Photo- and thermo- isomerization trajectories of various conversion pathways between nitro-spiropyran and its trans–trans–cis merocyanine form were produced and the role of nπ* states was ...investigated along the corresponding potential energy surface calculated using the ωB97XD functional and the cc-pVDZ basis set. The nondissociative nπ* states on the photoisomerization trajectories can switch from/to the dissociative photoactive ππ* state at two intersections between their energy surfaces. The photochromic properties inherited in hybrid compounds of nitro-spiropyran-containing 60fullerene are interpreted due to a reversible “dual energy bypass” ππ*↔nπ* mechanism in terms of both adiabatic absorption and highly effective nonadiabatic dissipative transitions between the excited states of the photochromic fragment, that prevents energy loss through the 60fullerene and in this way keeps the photochromic properties intact.
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.
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 Ag4 +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 β-actin mRNA.
The detailed structures of most of ligand‐stabilized metal nanoclusters (NCs) remain unknown due to the absence of crystal structure data for them. In such a situation, quantum‐chemical modeling is ...of particular interest. We compared the performance of different theoretical methods of geometry optimization and absorption spectra calculation for silver‐thiolate complexes. We showed that the absorption spectra calculated with the ADC(2) method were consistent with the spectra obtained with CC2 method. Three DFT functionals (B3LYP, CAM‐B3LYP, and M06‐2X) failed to reproduce the CC2 absorption spectra of the silver‐thiolate complexes.
The performance of different theoretical methods of geometry optimization and absorption spectra calculation for silver‐thiolate complexes was compared. It was shown that the absorption spectra calculated with the ADC(2) are consistent with the spectra obtained with CC2 method. Three DFT functionals (B3LYP, CAM‐B3LYP, and M06‐2X) failed to reproduce the CC2 absorption spectra of the silver‐thiolate complexes.
The photophysical and isomerization properties of hybrid molecular compounds that consist of photochromic nitro-substituted and halogenated spiropyran derivatives bonded to the surface of the ...60fullerene cage through the pyrrolidine bridge were investigated using various functionals and basis sets of TD-DFT and semiempirical quantum-chemical approaches. The role of nπ* states formed by the lone pairs of substituents in changing of the electronic structure and photochromic properties of spiropyran derivatives was evaluated. The Sππ(spiropyran) → intermediate nπ* states → Sππ(merocyanine) channel for phototransformation of the hybrid compound containing a nitro-substituted spiropyran moiety was established and compared with similar systems of halogenated spiropyrans attached to the 60fullerene bulk where photoinduced isomerization does not process due to high probability of internal conversion from the excited electronic state localized on the spiropyran fragment to the states of the pyrrolidino60fullerene.
In this experimental and theoretical joint study, we used single amino acids as model systems for studying protein–cluster interactions. We probed 12 natural amino acids with different functional ...groups as potential templates of fluorescent silver (Ag) nanoclusters obtained by sodium borohydride reduction of Ag ions. We also calculated the Gibbs free energies of the complexes formed between Ag+ ions, Ag atoms, and two-atom Ag clusters with the amino acids’ various functional groups. Only cysteine and tyrosine could form fluorescent complexes with Ag clusters. This agrees with the calculated Gibbs free energies for the Ag cluster–amino acid complexes. We also show that the tyrosine-based fluorescent Ag cluster could be obtained using a green synthetic method in which tyrosine, at alkali pH, acts as a reducing agent. The optimized structure of a complex of Ag3 + cluster with three semiquinone tyrosine rings is proposed. These results can be used in designing and synthesizing new peptide-templated biolabels.
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•Statistical absorption and emission spectra of Dmz&Trp@HSA generated in two-scale model and charge transfer is studied.
Spectroscopy is an important tool for detecting drug binding ...to amino acid sequences. One such important spectroscopic process is the fluorescence quenching due to charge transfer (CT) processes between a drug molecule and the chromophore center of Human Serum Albumin (HSA). We present a theoretical investigation of the CT occurring upon electronic excitation when a dimetridazole (Dmz) molecule incorporated in HSA interacts with tryptophan residue (Trp214). Structures of the donor–acceptor complexes were optimized using density-functional theory in vacuum as well as extracted from molecular dynamics (MD) trajectories of the Dmz and Trp214 complexes in HSA (Dmz&Trp214@HSA). Absorption, emission, and fluorescence quenching of the Trp214&Dmz complex in a large number of MD conformers were calculated using various quantum-mechanical approaches in order to generate statistical spectra that are then used for studying the CT between the non-bonded donor and the acceptor.
