DFT study of the adsorption of D-(L-)cysteine on flat and chiral stepped gold surfaces

First DFT-supported point of care and novel electrochemical biosensing: Determination of yellow fever NS1 antibody in human plasma

In our study, we developed a point of care electrochemical biosensing platform based on the functionalized cysteine-positioned gold electrode to diagnose yellow fever disease from human plasma samples. The developed platform underwent characterization through diverse methods encompassing cyclic voltammetry, electrochemical impedance spectroscopy, scanning electron microscopy, energy dispersive X-ray spectroscopy, and density-functional theory. The capacitive interaction between yellow fever virus non-structural antigen and antibody gave a cathodic signal at approximately -260 mV, and increased in proportion to the amount of non-structural antibody. The created electrochemical biosensor has an ability to detect 96 ag/mL of the yellow fever non-structural antibody with an extensive analytical range varied from 0.1 fg/mL to 1 μg/mL. The interference effects of various substances that could be found in human plasma, and the performance of the method were examined from the point of recovery and relative standard deviation for human plasma samples; hereby, the results confirmed the unprecedented selectivity and accuracy of the proposed method.

Chiral nanocrystals grown from MoS2 nanosheets enable photothermally modulated enantioselective release of antimicrobial drugs

The transfer of the concept of chirality from molecules to synthesized nanomaterials has attracted attention amongst multidisciplinary teams. Here we demonstrate heterogeneous nucleation and anisotropic accumulation of Au nanoparticles on multilayer MoS₂ planes to form chiroptically functional nanomaterials. Thiol amino acids with chiral conformations modulate asymmetric growth of gold nanoarchitectures on seeds of highly faceted Au/MoS₂ heterostructures. Consequently, dendritic plasmonic nanocrystals with partial chiral morphologies are synthesized. The chirality of dendritic nanocrystals inherited from cysteine molecules refers to the structural characteristics and includes specific recognition of enantiomeric molecules. With integration of the intrinsic photothermal properties and inherited enantioselective characteristics, dendritic Au/MoS₂ heterostructures exhibit chirality-dependent release of antimicrobial drugs from hydrogel substrates when activated by exogenous infrared irradiation. A three-in-one strategy involving synthesis of chiral dendritic heterostructures, enantioselective recognition, and controlled drug release system is presented, which improves nanomaterial synthetic technology and enhances our understanding of crucial chirality information.

Synthesis of Chiral Au Nanocrystals with Precise Homochiral Facets for Enantioselective Surface Chemistry

Metal surfaces with intrinsic chirality play an irreplaceable role in many significant enantioselective chemical processes such as enantioselective catalysis, sensing, and separation. Nonetheless, current methods for the precise preparation of such chiral surfaces suffer with issues of unscalable production and low surface areas. Herein, we report the synthesis of chiral Au nanoparticles with precisely determined homochiral facets. Though a scalable wet chemical method, {125̅8}^R and {85̅12}^S high-Miller-index facets are obtained with the l- and d-chiral Au nanocrystals, respectively. The growth process of these homochiral facets is investigated, and a new nanocrystal growth pathway is revealed. More importantly, the remarkable enantioselective recognition properties of these homochiral surfaces are demonstrated and enable an efficient electrochemical method for chiral discrimination of l-/d-tryptophan. These results provide a foundation of fundamental studies of heterogeneous enantioselective processes and may pave way for the development of nanocatalysts for enantioselective chemistry.

First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO2 (101) Anatase Surface Adopting a Full Periodic Approach

