Orbital-Resolved DFT+U for Molecules and Solids.

We present an orbital-resolved extension of the Hubbard U correction to density-functional theory (DFT). Compared to the conventional shell-averaged approach, the prediction of energetic, electronic and structural properties is strongly improved, particularly for compounds characterized by both localized and hybridized states in the Hubbard manifold. The numerical values of all Hubbard parameters are readily obtained from linear-response calculations. The relevance of this more refined approach is showcased by its application to bulk solids pyrite (FeS2) and pyrolusite (ß-MnO2), as well as to six Fe(II) molecular complexes. Our findings indicate that a careful definition of Hubbard manifolds is indispensable for extending the applicability of DFT+U beyond its current boundaries. The present orbital-resolved scheme aims to provide a computationally undemanding yet accurate tool for electronic structure calculations of charge-transfer insulators, transition-metal (TM) complexes and other compounds displaying significant orbital hybridization.

Modulation of Multidrug Resistance Protein 1-mediated Transport Processes by the Antiviral Drug Ritonavir in Cultured Primary Astrocytes.

The Multidrug Resistance Protein 1 (Mrp1) is an ATP-dependent efflux transporter and a major facilitator of drug resistance in mammalian cells during cancer and HIV therapy. In brain, Mrp1-mediated GSH export from astrocytes is the first step in the supply of GSH precursors to neurons. To reveal potential mechanisms underlying the drug-induced modulation of Mrp1-mediated transport processes, we investigated the effects of the antiviral drug ritonavir on cultured rat primary astrocytes. Ritonavir strongly stimulated the Mrp1-mediated export of glutathione (GSH) by decreasing the Km value from 200 nmol/mg to 28 nmol/mg. In contrast, ritonavir decreased the export of the other Mrp1 substrates glutathione disulfide (GSSG) and bimane-glutathione. To give explanation for these apparently contradictory observations, we performed in silico docking analysis and molecular dynamics simulations using a homology model of rat Mrp1 to predict the binding modes of ritonavir, GSH and GSSG to Mrp1. The results suggest that ritonavir binds to the hydrophilic part of the bipartite binding site of Mrp1 and thereby differently affects the binding and transport of the Mrp1 substrates. These new insights into the modulation of Mrp1-mediated export processes by ritonavir provide a new model to better understand GSH-dependent detoxification processes in brain cells.

N-glycosylation modulates enzymatic activity of Trypanosoma congolense trans-sialidase.

Trypanosomes cause the devastating disease trypanosomiasis, in which the action of trans-sialidase (TS) enzymes harbored on their surface is a key virulence factor. TS enzymes are N-glycosylated, but the biological functions of their glycans have remained elusive. In this study, we investigated the influence of N-glycans on the enzymatic activity and structural stability of TconTS1, a recombinant TS from the African parasite Trypanosoma congolense. We expressed the enzyme in Chinese hamster ovary Lec1 cells, which produce high-mannose type N-glycans similar to the TS N-glycosylation pattern in vivo. Our MALDI-TOF mass spectrometry data revealed that up to eight putative N-glycosylation sites were glycosylated. In addition, we determined that N-glycan removal via endoglycosidase Hf treatment of TconTS1 led to a decrease in substrate affinity relative to the untreated enzyme but had no impact on the conversion rate. Furthermore, we observed no changes in secondary structure elements of hypoglycosylated TconTS1 in CD experiments. Finally, our molecular dynamics simulations provided evidence for interactions between monosaccharide units of the highly flexible N-glycans and some conserved amino acids located at the catalytic site. These interactions led to conformational changes, possibly enhancing substrate accessibility and enzyme-substrate complex stability. The here-observed modulation of catalytic activity via N-glycans represents a so-far-unknown structure-function relationship potentially inherent in several members of the TS enzyme family.

Protein conformational changes at the oil/water-interface induced by premix membrane emulsification.

