Laser diagnostics of elementary processes in molecular beam scattering on surfaces

We survey the main aspects of the laser techniques to study the elementary processes that take place in the scattering of molecules from crystallographic surfaces. We discuss the salient features of the accommodation of the translational, rotational and vibrational degrees of freedom of the scattered molecules and we summarize the main results of a recent comparative study of molecular beam scattering on graphite and diamond.     

Electron-density-dependent fused-sphere surfaces derived from pseudopotential calculations

Fused-sphere surfaces can be used to mimic a molecular boundary associated with a constant value of the electron density. The simplest of such fused-sphere models are constructed by using the atomic radii for the spherical isodensity surfaces of individual atoms. In this work, we discuss the extension of this model to molecules containing atoms beyond the second row. In these many- electron systems, the computation of electron densities is usually simplified by adopting a pseudopotential (or effective-core potential) approach. Here, we discuss the performance of large- and small-core pseudo-potential calculations as a tool to derive atomic radii. Our results provide an optimum set of variable radii that can be used to build fused-sphere surfaces. This continuum of surfaces provides a simple approximation to the low-electron-density regions around molecules with heavy atoms.     

Pattern recognition strategies for molecular surfaces. II. Surface complementarity

Fuzzy logic based algorithms for the quantitative treatment of complementarity of molecular surfaces are presented. Therein, the overlapping surface patches defined in article I1 of this series are used. The identification of complementary surface patches can be considered as a first step for the solution of molecular docking problems. Standard technologies can then be used for further optimization of the resulting complex structures. The algorithms are applied to 33 biomolecular complexes. After the optimization with a downhill simplex method, for all these complexes one structure was found, which is in very good agreement with the experimental results.     

Prediction of solvation free energies from computed properties of solute molecular surfaces

We have shown that the solvation energies of a group of 12 solutes in 7 different solvents can be presented analytically in terms of quantities computed at the density functional B3P86/6‐31+G** level for the isolated solute molecules. These quantities include the molecular surface area and several properties of the electrostatic potential on the surface, e.g., the most positive and negative values, the average deviation of the potential, the positive and negative portions of the surface, and their average potentials. Overall, the average absolute deviation of the predicted from the experimental solvation free energies is 0.25 kcal/mol; the poorest results are obtained for the solute butanone, for which the average absolute deviation is 0.63 kcal/mol. The forms of the relationships reflect the natures of the solute–solvent interactions; for the solvents with low dielectric constants, these are primarily global, involving extended portions of the molecular surfaces, whereas for the more polar solvents, site‐specific interactions also play key roles. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 76: 643–647, 2000     

Helium atom scattering from oxide surfaces.

Many experimental methods of surface science employ electrons or photons of considerable incident energy as probe particles. However, insulating surfaces or delicate physisorbed layers may be damaged by these particles and should, therefore, be analyzed with a gentler probe: He atom scattering allows to determine the symmetry of the unit cell and the detection of phase transitions from diffraction measurements as well as the determination of surface and adsorbate vibrations by time-of-flight resolved detection. Herein, the application of He atom scattering to oxide surfaces is demonstrated on the basis of the examples of MgO and ZnO. MgO(001) is a very inert and stable surface, whereas hydrogen atoms are chemisorbed on the mixed-terminated ZnO(1010) and on both polar faces: ZnO(0001) and ZnO(0001). He atom scattering is very sensitive to the presence of hydrogen on surfaces. In addition ZnO reacts with molecules such as water, CO and CO(2). It is demonstrated that in combination with photoelectron spectroscopy and thermal desorption spectroscopy He atom scattering can also contribute to studies of surface chemistry.     

Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network

An algorithm for the identification of possible binding sites of biomolecules, which are represented as regions of the molecular surface, is introduced. The algorithm is based on the segmentation of the molecular surface into overlapping patches as described in the first article of this series.1 The properties of these patches (calculated on the basis of physical and chemical properties) are used for the analysis of the molecular surfaces of 7821 proteins and protein complexes. Special attention is drawn to known protein binding sites. A binding site identification algorithm is realized on the basis of the calculated data using a neural network strategy. The neural network is able to classify surface patches as protein-protein, protein-DNA, protein-ligand, or nonbinding sites. To show the capability of the algorithm, results of the surface analysis and the predictions are presented and discussed with representative examples.     

