In nanotechnology, amino acids (AAs) and polypeptides serve as biomolecular templates for the synthesis of copper nanoclusters (NCs) and nanoparticles, directing their size, stability, and structural geometry. To elucidate the underlying binding motifs, we performed density functional theory (DFT) calculations on all 20 proteinogenic amino acids complexed with copper, systematically analyzing their coordination preferences, electronic interactions and topology. Our computations of Cu+-AA binding energies (Gb) are in agreement with previous mass-spectrometry data. DFT calculations identified deprotonated amino acids (AAs) as the predominant sites for copper (Cu2, Cu8 and Cu20) nucleation. Among neutral AAs, arginine, histidine, and tryptophan exhibited the strongest interactions. Moreover, we compared the binding energy of copper, silver and gold with AAs/DNA nucleobases, which led us to a conclusion that Cu atoms possess higher mobility in biopolymer matrices than Au, but lesser mobility than silver. Moreover, several hydrated ion models have been regarded. We suppose, our results are of significant importance for the studies of copper nanostructures and copper-containing proteins.

Hydrogen peroxide (H2O2) is a type of reactive oxygen species widespread in biological tissues. It is an important biomarker of oxidative stress, cancers, asthma, etc. In this regard, development of precise and cost-effective sensors for detection of H2O2 in vitro and in vivo is of great significance for biomedicine. In this paper, a colorimetric method is introduced for sensing hydrogen peroxide using tyrosine-stabilized silver nanoparticles. In aqueous solutions, the colorimetric method demonstrated a linear range of 0.4-5 μM with a detection limit (LOD) of 150 nM, whereas in human blood serum the linear range was within 0.7-20 μM characterized by a LOD of 250 nM. Recovery tests in blood serum yielded results within the acceptable range 96-101%, confirming the method's accuracy and reliability. Possible mechanisms of silver nanoparticles/nanoclusters interaction with H2O2 during its detection were examined using fluorescence spectroscopy and dynamic light scattering methods.

Pterins are naturally occurring compounds widespread in living organisms. 5,6,7,8-Tetrahydrobiopterin (H(4)Bip) is a cofactor of several key enzymes, including NO-synthases and phenylalanine hydroxylase, whereas tetrahydrocyanopterin is a photoreceptor molecule in cyanobacteria. In this regard, tetrahydropterins (H(4)pterins) photochemistry and photophysics have been attracting our attention. H(4)pterins photodegrade in presence of molecular oxygen yielding dihydropterins (H(2)pterins) and oxidized pterins. Meanwhile, the excited states dynamics of H(4)pterins on a femto- and picosecond time-scale remains unclear. To shed light on this area, we perform time-resolved spectroscopy of H(4)Bip using fluorescence up-conversion as well as transient absorption spectroscopy techniques along with TD-DFT non-adiabatic molecular dynamics. We show that the lowest H(4)Bip exited state has a lifetime of ca. 200 fs. Using the BHandHLYP functional and multireference spin-flip (MRSF) method we demonstrate that starting from the S-4 state, H(4)Bip passes to the S-1 state within 50 fs, and after 200 fs a conical intersection with the ground S-0 state is achieved. As a whole, the excited state behavior of H(4)Bip is similar to DNA nucleobases, in particular guanine. These findings allow us to make some speculations about the biochemical role of H(4)pterins photophysics.

Silver nanoclusters (Ag NCs) are widely applied in the biosensing of metal ions, small organic molecules, nucleic acids, amino acids, and proteins due to their particular fluorescence and chemical properties. Organic matrices such as DNA are usually employed for Ag NC synthesis and stabilization. They make Ag NC/matrix complexes biocompatible and sensitive to the environment. It has recently been shown that Ag NCs based on DNA matrices are capable of self-assembly and rearrangement followed by a change in the fluorescence and absorbance characteristics. These attributes allow the development of sensors with target molecule detection visible even by the naked eye. Here we suggest a simple one-step turn-on highly specific microRNA-210 sensor based on a fluorescent Ag NC. The main feature of the sensor is the smart design of a binary matrix, which provides the appearance of a bright green fluorescence signal only after Ag NCs/DNA-matrix complexes are bonded to the target sequence. The microRNA detection assay requires no additional action because the process proceeds by itself. A comprehensive optimization of the binary probe structure and location was carried out. An approach to detection leading to minimal background signal was defined as follows. The approach involves the preliminary synthesis of non-fluorescent silver clusters using a single strand of the binary matrix containing a 5 '-CCCGTTTT-3 ' part. It was shown that these "dark" structures can be stored for at least a month before analysis. The fluorescence intensity of the green Ag NCs increases in the presence of the microRNA-210 sequence, and that dependence on the target concentration tends to be linear in the range of 5-500 nM. The sensor demonstrates specificity to the miR-210 sequence, and the LOD (limit of detection) was established as 5 nM in serum samples.

