Probing the interaction of the amino acid alanine with the surface of ZnO

Wavefunction-based quantum-chemicalab initiocalculations for core electron binding energies of small open shell molecules

Core electron binding energies (CEBEs), i.e. ionization energies of 1s core orbitals, are calculated by means of wavefunction-based quantum-chemicalab initiomethods for a series of small open-shell molecules containing first-row atoms. The calculations are performed in three steps: (a) Koopmans' theorem, where the orbitals of the electronic ground state are used unchanged also for the ions, (b) Hartree-Fock or self consistent field (SCF) approximation in which the orbitals are allowed to relax after 1s ionization (ΔSCF), (c) dynamic correlation effects on top of SCF. For open-shell molecules 1s ionization leads to ions in several spin states, mostly to a pair of a triplet and a singlet state. In several cases one or both of these ionic states are only poorly described by a single-reference SCF wavefunction, therefore a multi-reference complete active space self consistent field (CAS-SCF) wavefunction is used instead. The correlation effects are evaluated by means of our multi-reference coupled electron pair approximation program. The accuracy of the calculated CEBEs is in the order of 0.1-0.4 eV. This is in agreement with experimental results for NO and O₂. But there exist only very few gas phase data for CEBEs of open-shell molecules.

Strong Structural and Electronic Binding of Bovine Serum Albumin to ZnO via Specific Amino Acid Residues and Zinc Atoms

ZnO biointerfaces with serum albumin have attracted noticeable attention due to the increasing interest in developing ZnO-based materials for biomedical applications. ZnO surface morphology and chemistry are expected to play a critical role on the structural, optical, and electronic properties of albumin-ZnO complexes. Yet there are still large gaps in the understanding of these biological interfaces. Herein we comprehensively elucidate the interactions at such interfaces by using atomic force microscopy and nanoshaving experiments to determine roughness, thickness, and adhesion properties of BSA layers adsorbed on the most typical polar and non-polar ZnO single-crystal facets. These experiments are corroborated by force field (FF) and density-functional tight-binding (DFTB) calculations on ZnO-BSA interfaces. We show that BSA adsorbs on all the studied ZnO surfaces while interactions of BSA with ZnO are found to be considerably affected by the atomic surface structure of ZnO. BSA layers on the ( 000 1 ‾ ) surface have the highest roughness and thickness, hinting at a specific upright BSA arrangement. BSA layers on ( 10 1 ‾ 0 ) surface have the strongest binding, which is well correlated with DFTB simulations showing atomic rearrangement and bonding between specific amino acids (AAs) and ZnO. Besides the structural properties, the ZnO interaction with these AAs also controls the charge transfer and HOMO-LUMO energy positions in the BSA-ZnO complexes. This ZnO facet-specific protein binding and related structural and electronic effects can be useful for improving the design and functionality of ZnO-based materials and devices.

Covalent and Hydrogen Bonding in Adsorption of Alanine Molecules on Si(111)7×7

Molecular adsorption bonding configurations and specific interfacial chemistry of alanine on Si(111)7×7 have been determined by combining the results from scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) with ab initio calculations based on the density functional theory (DFT). XPS spectra of the N 1s region show that alanine molecules bind to the 7×7 surface by N-Si covalent bonding, while STM imaging reveals that such N-H dissociative adsorption of alanine occurs on an adjacent Si adatom-restatom pair, with the dehydrogenated alanine moiety and dissociated H atom occupying the Si adatom and restatom sites, respectively. At a sample bias above +2 V, the dehydrogenated alanine appears as a bright round protrusion, slightly off-center from a Si adatom site and leaning toward the opposite Si adatom across the dimer wall. The off-center character can be attributed to an electrostatic attraction between the electron-rich carbonyl O of the dehydrogenated alanine and electron-deficient nearest Si adatom across the dimer wall. Our DFT calculation also shows that the monodentate O-Si bonding configuration resulting from O-H dissociative adsorption is more thermodynamically favorable than the experimentally observed N-Si bonding configuration, suggesting that the interfacial dissociative adsorption reaction is a kinetically controlled rather than a thermodynamically driven process. Alanine molecules in the second adlayer (transitional layer) are found to attach to those in the first adlayer (interfacial layer) by N···HO hydrogen bonding, as supported by the presence of the N 1s feature at 401.0 eV. An alanine molecule H-bonded to a dehydrogenated alanine in the first adlayer has also been observed in STM as a brighter and larger protrusion close to the expected location of the free OH group in the dehydrogenated first-adlayer alanine. No thick zwitterionic alanine film can be obtained at room temperature possibly due to steric constraint caused by the methyl group.