Computational modeling of protein/surface systems is challenging since the conformational variations of the protein and its interactions with the surface need to be considered at once. Adoption of first-principles methods to this purpose is overwhelming and computationally extremely expensive so that, in many cases, dramatically simplified systems (e.g., small peptides or amino acids) are used at the expenses of modeling nonrealistic systems. In this work, we propose a cost-effective strategy for the modeling of peptide/surface interactions at a full quantum mechanical level, taking the adsorption of polyglycine on the TiO₂ (101) anatase surface as a test case. Our approach is based on applying the periodic boundary conditions for both the surface model and the polyglycine peptide, giving rise to full periodic polyglycine/TiO₂ surface systems. By proceeding this way, the considered complexes are modeled with a drastically reduced number of atoms compared with the finite-analogous systems, modeling the polypeptide structures at the same time in a realistic way. Within our modeling approach, full periodic density functional theory calculations (including implicit solvation effects) and ab initio molecular dynamics (AIMD) simulations at the PBE-D2* theory level have been carried out to investigate the adsorption and relative stability of the different polyglycine structures (i.e., extended primary, β-sheet, and α-helix) on the TiO₂ surface. It has been found that, upon adsorption, secondary structures become partially denatured because the peptide C═O groups form Ti-O═C dative bonds. AIMD simulations have been fundamental to identify these phenomena because thermal and entropic effects are of paramount importance. Irrespective of the simulated environments (gas phase and implicit solvent), adsorption of the α-helix is more favorable than that of the β-sheet because in the former, more Ti-O═C bonds are formed and the adsorbed secondary structure results less distorted with respect to the isolated state. Under the implicit water solvent, additionally, adsorbed β-sheet structures weaken with respect to their isolated states as the H-bonds between the strands are longer due to solvation effects. Accordingly, the results indicate that the preferred conformation upon adsorption is the α-helix over the β-sheet.

DFT study of cyclic glycine-alanine dipeptide binding to gold nanoclusters

In this work, we studied the interactions between cyclic glycine-alanine dipeptide c(GA) and gold nanoclusters (Au_nNCs, where n = 2-10) using density functional theory (DFT), atoms-in-molecules theory (AIM), and natural bond orbital analysis (NBO). This dipeptide (DP) consists of two amino acid residues (glycine and alanine); thus, the preference of both residues for binding to gold atoms was examined. The preference of alanine residue to the studied Au_nNCs was found to be greater than that of glycine residue. Two types of interactions were exhibited between the Au_nNCs and c(GA), the partially-covalent partially-electrostatic type and electrostatic interaction. Performance of two DFT functionals and different basis sets is assessed. The results benchmark the importance of the DFT functional with dispersion and long-range corrections, as well as the polarization functions in the basis sets for the gold lusters-peptide binding. The binding energy (ΔE_bind) values of the c(GA)-Au_nNCs complexes in gas and water implicit solvent were compared with those previously published for cyclic glycine-glycine DP-Au_nNCs complexes. It was found that the ΔE_bind values of the former complexes are greater than those of latter ones in water solvent.

Density functional theory study on adsorption of L-cysteine by Y, Zr, Nb, Mo-doped graphenes

The adsorption properties of l-cysteine (L-cys) on [Kr] 4d^1-4 (Y-Mo) doped graphenes with single and double vacancies are studied using density functional theory calculations with dispersion correction. The results showed that Y, Zr, Nb and Mo doped single-vacancy and double-vacancy graphenes show chemical adsorption characteristics towards L-cys. For the respective S, O and N-end adsorption, the binding strengths of L-cys on XSVs decrease from Y to Nb, and then increase. The binding strengths of L-cys on XDVs have no regular trend. Nb-doped graphene exhibits the most stable adsorption characteristics in the [Kr] 4d^1-4 element series, which is independent of the vacancy type. Zr-doped single and double vacancy graphene sensors have higher sensitivity than Y, Nb, Mo.

Chiral Surface and Geometry of Metal Nanocrystals

Chirality is a basic property of nature and has great importance in photonics, biochemistry, medicine, and catalysis. This importance has led to the emergence of the chiral inorganic nanostructure field in the last two decades, providing opportunities to control the chirality of light and biochemical reactions. While the facile production of 3D nanostructures has remained a major challenge, recent advances in nanocrystal synthesis have provided a new pathway for efficient control of chirality at the nanoscale by transferring molecular chirality to the geometry of nanocrystals. Interestingly, this discovery stems from a purely crystallographic outcome: chirality can be generated on high-Miller-index surfaces, even for highly symmetric metal crystals. This is the starting point herein, with an overview of the scientific history and a summary of the crystallographic definition. With the advance of nanomaterial synthesis technology, high-Miller-index planes can be selectively exposed on metallic nanoparticles. The enantioselective interaction of chiral molecules and high-Miller-index facets can break the mirror symmetry of the metal nanocrystals. Herein, the fundamental principle of chirality evolution is emphasized and it is shown how chiral surfaces can be directly correlated with chiral morphologies, thus serving as a guide for researchers in chiral catalysts, chiral plasmonics, chiral metamaterials, and photonic devices.

