DFT Study of Cysteine Adsorption on Au(111)

Novel mixed self-assembled monolayers of L-cysteine and methanol on gold surfaces under ambient conditions

In this work, we carried out an experimental and theoretical study on the formation of self-assembled monolayers of L-cysteine molecules on gold surfaces in the presence of methanol as a solvent. We report for the first time L-cysteine and methanol ordered structures forming a mixed self-assembled mono-layer on Au(100) surfaces under ambient conditions. Finger-like ordered structures with a relative height of 0.10-0.20 nm, average width of 2.0 nm and variable lengths were observed using scanning tunneling microscopy under room temperature and ambient pressure conditions. Using X-ray photoemission spectroscopy, it was determined that L-cysteine molecules bind to the gold surface through the sulfur atom of their thiol group in two molecular configurations: neutral and zwitterionic. We found that the finger-like structures are the result of complex interactions of L-cysteine molecules with gold surfaces and L-cysteine molecules with methanol molecules and among all three components of the system (L-cysteine + methanol + gold surfaces). These interactions were detected through attenuated total reflectance-Fourier transform infrared spectroscopy. Furthermore, adsorbate/substrate interactions were studied by employing ab initio calculations using density functional theory, resulting in molecular arrangements formed by chains of L-cysteine pairs surrounded by physisorbed methanol molecules.

Charge Transfer Surface-Enhanced Raman and Absorption Spectra of the Zwitterionic Form of Cysteine Adsorbed on M@Au12 (M = Au, Ag, Pt, and Pd) Nanoclusters

The effect of the core atom type of the M@Au₁₂ nanocluster (M = Au, Ag, Pt, and Pd) on the normal (NR) and charge-transfer surface-enhanced Raman spectroscopy (CT-SERS) of the zwitterion form of l-cysteine (ZWCYS) adsorbed on two different sites (D1 and D2) of the nanocluster is investigated separately in the gas phase and water. Because SERS requires the calculation of the absorption spectrum, the effect of the core atom type on the absorption spectrum of M@Au₁₂ and its complex with the ZWCYS has also been investigated. The vibrational bands that show the intensity enhancement in the CT-SERS of the ZWCYS interacting with the D1 site of M@Au₁₂ nanocluster in water are O─C═O asymmetric stretching (M = Au and Ag), NH₂ bending (M = Ag), S-H stretching (M = Ag, Pt, and Pd), CH₂ bending (M = Pt), and CH₂ symmetric stretching (M = Pt and Pd). The ZWCYS at the D₂ site of the M@Au₁₂ nanocluster in water exhibits intensity enhancement for O─C═O asymmetric stretching (M = Pt), NH₃ wagging (M = Au), and S-H stretching (M = Pd). The intensity of the vibrational bands of ZWCYS does not increase for M = Ag but decreases for O─C═O asymmetric stretching, S-H stretching, CH₂ symmetric stretching, CH₂ asymmetric stretching, and especially NH₂ symmetric stretching.

Chromatographic framework for coffee ring effect-driven separation of small molecules in surface enhanced Raman spectroscopy analysis

The applications of coffee ring effect (CRE) in analytical chemistry have been increasingly expanded from particles and macromolecules to small molecules, in particular coupled to surface-enhanced Raman spectroscopy (SERS). Despite the theory behind the formation of CRE itself from a single drop evaporation onto the dry surface is well established, the theoretical aspects of CRE-driven separation, especially the analyte-surface interactions involving small molecules, have not been conceived. Herein, we have developed a theoretical framework to describe the CRE-driven separation process of small molecules, using SERS analysis of dimethylarsinic acid (DMA^V), dimethylmonothioarsinic acid (DMMTA^V), and dimethyldithioarsinic acid (DMDTA^V) on gold nanofilm (AuNF) as an example. By combining the CRE theory for the radial flow and the Extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory for mass transfer between solution and AuNF surface, we adapted the conventional chromatographic theory to derive a modified van Deemter equation for the CRE-driven separation. By using this model, we predicted the travel distances of arsenicals based on the different affinity of analytes to the AuNF and evaluated the possibility of separation of unknown analytes by CRE-based SERS, demonstrating the successful adaptation of classic chromatographic theory to CRE-driven nanochromatography.

