Comparative study of gold and silver interactions with amino acids and nucleobases

Exploring the nanoscale: AFM-IR visualization of cysteine adsorption on gold nanoparticles

This study focuses on the adsorption process of L-cysteine (Cys), a sulfur-containing amino acid, onto monolayers of gold nanoparticles (AuNPs) prepared through distinct protocols on mica substrates. Two types of AuNPs were prepared using two different methods: the first employed a physical approach, which combined the Inert Gas Condensation (IGC) technique with the magnetron sputtering method, while the second utilized a chemical method involving the reduction of tetrachloroauric acid with trisodium citrate (TC). The characterization of AuNPs was performed using transmission electron microscopy (TEM) and atomic force microscopy (AFM), of up to 5 ± 1.3 nm for bare AuNPs obtained through vacuum techniques, and up to 12 ± 5 nm for negatively charged, citrate-stabilized TCAuNPs(-). The application of spectroscopic techniques based on the surface-enhanced effects allows for describing the adsorption process in both micro- and nanoscale systems: Cys/bare AuNPs and Cys/ TCAuNPs(-). The commonly used surface-enhanced Raman spectroscopy (SERS) technique provided insights into adsorption behaviours at the microscale level. In the case of TCAuNPs(-), an interaction involving the lone electron pair of sulfur (S) atom and metal surface, while on the bare AuNPs, S is adsorbed on the surface, but the cleavage of the SH group is not discernible. Nanoscale analysis was complemented using AFM combined with the surface-enhanced infrared absorption spectroscopy (AFM-SEIRA) technique. AFM-SEIRA map indicated the formation of hot spot which were predominantly located between aggregated TCAuNPs(-) and on specific NPs surfaces (area between NPs and gold-coated tip). Results from the SERS and AFM-SEIRA techniques were in good agreement, underscoring the comprehensive understanding achieved through the chosen experimental approach regarding the Cys interactions with layers of AuNPs.

Interaction of Au(III) with amino acids: a vade mecum for medicinal chemistry and nanotechnology

Au(III) is highly reactive. At odds with its reduced counterpart, Au(I), it is hardly present in structural databases. And yet, it is the starting reactant to form gold nanoclusters (AuNCs) and the constitutive component of a new class of drugs. Its reactivity is a world apart from that of the iso-electronic Pt(II) species. Rather than DNA, it targets proteins. Its interaction with amino acid residues is manifold. It can strongly interact with the residue backbones, amino acid side chains and protein ends, it can form appropriate complexes whose stabilization energy reaches up to more than 40 kcal mol-1, it can affect the pKa of amino acid residues, and it can promote charge transfer from the residues to the amount that it is reduced. Here, quantum chemical calculations provide quantitative information on all the processes where Au(III) can be involved. A myriad of structural arrangements are examined in order to determine the strongest interactions and quantify the amount of charge transfer between protonated and deprotonated residues and Au(III). The calculated interaction energies of the amino acid side chains with Au(III) quantitatively reproduce the experimental tendency of Au(III) to interact with selenocysteine, cysteine and histidine and negatively charged amino acids such as Glu and Asp. Also, aromatic residues such as tyrosine and tryptophan strongly interact with Au(III). In proteins, basic pH plays a role in the deprotonation of cysteine, lysine and tyrosine and strongly increases the binding affinity of Au(III) toward these amino acids. The amino acid residues in the protein can also trigger the reduction of Au(III) ions. Sulfur-containing amino acids (cysteine and methionine) and selenocysteine provide almost one electron to Au(III) upon binding. Tyrosine also shows a considerable tendency to act as a reductant. Other amino acids, commonly identified in Au-protein adducts, such as Ser, Trp, Thr, Gln, Glu, Asn, Asp, Lys, Arg and His, possess a notable reducing power toward Au(III). These results and their discussion form a vade mecum that can find application in medicinal chemistry and nanotech applications of Au(III).