Electronic structure variations of polar and nonpolar ZnO lattices with nitrogen-ion bombardment using synchrotron-based in situ photoemission and X-ray absorption spectroscopy

Surface polarity with different crystal orientations has been demonstrated as a crucial parameter in determining the physical properties and device applications in many transition metal oxide and semiconductor compound systems. The influences of surface polarity on electronic structures in nitrogen-incorporated ZnO lattices have been investigated in the present work. The successful doping of nitrogen atoms in ZnO lattices is suggested by the existence of N-related chemical bonds obtained from X-ray photoelectron spectroscopy analysis where a pronounced N-Zn peak intensity has been observed in the (000\bar 1)-terminated polar ZnO compound compared with the (10\bar 10)-terminated nonpolar ZnO compound. An energy shift of the valence band maximum towards the Fermi level has been resolved for both polar and nonpolar ZnO lattices, whereas a charge redistribution of the O 2p hybridized states is only resolved for o-plane ZnO with a polar surface. Angular-dependent X-ray absorption analyses at the O K-edge reveal enhanced surface-state contributions and asymmetric O 2p orbital occupations in the (000\bar 1)-terminated o-plane ZnO compound. The results shed light on the efficient nitrogen doping in ZnO lattices with polar surfaces. The comprehensive electronic structure investigations of correlations between impurity doping and surface polarity in ZnO lattices may also offer guidance for the material design in other transition metal oxide and semiconductor systems.

Platform for Screening Abiotic/Biotic Interactions Using Indicator Displacement Assays

This paper describes novel adaptations of optically sectioned planar format assays to screen compounds for their affinities to materials surfaces. The novel platform, which we name optically sectioned indicator displacement assays (O-IDA), makes use of displaceable dyes in a format adaptable to high-throughput multiwell plate technologies. We describe two approaches: the first being where the dye exhibits fluorescence in both the surface bound and unbound state and the second, where fluorescence is lost upon displacement of the dye from the surface. Half maximal inhibitory concentration (IC₅₀), binding affinity (K_i), and binding free energy (ΔG_ads) values can be extracted from the raw data. Representative biomolecules were tested for interactions with silica in an aqueous environment and ZnO(0001)-Zn and (10-10) facets in a nonaqueous environment. We provide the first experimental values for both the binding of small molecules to silica and the facet-dependent ZnO binding affinity of key amino acids associated with ZnO-specific oligopeptides. The specific data will be invaluable to those studying interactions at interfaces both experimentally and computationally. O-IDA provides a general framework for the high-throughput screening of molecule binding to materials surfaces, which has important applications in drug delivery, (bio-) catalysis, biosensing, and biomaterial engineering.

Selective photocatalytic conversion of methane into carbon monoxide over zinc-heteropolyacid-titania nanocomposites

Chemical utilization of vast fossil and renewable feedstocks of methane remains one of the most important challenges of modern chemistry. Herein, we report direct and selective methane photocatalytic oxidation at ambient conditions into carbon monoxide, which is an important chemical intermediate and a platform molecule. The composite catalysts on the basis of zinc, tungstophosphoric acid and titania exhibit exceptional performance in this reaction, high carbon monoxide selectivity and quantum efficiency of 7.1% at 362 nm. In-situ Fourier transform infrared and X-ray photoelectron spectroscopy suggest that the catalytic performance can be attributed to zinc species highly dispersed on tungstophosphoric acid /titania, which undergo reduction and oxidation cycles during the reaction according to the Mars-van Krevelen sequence. The reaction proceeds via intermediate formation of surface methyl carbonates.