We present combined experimental and modelling evidence that ß-lactoglobulin proteins employed as stabilizers of oil/water emulsions undergo minor but significant conformational changes during premix membrane emulsification processes. Circular Dichroism spectroscopy and Molecular Dynamics simulations reveal that the native protein structure is preserved as a metastable state after adsorption at stress-free oil/water interfaces. However, the shear stress applied to the oil droplets during their fragmentation in narrow membrane pores causes a transition into a more stable, partially unfolded interfacial state. The protein's ß-sheet content is reduced by up to 8% in a way that is largely independent of the pressure applied during emulsification, and is driven by an increase of contacts between the oil and hydrophobic residues at the expense of structural order within the protein core.

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 (Ki), and binding free energy (ΔGads) 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.

Atomistic Details of Chymotrypsin Conformational Changes upon Adsorption on Silica.

Adsorption of enzymes on solid surfaces may lead to conformational changes that reduce their catalytic conversion activity and are thus detrimental to the efficiency of biotechnology or biosensing applications. This work is a joint theoretical and experimental endeavor in which we identify and quantify the conformational changes that chymotrypsin undergoes when in contact with the surface of amorphous silica nanoparticles. For this purpose, we use circular dichroism spectroscopy, standard molecular dynamics, and advanced-sampling methods. Only the combination of these techniques allowed us to pinpoint a destabilization effect of silica on specific structural motifs of chymotrypsin. They are linked by the possibility of theoretically predicting CD spectra, allowing us to elucidate the source of the experimentally observed spectral changes. We find that chymotrypsin loses part of its helical content upon adsorption, with minor perturbation of its overall tertiary structure, associated with changes in the aromatic interactions. We demonstrate that the C-terminal helical fragment is unfolded as an isolated oligopeptide in pure water, folded as an α-helix as terminus of chymotrypsin in solution, and again partly disordered when the protein is adsorbed on silica. We believe that the joint methodology introduced in this manuscript has a direct general applicability to investigate any biomolecule-inorganic surface system. Methods to theoretically predict circular dichroism spectra from atomistic simulations were compared and improved. The drawbacks of the approaches are discussed; in particular, the limited capability of advanced-sampling MD schemes to explore the conformational phase space of large proteins and the dependency of the predicted ellipticity bands on the choice of calculation parameters.

Contact mechanics of highly porous oxide nanoparticle agglomerates.

Efficient nanopowder processing requires knowledge of the powder's mechanical properties. Due to the large surface area to volume ratio, nanoparticles experience relatively strong attractive interactions, leading to the formation of micron-size porous structures called agglomerates. Significant effort has been directed towards the development of models and experimental procedures to estimate the elasticity of porous objects such as nanoparticle agglomerates; however, none of the existing models has been validated for solid fractions below 0.1. Here, we measure the elasticity of titania (TiO[Formula: see text], 22 nm), alumina (Al[Formula: see text]O[Formula: see text], 8 nm), and silica (SiO[Formula: see text], 16 nm) nanopowder agglomerates by Atomic Force Microscopy, using a 3.75 [Formula: see text]m glass colloid for the stress-strain experiments. Three sample preparations with varying degree of powder manipulation are assessed. The measured Young's moduli are in the same order of magnitude as those predicted by the model of Kendall et al., thus validating it for the estimation of the Young's modulus of structures with porosity above 90 %.

Estimation of the free energy of adsorption of a polypeptide on amorphous SiO2 from molecular dynamics simulations and force spectroscopy experiments.

Estimating the free energy of adsorption of materials-binding peptides is fundamental to quantify their interactions across bio/inorganic interfaces, but is difficult to achieve both experimentally and theoretically. We employ a combination of molecular dynamics (MD) simulations and dynamical force-spectroscopy experiments based on atomic force microscopy (AFM) to estimate the free energy of adsorption ΔGads of a (GCRL) tetrapeptide on amorphous SiO2 in pure water. The results of both equilibrium, advanced sampling MD and non-equilibrium, steered MD are compared with those of two different approaches used to extract ΔGads from the dependence of experimentally measured adhesion forces on the applied AFM loading rates. In order to obtain unambiguous peak forces and bond loading rates from steered MD trajectories, we have developed a novel numerical protocol based on a piecewise-harmonic fit of the adhesion work profile along each trajectory. The interpretation of the experiments has required a thorough quantitative characterization of the elastic properties of polyethylene glycol linker molecules used to tether (GCRL)15 polypeptides to AFM cantilevers, and of the polypeptide itself. All obtained ΔGads values fall within a relatively narrow window between -5 and -9 kcal mol(-1), but can be associated with large relative error bars of more than 50%. Among the different approaches compared, Replica Exchange with Solute Tempering simulations augmented with MetaDynamics (RESTMetaD) and fitting of dynamic force spectroscopy experiments with the model of Friddle and De Yoreo lead to the most reliable ΔGads estimates.