Structural and Chemical Evolution of l-Cysteine Nanofilm on Si(111)-√3×√3-Ag: From Preferential Growth at Step Edges and Antiphase Boundaries at Room Temperature to Adsorbate-Mediated Metal Cluster Formation at Elevated Temperature

The interaction of cysteine molecules with the Si(111)-√3×√3-Ag surface has been investigated over the submonolayer to multilayer regime using X-ray photoelectron spectroscopy, scanning tunneling microscopy, and density functional theory calculations. With both upper step and lower step terraces, step edges, and antiphase boundaries, the √3×√3-Ag overlayer supported on Si(111) provides a rich two-dimensional template for studying site-specific biomolecular interactions. As an amino acid with three functional groups, cysteine is found to chemisorb through S-H bond cleavage and S-Ag bond linkage first at step edges and antiphase boundaries followed by island formation and expanded growth onto terraces. Intermolecular interactions are dominated by zwitterionic hydrogen bonding at higher coverages, producing a porous unordered interfacial layer composed of cysteine agglomerates at room temperature. Upon annealing, cysteine adsorbates induce structural transformation of the uniform √3×√3-Ag reconstructed surface lattice into metallic Ag clusters with a narrow size distribution and short-range ordering. Preferential nanoaggregate formation of cysteine at defect sites and cysteine-induced metal cluster formation promise a new approach to fabricating nanoclusters for potential applications in chemical sensing and catalysis.

Chemistry of cysteine assembly on Au(100): electrochemistry, in situ STM and molecular modeling

Cysteine (Cys) is an essential amino acid with a carboxylic acid, an amine and a thiol group. We have studied the surface structure and adsorption dynamics of l-cysteine adlayers on Au(100) from aqueous solution using electrochemistry, high-resolution electrochemical scanning tunnelling microscopy (in situ STM), and molecular modelling. Cys adsorption on this low-index Au-surface has been much less studied than Cys adsorption on Au(111)- and Au(110)-electrode surfaces. Chronopotentiometry was employed to monitor the adsorption dynamics at sub-second resolution and showed that adsorption is completed in 30 minutes at Cys concentrations above 100 μM. Two consecutive steps could be fitted to these data. Two separate reductive desorption peaks of Cys adlayers on Au(100) with a total coverage of 2.52 (±0.15) × 10-10 mol cm-2 were observed. In situ STM showed that the adsorbed Cys is organized in stripes with "fork-like" features which co-exist in (11 × 2)-2Cys and (7 × 2)-2Cys lattices, quite differently from Cys adsorption on Au(111)-electrode surfaces. Stripe structures with bright STM contrast in the center suggest that a second Cys adlayer on top of a first adlayer is formed, supporting the dual-peak reductive desorption of Cys adlayers. In addition, monolayers of both pure l-Cys and pure d-Cys and a 1 : 1 racemic mixture of l- and d-Cys on Au(100) were studied. Virtually identical macroscopic electrochemical features were found, but in situ STM discloses many more defects for the racemic mixture than for the pure enantiomers due to structural mismatch of l- and d-Cys. Density functional theory (DFT) calculations combined with a cluster model for the Au(100) surface were carried out to investigate the adsorption energy and geometry of the adsorbed monomer and dimer Cys species in different orientations, with detailed attention to the chirality effects. Optimized DFT geometries were used to construct model STM images, and kinetic Monte Carlo simulations undertaken to illuminate the growth of adsorbate rows and the mechanism of the adlayer formation as well as the Cys adsorption patterns specific to the Au(100)-electrode surface.