Detection of Brucella abortus by a platform functionalized with protein A and specific antibodies IgG

Oriented immobilization of antibodies on a sensor surface is critical for enhancing both the antigen-binding capacity and the sensitivity of immunosensors. In this study, we describe a strategy to adsorb immunoglobulin G (IgG) anti-Brucella antibodies onto a silicon surface, oriented by protein A obtained from Staphylococcus aureus (SpA). X-ray photoelectron spectroscopy and atomic force microscopy were used to characterize topographically, morphologically, and chemical changes of the sensor functionalization. The activity of the biosensor was assessed by confocal microscopy, scanning electronic microscopy, and bacteria capture assays (BCA). According to the BCA, the efficiency of Brucella abortus detection with the SpA-IgG anti Brucella biosensor was three-fold higher than that of the random orientated IgG anti Brucella biosensor. The limit of detection was 1 × 10⁶ CFU/ml. These data show that the orientation of antibodies immobilization is crucial to developing immunosensors for bacterial antigen detection as Brucella spp and improve its sensibility level. Functionalization with protein A increases Brucella detection by an antibody-coated surface. Functionalized silicon surface for Brucella detection was characterized by atomic force microscopy, X-ray photoelectron spectroscopy and confocal microscopy.

Interactions between Metal Oxides and Biomolecules: from Fundamental Understanding to Applications

Metallo-oxide (MO)-based bioinorganic nanocomposites promise unique structures, physicochemical properties, and novel biochemical functionalities, and within the past decade, investment in research on materials such as ZnO, TiO₂, SiO₂, and GeO₂ has significantly increased. Besides traditional approaches, the synthesis, shaping, structural patterning, and postprocessing chemical functionalization of the materials surface is inspired by strategies which mimic processes in nature. Would such materials deliver new technologies? Answering this question requires the merging of historical knowledge and current research from different fields of science. Practically, we need an effective defragmentation of the research area. From our perspective, the superficial accounting of material properties, chemistry of the surfaces, and the behavior of biomolecules next to such surfaces is a problem. This is particularly of concern when we wish to bridge between technologies in vitro and biotechnologies in vivo. Further, besides the potential practical technological efficiency and advantages such materials might exhibit, we have to consider the wider long-term implications of material stability and toxicity. In this contribution, we present a critical review of recent advances in the chemistry and engineering of MO-based biocomposites, highlighting the role of interactions at the interface and the techniques by which these can be studied. At the end of the article, we outline the challenges which hamper progress in research and extrapolate to developing and promising directions including additive manufacturing and synthetic biology that could benefit from molecular level understanding of interactions occurring between inanimate (abiotic) and living (biotic) materials.

Investigation into the effects of surface stripping ZnO nanosheets

ZnO nanosheets are polycrystalline nanostructures that are used in devices including solar cells and gas sensors. However, for efficient and reproducible device operation and contact behaviour the conductivity characteristics must be controlled and surface contaminants removed. Here we use low doses of argon bombardment to remove surface contamination and make reproducible lower resistance contacts. Higher doses strip the surface of the nanosheets altering the contact type from near-ohmic to rectifying by removing the donor-type defects, which photoluminescence shows to be concentrated in the near-surface. Controlled doses of argon treatments allow nanosheets to be customised for device formation.