Interactions of deprotonated phenylalanine with gold Clusters: Theoretical study with prospects for amino acid detection

Nanomaterials are widely used nowadays in industry and medicine. The specific properties of gold nanoclusters (Au NCs) are chemical stability, low cytotoxicity, low photobleaching, high sensitivity to the molecular environment. This set of properties allows to use Au NCs as nanosensors in bioimaging and diagnostics. We have investigated gold cluster complexes with proteinogenic amino acid phenylalanine (Phe). Detection of phenylalanine is essential for diagnostics of phenylketonuria, vitiligo, sclerosis, cancer, tuberculosis, etc. We have studied the complexes of Phe with Aunq clusters with atomic number equal 1-6, 8, 20 and a charge equal 0-2. We have established that the clusters Au40, Au21+ and Au32+ form the most stable complexes with Phe among NCs with charge 0, +1 and + 2, respectively. Intracomplex interactions have been studied using Atoms-In-Molecules (AIM) theory and Natural Bond Orbital (NBO) analysis. It has been shown that metal-ligand intracomplex interactions are partially covalent and partially electrostatic. Also, we have simulated the UV-vis absorption and Raman spectra of the Phe-Au NCs. We have established that the clusters possess prospective features if being used for colorimetric and Raman detection of Phe. Au20 cluster is remarkable for its six-times enhancement of the Raman signal. Moreover, our study provides insights into metal-ligand interactions for clusters synthesized inside a polypeptide globula. Hence, to the best of our knowledge this is a first attempt to perform a detailed analysis of Phe interactions with gold using quantum chemical calculations.

LSPR sensing for in situ monitoring the Ag dissolution of Au@Ag core-shell nanoparticles in biological environments

Silver nanoparticles (AgNPs) are extensively used as an antibacterial agent, and monitoring the dissolution behavior of AgNPs in native biological environments is critical in both optimizing their performance and regulating their safety. However, current assessment methods rely on sophisticated analytical tools that are off-site and time-consuming with potential underestimations, due to complicated sample preparation. Although localized surface plasmon resonance (LSPR) sensing offers a facile method for the detection of AgNP dissolution, it is limited by low sensitivity and poor nanoparticle stability in native biological environments. Herein, we constructed a highly sensitive and stable LSPR sensor using gold-silver core-shell nanoparticles (Au@AgNPs), in combination with polymeric stabilizing agents, for the direct measurement of the Ag shell dissolution in native biological media. The high sensitivity was attributed to the acute and large LSPR shift generated by bimetallic nanoparticles. The sensor was used for the real-time monitoring of the Ag dissolution of Au@AgNPs during their co-culture with both bacteria and fibroblast cells. The media pH was found to dominate the Ag dissolution process, where Au@AgNPs exhibited bactericidal effects in the bacteria environment with relatively low pH, but they showed little toxicity towards fibroblast cells at pH 7.4. The minimum inhibition concentration of Au@AgNPs for bacterial growth was found similar to that of AgNO3 in terms of released Ag amount. Thus, stabilized Au@AgNPs not only allow the in-situ monitoring of Ag dissolution via LSPR sensing but also constitute an effective antibacterial agent with controlled toxicity, holding great potential for future biomedical and healthcare applications.

Reversible chirality inversion of an AuAgx-cysteine coordination polymer by pH change

Responsive chiral systems have attracted considerable attention, given their potential for diverse applications in biology, optoelectronics, photonics, and related fields. Here we show the reversible chirality inversion of an AuAgx-cysteine (AuAgx-cys) coordination polymer (CP) by pH changes. The polymer can be obtained by mixing HAuCl4 and AgNO3 with L-cysteine (or D-cysteine) in appropriate proportions in H2O (or other surfactant solutions). Circular dichroism (CD) spectrum is used to record the strong optical activity of the AuAg0.06-L-cys enantiomer (denoted as L0.06), which can be switched to that of the corresponding D0.06 enantiomer by alkalization (final dispersion pH > 13) and can be switched back after neutralization (final dispersion pH <8). Multiple structural changes at different pH values (≈9.6, ≈13) are observed through UV-Vis and CD spectral measurements, as well as other controlled experiments. Exploration of the CP synthesis kinetics suggests that the covalent bond formation is rapid and then the conformation of the CP materials would continuously evolve. The reaction stoichiometry investigation shows that the formation of CP materials with chirality inversion behavior requires the balancing between different coordination and polymerization processes. This study provides insights into the potential of inorganic stereochemistry in developing promising functional materials.

Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study

Tubulin has been recently reported to form a large family consisting of various gene isoforms; however, the differences in the molecular features of tubulin dimers composed of a combination of these isoforms remain unknown. Therefore, we attempted to elucidate the physical differences in the molecular motility of these tubulin dimers using the method of measurable pico-meter-scale molecular motility, diffracted X-ray tracking (DXT) analysis, regarding characteristic tubulin dimers, including neuronal TUBB3 and ubiquitous TUBB5. We first conducted a DXT analysis of neuronal (TUBB3-TUBA1A) and ubiquitous (TUBB5-TUBA1B) tubulin dimers and found that the molecular motility around the vertical axis of the neuronal tubulin dimer was lower than that of the ubiquitous tubulin dimer. The results of molecular dynamics (MD) simulation suggest that the difference in motility between the neuronal and ubiquitous tubulin dimers was probably caused by a change in the major contact of Gln245 in the T7 loop of TUBB from Glu11 in TUBA to Val353 in TUBB. The present study is the first report of a novel phenomenon in which the pico-meter-scale molecular motility between neuronal and ubiquitous tubulin dimers is different.