The reaction of Cu(NCMe)4PF6 with aromatic acetylenes HC2R and triphosphine 1,1,1-tris(diphenylphosphino)methane in the presence of NEt3 results in the formation of hexanuclear Cu(I) clusters ...with the general formula Cu6(C2R)4{(PPh2)3CH}2PF62 (R = 4-X-C6H4 (1–5) and C5H4N (6); X = NMe2 (1), OMe (2), H (3), Ph (4), CF3 (5)). The structural motif of the complexes studied consists of a Cu6 metal core supported by two phosphine ligands and stabilized by σ- and π-coordination of the alkynyl fragments (together with coordination of pyridine nitrogen atoms in cluster 6). The solid state structures of complexes 2–6 were determined by single crystal XRD analysis. The structures of the complexes in solution were elucidated by 1H, 31P, 1H–1H COSY NMR spectroscopy, and ESI mass spectrometry. Clusters 1–6 exhibit moderately strong phosphorescence in the solid state with quantum yields up to 17%. Complexes 1–5 were found to form solvates (acetone, acetonitrile) in the solid state. The coordination of loosely bound solvent molecules strongly affects emission characteristics and leads to solvato- and vapochromic behavior of the clusters. Thus, solvent-free and acetonitrile solvated forms of 3 demonstrate contrasting emission in orange (615 nm) and blue (475 nm) regions, respectively. The computational studies show that alkynyl-centered IL transitions mixed with those of MLCT between the Cu6 metal core and the ligand environment play a dominant role in the formation of excited states and can be considerably modulated by weakly coordinating solvent molecules leading to luminescence vapochromism.
For the first time, lonsdaleite-rich impact diamonds from one of the largest Popigai impact crater (Northern Siberia) with a high concentration of structural defects are investigated under ...hydrostatic compression up to 25 GPa. It is found that, depending on the nature of a sample, the bulk modulus for lonsdaleite experimentally obtained by X-ray diffraction in diamond-anvil cells is systematically lower and equal to 93.3–100.5% of the average values of the bulk moduli of a diamond matrix. Density functional theory calculations reveal possible coexistence of a number of diamond/lonsdaleite and twin diamond biphases. Among the different mutual configurations, separate inclusions of one lonsdaleite (001) plane per four diamond (111) demonstrate the lowest energy per carbon atom, suggesting a favorable formation of single-layer lonsdaleite (001) fragments inserted in the diamond matrix. Calculated formation energies and experimental diamond (311) and lonsdaleite (331) powder X-ray diffraction patterns indicate that all biphases could be formed under high-temperature, high-pressure conditions. Following the equation of states, the bulk modulus of the diamond (111)/lonsdaleite (001) biphase is the largest one among all bulk moduli, including pristine diamond and lonsdaleite.
Luminescent metal nanoclusters (NCs) stabilized by natural proteins are of special interest in bioimaging applications. However, the detailed structure of the protein-templated NCs and the nature of ...their emissive states remain poorly understood. A fair amount of nonluminescent metal ions and clusters complexed to the proteins hinders probing of the structure of the emitting clusters using mass spectroscopy, infrared, or other conventional spectroscopy methods. In this respect, only luminescent excitation spectra distinguish the emitting NCs. In this experimental and theoretical joint study, we modeled the fluorescent excitation and excitation anisotropy spectra of protein-based silver (Ag) NCs. We varied the synthesis conditions and studied the spectral properties of Ag clusters on bovine serum albumin (BSA) and lysozyme, which had already been used as templates, as well as on HMG box (HMGB1) and histone H1 (H1) proteins. We also calculated the electronic spectra of quantum mechanics-optimized Ag–thiolate, Ag–semiquinone, and Ag–formaldehyde complexes with two confined electrons using second-order algebraic diagrammatic construction ADC(2) and resolution-of-identity approximate coupled-cluster singles-and-doubles (RI-CC2) methods and compared them with the experimental spectra. We propose a model for the fluorescent Ag–protein complexes in which two reduced Ag atoms are sufficient to form the fluorescent core of the complex. The proposed structural model of the luminescent centers in the Ag–protein complexes differs from the common view that the fluorescent metal NCs in proteins contain about 10 or more metal atoms. The fluorescent Ag clusters formed on the four investigated natural protein matrices exhibited two different spectral and structural patterns. Deprotonated free cysteine residues stabilized the fluorescent Ag3 +1 core formed in the BSA matrix. The second type of fluorescent center was realized in the H1, HMGB1, and lysozyme protein matrixes. In this case, tyrosine residues probably stabilize the fluorescent Ag2 centers.
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