Experimental characterization and simulation of amino acid and peptide interactions with inorganic materials

Inspired by nature, many applications and new materials benefit from the interplay of inorganic materials and biomolecules. A fundamental understanding of complex organic-inorganic interactions would improve the controlled production of nanomaterials and biosensors to the development of biocompatible implants for the human body. Although widely exploited in applications, the interaction of amino acids and peptides with most inorganic surfaces is not fully understood. To date, precisely characterizing complex surfaces of inorganic materials and analyzing surface-biomolecule interactions remain challenging both experimentally and computationally. This article reviews several approaches to characterizing biomolecule-surface interactions and illustrates the advantages and disadvantages of the methods presented. First, we explain how the adsorption mechanism of amino acids/peptides to inorganic surfaces can be determined and how thermodynamic and kinetic process constants can be obtained. Second, we demonstrate how this data can be used to develop models for peptide-surface interactions. The understanding and simulation of such interactions constitute a basis for developing molecules with high affinity binding domains in proteins for bioprocess engineering and future biomedical technologies.

Understanding the Nature of Amino Acid Interactions with Pd(111) or Pd-Au Bimetallic Catalysts in the Aqueous Phase

The interaction of methionine (Met) with different bimetallic-segregated surfaces comprising a uniform distribution of strips and islands of Au on the Pd(111) surface was examined using molecular dynamics (MD) simulations. Out of all the segregated and uniformly doped surfaces studied, the design of Pd-Au islands showed some reduction in the interaction energy (E_int = -43.7 kJ/mol) as compared to that of the pure Pd(111) surface (E_int = -50 kJ/mol) for a single Met molecule. However, at a higher coverage of 9 Met molecules/simulation cell, none of the Pd-Au alloy surfaces showed any improvement as compared to the Pd(111) surface. In order to develop a comprehensive understanding of the nature of the nonbonded interaction of aqueous biogenic impurities with the Pd catalyst surface, the MD study was extended to include a variety of aliphatic, S-containing, aromatic, and polar amino acids. The potential of mean force (PMF) profiles were observed to be distinct for each class of amino acids with substantial differences among amino acids with acidic and basic side chains. The side chains of all the polar and aromatic amino acids showed direct contact with the surface while aliphatic amino acids had their hydrophobic side chain aligned away from the surface. Interestingly, lysine (Lys) and tyrosine (Tyr) were the only two amino acids which interacted preferentially via the distant backbone nitrogen and backbone oxygen, respectively, despite their side chains being in direct contact with the metal surface. The strength of interaction was correlated with the size of the amino acid; the interaction energies were observed to be the maximum for large molecules such as arginine (Arg, E_int = -87.7 kJ/mol) and tryptophan (Trp, E_int = -73.4 kJ/mol), while it was a minimum for aliphatic amino acids such as alanine (Ala, E_int = -10.9 kJ/mol). The study is focused on examining the sensitivity of the choice of the preferential interaction site, conformational preferences, and interaction energies to the side-chain specificity.

XPS investigation of titanium contact formation to ZnO nanowires

Ti is often used to form an initial Ohmic interface between ZnO and Au due to its low work function, and the TiO₂/ZnO heterojunction is also of great importance for many practical applications of nanoparticles. Here, Ti has been controllably deposited onto hydrothermally grown ZnO nanowires and the formation of metal-semiconductor contact has been investigated using x-ray photoelectron spectroscopy (XPS), photoluminescence (PL) spectroscopy and scanning electron microscopy. XPS results showed that that the Ti initially reacts with surface oxygen species to form TiO₂, and further deposition results in the formation of oxides with oxidation state numbers lower than four, and eventually metallic Ti on top of the TiO₂. The formation of TiC was also observed. XPS showed that the onset of metallic Ti coincided with a Zn 3p core level shift to lower binding energy, indicating upwards band bending and the formation of a rectifying contact. Annealing caused a near-complete conversion of the metallic Ti to TiO₂ and caused the Zn 3p to shift back to its original higher binding energy, resulting in downwards band bending and a more Ohmic contact. PL measurements showed that the optical properties of the nanowires are not affected by the contact formation.

