Mikhail Ryazantsev | Saint Petersburg State University (original) (raw)
Light Sensitive Proteins: Rhodopsins by Mikhail Ryazantsev
ACS Physical Chemistry Au, 2014
Genetically encoded voltage indicators (GEVIs) have found wide applications as molecular tools fo... more Genetically encoded voltage indicators (GEVIs) have found wide applications as molecular tools for visualization of changes in cell membrane potential. Among others, several classes of archaerhodopsin-3-based GEVIs have been developed and have proved themselves promising in various molecular imaging studies. To expand the application range for this type of GEVIs, new variants with absorption band maxima shifted toward the first biological window and enhanced fluorescence signal are required. Here, we integrate computational and experimental strategies to reveal structural factors that distinguish far-red bright archaerhodopsin-3-based GEVIs, Archers, obtained by directed evolution in a previous study (McIsaac et al., PNAS, 2014) and the wild-type archaerhodopsin-3 with an extremely dim fluorescence signal, aiming to use the obtained information in subsequent rational design. We found that the fluorescence can be enhanced by stabilization of a certain conformation of the protein, which, in turn, can be achieved by tuning the pKa value of two titratable residues. These findings were supported further by introducing mutations into wild-type archeorhodopsin-3 and detecting the enhancement of the fluorescence signal. Finally, we came up with a rational design and proposed previously unknown Archers variants with red-shifted absorption bands (λmax up to 640 nm) and potential-dependent bright fluorescence (quantum yield up to 0.97%).
International Journal of Molecular Sciences
A typical feature of proteins from the rhodopsin family is the sensitivity of their absorption ba... more A typical feature of proteins from the rhodopsin family is the sensitivity of their absorption band maximum to protein amino acid composition. For this reason, studies of these proteins often require methodologies that determine spectral shift caused by amino acid substitutions. Generally, quantum mechanics/molecular mechanics models allow for the calculation of a substitution-induced spectral shift with high accuracy, but their application is not always easy and requires special knowledge. In the present study, we propose simple models that allow us to estimate the direct effect of a charged or polar residue substitution without extensive calculations using only rhodopsin three-dimensional structure and plots or tables that are provided in this article. The models are based on absorption maximum values calculated at the SORCI+Q level of theory for cis- and trans-forms of retinal protonated Schiff base in an external electrostatic field of charges and dipoles. Each value corresponds...
International Journal of Molecular Sciences
Membrane potential is a fundamental property of biological cells. Changes in membrane potential c... more Membrane potential is a fundamental property of biological cells. Changes in membrane potential characterize a vast number of vital biological processes, such as the activity of neurons and cardiomyocytes, tumorogenesis, cell-cycle progression, etc. A common strategy to record membrane potential changes that occur in the process of interest is to utilize organic dyes or genetically-encoded voltage indicators with voltage-dependent fluorescence. Sensors are introduced into target cells, and alterations of fluorescence intensity are recorded with optical methods. Techniques that allow recording relative changes of membrane potential and do not take into account fluorescence alterations due to factors other than membrane voltage are already widely used in modern biological and biomedical studies. Such techniques have been reviewed previously in many works. However, in order to investigate a number of processes, especially long-term processes, the measured signal must be corrected to ex...
Journal of the American Chemical Society, 2012
Detailed knowledge of the molecular mechanisms that control the spectral properties in the rhodop... more Detailed knowledge of the molecular mechanisms that control the spectral properties in the rhodopsin protein family is important for understanding the functions of these photoreceptors and for the rational design of artificial photosensitive proteins. Here we used a high-level ab initio QM/MM method to investigate the mechanism of spectral tuning in the chloride-bound and anion-free forms of halorhodopsin from Natronobacterium pharaonis (phR) and the interprotein spectral shift between them. We demonstrate that the chloride ion tunes the spectral properties of phR via two distinct mechanisms: (i) electrostatic interaction with the chromophore, which results in a 95 nm difference between the absorption maxima of the two forms, and (ii) induction of a structural reorganization in the protein, which changes the positions of charged and polar residues and reduces this difference to 29 nm. The present study expands our knowledge concerning the role of the reorganization of the internal H-bond network for color tuning in general and provides a detailed investigation of the tuning mechanism in phR in particular.
Physical Chemistry Chemical Physics, 2020
Accurate prediction of water molecules in protein cavities is an important factor for obtaining h... more Accurate prediction of water molecules in protein cavities is an important factor for obtaining high-quality rhodopsin QM/MM models.
ACS omega, Jan 31, 2018
Rhodopsins are seven α-helical membrane proteins that are of great importance in chemistry, biolo... more Rhodopsins are seven α-helical membrane proteins that are of great importance in chemistry, biology, and modern biotechnology. Any in silico study on rhodopsin properties and functioning requires a high-quality three-dimensional structure. Due to particular difficulties with obtaining membrane protein structures from the experiment, in silico prediction of the three-dimensional rhodopsin structure based only on its primary sequence is an especially important task. For the last few years, significant progress was made in the field of protein structure prediction, especially for methods based on comparative modeling. However, the majority of this progress was made for soluble proteins and further investigations are needed to achieve similar progress for membrane proteins. In this paper, we evaluate the performance of modern protein structure prediction methodologies (implemented in the Medeller, I-TASSER, and Rosetta packages) for their ability to predict rhodopsin structures. Three w...