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.

We have studied the excited states and structural properties for the complexes of cytosine (dC)10 chains with silver ions (Ag+) in a wide range of the Ag+ to DNA ratio (r) and pH conditions using circular dichroism, steady-state absorption, and fluorescence spectroscopy along with the ultrafast fluorescence upconversion technique. We also calculated vertical electronic transition energies and determined the nature of the corresponding excited states in some models of the cytosine-Ag+ complexes. We show that (dC)10 chains in the presence of silver ions form a duplex stabilized by C-Ag+-C bonds. It is also shown that the i-motif structure formed by (dC)10 chains is destabilized in the presence of Ag+ ions. The excited-state properties in the studied complexes depend on the amount of binding ions and the binding sites, which is supported by the calculations. In particular, new low-lying excited states appear when the second Ag+ ion interacts with the O atom of cytosine in the C-Ag+-C pairs. A similar picture is observed in the case when one Ag+ ion interacts with one cytosine via the N7 atom.

Pteridines are important low molecular weight biomarkers used in the diagnostics of inflammation, oxidative stress, phenylketonuria, cancer, etc. In this experimental study, we present a simple and selective approach to determine pteridines (pterin, leucopterin and folic acid) and nucleobase guanine concentration using luminescent gold clusters stabilized by aromatic amino acids. We synthesized several new gold clusters (AA-Au NCs) stabilized by various aromatic amino acids - 3,4-dihydroxy-L-phenylalanine (DOPA), L-tryptophan (Trp), L-tyrosine (Tyr) and L-phenylalanine (Phe), emitting in the violet-green spectral range. Their luminescence appeared to be sensitive to the presence of pterin, leucopterin, folic acid and guanine depending on the stabilizing matrix. Thus, a facile and cost-effective approach for the detection of pteridines is proposed. AA-Au NC-based sensors work according to "turn-off" and "turn-on" mechanisms. The possible physical origins of their luminescence quenching and enhancement are discussed.

In this experimental study, we developed a simple and selective approach to determine the concentrations of human serum albumin (HSA) and total amount of immunoglobulins (Ig) in real human serum (HS) sample using luminescent gold nanoclusters (Au NCs). In doing so, Au NCs were grown directly on the HS proteins without any sample pretreatment. We synthesized Au NCs on HSA and Ig and studied their photophysical properties. Using combined fluorescent and colorimetric assay we were able to obtain protein concentrations with a high degree of accuracy relative to techniques currently used in clinical diagnostics. We used method of standard additions to determine both HSA and Ig concentrations in HS by the Au NCs absorbance and fluorescence signals. A simple and cost-effective method developed in this work represents an excellent alternative to the techniques currently used in clinical diagnostics.

L-DOPA, or l-3,4-dihydroxyphenylalanine is an aromatic amino acid, which plays a significant role in human metabolism as a precursor of important neurotransmitters. We develop a fast and simple colorimetric method for the detection of L-DOPA in biological fluids. The method is based on the reduction of silver ions with L-DOPA and the subsequent formation of L-DOPA stabilized silver nanoparticles (Ag NPs). In this novel approach, L-DOPA works as both reducing and stabilizing agent, which provides selectivity and simplifies the procedure. HR-TEM images show very narrow Ag NPs distribution with an average size of 24 nm. Such sensor design is suggested for the first time. We also calculate vertical ionization potential, vertical electron affinity, and Gibbs free energy change of different ionic forms of L-DOPA and amino acids at the M06-2X/def2-TZVP level for the gas phase in comparison with that of silver. A model of silver ions reduction by aromatic amino acids is proposed: the ionic forms with charge −1 are suggested to reduce silver ions. High selectivity against aromatic amino acids, dopamine and serotonin is achieved by tuning pH and involving two L-DOPA forms with charged both hydroxyphenolate and carboxylate groups in the stabilization of uniform-sized Ag NPs. The method is applicable for the determination of L-DOPA in human serum with the 50 nM limit of detection and the linear range up to 5 μM. Ag NPs formation and coloring the solution proceeds in a few minutes. The suggested colorimetric method has potential application in clinical trials.

