Ab initio studies of a water layer at transition metal surfaces

This paper presents a detailed study of a water adlayer adsorbed on Pt(111) and Rh(111) surfaces using periodic density functional theory methods. The interaction between the metal surface and the water molecules is assessed from molecular dynamics simulation data and single point electronic structure calculations of selected configurations. It is argued that the electron bands around the Fermi level of the metal substrate extend over the water adlayer. As a consequence in the presence of the water layer the surface as a whole still maintains its metallic conductivity-a result of a crucial importance for understanding the process of electron transfer through the water/metal interface and electrochemical reactions in particular. Our results also indicate that there exists a weak bond between the hydrogen of the water and the Rh metal atoms as opposed to the widespread (classical) models based on purely repulsive interaction. This suggests that the commonly used classical interactions potentials adopted for large scale molecular dynamics simulations of water/metal interfaces may need revision. Two adsorption models of water on transition metals with the OH bonds pointing towards or away of the surface are also examined. It is shown that due to the very close values of their adsorption energies one should consider the real structure of water on the surface as a mixture of these simple "up" and "down" models. A model for the structure of the adsorbed water layer on Rh(111) is proposed in terms of statistical averages from molecular dynamics simulations.     

Non-specific adhesion on biomaterial surfaces driven by small amounts of protein adsorption

This work explores how long-range non-specific interactions, resulting from small amounts of adsorbed fibrinogen, potentially influence bioadhesion. Such non-specific interactions between protein adsorbed on a biomaterial and approaching cells or bacteria may complement or even dominate ligand–receptor mating. This work considers situations where the biomaterial surface and the approaching model cells (micron-scale silica particles) exhibit strong electrostatic repulsion, as may be the case in diagnostics and lab-on-chip applications. We report that adsorbed fibrinogen levels near 0.5 mg/m² produce non-specific fouling. For underlying surfaces that are less fundamentally repulsive, smaller amounts of adsorbed fibrinogen would have a similar effect. Additionally, it was observed that particle adhesion engages sharply and only above a threshold loading of fibrinogen on the collector. Also, in the range of ionic strength, I, below about 0.05 M, increases in I reduce the fibrinogen needed for microparticle capture, due to screening of electrostatic repulsions. Surprisingly, however, ionic strengths of 0.15 M reduce fibrinogen adsorption altogether. This observation opposes expectations based on DLVO arguments, pointing to localized electrostatic attractions and hydration effects to drive silica–fibrinogen adhesion. These behaviors are benchmarked against microparticle binding on silica surfaces carrying small amounts of a polycation, to provide insight into the role of electrostatics in fibrinogen-driven non-specific adhesion.     

Ab initio modeling of TiO2 nanosheets

We present density functional calculations on 1–6 monolayer (ML) thick TiO₂ films peeled off from the main low-index surfaces of anatase. The structure of the films is optimized both by constraining the lattice constants to those of bulk anatase, and by allowing them to relax. It is found that the stability order of the films does not follow that of the surfaces from which they are derived, and does not increase monotonously with film thickness. Furthermore, relaxing the lattice constants can induce large modifications in the film structure. In particular, two anomalously stable films are found. One derives from the 2 ML (001) film, and rearranges to a lepidocrocite-TiO₂ nanosheet. The other one derives from a 4 ML (101) film, and gives rise to a novel phase, where all the Ti ions are fivefold coordinated.     

Ab initio dipole polarizability surfaces of water molecule: static and dynamic at 514.5 nm

Coupled cluster calculations with a carefully designed basis set have been performed to obtain both static, alpha, and dynamic at 514.5 nm, alpha(514.5 nm), dipole polarizability surfaces of water. We employed a medium size basis set (13s10p6d3f9s6p2d1f)[9s7p6d3f6s5p2d1f] consisting of 157 contracted Gaussian-type functions that yields values near the Hartree-Fock limit for alpha [G. Maroulis, J. Chem. Phys. 94, 1182 (1991)]. The alpha and alpha(514.5 nm) surfaces were able to reproduce all the experimentally available information about the dipole polarizability of water, especially the Raman spectra of gaseous H(2)O, D(2)O, and HDO. Vibrational averages for the dipole polarizability of water molecule are also reported.     