Physisorption of enzymatically active chymotrypsin on titania colloidal particles.

In this study we use a straightforward experimental method to probe the presence and activity of the proteolytic enzyme α-chymotrypsin adsorbed on titania colloidal particles. We show that the adsorption of α-chymotrypsin on the particles is irreversible and pH-dependent. At pH 8 the amount of adsorbed chymotrypsin is threefold higher compared to the adsorption at pH 5. However, we observe that the adsorption is accompanied by a substantial loss of enzymatic activity, and only around 6-9% of the initial enzyme activity is retained. A Michaelis-Menten kinetics analysis of both unbound and TiO2-bound chymotrypsin shows that the K(M) value is increased from ∼10 µM for free chymotrypsin to ∼40 µM for the particle bound enzyme. Such activity decrease could be related by the hindered accessibility of substrate to the active site of adsorbed chymotrypsin, or by adsorption-induced structural changes. Our simple experimental method does not require any complex technical equipment, can be applied to a broad range of hydrolytic enzymes and to various types of colloidal materials. Our approach allows an easy, fast and reliable determination of particle surface-bound enzyme activity and has high potential for development of future enzyme-based biotechnological and industrial processes.

Label-free sensing of adenosine based on force variations induced by molecular recognition.

We demonstrate a simple force-based label-free strategy for the highly sensitive sensing of adenosine. An adenosine ssDNA aptamer was bound onto an atomic force microscopy (AFM) probe by covalent modification, and the molecular-interface adsorption force between the aptamer and a flat graphite surface was measured by single-molecule force spectroscopy (SMFS). In the presence of adenosine, the molecular recognition between adenosine and the aptamer resulted in the formation of a folded, hairpin-like DNA structure and hence caused a variation of the adsorption force at the graphite/water interface. The sensitive force response to molecular recognition provided an adenosine detection limit in the range of 0.1 to 1 nM. The addition of guanosine, cytidine, and uridine had no significant interference with the sensing of adenosine, indicating a strong selectivity of this sensor architecture. In addition, operational parameters that may affect the sensor, such as loading rate and solution ionic strength, were investigated.

Selective covalent immobilization of ferritin on alumina.

Selective and specific covalent immobilization and simultaneous suppression of nonspecific adsorption of the protein ferritin (FN) on the surfaces of polycrystalline α-alumina colloidal particles and single α-alumina crystals is demonstrated. FN immobilization is obtained by using a classical immobilization route and by combining either the organic silane 3-(triethoxysilyl)propylsuccinic anhydride (TESPSA) or (3-aminopropyl)triethoxysilane (APTES) with the zero-length cross linking system N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (EDC)/N-hydroxysuccinimide (NHS). The combination of APTES or TESPSA with EDC/NHS leads to a stable FN binding via amide bonds. However, the authors demonstrate that the TESPSA-EDC/NHS system enables an overall higher amount of covalent immobilization and a simultaneous suppression of nonspecific FN adsorption. After TESPSA functionalization negatively charged carboxylic groups are formed and can at the same time both electrostatically repel the overall negatively charged FN proteins and react with EDC/NHS for FN covalent immobilization. Moreover, the authors show that by specifically controlling the FN concentration during the immobilization reaction, the molecule distribution and density of bound FN can be easily tuned. The approach presented enables to selectively immobilize FN at mild conditions on substrates with different geometries and is therefore relevant for the fabrication of biomimetic nanomaterials and two-dimensional FN arrays.