A Redox-Based Autoinduction Strategy to Facilitate Expression of 5xCys-Tagged Proteins for Electrobiofabrication

Biofabrication utilizes biological materials and biological means, or mimics thereof, for assembly. When interfaced with microelectronics, electrobiofabricated assemblies enable exquisite sensing and reporting capabilities. We recently demonstrated that thiolated polyethylene glycol (PEG-SH) could be oxidatively assembled into a thin disulfide crosslinked hydrogel at an electrode surface; with sufficient oxidation, extra sulfenic acid groups are made available for covalent, disulfide coupling to sulfhydryl groups of proteins or peptides. We intentionally introduced a polycysteine tag (5xCys-tag) consisting of five consecutive cysteine residues at the C-terminus of a Streptococcal protein G to enable its covalent coupling to an electroassembled PEG-SH film. We found, however, that its expression and purification from E. coli was difficult, owing to the extra cysteine residues. We developed a redox-based autoinduction methodology that greatly enhanced the yield, especially in the soluble fraction of E. coli extracts. The redox component involved the deletion of oxyRS, a global regulator of the oxidative stress response and the autoinduction component integrated a quorum sensing (QS) switch that keys the secreted QS autoinducer-2 to induction. Interestingly, both methods helped when independently employed and further, when used in combination (i.e., autodinduced oxyRS mutant) the results were best—we found the highest total yield and highest yield in the soluble fraction. We hypothesize that the production host was less prone to severe metabolic perturbations that might reduce yield or drive sequestration of the -tagged protein into inclusion bodies. We expect this methodology will be useful for the expression of many such Cys-tagged proteins, ultimately enabling a diverse array of functionalized devices.

Improving SERS Sensitivity toward Trace Sulfonamides: The Key Role of Trade-Off Interfacial Interactions among the Target Molecules, Anions, and Cations on the SERS Active Surface

In recent years, ensuring the rational use and effective control of antibiotics has been a major focus in the eco-environment, which requires an effective monitoring method. However, on-site rapid detection of antibiotics in water environments remains a challenging issue. In this study, surface-enhanced Raman spectroscopy (SERS) was used to systematically achieve selective, rapid, and highly sensitive detection of sulfonamides, based on their fingerprint characteristics. The results show that the trade-off between the competitive and coadsorption behaviors of target molecules and agglomerates (inorganic salts) on the surface of the SERS substrate determines whether the molecules can be detected with high sensitivity. Based on this, the qualitative differentiation and quantitative detection of three structurally similar antibiotics, sulfadiazine, sulfamerazine, and sulfamethazine, were achieved, with the lowest detectable concentration being 1 μg/L for sulfadiazine and 50 μg/L for sulfamerazine and sulfamethazine.

Amino-acid interactions with the Au(111) surface: adsorption, band alignment, and interfacial electronic coupling

The charge transport properties of biological molecules like peptides and proteins are intensively studied for the great flexibility, redox-state variability, long-range efficiency, and biocompatibility of potential bioelectronic applications. Yet, the electronic interactions of biomolecules with solid metal surfaces, determining the conductivities of the biomolecular junctions, are hard to predict and usually unavailable. Here, we present accurate adsorption structures and energies, electronic band alignment, and interfacial electronic coupling data for all 20 natural amino acids computed using the DFT+Σ scheme based on the vdW-DF and OT-RSH functionals. For comparison, data obtained using the popular PBE functional are provided as well. Tryptophan, compared to other amino acids, is shown to be distinctly exceptional in terms of the electronic properties related to charge transport. Its high adsorption energy, frontier-orbital levels aligned relatively close to the Fermi energy of gold and strong interfacial electronic coupling make it an ideal candidate for facilitating charge transfer on such heterogeneous interfaces. Although the amino acids in peptides and proteins are affected by the structural interactions hindering their contact with the surface, knowledge of the single-molecule surface interactions is necessary for a detailed understanding of such structural effects and tuning of potential applications.