Ab initio computed diabatic potential energy surfaces of OH-HCl

The two four-dimensional diabatic potential energy surfaces (DPESs) for OH-HCl are computed that correlate with the twofold degenerate (2)Pi ground state of the free OH radical. About 20 000 points on the surface are obtained by the ab initio coupled-cluster and multi-reference configuration interaction methods. Analytic forms for the diabatic potential energy surfaces are derived as expansions in complete sets of orthogonal functions depending on the three intermolecular angles. The numeric computation of the angular expansion coefficients is discussed. The distance-dependence of the angular coefficients is represented by the reproducing kernel Hilbert space method. It is checked that both diabatic potentials converge for large intermolecular separations to the values computed directly from the electrostatic multipole expansion. The final DPESs are discussed and illustrated by some physically meaningful one- and two-dimensional cuts through them.     

Ab initio potential energy surfaces and nonadiabatic interactions in the H+ +NO collision system

Ab initio calculations on the H(+)+NO system have been carried out in Jacobi coordinates at the multireference configuration interaction level employing Dunning's correlation-consistent polarized valence triple zeta basis set to analyze the role of low-lying electronic excited states in influencing the collision dynamics relevant to the experimental collision energy range of 9.5-30 eV. The lowest two adiabatic potential energy surfaces, asymptotically correlating to H(+)+NO(X (2)Pi) and H((2)S)+NO(+)(X (1)Sigma(+)), have been obtained. Using ab initio procedures, the (radial) nonadiabatic couplings and the mixing angle between the lowest two electronic states (1 (2)A' and 2 (2)A') have been obtained to yield the corresponding quasidiabatic potential energy matrix. The strengths of the computed vibrational coupling matrix elements reflect a similar trend, as has been observed experimentally in the magnitudes of the state-to-state transition probability for the inelastic vibrational excitations [J. Krutein and F. Linder, J. Chem. Phys. 71, 559 (1979); F. A. Gianturco et al., J. Phys. B 14, 667 (1981)].     

Ab initio study of magnetic interactions of manganese-oxide clusters

The manganese clusters have attracted much attention in relation with the oxygen evolving center (OEC) in photosystem II (PS II) system, which catalyzes the water oxidation reaction. Previously, we examined various spin-structures of Mn(II)₄O₄ model clusters, of which all of magnetic interactions are antiferromagnetic. In this study, we investigated electronic and magnetic structures of simple model clusters, Mn₄O₄(OAc)₆ and Mn₃CaO₄(OAc)₆ using spin unrestricted B3LYP (UB3LYP) method. The UB3LYP method is a standard tool for this study and has been in fact employed by many researchers. However, several peculiar features are observed for these model clusters: for instance the most stable spin state becomes the highest spin state for Mn(IV)₄O₄(OAc)₆ although this model cluster consists of superexchange type of units, Mn(IV)₂O₂ that usually favors antiferromagnetic spin alignments. Implications of the comparative results are discussed in relation to the electrophilic (or radical) mechanism for the O-O bond formation in the OEC.     

Ab initio periodic study of the conformational behavior of glycine helical homopeptides

Representative helicoidal conformations of polyglycine infinite chains have been investigated by using periodic boundary conditions, the B3LYP hybrid functional, and large basis sets, by means of the CRYSTAL code. The exploitation of the helix roto‐translational symmetry permits to optimize at a relatively low cost the structure of systems whose unit cell contains more than 300 atoms, much larger than the one investigated till now. In the present calculations, the helix symmetry is exploited at three levels. First, for the automatic generation of the structure. Second, for the calculation of the one‐ and two‐electron integrals that enter into the Fock matrix definition. Only the irreducible wedge of the Fock matrix is computed. Finally, for the diagonalization of the Fock matrix, where each irreducible representation is separately treated. The efficiency and accuracy of the computational scheme are documented, by considering cells containing up to 47 glycine residues. Results are compared with previous calculations and available experimental data. The role of hydrogen bonding in stabilizing polyglycine conformers is also addressed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Driving forces for protein adsorption at solid surfaces

Under most conditions proteins show a strong tendency to adsorb at interfaces. The general principles underlying the interaction between proteins and solid surfaces in an aqueous environment are discussed. These principles are illustrated by experimental results obtained with well-defined systems. The approach is mainly based on thermodynamic arguments.     