Molecular dynamics simulations of the amino acid-ZnO (10-10) interface: a comparison between density functional theory and density functional tight binding results.

We investigate the adsorption behavior of four different amino acids (glutamine, glutamate, serine, cysteine) on the zinc oxide (101̄0) surface, comparing the geometry and energy associated with a number of different adsorption configurations. In doing this, we highlight the benefits and limits of using density-functional tight-binding (DFTB) with respect to standard density functional theory (DFT). The DFTB method is found to reliably reproduce the DFT adsorption geometries. Analysis of the adsorption configurations emphasizes the fundamental role of the first hydration layer in mediating the interactions between the amino acids and the surface. Direct surface-molecule bonds are found to form predominantly via the carboxylate groups of the studied amino acids. No surface-mediated chemical reactions are observed, with the notable exception of a proton transfer from the thiol group of cysteine to a hydroxyl group of the surface hydration layer. The adsorption energies are found to be dominated both by the formation of direct or indirect surface-molecule hydrogen bonds, but also by the rearrangement of the hydrogen-bond network in surface proximity in a non-intuitive way. Energetic comparisons between DFTB and DFT are made difficult on one side by the long time necessary to achieve convergence of potential energy values in MD simulations and on the other side by the necessity of including higher-order corrections to DFTB to obtain a good description of the hydrogen bond energetics. Overall, our results suggest that DFTB is a good reference method to set the correct chemical states and the initial geometries of hybrid biomolecule/ZnO systems to be simulated with non-reactive force fields.

Direct force measurements on peeling heteropolymer ssDNA from a graphite surface using single-molecule force spectroscopy.

We report here a systematic investigation of the interactions between two heteropolymer DNA single-strands (ssDNA) and graphite surfaces using AFM-based single-molecule force spectroscopy (SMFS). For this purpose, force-displacement (FD) curves are recorded by peeling single-molecule ssDNA from graphite. We find that the unbinding forces are affected both by the DNA sequences and the ionic strength of the liquid environment. In particular, the unbinding force decreases with the increase of ionic strength. Dynamic force measurements indicate that the unbinding force increases nonlinearly with the logarithm of the applied loading rate. The force data at different loading rates can be fitted with a recently developed single-barrier adsorption model, which is used here as a mean of quantifying the differences in the adsorption between different sequences. In addition, we investigate the effect of DNA hybridization and the presence of mismatch pairing defects and find that flawless hybridization to a complementary oligomer significantly decreases the unbinding force but mismatched hybridization has no obvious effect on it. These results can help optimize a recently envisaged SMFS-based biosensing technology for label-free DNA detection.

Specific material recognition by small peptides mediated by the interfacial solvent structure.

We present evidence that specific material recognition by small peptides is governed by local solvent density variations at solid/liquid interfaces, sensed by the side-chain residues with atomic-scale precision. In particular, we unveil the origin of the selectivity of the binding motif RKLPDA for Ti over Si using a combination of metadynamics and steered molecular dynamics simulations, obtaining adsorption free energies and adhesion forces in quantitative agreement with corresponding experiments. For an accurate description, we employ realistic models of the natively oxidized surfaces which go beyond the commonly used perfect crystal surfaces. These results have profound implications for nanotechnology and materials science applications, offering a previously missing structure-function relationship for the rational design of materials-selective peptide sequences.

A Classical Potential to Model the Adsorption of Biological Molecules on Oxidized Titanium Surfaces.