Bacteriophage Capsid Modification by Genetic and Chemical Methods

Bacteriophages are viruses whose ubiquity in nature and remarkable specificity to their host bacteria enable an impressive and growing field of tunable biotechnologies in agriculture and public health. Bacteriophage capsids, which house and protect their nucleic acids, have been modified with a range of functionalities (e.g., fluorophores, nanoparticles, antigens, drugs) to suit their final application. Functional groups naturally present on bacteriophage capsids can be used for electrostatic adsorption or bioconjugation, but their impermanence and poor specificity can lead to inconsistencies in coverage and function. To overcome these limitations, researchers have explored both genetic and chemical modifications to enable strong, specific bonds between phage capsids and their target conjugates. Genetic modification methods involve introducing genes for alternative amino acids, peptides, or protein sequences into either the bacteriophage genomes or capsid genes on host plasmids to facilitate recombinant phage generation. Chemical modification methods rely on reacting functional groups present on the capsid with activated conjugates under the appropriate solution pH and salt conditions. This review surveys the current state-of-the-art in both genetic and chemical bacteriophage capsid modification methodologies, identifies major strengths and weaknesses of methods, and discusses areas of research needed to propel bacteriophage technology in development of biosensors, vaccines, therapeutics, and nanocarriers.

Combined NMR and Computational Study of Cysteine Oxidation during Nucleation of Metallic Clusters in Biological Systems

The widespread biomedical applications of silver and gold nanoparticles (AgNPs and AuNPs, respectively) prompt the need for mechanistic evaluation of their interaction with biomolecules. In biological media, metallic NPs are known to transform by various pathways, especially in the presence of thiols. The interplay between metallic NPs and thiols may lead to unpredictable consequences for the health status of an organism. This study explored the potential events occurring during biotransformation, dissolution, and reformation of NPs in the thiol-rich biological media. The study employed a model system evaluating the interaction of cysteine with small-sized AgNPs and AuNPs. The interplay of cysteine on transformation and reformation pathways of these NPs was experimentally investigated by nuclear magnetic resonance (NMR) spectroscopy and supported by light scattering techniques and transmission electron microscopy (TEM). As the main outcome, Ag- or Au-catalyzed oxidation of cysteine to cystine was found to occur through generation of reactive oxygen species (ROS). Computational simulations confirmed this mechanism and the role of ROS in the oxidative dimerization of biothiol during NPs reformation. The obtained results represent valuable mechanistic data about the complex events during the transport of metallic NPs in thiol-rich biological systems that should be considered for the future biomedical applications of metal-based nanomaterials.

Controlling the Surface Functionalization of Ultrasmall Gold Nanoparticles by Sequence-Defined Macromolecules

Ultrasmall gold nanoparticles (diameter about 2 nm) were surface-functionalized with cysteine-carrying precision macromolecules. These consisted of sequence-defined oligo(amidoamine)s (OAAs) with either two or six cysteine molecules for binding to the gold surface and either with or without a PEG chain (3400 Da). They were characterized by 1 H NMR spectroscopy, 1 H NMR diffusion-ordered spectroscopy (DOSY), small-angle X-ray scattering (SAXS), and high-resolution transmission electron microscopy. The number of precision macromolecules per nanoparticle was determined after fluorescent labeling by UV spectroscopy and also by quantitative 1 H NMR spectroscopy. Each nanoparticle carried between 40 and 100 OAA ligands, depending on the number of cysteine units per OAA. The footprint of each ligand was about 0.074 nm2 per cysteine molecule. OAAs are well suited to stabilize ultrasmall gold nanoparticles by selective surface conjugation and can be used to selectively cover their surface. The presence of the PEG chain considerably increased the hydrodynamic diameter of both dissolved macromolecules and macromolecule-conjugated gold nanoparticles.

First-Principles Insights into the Interface Chemistry between 4-Aminothiophenol and Zinc Phosphide (Zn3P2) Nanoparticles

Accurate prediction of the structures, stabilities, and electronic structures of hybrid inorganic/organic systems is an essential prerequisite for tuning their electronic properties and functions. Herein, the interface chemistry between the 4-aminothiophenol (4ATP) molecule and the (001), (101), and (110) surfaces of zinc phosphide (Zn₃P₂) has been investigated by means of first-principles density functional theory calculation with a correction for van der Waals interactions. In particular, the atomic-level insights into the fundamental aspects of the 4ATP adsorption, including the lowest-energy adsorption configurations, binding energetics, structural parameters, and electronic properties are presented and discussed. The 4ATP molecule is demonstrated to bind most strongly onto the least stable Zn₃P₂(001) surface (E _ads = -1.91 eV) and least strongly onto the most stable Zn₃P₂(101) surface (E _ads = -1.21 eV). Partial density of states analysis shows that the adsorption of 4ATP on the Zn₃P₂ surfaces is characterized by strong hybridization between the molecule's sulfur and nitrogen p-orbitals and the d-orbitals of the interacting surface Zn ions, which gave rise to electron density accumulation around the centers of the newly formed Zn-S and Zn-N chemical bonds. The thermodynamic crystal morphology of the nonfunctionalized and 4ATP-functionalized Zn₃P₂ nanoparticles was obtained using Wulff construction based on the calculated surface energies. The stronger binding of the 4ATP molecule onto the less stable (001) and (110) surfaces in preference to the most stable (101) facet resulted in the modulation of the Zn₃P₂ nanocrystal shape, with the reactive (001) and (110) surfaces becoming more pronounced in the equilibrium morphology.