Ab initio potential energy surfaces for BH+2

Preliminary ab initio calculations for the BH⁺₂ potential surface are presented. The reaction B⁺¹S) + H₂ → BH⁺ (B₂ (B²σ⁺) + H is shown to be most likely to occur for C_2v and near C_2v geometrics where there are avoided crossings between the 1 ¹A₁ and 2 ¹A₁ surfaces and between the 2 ¹A₁ and 3 ¹A₁ surfaces which should facilitate non-adiabatic transitions. Bent geometries are alos preferred for the reaction B⁺(¹S) + H₂ → BH⁺(A²π) + H for which there are avoided crossings in C₂ sysmmetry between surfaces correlating with 1 ¹A₁ and 1 ¹B₂ surfaces.     

Ab initio molecular dynamics study of glycine intramolecular proton transfer in water

We use ab initio molecular-dynamics simulations to quantify structural and thermodynamic properties of a model proton transfer reaction that converts a neutral glycine molecule, stable in the gas phase, to the zwitterion that predominates in aqueous solution. We compute the potential of mean force associated with the direct intramolecular proton transfer event in glycine. Structural analyses show that the average hydration number (N(w)) of glycine is not constant along the reaction coordinate, but rather progresses from N(w) = 5 in the neutral molecule to N(w) = 8 for the zwitterion. We report the free-energy difference between the neutral and charged glycine molecules, and the free-energy barrier to proton transfer. Finally, we identify the approximations inherent in our method and estimate the corresponding corrections to our reported thermodynamic predictions.     

Ab initio and microcalorimetric investigations of alkene adsorption on phosphotungstic acid

The adsorption of ethene, propene, 1-butene, trans-2-butene, and isobutene on phosphotungstic acid has been characterized by density functional theory (DFT) calculations and microcalorimetric experiments. The DFT-calculated chemisorption energies to form the corresponding alkoxides for ethene, propene, 1-butene, trans-2-butene, and isobutene were -86.8, -90.3, -102.6, -79.9, and -91.4 kJ mol(-1), respectively (for their most-favorable binding modes). The relative chemisorption energies to form the alkoxides are dictated by the strength of interaction of the acidic proton with the carbon atom of the double bond that becomes protonated. The activation barrier for chemisorption was greatest for alkenes with primary (1 degrees) carbenium-like transition states followed by secondary (2 degrees) and tertiary (3 degrees) transition states. The adsorption enthalpy established from microcalorimetric experiments with propene and isobutene was approximately -100 kJ mol(-1), which is close to the DFT-calculated values. Chemisorption of ethene on phosphotungstic acid during microcalorimetric experiments was minimal, presumably because of the large activation barrier associated with a 1 degrees carbenium-like transition state. The results from this study are compared with those in the literature for the adsorption of alkenes on zeolites, which have a similar adsorption mechanism. Our results suggest that alkene adsorption is stronger on phosphotungstic acid than on zeolites, as supported by the more exothermic chemisorption energies. Additionally, activation barriers for alkene adsorption are lower over phosphotungstic acid than over zeolites.     

Ab initio molecular orbital study of the flavin-catalyzed dehydrogenation reaction of glycine - protein transport channel driving hydride-transfer mechanism

The reaction mechanism of flavin-catalyzed dehydrogenation of glycine has been studied by ab initio molecular orbital calculations using the 6-31G* basis set. 10-Methyl isoalloxazine (10-MIA) has been used as the flavin model compound. The results showed that when we assume a proton transport channel in amino acid oxidase, which is switched on by the substrate anion, the O12-protonated 10-MIA [10-MIAH⁺(O12)] is generated. The main structure of 10-MIAH⁺(O12) is one in which the central ring is expressed by an NAD⁺-like structure, which is favorable for driving the hydride-transfer reaction, i.e., the abstraction of the α-hydrogen of glycine by the hydride-transfer mechanism. We have found that this protonation results in a dramatic lowering of the activation energy of the reaction. The proposed mechanism is summarized as follows: the hydride transfer proceeds via two-electron transfer and synchronous intramolecular proton transfer → intermolecular proton transfer. Received: 10 August 1998 / Accepted: 17 September 1998 / Published online: 8 February 1999     

Radiation-induced degradation of hydroxyapatite/poly L-lactide composite biomaterial

The effects of gamma irradiation on the structure and properties of hydroxyapatite/poly L-lactide (HAp/PLLA) biomaterial have been investigated. Effects of radiation on microstructure, degradation of polymer part and thermal stability of composite were determined by scanning electronic microscopy (SEM), gel permeation chromatography (GPC) and thermogravimetric analysis (TGA), respectively. Mechanical properties were obtained through mechanical strength and elasticity modulus. Presented results show that properties of HAp/PLLA decay with irradiation dose, but for doses required for sterilization, changes and damaging effects are acceptable.     