Low-Index ZnO Crystal Plane-Specific Binding Behavior of Whole Immunoglobulin G Proteins

Crystallographic surface-resolved examination of protein-ZnO interactions can greatly enhance the fundamental understanding of protein adsorption on these technologically important solid surfaces which, in turn, will be tremendously valuable for the emerging applications of ZnO-based biomaterials and biosensors. We examine experimentally and via computer simulations the intriguing differences in the adsorption preferences and binding behavior of whole immunoglobulin G (IgG) proteins to various, low-index ZnO crystal surfaces at the individual biomolecule level. By performing direct atomic force microscopy imaging, we determine that IgG predominantly binds to the ZnO plane of (101̅0) relative to the other three low-index planes of (0001), (0001̅), and (112̅0). This phenomenon is highly unusual, particularly considering the fact that the average binding energy of amino acids (AAs) on the ZnO (0001) facet is higher than that on the (101̅0) plane. In conjunction with combined Monte Carlo-molecular dynamics simulations, we further explain the possible origins of our unusual experimental findings with critical factors such as the specific spatial locations of strongly binding AAs in the protein and their spatial distributions on the exterior surface of the protein.

Functionalization of nanostructured cerium oxide films with histidine

The surfaces of polycrystalline cerium oxide films were modified by histidine adsorption under vacuum and characterized by the synchrotron based techniques of core and valence level photoemission, resonant photoemission and near edge X-ray absorption spectroscopy, as well as atomic force microscopy. Histidine is strongly bound to the oxide surface in the anionic form through the deprotonated carboxylate group, and forms a disordered molecular adlayer. The imidazole ring and the amino side group do not form bonds with the substrate but are involved in the intermolecular hydrogen bonding which stabilizes the molecular adlayer. The surface reaction with histidine results in water desorption accompanied by oxide reduction, which is propagated into the bulk of the film. Previously studied, well-characterized surfaces are a guide to the chemistry of the present polycrystalline surface and histidine bonds via the carboxylate group in both cases. In contrast, bonding via the imidazole group occurs on the well-ordered surface but not in the present case. The morphology and structure of the cerium oxide are decisive factors which define the adsorption geometry of the histidine adlayer.

Peptide-directed crystal growth modification in the formation of ZnO

ZnO-binding peptides, differing only by Met or Cys at position 5 modify the mechanism of ZnO crystal growth.

Efficient and facile tuning of Vulcan XC72 with ultra-small Pt nanoparticles for electrocatalytic applications

In this work, we report a facile and straightforward approach for the preparation of electroactive catalysts based on the anchoring of crystalline, ultrafine Pt nanoparticles on the surface of amino-functionalized Vulcan XC72.

Characterization of functionalized multiwalled carbon nanotubes for use in an enzymatic sensor

Carbon nanotubes (CNT) have proven to be materials with great potential for the construction of biosensors. Development of fast, simple, and low cost biosensors to follow reactions in bioprocesses, or to detect food contaminants such as toxins, chemical compounds, and microorganisms, is presently an important research topic. This report includes microscopy and spectroscopy to characterize raw and chemically modified multiwall carbon nanotubes (MWCNTs) synthesized by chemical vapor deposition with the intention of using them as the active transducer in bioprocessing sensors. MWCNT were simultaneously purified and functionalized by an acid mixture involving HNO3-H2SO4 and amyloglucosidase attached onto the chemically modified MWCNT surface. A 49.0% decrease in its enzymatic activity was observed. Raw, purified, and enzyme-modified MWCNTs were analyzed by scanning and transmission electron microscopy and Raman and X-ray photoelectron spectroscopy. These studies confirmed purification and functionalization of the CNTs. Finally, cyclic voltammetry electrochemistry was used for electrical characterization of CNTs, which showed promising results that can be useful for construction of electrochemical biosensors applied to biological areas.