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.

Tuning Structure and Dynamics of Blue Copper Azurin Junctions via Single Amino-Acid Mutations

In the growing field of biomolecular electronics, blue-copper Azurin stands out as one of the most widely studied protein in single-molecule contacts. Interestingly, despite the paramount importance of the structure/dynamics of molecular contacts in their transport properties, these factors remain largely unexplored from the theoretical point of view in the context of single Azurin junctions. Here we address this issue using all-atom Molecular Dynamics (MD) of Pseudomonas Aeruginosa Azurin adsorbed to a Au(111) substrate. In particular, we focus on the structure and dynamics of the free/adsorbed protein and how these properties are altered upon single-point mutations. The results revealed that wild-type Azurin adsorbs on Au(111) along two well defined configurations: one tethered via cysteine groups and the other via the hydrophobic pocket surrounding the Cu 2 + . Surprisingly, our simulations revealed that single amino-acid mutations gave rise to a quenching of protein vibrations ultimately resulting in its overall stiffening. Given the role of amino-acid vibrations and reorientation in the dehydration process at the protein-water-substrate interface, we suggest that this might have an effect on the adsorption process of the mutant, giving rise to new adsorption configurations.

Triptycene Tripods for the Formation of Highly Uniform and Densely Packed Self-Assembled Monolayers with Controlled Molecular Orientation

When employing self-assembled monolayers (SAMs) for tuning surface and interface properties, organic molecules that enable strong binding to the substrate, large-area structural uniformity, precise alignment of functional groups, and control of their density are highly desirable. To achieve these goals, tripod systems bearing multiple bonding sites have been developed as an alternative to conventional monodentate systems. Bonding of all three sites has, however, hardly been achieved, with the consequence that structural uniformity and orientational order in tripodal SAMs are usually quite poor. To overcome that problem, we designed 1,8,13-trimercaptomethyltriptycene (T1) and 1,8,13-trimercaptotriptycene (T2) as potential tripodal SAM precursors and investigated their adsorption behavior on Au(111) combining several advanced experimental techniques and state-of-the-art theoretical simulations. Both SAMs adopt dense, nested hexagonal structures but differ in their adsorption configurations and structural uniformity. While the T2-based SAM exhibits a low degree of order and noticeable deviation from the desired tripodal anchoring, all three anchoring groups of T1 are equally bonded to the surface as thiolates, resulting in an almost upright orientation of the benzene rings and large-area structural uniformity. These superior properties are attributed to the effect of conformationally flexible methylene linkers at the anchoring groups, absent in the case of T2. Both SAMs display interesting electronic properties, and, bearing in mind that the triptycene framework can be functionalized by tail groups in various positions and with high degree of alignment, especially T1 appears as an ideal docking platform for complex and highly functional molecular films.

Adsorption of Amino Acids on Gold: Assessing the Accuracy of the GolP-CHARMM Force Field and Parametrization of Au-S Bonds

The interaction of amino acids with metal electrodes plays a crucial role in bioelectrochemistry and the emerging field of bionanoelectronics. Here we present benchmark calculations of the adsorption structure and energy of all natural amino acids on Au(111) in vacuum using a van-der-Waals density functional (revPBE-vdW) that showed good performance on the S22 set of weakly bound dimers (mean relative unsigned error (MRUE) wrt CCSD(T)/CBS = 13.3%) and adsorption energies of small organic molecules on Au(111) (MRUE wrt experiment = 11.2%). The vdW-DF results are then used to assess the accuracy of a popular force field for Au-amino acid interactions, GolP-CHARMM, which explicitly describes image charge interactions via rigid-rod dipoles. We find that while the force field underestimates adsorption distances, it does reproduce the binding energy rather well (MRUE wrt revPBE-vdW = 11.3%) with the MRUE decreasing in the order Cys, Met > amines > aliphatic > carboxylic > aromatic. We also present a parametrization of the bonding interaction between sulfur-containing molecules and the Au(111) surface and report force field parameters that are compatible with GolP-CHARMM. We believe the vdW-DF calculations presented herein will provide useful reference data for further force field development, and that the new Au-S bonding parameters will enable improved simulations of proteins immobilized on Au-electrodes via S-linkages.