External strain-enhanced cysteine enantiomeric separation ability on alloyed stepped surfaces

Using density functional theory with an accurate treatment of van der Waals interactions, we investigate the enantioselective recognition and separation of chiral molecules on stepped metal surfaces. Our calculations demonstrate that the separation ability of metal substrates can be significantly enhanced by surface decoration and external strain. For example, applying 2% tensile strain to the Ag-alloyed Au(532) surface leads to a dramatic increase (by 89%) in cysteine enantioselectivity as compared to that of pristine Au(532). Analysis on the computed binding energies shows that the interaction energy is the predominant factor that affects the separation efficiency in strongly bound systems. Our study presents a new strategy to modify the enantioselectivity of stepped metal surfaces and paves the way for exploring high efficiency chiral separation technology in pharmaceutical industry.

A Surface Mediated Supramolecular Chiral Phenomenon for Recognition of l- and d-Cysteine

Chiral recognition is of fundamental importance in chemistry and life sciences and the principle of chiral recognition is instructive in chiral separation and enantioselective catalysis. Non-chiral Ag nanoparticles (NPs) conjugated with chiral cysteine (Cys) molecules demonstrate strong circular dichroism (CD) responses in the UV range. The optical activities of the l-/d-Cys capped Ag NPs are associated with the formation of order arrangements of chiral molecules on the surface of Ag NPs, which are promoted by the electrostatic attraction and hydrogen bonding interaction. The intensity of the chiroptical response is related to the total surface area of Ag NPs in the colloidal solution. The anisotropy factor on the order of 10-2 is acquired for Ag NPs with the size varying from ~2.4 to ~4.5 nm. We demonstrate a simple and effective method for the fabrication of a quantitative chiral sensing platform, in which mesoporous silica coated Ag nanoparticles (Ag@mSiO₂) were used as chiral probes for recognition and quantification of Cys enantiomers.

Density-functional tight-binding approach for metal clusters, nanoparticles, surfaces and bulk: application to silver and gold

Density-functional based tight-binding (DFTB) is an efficient quantum mechanical method that can describe a variety of systems, going from organic and inorganic compounds to metallic and hybrid materials. The present topical review addresses the ability and performance of DFTB to investigate energetic, structural, spectroscopic and dynamical properties of gold and silver materials. After a brief overview of the theoretical basis of DFTB, its parametrization and its transferability, we report its past and recent applications to gold and silver systems, including small clusters, nanoparticles, bulk and surfaces, bare and interacting with various organic and inorganic compounds. The range of applications covered by those studies goes from plasmonics and molecular electronics, to energy conversion and surface chemistry. Finally, perspectives of DFTB in the field of gold and silver surfaces and NPs are outlined.

Chirality in adsorption on solid surfaces

In the present review we survey the main advances made in recent years on the understanding of chemical chirality at solid surfaces. Chirality is an important topic, made particularly relevant by the homochiral nature of the biochemistry of life on Earth, and many chiral chemical reactions involve solid surfaces. Here we start our discussion with a description of surface chirality and of the different ways that chirality can be bestowed on solid surfaces. We then expand on the studies carried out to date to understand the adsorption of chiral compounds at a molecular level. We summarize the work published on the adsorption of pure enantiomers, of enantiomeric mixtures, and of prochiral molecules on chiral and achiral model surfaces, especially on well-defined metal single crystals but also on other flat substrates such as highly ordered pyrolytic graphite. Several phenomena are identified, including surface reconstruction and chiral imprinting upon adsorption of chiral agents, and the enhancement or suppression of enantioselectivity seen in some cases upon adsorption of enantiomixtures of chiral compounds. The possibility of enhancing the enantiopurity of adsorbed layers upon the addition of chiral seeds and the so-called "sergeants and soldiers" phenomenon are presented. Examples are provided where the chiral behavior has been associated with either thermodynamic or kinetic driving forces. Two main approaches to the creation of enantioselective surface sites are discussed, namely, via the formation of supramolecular chiral ensembles made out of small chiral adsorbates, and by adsorption of more complex chiral molecules capable of providing suitable chiral environments for reactants by themselves, via the formation of individual adsorbate:modifier adducts on the surface. Finally, a discussion is offered on the additional effects generated by the presence of the liquid phase often required in practical applications such as enantioselective crystallization, chiral chromatography, and enantioselective catalysis.

