlorine on and from rutile TiO2{110}: a theoretical investigation.

The adsorption, diffusion and desorption of chlorine on and from stoichiometric, reduced and partially reduced (defective) rutile TiO2{110} are investigated using ab initio density functional theory (DFT) calculations. Theoretical results are compared with experimental investigations, and microkinetic simulations based on DFT values are then used to verify the diffusion mechanisms assumed in the experimental investigations.     

Interaction of organic molecules with the TiO2 (110) surface: ab inito calculations and classical force fields

We have studied the adsorption of a number of organic molecules consisting of methyl, benzyl, and carboxylic groups on the rutile TiO2 (110) surface using both ab initio and atomistic simulation techniques. We have tested the applicability of a simple embedded cluster model to studying the adsorption of small organic molecules on the perfect rutile TiO2 (110) surface, and used this model to develop a classical force field for the interactions of a wide class of organic molecules consisting of these groups with the rutile TiO2 (110) surface. The force field accounts for physisorption and ionic bonding of organic molecules at the surface. It allows the reproduction of adsorption energies and of geometries of organic molecules on the rutile surface. It should be useful for studying diffusion of these molecules and their manipulation with use of AFM and STM tips.     

Ion adsorption at the rutile-water interface: linking molecular and macroscopic properties

A comprehensive picture of the interface between aqueous solutions and the (110) surface of rutile (alpha-TiO2) is being developed by combining molecular-scale and macroscopic approaches, including experimental measurements, quantum calculations, molecular simulations, and Gouy-Chapman-Stern models. In situ X-ray reflectivity and X-ray standing-wave measurements are used to define the atomic arrangement of adsorbed ions, the coordination of interfacial water molecules, and substrate surface termination and structure. Ab initio calculations and molecular dynamics simulations, validated through direct comparison with the X-ray results, are used to predict ion distributions not measured experimentally. Potentiometric titration and ion adsorption results for rutile powders having predominant (110) surface expression provide macroscopic constraints of electrical double layer (EDL) properties (e.g., proton release) which are evaluated by comparison with a three-layer EDL model including surface oxygen proton affinities calculated using ab initio bond lengths and partial charges. These results allow a direct correlation of the three-dimensional, crystallographically controlled arrangements of various species (H2O, Na+, Rb+, Ca2+, Sr2+, Zn2+, Y3+, Nd3+) with macroscopic observables (H+ release, metal uptake, zeta potential) and thermodynamic/electrostatic constraints. All cations are found to be adsorbed as "inner sphere" species bonded directly to surface oxygen atoms, while the specific binding geometries and reaction stoichiometries are dependent on ionic radius. Ternary surface complexes of sorbed cations with electrolyte anions are not observed. Finally, surface oxygen proton affinities computed using the MUSIC model are improved by incorporation of ab initio bond lengths and hydrogen bonding information derived from MD simulations. This multitechnique and multiscale approach demonstrates the compatibility of bond-valence models of surface oxygen proton affinities and Stern-based models of the EDL structure, with the actual molecular interfacial distributions observed experimentally, revealing new insight into EDL properties including specific binding sites and hydration states of sorbed ions, interfacial solvent properties (structure, diffusivity, dielectric constant), surface protonation and hydrolysis, and the effect of solution ionic strength.     

O2 interaction and reactivity on a model hydroxylated rutile(110) surface

Recently several theoretical studies have examined oxygen adsorption on the clean, reduced TiO2(110) surface. However the photocatalytic behavior of TiO2 and the scavenging ability of oxygen are known to be influenced by the presence of surface hydroxyls. In this paper the chemistry of O2 on the hydroxylated TiO2 surface is investigated by means of first-principles total energy calculations and molecular dynamics (MD) simulations. The MD trajectories show a direct, spontaneous reaction between O2 and the surface hydroxyls, thus supporting the experimental hypothesis that the reaction does not necessarily pass through a chemisorbed O2 state. Following this reaction, the most stable chemisorbed intermediates are found to be peroxide species HO2 and H2O2. Although these intermediates are very stable on the short time scale of MD simulations, the energetics suggests that their further transformation is connected to a new 300 K feature observed in the experimental water temperature programmed desorption (TPD) spectrum. The participation of two less stable intermediate states, involving terminal hydroxyls and/or chemisorbed water plus oxygen adatoms, to the desorption process, is not supported by the total energy calculations. Analysis of the projected density of states, however, suggests the possibility that these intermediates have a role in completing the surface oxidation immediately before desorption.     