Advances in the design of amino acid and peptide synthesized gold nanoparticles for their applications

The field of therapeutics and diagnostics is advanced by nanotechnology-based approaches including the spatial-temporal release of drugs, targeted delivery, enhanced accumulation of drugs, immunomodulation, antimicrobial action, and high-resolution bioimaging, sensors and detection. Various compositions of nanoparticles (NPs) have been developed for biomedical applications; however, gold NPs (Au NPs) have attracted tremendous attention due to their biocompatibility, easy surface functionalization and quantification. Amino acids and peptides have natural biological activities as such, their activities enhance several folds in combination with NPs. Although peptides are extensively used to produce various functionalities of Au NPs, amino acids have also gained similar interests in producing amino acid-capped Au NPs due to the availability of amine, carboxyl and thiol functional groups. Henceforth, a comprehensive review is needed to timely bridge the synthesis and the applications of amino acid and peptide-capped Au NPs. This review aims to describe the synthesis mechanism of Au NPs using amino acids and peptides along with their applications in antimicrobial, bio/chemo-sensors, bioimaging, cancer therapy, catalysis, and skin regeneration. Moreover, the mechanisms of various activities of amino acid and peptide capped-Au NPs are presented. We believe this review will motivate researchers to better understand the interactions and long-term activities of amino acid and peptide-capped Au NPs for their success in various applications.

Dual-emissive phenylalanine dehydrogenase-templated gold nanoclusters as a new highly sensitive label-free ratiometric fluorescent probe: heavy metal ions and thiols measurement with live-cell imaging

Phenylalanine dehydrogenase (PheDH) has been proposed as an ideal protein scaffold for the one-step and green synthesis of highly efficient multifunctional gold nanoclusters. The PheDH-stabilized fluorescent gold nanoclusters (PheDH-AuNCs) with dual emission/single excitation exhibited excellent and long-term stability, high water solubility, large Stokes shift and intense photoluminescence. Selectivity studies demonstrated that the red fluorescence emission intensity of PheDH-AuNCs was obviously decreased in less than 10 min by the addition of mercury, copper, cysteine or glutathione under the single excitation at 360 nm, without significant change in the blue emission of the PheDH-AuNCs. Therefore, the as-prepared PheDH-AuNCs as a new excellent fluorescent probe were successfully employed to develop a simple, rapid, low cost, label- and surface modification-free nanoplatform for the ultrasensitive and selective detection of Hg2+, Cu2+, Cys and GSH through a ratiometric fluorescence system with wide linear ranges and detection limits of 1.6, 2.4, 160 and 350 nM, respectively which were lower than previous reports. In addition, the results showed that PheDH-AuNCs can be used for the detection of toxic heavy metal ions and small biomarker thiols in biological and aqueous samples with acceptable recoveries. Interestingly, PheDH-AuNCs also displayed a promising potential for live-cell imaging due to their low toxicity and great chemical- and photo-stability.

Density Functional Theory Computation and Machine Learning Studies of Interaction between Au3 Clusters and 20 Natural Amino Acid Molecules

The optimal adsorption sites and the binding energies of neutral Au₃ clusters with 20 natural amino acids under the gas phase and water solvation were systematically investigated based on density functional theory (DFT) calculations. The calculation results showed that in the gas phase Au₃ tends to bind with N atoms of amino groups in amino acids, except methionine, which tends to bind with Au₃ through S atoms. Under water solvation, Au₃ clusters tended to bind to N atoms of amino groups and N atoms of side chain amino groups in amino acids. However, methionine and cysteine bind more strongly to the gold atom through the S atom. Based on the binding energy data of Au₃ clusters and 20 natural amino acids under water solvation calculated by DFT, a machine learning model (gradient boosted decision tree) was proposed to predict the optimal binding Gibbs free energy (ΔG) of the interaction between Au₃ clusters and amino acids. The main factors affecting the strength of the interaction between Au₃ and amino acids were uncovered by the feature importance analysis.