Modeling and simulation of protein-surface interactions: achievements and challenges

Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.

Three steps to gold: mechanism of protein adsorption revealed by Brownian and molecular dynamics simulations

The addition of three N-terminal histidines to β-lactamase inhibitor protein was shown experimentally to increase its binding potency to an Au(111) surface substantially but the binding mechanism was not resolved. Here, we propose a complete adsorption mechanism for this fusion protein by means of a multi-scale simulation approach and free energy calculations. We find that adsorption is a three-step process: (i) recognition of the surface predominantly by the histidine fusion peptide and formation of an encounter complex facilitated by a reduced dielectric screening of water in the interfacial region, (ii) adsorption of the protein on the surface and adoption of a specific binding orientation, and (iii) adaptation of the protein structure on the metal surface accompanied by induced fit. We anticipate that the mechanistic features of protein adsorption to an Au(111) surface revealed here can be extended to other inorganic surfaces and proteins and will therefore aid the design of specific protein-surface interactions.

Simulation of Gold Functionalization with Cysteine by Reactive Molecular Dynamics

The anchoring mechanism of cysteine to gold in water solution is characterized in detail by means of a combination of quantum chemistry (QC) and reactive classical molecular dynamics (RC-MD) calculations. A possible adsorption-reaction route is proposed, through RC-MD simulations based on a modified version of the protein reactive force field (ReaxFF), in which gold-protein interactions have been included after accurate parametrization at the QC level. The computational results confirm recent experimental findings regarding the mechanism as a two-step binding, namely, a slow physisorption followed by a fast chemisorption. The reaction barriers are estimated through the nudged elastic band approach and checked by QC calculations. Surface reconstructions, induced by the strong adsorption of the molecule, are identified, and their role, as further adsorbate stabilizers, is properly disclosed. The satisfactory agreement with QC data and experiments confirm the reliability of the simulations and the unique opportunity they provide to follow locally molecule adsorption on selected materials.

Surface-site reactivity in small-molecule adsorption: A theoretical study of thiol binding on multi-coordinated gold clusters

BACKGROUND

The adsorption of organic molecules on metal surfaces has a broad array of applications, from device engineering to medical diagnosis. The most extensively investigated class of metal-molecule complexes is the adsorption of thiols on gold.

RESULTS

In the present manuscript, we investigate the dependence of methylthiol adsorption structures and energies on the degree of unsaturation at the metal binding site. We designed an Au20 cluster with a broad range of metal site coordination numbers, from 3 to 9, and examined the binding conditions of methylthiol at the various sites.

CONCLUSION

We found that despite the small molecular size, the dispersive interactions of the backbone are a determining factor in the molecular affinity for various sites. Kink sites were preferred binding locations due to the availability of multiple surface atoms for dispersive interactions with the methyl groups, whereas tip sites experienced low affinity, despite having low coordination numbers.

Novel insights into l-cysteine adsorption on transition metal doped graphene: influences of the dopant and the vacancy

Unprotonated l-cysteine is docked on single-vacancy and double-vacancy graphenes doped with transition metals from Sc to Zn. The adsystems exhibit interesting adsorption stability and magnetism.

Emerging enantiomeric resolution materials with homochiral nano-fabrications

The major scientific challenge of enantiomeric separation is to develop simple, rapid, and sensitive routine analytical methods. Generally, enantio-resolution is still based on "three-point interaction" theory, which indicates that homochiral sites are needed for enantio-selective interaction. However, in recent years, advanced materials with precise homochiral fabrication at the nanoscale have been synthesized, and have shown great potential in development of high-throughput enantio-resolution methods. This tutorial review summarizes fabrication and applications of homochiral materials for enantio-selective recognition and separation. These materials, which include intrinsic and restructured chiral metal surfaces, plasmonic nanostructures, coordination polymers, organic polymer sensors, and molecularly imprinted polymers, have been applied as sensors or chiral stationary phases (CSPs) for efficient enantio-resolution.