Potential-energy and free-energy surfaces of glycyl-phenylalanyl-alanine (GFA) tripeptide: experiment and theory

The free-energy surface (FES) of glycyl-phenylalanyl-alanine (GFA) tripeptide was explored by molecular dynamics (MD) simulations in combination with high-level correlated ab initio quantum chemical calculations and metadynamics. Both the MD and metadynamics employed the tight-binding DFT-D method instead of the AMBER force field, which yielded inaccurate results. We classified the minima localised in the FESs as follows: a) the backbone-conformational arrangement; and b) the existence of a COOH...OC intramolecular H-bond (families CO(2)H(free) and CO(2)H(bonded)). Comparison with experimental results showed that the most stable minima in the FES correspond to the experimentally observed structures. Remarkably, however, we did not observe experimentally the CO(2)H(bonded) family (also predicted by metadynamics), although its stability is comparable to that of the CO(2)H(free) structures. This fact was explained by the former's short excited-state lifetime. We also carried out ab initio calculations using DFT-D and the M06-2X functional. The importance of the dispersion energy in stabilising peptide conformers is well reflected by our pioneer analysis using the DFT-SAPT method to explore the nature of the backbone/side-chain interactions.     

Structure, energetics, and dynamics of water adsorbed on the muscovite (001) surface: a molecular dynamics simulation

Molecular dynamics (MD) computer simulations of liquid water adsorbed on the muscovite (001) surface provide a greatly increased, atomistically detailed understanding of surface-related effects on the spatial variation in the structural and orientational ordering, hydrogen bond (H-bond) organization, and local density of H2O molecules at this important model phyllosilicate surface. MD simulations at constant temperature and volume (statistical NVT ensemble) were performed for a series of model systems consisting of a two-layer muscovite slab (representing 8 crystallographic surface unit cells of the substrate) and 0 to 319 adsorbed H2O molecules, probing the atomistic structure and dynamics of surface aqueous films up to 3 nm in thickness. The results do not demonstrate a completely liquid-like behavior, as otherwise suggested from the interpretation of X-ray reflectivity measurements and earlier Monte Carlo simulations. Instead, a more structurally and orientationally restricted behavior of surface H2O molecules is observed, and this structural ordering extends to larger distances from the surface than previously expected. Even at the largest surface water coverage studied, over 20% of H2O molecules are associated with specific adsorption sites, and another 50% maintain strongly preferred orientations relative to the surface. This partially ordered structure is also different from the well-ordered 2-dimensional ice-like structure predicted by ab initio MD simulations for a system with a complete monolayer water coverage. However, consistent with these ab initio results, our simulations do predict that a full molecular monolayer surface water coverage represents a relatively stable surface structure in terms of the lowest diffusional mobility of H2O molecules along the surface. Calculated energies of water adsorption are in good agreement with available experimental data.     

Molecular dynamics simulations of the adsorption of bone morphogenetic protein-2 on surfaces with medical relevance

Bone morphogenetic protein-2 (BMP-2) plays a crucial role in osteoblast differentiation and proliferation. Its effective therapeutic use for ectopic bone and cartilage regeneration depends, among other factors, on the interaction with the carrier at the implant site. In this study, we used classical molecular dynamics (MD) and a hybrid approach of steered molecular dynamics (SMD) combined with MD simulations to investigate the initial stages of the adsorption of BMP-2 when approaching two implant surfaces, hydrophobic graphite and hydrophilic titanium dioxide rutile. Surface adsorption was evaluated for six different orientations of the protein, two end-on and four side-on, in explicit water environment. On graphite, we observed a weak but stable adsorption. Depending on the initial orientation, hydrophobic patches as well as flexible loops of the protein were involved in the interaction with graphite. On the contrary, BMP-2 adsorbed only loosely to hydrophilic titanium dioxide. Despite a favorable interaction energy between protein and the TiO(2) surface, the rapid formation of a two-layer water structure prevented the direct interaction between protein and titanium dioxide. The first water adlayer had a strong repulsive effect on the protein, while the second attracted the protein toward the surface. For both surfaces, hydrophobic graphite and hydrophilic titanium dioxide, denaturation of BMP-2 induced by adsorption was not observed on the nanosecond time scale.     