Engineering Geobacter pili to produce metal:organic filaments

The organized self-assembly of conductive biological structures holds promise for creating new bioelectronic devices. In particular, Geobacter sulfurreducens type IVa pili have proven to be a versatile material for fabricating protein nanowire-based devices. To scale the production of conductive pili, we designed a strain of Shewanella oneidensis that heterologously expressed abundant, conductive Geobacter pili when grown aerobically in liquid culture. S. oneidensis expressing a cysteine-modified pilin, designed to enhance the capability to bind to gold, generated conductive pili that self-assembled into biohybrid filaments in the presence of gold nanoparticles. Elemental composition analysis confirmed the filament-metal interactions within the structures, which were several orders of magnitude larger than previously described metal:organic filaments. The results demonstrate that the S. oneidensis chassis significantly advances the possibilities for facile conductive protein nanowire design and fabrication.

Silver cluster interactions with Pterin: Complex structure, binding energies and spectroscopy

Metal nanoclusters (NCs) are widely present today in biosensing, bioimaging, and diagnostics due to their small size, great biocompatibility, and sensitivity to the biomolecular environment. Silver (Ag) NCs often possess intense fluorescence, photostability, and low photobleaching, which is in high demand during the detection of organic molecules. Pterins are small compounds, which are used in medicine as biomarkers of oxidative stress, cardiovascular diseases, neurotransmitter synthesis, inflammation and immune system activation. It is experimentally possible to detect pterin (Ptr) through the adsorption on Ag colloid. We optimized geometries and evaluated the binding energy in Ptr-Ag_n^q complexes (n = 1-6; q = 0, +1, +2) using quantum chemistry methods. Different Ptr atoms were preferential for silver attachment depending on NC charge and size. The highest E_b was obtained for the complexes between the Ptr⁰ and Ag₃²⁺ (-50.8 kcal mol^-1), between Ptr^-1 and Ag₃²⁺ (-64.8 kcal mol^-1), which means that these complexes should be formed preferably in aqueous solutions in acidic and alkaline media, respectively. The colorimetric detection of pterin with silver clusters does not seem to be promising. However, intense S_0→S₁ transitions of Ag₅⁺ complexes look promising for luminescent Ptr detection. SERS detection of pterin is better to be done at pH > 8 since deprotonated pterin Raman undergo more dramatic changes upon addition of Ag than the neutral pterin. The characteristics of absorption and vibrational spectra of silver-pterin should be exploited during biosensor development.

Functionalisation of Inorganic Material Surfaces with Staphylococcus Protein A: A Molecular Dynamics Study

Staphylococcus protein A (SpA) is found in the cell wall of Staphylococcus aureus bacteria. Its ability to bind to the constant Fc regions of antibodies means it is useful for antibody extraction, and further integration with inorganic materials can lead to the development of diagnostics and therapeutics. We have investigated the adsorption of SpA on inorganic surface models such as experimentally relevant negatively charged silica, as well as positively charged and neutral surfaces, by use of fully atomistic molecular dynamics simulations. We have found that SpA, which is itself negatively charged at pH7, is able to adsorb on all our surface models. However, adsorption on charged surfaces is more specific in terms of protein orientation compared to a neutral Au (111) surface, while the protein structure is generally well maintained in all cases. The results indicate that SpA adsorption is optimal on the siloxide-rich silica surface, which is negative at pH7 since this keeps the Fc binding regions free to interact with other species in solution. Due to the dominant role of electrostatics, the results are transferable to other inorganic materials and pave the way for new diagnostic and therapeutic designs where SpA might be used to conjugate antibodies to nanoparticles.

Synthesis of silver and gold nanoparticles-enzyme-polymer conjugate hybrids as dual-activity catalysts for chemoenzymatic cascade reactions

Novel hybrids containing silver or gold nanoparticles have been synthesized in aqueous media and at room temperature using enzymes or tailor-made enzyme-polymer conjugates, which directly induced the formation of inorganic silver or gold species. The choice of pH, protein, or bioconjugate strongly affected the final metallic nanoparticles hybrid formation. Using Candida antarctica lipase (CALB) in a solution, nanobiohybrids containing Ag₂O nanoparticles of 9 nm average diameter were obtained. The use of tailor-made bioconjugates, for example, the CALB modified with dextran-aspartic acid polymer (Dext6kDa), resulted in a nanobiohybrid containing smaller Ag(0)/Ag₂O nanoparticles. In the case of nanobiohybrids based on gold, Au(0) species were found in all cases. The Au-CALB hybrid contained spherical nanoparticles with 18 nm average diameter size, with a minor range of larger ones (>100 nm) while the AuNPs-CALB-Dext6kDa hybrid was formed by much smaller nanoparticles (9 nm, minor range of 22 nm), and also nanorods of 20-30/40-50 nm length. Using Thermomyces lanuginosus lipase (TLL), apart from the nanoparticle formation, nanoflowers with a diameter range of 100-200 nm were obtained. All nanobiohybrids maintained (dual) enzymatic and metallic activities. For instance, these nanobiohybrids exhibited exquisite dual-activity for hydrolysis/cycloisomerization cascades starting from allenic acetates. By merging the transition metal reactivity with the inherent lipase catalysis, allenic acetates directly converted to the corresponding O-heterocycles in enantiopure form catalysed by AgNPs-CALB-Dext6kDa, taking advantage of a kinetic resolution/cyclization pathway. These results showed the high applicability of these novel hybrids, offering new opportunities for the design of novel reaction cascades.