Ag Nanometallic Surfaces for Self-Assembled Ordered Morphologies of Zein

Nanometallic surfaces of Ag nanoparticles (NPs) catalyzed the self-aggregation behavior of zein in different ordered morphologies such as cubes, rectangles, and bars. This was studied in a ternary in situ reaction (AgNO₃ + zein + water), where zein performed the reduction as well as stabilization of Ag NPs. This reaction produced small Ag NPs of less than 10 nm predominantly bound with {111} crystal planes, which attracted the surface adsorption of zein. Surface-adsorbed zein initiated the protein seeding and converted the tertiary structure of protein into open β-pleated structure with aqueous exposed hydrophobic domains. A layered deposition of β-pleats on different crystal planes of Ag NPs derived them to nearly monodispersed cubic morphologies. The mechanistic aspects of self-aggregation of zein in the presence of nanometallic surfaces hold possible scenarios for simple and straightforward routes of protein crystallization.

Adjusting the Linear Range of Au-MOF Fluorescent Probes for Real-Time Analyzing Intracellular GSH in Living Cells

A series of Au-loaded metal-organic frameworks (MOFs) were synthesized in this study and further employed for real-time quantitative analysis of intracellular glutathione (GSH) level. Different linear ranges can be acquired by altering the size of gold and MOF particles, or adjusting the proportion of 2-aminoterephthalic acid/1,4-benzenedicarboxylate linkers, which is also observed on fluorescein isothiocyanate-attached Au-MOFs. Further study reveals that the flexible molecular chain of GSH with the -COOH/-NH₂ and -SH terminals may readily tie on relevant gold nanoparticles through its -NH₂/-COOH groups, which then restricts the intramolecular motions of fluorescence probes and thus induces marked fluorescence enhancement. On the basis of these observations, the intracellular GSH levels of different cells including L02 cells, Hela, and U87 as well as HepG2 cancer cells can be rapidly evaluated by these Au-MOF probes.

The long and successful journey of electrochemically active amino acids. From fundamental adsorption studies to potential surface engineering tools

Proteins have been the subject of electrochemical studies. It is possible to apply electrochemical techniques to obtain information about their structure due to the presence of five electroactive amino acids that can be oriented to the outside of the peptidic chain. These amino acids are L-Tryptophan (L-Trp), L-Tyrosine (L-Tyr), L-Histidine (L-His), L-Methionine (L-Met) and L-Cysteine (L-Cys); their electrochemical behavior being subject of extensive research, but it is still controversial. No spectroscopic investigations have been reported on L-Trp, and due to the short life time of the intermediates, ex situ techniques cannot be employed, leading to a never-ending discussion about possible intermediates. In the L-Tyr and L-His cases, spectroelectrochemical studies were performed and different intermediates were observed, suggesting that some intermediates may be observed under specific conditions, as proposed for L-Cys. This amino acid is the most interesting among the electroactive ones because of the presence of a thiol moiety at its side chain, leading to a wide range of oxidation states. It can adsorb onto surfaces of different crystallographic orientation in stereoselective conformation, modifying the surface for different applications.as a surface engineering tool since it plays the role of as an anchor for the growing of nanocrystals inside proteic templates.

Linkage, charge state and layer of L-Cysteine on copper surfaces

The control of linkage and charge state between biomolecules and metals represents a key issue for the architect of bioactive systems. In this paper, the linkage, charge state and layer of L-Cysteine (L-Cys) self-assembled films were handled on copper surfaces at pH=6.86. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) were performed to measure the film quality and the details of self-assembled progress. X-ray photoelectron spectroscopy (XPS) and quantum chemical calculations of density functional theory (DFT) were used to characterize the linkage, charge state and layer of the L-Cys molecules on copper surfaces. The results indicate that, from 0s to 24h, the self-assembled process can be classified as three steps, fast adsorption at the beginning, and then rearrangement to form a monolayer, and then the formation of double layer. And L-Cys molecules link to the copper surface through CuS bond, not CuN bond. The thickness of monolayer is 10.5Å. Then the L-Cys molecules of second layer recline on the first layer. Finally, by the interaction of amine group and carboxylic acid group between the two layers, the second self-assembled film stands uprightly, and the -S^- group of the second layer point outward. The thickness of the double layer is 19.7Å. All the Cu/L-Cys films have negative charges because the pH (6.86) of the self-assembled solution is more than the isoelectric point of the L-Cys (5.05).