Preferred conformation of the glycosidic linkage of methyl-beta-mannose

The conformational preference of the glycosidic linkage of methyl-beta-mannose was studied in the gas phase and in aqueous solution by ab initio calculations, and by molecular dynamics (MD) and Car-Parrinello molecular dynamics (CPMD) simulations. MD simulations were performed with various water potential functions to study the impact of the chosen water potential on the predicted conformational preference of the glycosidic linkage of the carbohydrate in solution. This study shows that the trans (t) orientation of the glycosidic linkage of methyl-beta-mannose is preferred over its gauche clockwise (g+) orientation in solution. CPMD simulations clearly indicate that this preference is due to intermolecular hydrogen bonding with surrounding water molecules, whereas no such information could be demonstrated by MD simulations. This study demonstrates the importance of ab initio molecular dynamics simulations in studying the structural properties of carbohydrate-water interactions.     

Modeling water exchange on an aluminum polyoxocation

For the first time, water exchange on a polymeric complex has been modeled using a combination of gas-phase ab initio calculations and molecular dynamics (MD) simulations. The GaO4Al12(OH)24(H2O)12(7+)aq ion (GaAl12) was chosen because high-quality experimental data exist, including an activation enthalpy (+63 +/- 7 kJ/mol) and an activation volume (+3 +/- 1 cm3/mol). We took a two-step approach. First, the local solvent structure and the initial states for reaction were inferred from the molecular dynamics simulations. Second, we used this information to evaluate initial-state structures in the ab initio calculations. The energy differences between the initial and transition states from the ab initio calculations varied from +59 kJ/mol to +53 kJ/mol depending upon details, closely approximating the activation enthalpy.     

Adsorption of 2-chloropyridine on oxides--an infrared spectroscopic study

The adsorption of 2-chloropyridine on SiO(2), TiO(2), ZrO(2), SiO(2)-Al(2)O(3) and H-mordenite has been studied by IR spectroscopy. The different modes of interaction with oxide surfaces, i.e. hydrogen-bonding and adsorption at Br?nsted or Lewis acid sites, was modelled by ab initio calculations at the B3LYP/DZ+(d) level. Adsorption on SiO(2) results in hydrogen bonding to surface hydroxyl groups, whereas the spectra obtained following adsorption on TiO(2) and ZrO(2) display evidence for electron transfer at Lewis acidic surface sites. Protonation of 2-chloropyridine at Br?nsted acidic sites was detected only for adsorption on SiO(2)-Al(2)O(3) and H-mordenite, indicating the presence of Br?nsted acidic sites on these oxide surfaces with pK(a) values 相似文献   

First principles and classical molecular dynamics simulations of solvated benzene

We have performed extensive ab initio and classical molecular dynamics (MD) simulations of benzene in water in order to examine the unique solvation structures that are formed. Qualitative differences between classical and ab initio MD simulations are found and the importance of various technical simulation parameters is examined. Our comparison indicates that nonpolarizable classical models are not capable of describing the solute-water interface correctly if local interactions become energetically comparable to water hydrogen bonds. In addition, a comparison is made between a rigid water model and fully flexible water within ab initio MD simulations which shows that both models agree qualitatively for this challenging system.     

Like-charge guanidinium pairing from molecular dynamics and ab initio calculations

Pairing of guanidinium moieties in water is explored by molecular dynamics simulations of short arginine-rich peptides and ab initio calculations of a pair of guanidinium ions in water clusters of increasing size. Molecular dynamics simulations show that, in an aqueous environment, the diarginine guanidinium like-charged ion pairing is sterically hindered, whereas in the Arg-Ala-Arg tripeptide, this pairing is significant. This result is supported by the survey of protein structure databases, where it is found that stacked arginine pairs in dipeptide fragments exist solely as being imposed by the protein structure. In contrast, when two arginines are separated by a single amino acid, their guanidinium groups can freely approach each other and they frequently form stacked pairs. Molecular dynamics simulations results are also supported by ab initio calculations, which show stabilization of stacked guanidinium pairs in sufficiently large water clusters.     

Free energy perturbation study of water dimer dissociation kinetics

An efficient approach is described for using accurate ab initio calculations to determine the rates of elementary condensation and evaporation processes that lead to nucleation of aqueous aerosols. The feasibility of the method is demonstrated in an application to evaporation rates of water dimer at 230 K. The method, known as ABC-FEP (ab initio/classical free energy perturbation), begins with a calculation of the potential of mean force for the dissociation (evaporation) of small water clusters using a molecular dynamics (MD) simulation with a model potential. The free energy perturbation is used to calculate how changing from the model potential to a potential calculated from ab initio methods would alter the potential of mean force. The difference in free energy is the Boltzmann-weighted average of the difference between the ab initio and classical potential energies, with the average taken over a sample of configurations from the MD simulation. In principle, the method does not require a highly accurate model potential, though more accurate potentials require fewer configurations to achieve a small sampling error in the free energy perturbation step. To test the feasibility of obtaining accurate potentials of mean force from ab initio calculations at a modest number of configurations, the free energy perturbation method has been used to correct the errors when some standard models for bulk water (SPC, TIP4P, and TIP4PFQ) are applied to water dimer. To allow a thorough exploration of sampling issues, a highly accurate fit to results of accurate ab initio calculations, known as SAPT-5s, as been used a proxy for the ab initio calculations. It is shown that accurate values for a point on the potential of mean force can be obtained from any of the water models using ab initio calculations at only 50 configurations. Thus, this method allows accurate simulations of small clusters without the need to develop water models specifically for clusters.     