Minimal molecular surfaces and their applications

This article presents a novel concept, the minimal molecular surface (MMS), for the theoretical modeling of biomolecules. The MMS can be viewed as a result of the surface free energy minimization when an apolar molecule, such as protein, DNA or RNA is immersed in a polar solvent. Based on the theory of differential geometry, the MMS is created via the mean curvature minimization of molecular hypersurface functions. A detailed numerical algorithm is presented for the practical generation of MMSs. Extensive numerical experiments, including those with internal and open cavities, are carried out to demonstrated the proposed concept and algorithms. The proposed MMS is typically free of geometric singularities. Application of the MMS to the electrostatic analysis is considered for a set of twenty six proteins.     

Electrochemical and photochemical control of host-guest complexation at surfaces

The application of electrochemistry or photochemistry to modulate supramolecular interactions between host-guest systems in solution is a burgeoning field. In particular, the speed and reversibility associated with electrochemically or photochemically actuated supramolecular interactions has allowed the creation and modulation of novel solution-based devices. In recent years, great advances have been made in transferring these systems from the solution to the solid state, to facilitate the development of molecular-electronics components that can operate in unison under the influence of an externally applied stimulus. These studies pave the way for the creation of responsive surfaces with advanced materials and nanotechnology applications.     

Pattern recognition strategies for molecular surfaces. I. Pattern generation using fuzzy set theory

A new method for the characterization of molecules based on the model approach of molecular surfaces is presented. We use the topographical properties of the surface as well as the electrostatic potential, the local lipophilicity/hydrophilicity, and the hydrogen bond density on the surface for characterization. The definition and the calculation method for these properties are reviewed shortly. The surface is segmented into overlapping patches with similar molecular properties. These patches can be used to represent the characteristic local features of the molecule in a way that is beyond the atomistic resolution but can nevertheless be applied for the analysis of partial similarities of different molecules as well as for the identification of molecular complementarity in a very general sense. The patch representation can be used for different applications, which will be demonstrated in subsequent articles.     

Localized electron traps on extended molecular surfaces

We have previously alluded to the fact that concentrated charge pockets can form on molecular surfaces that can act to stabilize excess electrons. These charge pockets are formed from systems, which posses a network of hydrogen bonded OH groups on one side of the surface and hydrogen atoms on the opposite side of the molecular surface. In this work, we have increased the size of our recently reported molecular surfaces (Jalbout and Adamowicz, Mol Phys, 2006, 19, 3101) while keeping the number of OH groups constant, to investigate localized charge concentration on extended frameworks. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

A method for determining the mean translational energy of particles desorbed from solid surfaces

A method for determinig the mean molecular translational energy in gas flows of low intensity (10¹²–10¹⁴ molec. s^–1) has been proposed. The method was verified using various gases (H₂, N₂, O₂, and CO₂ flowing into a vacuum out of a heated capillary. The translational energies were determined for CO and N₂ molecules desorbing from the surface of polycrystalline Ir. The translational temperature (T _tr) measured for CO equals 650±90 K and almost coincides with the surface temperature (T _s = 600 K). In the case of nitrogen molecules,T _tr = 4600±500 K atT _s = 500 K. The method proposed is applicable to the determination of the spatial distribution of molecular beam particles.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 30–34, January, 1995.The authors express their gratitude to A. V. Sklyarov for fruitful discussions during the elaboration of the theoretical basis and technical realization of the method.The reseach was carried out with the partial financial support of the International Science Foundation (Grant MBN 000).     

Segregation of inorganic ions at surfaces of polar nonaqueous liquids.

We present a short review of recent computational and experimental studies on surfaces of solutions of inorganic salts in polar nonaqueous solvents. These investigations complement our knowledge of aqueous interfaces and show that liquids such as formamide, liquid ammonia, and ethylene glycol can also surface-segregate large polarizable anions like iodide, albeit less efficiently than water. For liquids whose surfaces are covered with hydrophobic groups (e.g. methanol), the surface-ion effect all but disappears. Based on the present data a general picture of inorganic-ion solvation at the solution-vapor interface of polar liquids is outlined.     

Ammoniated solvation of excess electrons on molecular surfaces

As previously asserted, we have proposed a set of hypothetical molecular surfaces that possessed an extended hydrogen‐bonded network on one of the sides and hydrogen atoms on the opposite side. The uneven distribution of the OH groups (which increases the total dipole moment of the system) coupled to the partial positive charge of the hydrogen atoms creates charge pockets capable of trapping excess electrons. In this work we consider the ability of ammonia (NH₃) in solvating excess electrons in charge pockets on molecular surfaces. The anions are stable with respect to vertical electron detachment, and serve as another example by which electrons can be solvated on molecular surfaces. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Water order profiles on phospholipid/cholesterol membrane bilayer surfaces