Specific pH effect for selective colorimetric assay of glutathione using anti-aggregation of label-free gold nanoparticles

An operationally simple colorimetric method for measuring glutathione (GSH) concentration was developed using anti-aggregation of gold nanoparticles (AuNPs) in this work.

l-Cysteine electrooxidation in alkaline and acidic media: a combined spectroelectrochemical and computational study

The wide possibilities of l-cysteine and l-cystine adsorbed and/or oxidized species onto Pt were explored by FTIR experiments and DFT calculations.

Density functional theory simulation of the adsorption of sulphur multilayers on Au(100)

The adsorption of sulphur multilayers on Au(100) has been studied using density functional theory (DFT) within the generalized gradient approximation (GGA). The first sulphur layer was adsorbed on the four-fold sites of the unreconstructed Au(100) surface forming a lattice. The experimental parameters of the lattice were reproduced taking into account the surface expansion of the topmost Au(100) layer. This expansion should occur when gold islands are formed after the lifting of hex-reconstruction, which allows the lateral movement of the gold atoms. The second sulphur layer, on top of the lattice, consisted of eight S atoms (octomer phase) in a quasi-rectangular arrangement. The structural optimization of the octomer phase was achieved in a specific spatial orientation with respect to the lattice. The analysis of Bader atomic charges and the projected density of states (PDOS) demonstrated that charge transfer from the Au(100) surface to the sulphur layers, sulphur chemisorption and sulphur-sulphur inter-layer mixing of electronic states control the formation of sulphur multilayers.

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.

Nanoparticle Surface Specific Adsorption of Zein and Its Self-assembled Behavior of Nanocubes Formation in Relation to On-Off SERS: Understanding Morphology Control of Protein Aggregates

Zein, an industrially important protein, is characterized in terms of its food and pharmaceutical coating applications by using surface enhanced Raman spectroscopy (SERS) on Au, Ag, and PbS nanoparticles (NPs). Its specific surface adsorption behavior on Ag NPs produced self-assembled zein nanocubes which demonstrated on and off SERS activity. Both SERS characterization as well as nanocube formation of zein helped us to understand the complex protein aggregation behavior in shape controlled morphologies, a process with significant ramifications in protein crystallization to achieve ordered morphologies. Interestingly, nanocube formation was promoted in the presence of Ag rather than Au or PbS NPs under in situ synthesis and discussed in terms of specific adsorption. Zein fingerprinting was much more clear and enhanced on Au surface in comparison to Ag while PbS did not demonstrate SERS due to its semiconducting nature.

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.

Biosensors based on modularly designed synthetic peptides for recognition, detection and live/dead differentiation of pathogenic bacteria

Rapid and sensitive detection of bacterial pathogens is critical for assessing public health, food and environmental safety. We report the use of modularly designed and site-specifically oriented synthetic antimicrobial peptides (sAMPs) as novel recognition agents enabling detection and quantification of bacterial pathogens. The oriented assembly of the synthetic peptides on electrode surfaces through an engineered cysteine residue coupled with impedimetric detection facilitated rapid and sensitive detection of bacterial pathogens with a detection limit of 10(2)CFU/mL for four bacterial strains including Escherichia coli (E. coli), Pseudomonas aeruginosa (P. aeruginosa), Staphylococcus aureus (S. aureus) and Staphylococcus epidermidis (S. epidermidis). The approach enabled differentiation between live and dead bacteria. The fabrication of the sAMPs functionalized surface and the importance of the sAMPs orientation for providing optimum recognition and detection ability against pathogens are discussed. The proposed methodology provides a universal platform for the detection of bacterial pathogens based on engineered peptides, as alternative to the most commonly used immunological and gene based assays. The method can also be used to fabricate antimicrobial coatings and surfaces for inactivation and screening of viable bacteria.

Surface and shape modification of mackinawite (FeS) nanocrystals by cysteine adsorption: a first-principles DFT-D2 study

The surface and shape modulation of mackinawite (FeS) nanoparticles by amino acid cysteine adsorption is investigated using a first-principles density functional theory calculations, corrected for dispersion-interactions (DFT-D2).