Silver Cluster Interactions with Tyrosine: Towards Amino Acid Detection

Tyrosine (Tyr) is involved in the synthesis of neurotransmitters, catecholamines, thyroid hormones, etc. Multiple pathologies are associated with impaired Tyr metabolism. Silver nanoclusters (Ag NCs) can be applied for colorimetric, fluorescent, and surface-enhanced Raman spectroscopy (SERS) detection of Tyr. However, one should understand the theoretical basics of interactions between Tyr and Ag NCs. Thereby, we calculated the binding energy (Eb) between Tyr and Agnq (n = 1-8; q = 0-2) NCs using the density functional theory (DFT) to find the most stable complexes. Since Ag NCs are synthesized on Tyr in an aqueous solution at pH 12.5, we studied Tyr-1, semiquinone (SemiQ-1), and Tyr-2. Ag32+ and Ag5+ had the highest Eb. The absorption spectrum of Tyr-2 significantly red-shifts with the attachment of Ag32+, which is prospective for colorimetric Tyr detection. Ag32+ interacts with all functional groups of SemiQ-1 (phenolate, amino group, and carboxylate), which makes detection of Tyr possible due to band emergence at 1324 cm-1 in the vibrational spectrum. The ground state charge transfer between Ag and carboxylate determines the band emergence at 1661 cm-1 in the Raman spectrum of the SemiQ-1-Ag32+ complex. Thus, the prospects of Tyr detection using silver nanoclusters were demonstrated.

Chiral Recognition on Bare Gold Surfaces by Quartz Crystal Microbalance

Quartz crystal microbalance (QCM) is one of the powerful tools for the studies of molecular recognition and chiral discrimination. Its efficiency mainly relies on the design of the functional sensitive layer on the electrode surface. However, the organic sensitive layer may easily cause dissipation of oscillation or detachment and weaken the signal transfer during the molecular recognition processes. In this work, we reveal for the first time that the bare metal surface without the organic selector layer has the capability for chiral recognition in the QCM system. During the adsorption of various chiral amino acids, relatively higher selectivity of D-enantiomers on gold (Au) surface was shown by the QCM detection. Based on analyses of the surface crystalline structure and density functional theory calculations, we demonstrate that the chiral nature of Au surface plays an important role in the selective binding of specific D-amino acids. These results may open new insights on chiral detection by QCM system. It will also promote the construction of novel chiral sensing systems with both efficient detection and separation capability.

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.

Theoretical Study of the Binding of the Thiol-Containing Cysteine Amino Acid to the Silver Surface Using a Cluster Model

Computational approaches within the framework of density functional theory (DFT) were employed to elucidate the binding mechanism of the cysteine amino acid on silver nanoparticles using several small silver clusters Ag_n with n = 2-10 as surface models. The long-range corrected LC-BLYP functional and correlation consistent basis sets cc-pVTZ-PP and cc-pVTZ were used to determine the structural features, energetics, and spectroscopic and electronic properties of the resulting complexes. In vacuum and highly acidic conditions, cysteine molecules prefer to adsorb on silver clusters via their amine group. In aqueous solution, the thiolate head turns out to be the most energetically favorable binding site. The cysteine affinity of silver clusters is greatly altered in different conditions, i.e., acidic solution < vacuum < aqueous solution, and is strongly dependent on the cluster size. As compared to free clusters, the frontier orbital energy gap of the ones capped by cysteine is significantly improved, which corresponds to stronger stability, especially in aqueous solution. The analysis of frontier orbitals also reveals that both forward and backward electron donations exhibit comparable contributions to the enhancement of stabilizing interactions. As for an application, a chemical enhancement mechanism of the surface-enhanced Raman scattering (SERS) procedure of cysteine by silver clusters was also analyzed.

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.