The behavior of titanium implants in physiological environments is governed by the thin oxide layer that forms spontaneously on the metal surface and mediates the interactions with adsorbate molecules. In order to study the adsorption of biomolecules on titanium in a realistic fashion, we first build up a model of an oxidized Ti surface in contact with liquid water by means of extensive first-principles molecular dynamics simulations. Taking the obtained structure as reference, we then develop a classical potential to model the Ti/TiOx/water interface. This is based on the mapping with Coulomb and Lennard-Jones potentials of the adsorption energy landscape of single water and ammonia molecules on the rutile TiO2(110) surface. The interactions with arbitrary organic molecules are obtained via standard combination rules to established biomolecular force fields. The transferability of our potential to the case of organic molecules adsorbing on the oxidized Ti surface is checked by comparing the classical potential energy surfaces of representative systems to quantum mechanical results at the level of density functional theory. Moreover, we calculate the heat of immersion of the TiO2 rutile surface and the detachment force of a single tyrosine residue from steered molecular dynamics simulations, finding good agreement with experimental reference data in both cases. As a first application, we study the adsorption behavior of the Arg-Gly-Asp (RGD) peptide on the oxidized titanium surface, focusing particularly on the calculation of the free energy of desorption.

Atomically smooth stress-corrosion cleavage of a hydrogen-implanted crystal.

We present a quantum-accurate multiscale study of how hydrogen-filled discoidal "platelet" defects grow inside a silicon crystal. Dynamical simulations of a 10-nm-diameter platelet reveal that H2 molecules form at its internal surfaces, diffuse, and dissociate at its perimeter, where they both induce and stabilize the breaking up of highly stressed silicon bonds. A buildup of H2 internal pressure is neither needed for nor allowed by this stress-corrosion growth mechanism, at odds with previous models. Slow platelet growth up to micrometric sizes is predicted as a consequence, making atomically smooth crystal cleavage possible in implantation experiments.

Water structuring and collagen adsorption at hydrophilic and hydrophobic silicon surfaces.

The adsorption of a collagen fragment on both a hydrophobic, hydrogen-terminated and a hydrophilic, natively oxidised Si surface is investigated using all-atom molecular dynamics. While favourable direct protein-surface interactions via localised contact points characterise adhesion to the hydrophilic surface, evenly spread surface/molecule contacts and stabilisation of the helical structure occurs upon adsorption on the hydrophobic surface. In the latter case, we find that adhesion is accompanied by a mutual fit between the hydrophilic/hydrophobic pattern within the protein and the layered water structure at the solid/liquid interface, which may provide an additional driving force to the classic hydrophobic effect.

Vacancy segregation in the initial oxidation stages of the TiN(100) surface.

The well-known corrosion resistance and biocompatibility of TiN depend on the structural and chemical properties of the stable oxide film that forms spontaneously on its surface after exposure to air. In the present work, we focus on the atomistic structure and stability of the TiN(100) surface in contact with an oxidizing atmosphere. The early oxidation stages of TiN(100) are investigated by means of first-principles molecular dynamics (FPMD). We observe selective oxidation of Ti atoms and formation of an ultrathin Ti oxide layer, while Ti vacancies are left behind at the metal/oxide interface. Within the formalism of ab initio thermodynamics we compute the segregation energies of vacancies and vacancy clusters at the metal/oxide interface, comparing the stability of the system obtained by FPMD simulations with ideally reconstructed models. We find that the localization of Ti vacancies in the thin oxide layer and at the TiN/oxide interface is thermodynamically stable and may account for the early removal of N atoms from the interface by segregation of N vacancies from the bulk reservoir. We suggest that superficial oxidation may proceed along two distinct possible pathways: a thermodynamically stable path along the potential energy minimum surface and a metastable, kinetically driven path that results from the high heat release during the dissociation of O(2).

Structure and energetics of diphenylalanine self-assembling on Cu(110).

We investigate the dynamical features of the adsorption of diphenylalanine molecules on the Cu(110) surface and of their assembling into supramolecular structures by a combination of quantum and classical atomistic modeling with dynamic scanning tunneling microscopy and spectroscopic experiments. Our results reveal a self-assembling mechanism in which isolated adsorbed molecules change their conformation and adsorption mode as a consequence of their mutual interactions. In particular, the formation of zwitterions after proton transfer between initially neutral molecules is found to be the key event of the assembling process, which stabilizes the supramolecular structures. Because of the constraints on the intermolecular bonds exerted by the surface-molecule interactions, the assembly process is strictly stereoselective, and may suggest a general model for patterning and functionalization of bare metal surfaces with short chiral peptides.