Ab initio molecular dynamics study of methanol adsorption on copper clusters

The preferential structures of small copper clusters Cun (n=2-9) and the adsorption of methanol molecules on these clusters are examined with first principles, molecular dynamics simulations. The results show that the copper clusters undergo systematic changes in bond length and bond order associated with altering their preferential structures from one-dimensional structures, to two-dimensional and three-dimensional structures. The results also indicate that low coordination number sites on the copper clusters are both the most favorable for methanol adsorption and have the greatest localization of electronic charge. The simulations predict that charge transfer between the neutral copper clusters and the incident methanol molecules is a key process by which adsorption is stabilized. Importantly, the changes in the dimensionality of the copper clusters do not significantly influence methanol adsorption.     

Ab initio studies of layering behavior of liquid sodium surfaces and interfaces

We have studied the liquid surface of sodium with extensive ab initio molecular dynamics simulations based on ensemble density-functional theory. We find clear evidence of layering in the direction perpendicular to the surface that persists to temperatures more than 100 K above the melting point. We also observe clear Friedel oscillations in the electronic density response to the presence of a surface, but their direct effect on atomic layering is ruled out. A careful finite-size effect analysis accompanies our results, showing that liquid slabs 20-25 A thick capture the essential details of the surface structure. We conclude that geometrical confinement is the common cause for layer formation, which is similar to what happens at a liquid-solid interface: at a free liquid surface, the rapid decay of the electronic density from the bulk liquid value to zero in the vapor forms a hard wall against which the atoms pack. Finally, we predict x-ray reflectivities from ab initio molecular dynamics data that include some of the large surface-normal wave vector-transfer regions that, for alkali metals, are not accessible to experiments.     

Ab initio and DFT calculations of three-body interactions in chiral mixtures

In order to elucidate the enthalpic stabilization of a 2-methyl-1,4-butanediol system (2M14BD) and a 3-chloro-1,2-propanediol (3C12PDO) system by mixing of each (R)- and (S)-enantiomers, three-body interaction energies are obtained by PW91/6-311G** and MP2/6-311G** level calculations. The differences between homochiral interactions and heterochiral interactions in a 3C12PDO system are found. On the other hand, in 2M14BD systems, very slight differences can be observed between the three-body interaction energies of the three ternary systems. Further, the relationship between excess enthalpies and chiral interactions is discussed.     

Ab initio computational modeling of long loops in G-protein coupled receptors

A newly developed approach for predicting the structure of segments that connect known elements of secondary structure in proteins has been applied to some of the longer loops in the G-protein coupled receptors (GPCRs) rhodopsin and the dopamine receptor D2R. The algorithm uses Monte Carlo (MC) simulation in a temperature annealing protocol combined with a scaled collective variables (SCV) technique to search conformation space for loop structures that could belong to the native ensemble. Except for rhodopsin, structural information is only available for the transmembrane helices (TMHs), and therefore the usual approach of finding a single conformation of lowest energy has to be abandoned. Instead the MC search aims to find the ensemble located at the absolute minimum free energy, i.e., the native ensemble. It is assumed that structures in the native ensemble can be found by an MC search starting from any conformation in the native funnel. The hypothesis is that native structures are trapped in this part of conformational space because of the high-energy barriers that surround the native funnel. In this work it is shown that the crystal structure of the second extracellular loop (e2) of rhodopsin is a member of this loop’s native ensemble. In contrast, the crystal structure of the third intracellular loop is quite different in the different crystal structures that have been reported. Our calculations indicate, that of three crystal structures examined, two show features characteristic of native ensembles while the other one does not. Finally the protocol is used to calculate the structure of the e2 loop in D2R. Here, the crystal structure is not known, but it is shown that several side chains that are involved in interaction with a class of substituted benzamides assume conformations that point into the active site. Thus, they are poised to interact with the incoming ligand.