Self-assembled monolayers of thiols adsorbed on Au/ZnO-functionalized silica nanosprings: photoelectron spectroscopy-analysis and detection of vaporized explosives

Self-assembled monolayers (SAMs) of thiols of L-cysteine, 6-mercaptohexanol, 4-mercaptobenzoic acid, DL-thioctic acid and 11-(1-pyrenyl)-1-undecathiol, which have been selected for their propensity to interact with vaporized explosives, have been attached from solution onto gold decorated ZnO-coated nanosprings. X-ray and ultraviolet photoelectron spectroscopies (XPS and UPS) have been used to investigate the surface electronic structure of the SAMs coated nanosprings. On the basis of XPS analysis, it has been determined that the packing densities of L-cysteine, 6-mercaptohexanol, 4-mercaptobenzoic acid, DL-thioctic acid and 11-(1-pyrenyl)-1-undecathiol on gold (zinc oxide) are 5.42 × 10(14) (2.83 × 10(14)), 3.26 × 10(14) (2.54 × 10(14)), 9.50 × 10(13), 2.55 × 10(14) (1.12 × 10(14)), and 5.23 × 10(13) molecules/cm(2), respectively. A single S 2p core level doublet is observed for 4-mercaptobenzoic acid and 11-(1-pyrenyl)-1-undecathiol, which is assigned to the S-Au bond. The S 2p core level for L-cysteine, 6-mercaptohexanol, and DL-thioctic acid consist of two doublets, where one is S-Au bond and the other is the S-Zn bond. Analysis of the C/S ratios agrees well with the stoichiometry of the respective thiols. UPS analysis shows that the hybridization of S 3p states and Au d-bands produces antibonding and bonding states, above and below the Au d-bands, which is characteristic of molecular chemisorption on Au nanoparticles. Gas sensors were constructed with thiolated nanosprings and their responsiveness to ammonium nitrate at 100-150 °C was tested. Nanosprings sensors functionalized with 4-mercaptobenzoic acid and 6-mercaptohexanol showed the strongest responses by a factor of 4 to 5 relative to the less responsive thiols. The response to ammonium nitrate can be correlated to the packing density and ordering of the SAMs.

Cysteine on TiO2(110): a theoretical study by reactive dynamics and photoemission spectra simulation

Owing to the importance of bioinorganic interface properties for the biocompatibility of implants and for biosensing technology, it has become indispensable to gain understanding of their crucial structure-property relations at the atomistic level. Motivated by this fact, we use cysteine amino acid on perfect and defective TiO2(110) surfaces as model systems and study adsorption by means of classical all-atom reactive molecular dynamics and ab initio O 1s, N 1s, and S 2p photoemission spectra (XPS) simulations of the most relevant adsorbate structures. By analysis of the dynamics results and a detailed comparison with spectra recently collected for this adsorbate, we obtain conclusions of both general and particular character. It is shown that the interaction of cysteine with the TiO2(110) surface has multipoint character involving the carboxylic group as well as the amino and sulfur groups. The proton-transfer reactivity of cysteine is enhanced by the presence of the surface, and different forms of cysteines are confirmed to be present in the adsorbate. A general conclusion is that reactive force field dynamics combined with selected spectroscopy provides a viable path to understanding bioinorganic surfaces with ramifications for the design of such surfaces for future technological applications.

Characterization of two-dimensional chiral self-assemblies L- and D-methionine on Au(111)

A combination of XPS, in situ RAIRS, LEED, and STM experiments together with ab initio DFT calculations were used to elucidate the self-assembly properties at the atomic level, and enabled the interpretation of the expression of surface chirality upon adsorption of both enantiomers of methionine on a clean Au(111) surface under UHV conditions. The combination of experimental results, in particular, LEED and STM data with quantum chemical calculations is shown to be a successful setup strategy for addressing this challenge. It was found that the methionine molecular self-assembly consists of the first molecule lying parallel to the gold surface and the second interacting with the first methionine through a 2D H-bond network. The interaction with the gold surface is weak. The stability of the assembly is mainly due to the presence of intermolecular H bonds, resulting in the formation of ziplike dimer rows on the Au(111) surface. The methionine molecules interact with each other via their amino acid functional groups. The assembly shows an asymmetric pattern due to a slightly different orientation of the methionine molecules with respect to the surface. Simulations of the STM image of methionine assemblies were consistent with the experimental STM image. The present study shows another example of Au(111) stabilizing a self-assembled biological layer, which is not chemically perturbed by the surface.