Quantification of zinc atoms in a surface alloy on copper in an industrial-type methanol synthesis catalyst

Methanol has recently attracted renewed interest because of its potential importance as a solar fuel. Methanol is also an important bulk chemical that is most efficiently formed over the industrial Cu/ZnO/Al2O3 catalyst. The identity of the active site and, in particular, the role of ZnO as a promoter for this type of catalyst is still under intense debate. Structural changes that are strongly dependent on the pretreatment method have now been observed for an industrial-type methanol synthesis catalyst. A combination of chemisorption, reaction, and spectroscopic techniques provides a consistent picture of surface alloying between copper and zinc. This analysis enables a reinterpretation of the methods that have been used for the determination of the Cu surface area and provides an opportunity to independently quantify the specific Cu and Zn areas. This method may also be applied to other systems where metal-support interactions are important, and this work generally addresses the role of the carrier and the nature of the interactions between carrier and metal in heterogeneous catalysts.

Spectroscopic evidence for neutral and anionic adsorption of (S)-glutamic acid on Ag(111)

We report here on a combined photoemission and vibrational spectroscopy investigation of (S)-glutamic acid adsorption on Ag(111). We show that, in the temperature range 250 K ≤ T ≤ 400 K, non-zwitterionic adsorption takes place and the anionic form prevails at nonvanishing coverage. Significant conformational changes of the self-assembled layer must occur above 300 K, corresponding to a substantial reduction of the sticking probability and a modification of the vibrational spectrum. The similarity of behavior with respect to glutamic acid adsorption on the previously investigated Ag(100) and Ag(110) surfaces is also discussed.

(S)-glutamic acid on Ag(100): self-assembly in the nonzwitterionic form

The fundamental understanding of adsorption and self-organization of biological molecules at surfaces is of greatest importance for a huge variety of possible applications, ranging from molecular electronics to the study of biocompatible materials, hygiene, and biofouling. In spite of that, the characterization of the interactions of organic molecules of biological interest with surfaces is far from being complete. In the present paper we report on a combined microscopic (scanning tunneling microscopy (STM)) and spectroscopic (X-ray photoemission spectroscopy and high-resolution electron energy loss spectroscopy) study of glutamic acid (Glu) adsorption and self-assembly on Ag(100) at different temperature. STM allows one to determine the structures of the Glu layers, for which empirical models are proposed, while photoemission spectra exclude adsorption in the zwitterionic form, which is the most common especially for weakly interacting substrates.

Biomolecule-biomaterial interaction: a DFT-D study of glycine adsorption and self-assembly on hydroxylated Cr2O3 surfaces

The adsorption of glycine, the building block of amino acids, on hydroxylated (0001)-Cr2O3 model surfaces, representing the stainless steel passive film surface, was modeled by means of the GGA + U method. The roles of glycine coverage and surface termination (hydroxylated Cr- and O-terminated surfaces) on the adsorption mode and self-assembly properties were explored. The hydroxylated Cr-terminated Cr2O3 surface, which presents two types of (H)OH groups exhibiting different acidic character, is more reactive than the hydroxylated O-terminated surface, where one single type of OH group is present, for all adsorption modes and coverages considered. Outer sphere adsorption occurs in the zwitterion form, stabilized at low coverage through H-bond formation with coadsorbed water molecules, and at the monolayer coverage by glycine self-assembling. The OH substitution by glycinate is favored on the hydroxylated Cr-terminated surface and not on the O-terminated one. The inclusion of dispersion forces does not change the observed tendencies. An atomistic thermodynamics approach suggests that outer sphere adsorption is thermodynamically favored over inner sphere adsorption in the whole domain of glycine concentration. The obtained SAM's free energies of formation are rationalized in a model considering the balance between sublimation and solvation free energies, and extrapolated to other amino acids, to predict the SAMs formation above hydroxylated surfaces. It is found that hydrophobic AA tend to self-assemble at the surface, whereas hydrophilic ones do not.