Gold (Au) nanoclusters (NCs) are novel materials with low cytotoxicity and high chemical stability. These properties are in high demand during the bioimaging. Moreover, the optical properties of gold clusters allow to use them as colorimetric and luminescent bionanosensors. Pterins are low molecular weight organic compounds, which are used in medicine as biomarkers of phenylketonuria, vitiligo, inflammation and immune system activation, cancer, COVID-19, etc. We have investigated the possibility of gold nanosensors usage to detect pterin (Ptr). Ptr-Aun structures (n = 1-6; q = 0-2) Gibbs energy of complexation (Eb) have been obtained using density functional theory. The highest Eb was determined for the complexes of Au62+ and Au32+ in acidic and alkaline aqueous solution, respectively. The detection of pterin with gold clusters seems to be prospective using both colorimetric and fluorescent detection because of the intense S0 & RARR;S1 transition in the absorption spectrum of the Au5+complex. Raman detection of pterin should be performed at alkaline pH because of the dramatic changes in the spectrum of Ptr-1 upon the addition of Au clusters. We believe that these tunable changes of the pterin spectra due to Au clusters and nanoparticles attachment could be exploited in further studies on nanosensor design.

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-Agnq 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 Eb 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 S0 -> 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.

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.

Theoretical calculations of excited states in the complexes of gold and silver three-atom nanoclusters with carbon quantum nanodots are performed using the M062X functional and the def2SVP {H}/def2TZVP/def2TZVPP{Ag, Au} hybrid basis set. A subsequent calculation of the excited states is performed in an approximation of the time-dependent density functional theory implemented in Gaussian09. The chromophore centers of the nanodots are modeled by heterocyclic molecules of isoquino-diazaanthracene and benzopyrano-diazanaphthalene. The clusters are attached to the nanodots using ethyl mercaptan and methoxyethane bridges of various lengths. The energy transfer channels are considered depending on the mutual arrangement of energy levels of clusters and heterocycles.

Fluorescent beacons based on silver (Ag) clusters for DNA/RNA detection represent a new type of turn-on probe that fluoresces upon hybridization to target nucleobase sequences. Physical-chemical mechanisms of their fluorescence activation still remain poorly understood. We studied in detail the fluorescence activation of dark Ag clusters induced by interactions of Ag-DNA complexes with different DNA sequences. In all cases, the final result depends neither on the location of the precursors (dark clusters) nor on their spectral properties. The reaction of fluorescence activation is a process similar to the growth of fluorescent silver clusters on dsDNA matrices. In both cases, reactants are dark clusters and two adjacent DNA strands. The latter form a double-stranded template for cluster nucleation. We found the optimized structure of a green fluorescent Ag-4(+2) cluster assembled on a C3/C3 DNA dimer in two different ssDNA pairs using QM modeling. The calculated absorption spectra match nicely the experimental ones, which proves the optimized structures. We conclude that apparent fluorescence activation in the studied systems results from reassembling Ag clusters on the new dsDNA template formed upon hybridization with the target. The suggested mechanism of "fluorescence activation" offers a way to design new light-up DNA probes. Two DNA strands making up the dsDNA template providing a high yield of bright Ag clusters can be used as the halves with the "stick" tails hybridizing with the base sequence of the target DNA. In this way, we have designed a light-up Ag cluster probe for beta-actin mRNA.

In this work we designed, synthesized and characterized luminescent metal nanoclusters (NCs) on human serum albumin (HSA) and immunoglobulins (Ig). We demonstrate that the approach developed allows one to determine the relative content of albumins and immunoglobulins in biologically relevant protein mixtures based on the luminescent properties of the NCs. Fast and inexpensive approach which allows to determine concentrations of immunoglobulins (Ig) and serum albumin (HSA) in blood serum might be useful in clinical diagnostics.

The mechanism of fluorescence quenching of the human serum albumin by transferring the energy of the photoinduced electronic excitation from the single tryptophan residue in the structure to the nitrospiropyran donor introduced into its environment is studied by the hybrid computer simulation, including the classical molecular dynamics and the semi-empirical photo-physical calculations for generating the statistical spectra of tryptophan emission and spectra of nitrospiropyran absorption. The probability of the electronic excitation redistribution between the donor and the acceptor is estimated, followed by the photochromic conversion of nitrospiropyran to the merocyanine form, which is readily identifiable due to a significant shift of the longwave absorption band and can be treated as a luminescence detector of the ongoing photoprocesses. The mechanisms of the energy transfer between nonequilibrium fragments in typical combinations of their complex are considered in detail. The general scheme and technical specifics of modeling the optical spectra are illustrated using a simple system of the anthracene molecule in argon. A discussion of several other advanced hybrid approaches of the classical methods in combination with the quantum-mechanical calculations, developed at different theoretical levels and applied in the current computational molecular spectroscopy, is presented.