A comparative study of nitrogen physisorption on different C70 crystal structures using an ab initio based potential

Quantum mechanical calculations are performed using the recently developed hybrid method for interaction energies to determine atom site Lennard-Jones potential parameters for the interactions of molecular nitrogen with C(70) molecules. This ab initio based potential is used in grand canonical Monte Carlo simulations to predict surface adsorption properties of N(2) on five known C(70) structures: rhombohedral, fcc, ideal hcp, deformed hcp, and monoclinic crystals. Because of the presence of five-membered carbon rings and the surface curvature of C(70) molecule, the Lennard-Jones potential parameters for nitrogen-carbon interactions obtained from ab initio based calculations are found to be different from that with planar graphite. The simulation results obtained from these two sets of force fields are compared and shown to differ, particularly at low coverage, where the nitrogen-carbon interactions are more important than the nitrogen-nitrogen interactions. The surface area, monolayer capacity, and isosteric heat of adsorption are calculated for various C(70) crystals and found to change appreciably as a result of the shear-induced phase transformation from hcp to rhombohedral lattice.     

Adsorption of polyacrylic acid on aluminium oxide: DRIFT spectroscopy and ab initio calculations

Diffuse reflectance Fourier transform infrared (DRIFT) spectroscopy was used to study the adsorption process of the water-soluble polyacrylic acid (PAA) polymer on hydrous δ-Al₂O₃. Vibrational assignment of PAA, sodium polyacrylate, (Na–PA) and the PA-oxide surface complex was achieved by comparison of observed band position and intensity in the DRIFT spectra with wavenumbers and intensities from ab initio quantum mechanical calculations. The presented data of polyacrylic acid suggest that IR data calculated ab initio on relatively short oligomers (quantum-mechanical oligomer approach) may provide valuable information regarding the interpretation of polyelectrolyte infrared spectra. Batch adsorption experiments were performed to sorb PAA onto the δ-Al₂O₃ surface. The results obtained from DRIFT studies were compared with adsorption isotherm experiments in order to relate the level of PAA coverage to the nature of the surface complex. Ab initio molecular orbital calculations on PAA/Al₂O₃ clusters were used to model possible surface complexes. Strong correlation were found between theoretical and observed DRIFT frequencies of the antisymmetric R-COO⁻ vibration. A number of possible configurations of the polyacrylic acid/aluminate surface complex were tested via ab initio calculations. These possible configurations included different di-aluminium octahedral Al³⁺ surface models. Results obtained from adsorption isotherm experiments, DRIFT spectra and ab initio calculations indicate that the carboxylate oxygens bridge an Al³⁺-octahedral dimer [Al₂(OH)₂4(H₂O)2(OH)] in a ligand-exchange inner sphere complex.     

DFT study of the adsorption of microsolvated glycine on a hydrophilic amorphous silica surface

Density functional theory (DFT) periodic ab initio molecular dynamics calculations are used to study the adsorption of gaseous and microsolvated glycine on a hydroxylated, hydrophilic silica surface. The silica model is presented and the interaction of water with surface silanols is studied. The heat of interaction of water is higher with the associated silanols (be they terminal or geminal ones) studied here than with isolated silanols presented in past works. Glycine is stabilized in a parallel mode on the hydroxylated surface. Terminal silanols do not allow the stabilization of the zwitterionic form, whereas geminal silanols do. Molecular dynamics (MD) first-principle calculations show that microsolvated zwitterion glycine directly binds through the carboxylate function to a surface silanol rather than through water molecules. The adsorption mode, whether with or without additional water molecules, is parallel to the surface. The ammonium function does not interact directly with the silanol groups but rather through water molecules. Thus, the carboxylate and ammonium functions exhibit two different reactivities towards silanols. The calculated free energies, taking into account the chemical potentials of water and glycine in the gas phase, suggest the existence of a thermodynamic domain in which the glycine is present in the gas phase as well as strongly adsorbed on specific sites of the surface.