Density functional theory study on the interactions of L-cysteine with graphene: adsorption stability and magnetism

Understanding the interactions between graphene and biomolecules is of fundamental relevance to the area of nanobiotechnology. Herein, we take l-cysteine as the probe biomolecule and investigate its adsorption on pristine graphene and B-, N-, Al-, Ni-, Ga-, Pd-doped graphene using density functional theory calculations. Three kinds of upright adsorption configurations, via unprotonated functional groups (-SH, -NH2, -COOH), are considered. The calculations reveal pristine graphene physically adsorbs l-cysteine. N-doped graphene shows physisorption towards the S-end and N-end l-cysteine, and chemisorption towards the O-end radical. Strong chemisorption, with site-specific preference, occurs on Al-, Ni-, Ga- and Pd-doped graphene, accompanied by severe structural changes. Spin polarization with an unusual mirror symmetry on Ni- and Pd-doped graphene is induced by chemisorption of unprotonated l-cysteine, except for O-end adsorption on Pd-doped graphene. The magnetization arises mainly from spin polarization of the C 2pz orbital, with a minor magnetism located on Ni or Pd. The influence of van der Waals forces is also evaluated. A thorough analysis of the adsorption stability and magnetism of these systems would be beneficial to facilitate applications in graphene-based biosensing, biomolecule immobilization, magnetic bio-separation and other fields in bionanotechnology.

Self-assembly of mono- and bidentate oligoarylene thiols onto polycrystalline Au

Four thiolated oligoarylene molecules (i) 4-methoxy-terphenyl-4″-methanethiol (MTM), (ii) 4-methoxy-terphenyl-3″,5″-dimethanethiol (MTD), (iii) 4-nitro-terphenyl-4″-methanethiol (NTM), and (iv) 4-nitro-terphenyl-3″,5″-dimethanethiol (NTD) were synthesized and self-assembled as monolayers (SAMs) on polycrystalline Au electrodes of organic field-effect transistors (OFETs). SAMs were characterized by contact angle and AC/DC electrochemical measurements, whereas atomic force microscopy was used for imaging the pentacene films grown on the coated electrodes. The electrical properties of functionalized OFETs, the electrochemical SAMs features and the morphology of pentacene films were correlated to the molecular organization of the thiolated oligoarylenes on Au, as calculated by means of the density functional theory. This multi-methodological approach allows us to associate the systematic replacement of the SAM anchoring head group (viz. methanethiol and dimethanethiol) and/or terminal tail group (viz. nitro-, -NO2, and methoxy, -OCH3) with the change of the electrical features. The dimethanethiol head group endows SAMs with higher resistive features along with higher surface tensions compared with methanethiol. Furthermore, the different number of thiolated heads affects the kinetics of Au passivation as well as the pentacene morphology. On the other hand, the nitro group confers further distinctive properties, such as the positive shift of both threshold and critical voltages of OFETs with respect to the methoxy one. The latter experimental evidence arise from its electron-withdrawing capability, which has been verified by both DFT calculations and DC electrochemical measurements.

Interaction of Nucleic Acid Bases with the Au(111) Surface

The fate of an individual DNA molecule when it is deposited on a hard inorganic surface in a "dry" environment is unknown, while it is a crucial determinant for nanotechnology applications of nucleic acids. In the absence of experimental approaches that are able to unravel the three-dimensional atomic structure of the target system, here we tackle the first step toward a computational solution of the problem. By using first-principles quantum mechanical calculations of the four nucleobases on the Au(111) surface, we present results for the geometries, energetics, and electronic structure, in view of developing a force field that will enable classical simulations of DNA on Au(111) to investigate the structural modifications of the duplex in these non-native conditions. We fully characterize each system at the individual level. We find that van der Waals interactions are crucial for a correct description of the geometry and energetics. However, the mechanism of adsorption is well beyond pure dispersion interactions. Indeed, we find charge sharing between the substrate and the adsorbate, the formation of hybrid orbitals, and even bonding orbitals. Yet, this molecule-surface association is qualitatively distinct from the thiol adsorption mechanism: we discuss such differences and also the relation to the adsorption mechanism of pure aromatic molecules.