Metal nanoclusters (NCs) have gained much attention in the last decade. In solution, metal nanoclusters can be stabilized by proteins, and, thus, exhibit many advantages in biocatalysis, biosensing, and bioimaging. In spite of much progress in the synthesis of polypeptide-stabilized gold (Au) clusters, their structure, as well as amino acid-cluster and amino acid-Au+ interactions, remain poorly understood. It is not entirely clear which amino acid (AA) residues and sites in the protein are preferred for binding. The understanding of NC-protein interactions and how they evolve in the polypeptide templates is the key to designing Au NCs. In this work, binding of gold ion Au+ and diatomic neutral gold nanocluster Au2 with a full set of α-proteinogenic amino acids is studied using Density Functional Theory (DFT) and the ab initio RI-MP2 method in order to find the preferred sites of gold interaction in proteins. We demonstrated that the interaction of gold cations and clusters with protonated and deprotonated amino acid residues do not differ greatly. The binding affinity of AAs to the Au2 cluster increases in the following order: Cys(-H+) > Asp(-H+) > Tyr(-H+) > Glu(-H+) > Arg > Gln, His, Met ≫ Asn, Pro, Trp > Lys, Tyr, Phe > His(+H+) > Asp > Lys(+H+) > Glu, Leu > Arg(+H+) > Ile, Val, Ala > Thr, Ser > Gly, Cys, which agrees with the available experimental data that gold cluster synthesis occurs in a wide range of pH - amino acid residues with different protonation states are involved in this process. The significant difference in the binding energy of metal atoms with nucleobases and amino acids apparently means that unlike on DNA templates, neutral metal atoms are strongly bound to amino acid residues and can't freely diffuse in a polypeptide globula. This fact allows one to conclude that formation of metal NCs in proteins occurs through the nucleation of reduced Au atoms bound to the neighboring amino acid residues, and the flexibility of the amino acid residue side-chains and protein chain as a whole plays a significant role in this process.

Metal nanoparticles and nanoclusters are progressively studied for use in various biomedical applications such as imaging, drug delivery, and therapies. Therefore, considering the interaction of biopolymers with metal nanostructures becomes vital for their efficient application. Luminescent metal nanoclusters are now widely considered as potential sensor applications. In this work we considered the interaction of silver nanoparticles with some proteins and oligonucleotides. We observed that biomolecules in some cases can effectively dissolve nanoparticles and lead to the formation of silver nanoclusters.

The mechanisms underlying the sensory activity of silver clusters (Ag NCs) synthesized on oligonucleotide matrices are not understood yet. It is known that close proximity of cytosine and guanine rich sequences causes colour changes in the luminescence of Ag NCs. We studied two types of fluorescence activation of Ag NCs due to close proximity of two DNA strands. We concluded that the activation phenomenon could be explained by the same mechanism, namely by the reassembling of the silver atoms on the double-stranded DNA formed upon hybridization. Our results could be useful for further Ag NCs-based sensors development.

Binding of silver ion (Ag+) and two atomic neutral silver cluster (Ag2) with a set of amino acids has been studied using Density Functional Theory (DFT) and ab initio MP2 method. We show that binding energy with Ag2 is higher for deprotonated anionic amino acids. Cysteine, aspartic acid, and tyrosine with deprotonated side chain exhibit the highest binding energy (Gbind) values among all the amino acids: − 30.1 kcal mol−1, − 30.7 kcal mol−1, and − 30.9 kcal mol−1, respectively. Binding energies of deprotonated cysteine, glutamic acid, tyrosine, and aspartic acid with silver ion Ag+ are reported here for the first time. Natural bond orbital (NBO) analysis has also been performed to calculate charge transfer, natural populations, occupancies, and Wiberg bond indices of the amino acid–Ag2 complexes. Atoms-in-molecules (AIM) theory was used to establish the nature of interactions. It was shown that, in most cases, the bonds between amino acid and Ag2 cluster are partially electrostatic and partially covalent.