Water is pivotal in the stabilization of macromolecular biological structures, although the dynamic ensemble structure of water near to molecular surfaces has yet to be fully understood. We show, through molecular simulation and fluorescence measurements, that water at the membrane surface is substantially more ordered than bulk water, due to a loss of hydrogen bonding between water molecules, coupled with an alignment of lipid and water dipole moments. Ordering of the water leads to a gradient in the effective dielectric permittivity, which is evident in both the molecular simulations and the fluorescence measurements. A lower effective dielectric permittivity was correlated with a decreasing degree of hydrogen bonding over the same spatial range. The water molecules closest to the lipid headgroup oxygen atoms form hydrogen bonds which exhibit a mean lifetime of 6.3 ps, compared with a mean lifetime of water-water hydrogen bonds of less than 2 ps. Membranes made up purely of phosphatidylcholine (PC) were compared with those made with a PC/cholesterol ratio relevant to cell membranes. Clear differences were found between these membrane configurations. These observations point to molecular structural differences in the surface environments of membranes and may underlie regional differences in the surface biophysical properties of membrane microdomains.     

Monte carlo simulations of polydisperse polymers grafted on spherical surfaces

This article presents effects of polydispersity in polymers grafted on spherical surfaces on grafted polymer chain conformations, grafted layer thickness, and free‐end monomer distribution within the grafted layer. At brush‐like grafting densities, as polydispersity index (PDI) increases, the scaling exponent of radius of gyration of grafted chains approaches that of a single chain grafted on the same nanoparticle, because polydispersity alleviates monomer crowding within the brush. At high PDI, the chains shorter than the number average chain length, N_n, have more compressed conformations, and the chains longer than N_n overall stretch less than in the monodisperse case. As seen in polydisperse flat brushes at high grafting densities, the grafted layer thickness on spherical nanoparticle increases with PDI. Polydispersity eliminates the region near the surface devoid of free‐end monomers seen in monodisperse cases, and it reduces the width of free‐end monomer distribution and shifts the free‐end monomer distribution close to the surface. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012     

Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST

The expulsion of water from surfaces upon molecular recognition and nonspecific association makes a major contribution to the free energy changes of these processes. In order to facilitate the characterization of water structure and thermodynamics on surfaces, we have incorporated Grid Inhomogeneous Solvation Theory (GIST) into the CPPTRAJ toolset of AmberTools. GIST is a grid‐based implementation of Inhomogeneous Fluid Solvation Theory, which analyzes the output from molecular dynamics simulations to map out solvation thermodynamic and structural properties on a high‐resolution, three‐dimensional grid. The CPPTRAJ implementation, called GIST‐cpptraj, has a simple, easy‐to‐use command line interface, and is open source and freely distributed. We have also developed a set of open‐source tools, called GISTPP, which facilitate the analysis of GIST output grids. Tutorials for both GIST‐cpptraj and GISTPP can be found at ambermd.org. © 2016 Wiley Periodicals, Inc.     

Interactions of aminomethylphosphonic acid and sarcosine with montmorillonite interlayer surfaces

The smectite clay, montmorillonite, can be found in many soils throughout the world. In addition to its importance in agriculture and soil remediation, montmorillonite has extensive applications in industry both in its natural form and as a component of composite materials. The adsorptive properties of montmorillonite have been explored in relation to its interactions with the common herbicide glyphosate. This herbicide, when exposed to microorganisms in the soil is degraded, forming two products: aminomethylphosphonic acid (AMPA) and sarcosine. The atomic‐level interactions of these compounds with the montmorillonite interlayer surfaces are studied here using molecular mechanics. The final outcomes of these calculations are analyzed in terms of the proximity of the montmorillonite surface to the moieties of the degradation products. The phosphonate moiety was found to be the most important source of interactions for AMPA, while for sarcosine there was an even distribution between the amino and carboxylic moieties, and Na⁺ ion mediated surface complexes. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Adsorption of benzotriazole on copper surfaces in a hydrochloric acid solution

The adsorption of benzotriazole (BTA) on commercial copper surfaces in hydrochloric (HCl) acid concentrations from 1 × 10^?3 to 5 × 10^?1 M was investigated using gravimetric measurements. BTA in bulk solution was tested in concentrations from 1 × 10^?5 to 1 × 10^?1 M at temperatures from 298 to 328 K. The adsorption mechanism is discussed using the objective function (OF) and in terms of applicability of the conventional isotherm models. The best fit was obtained using the Frumkin equation. The projected molecular area of BTA was calculated to elucidate inhibitor orientation in the adsorption process. Copyright © 2006 John Wiley & Sons, Ltd.