Journal of Chemical Theory and Computation
Journal of the American Chemical Society, 2011
The molecular dynamics (MD) trajectories were calculated using the velocity Verlet algorithm 1 ac... more The molecular dynamics (MD) trajectories were calculated using the velocity Verlet algorithm 1 accordingtotheclassical Newton'sequa?ons whichweresolvednumerically.At ?me(t)thealgorithmrequirescoordinates,veloci?esandforces asinput.Inthefirststepof thealgorithmthecoordinatesforthenew?mestep(t+dt)aredetermined:
Physical Chemistry Chemical Physics, 2009
Acceleration of the Z to E photoisomerization of penta-2,4-dieniminium by hydrogen out-of-plane m... more Acceleration of the Z to E photoisomerization of penta-2,4-dieniminium by hydrogen out-of-plane motion: Theoretical study on a model system of retinal protonated Schiff base submitted by: Masato Sumita, Mikhail N. Ryazantsev, and Kazuya Saito contents: Potential energy surfaces with the interpolated point at θ 1 = 50 • The Cartesian coordinates of the stationary points in the S 1 and S 0 states and the S 1 /S 0 degeneracy points (inÅ).
Photopharmacology by Mikhail Ryazantsev
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
European Journal of Pharmacology, 2023
ACS Chemical Neuroscience
Azobenzene-based quaternary ammonium compounds provide optical control of ion channels and are co... more Azobenzene-based quaternary ammonium compounds provide optical control of ion channels and are considered promising agents for regulation of neuronal excitability and for restoration of the photosensitivity of retinal cells. However, the selectivity of the action of these compounds remains insufficiently known. We studied the action of DENAQ (diethylamine-azobenzene-quaternary ammonium) and DMNAQ (dimethylamine-azobenzene-quaternary ammonium) on ionotropic glutamate receptors in rat brain neurons. In the dark, both compounds applied extracellularly caused fast and reversible inhibition of NMDA (N-methyl-d-aspartate) receptor-mediated currents with IC50 values of 10 and 5 μM, respectively. Light-induced transformation of DENAQ and DMNAQ to their cis forms caused the IC50 values to increase to 30 and 27 μM, respectively. Detailed analysis of this action revealed a complex nature consisting of fast inhibitory and slower potentiating effects. The AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptors were only weakly affected independently on illumination. We conclude that, in addition to their long-lasting intracellular action, which persists after washout, azobenzene-based quaternary ammonium compounds should affect glutamatergic transmission and synaptic plasticity during treatment. Our findings also extend the list of soluble photoswitchable inhibitors of NMDA receptors. While the site(s) and mechanisms of action are unclear, the effect of DENAQ demonstrates strong pH dependence. At acidic pH values, DENAQ potentiates both NMDA and AMPA receptors.
Papers by Mikhail Ryazantsev
ACS Physical Chemistry Au, Apr 29, 2024
Genetically encoded voltage indicators (GEVIs) have found wide applications as molecular tools fo... more Genetically encoded voltage indicators (GEVIs) have found wide applications as molecular tools for visualization of changes in cell membrane potential. Among others, several classes of archaerhodopsin-3-based GEVIs have been developed and have proved themselves promising in various molecular imaging studies. To expand the application range for this type of GEVIs, new variants with absorption band maxima shifted toward the first biological window and enhanced fluorescence signal are required. Here, we integrate computational and experimental strategies to reveal structural factors that distinguish far-red bright archaerhodopsin-3-based GEVIs, Archers, obtained by directed evolution in a previous study (McIsaac et al., PNAS, 2014) and the wild-type archaerhodopsin-3 with an extremely dim fluorescence signal, aiming to use the obtained information in subsequent rational design. We found that the fluorescence can be enhanced by stabilization of a certain conformation of the protein, which, in turn, can be achieved by tuning the pKa value of two titratable residues. These findings were supported further by introducing mutations into wild-type archeorhodopsin-3 and detecting the enhancement of the fluorescence signal. Finally, we came up with a rational design and proposed previously unknown Archers variants with red-shifted absorption bands (λmax up to 640 nm) and potential-dependent bright fluorescence (quantum yield up to 0.97%).
Journal of Physical Chemistry B, Apr 13, 2020
The ultrafast photochemistry of the [Cr(NCS)6]3- complex upon excitation to the 4T2 ligand-field ... more The ultrafast photochemistry of the [Cr(NCS)6]3- complex upon excitation to the 4T2 ligand-field (LF) state was studied in dimethylsulfoxide (DMSO) and N,N-dimethylformamide (DMF) in a wide temporal range (100 fs - 9 ms) by a combination of femtosecond and nanosecond transient absorption spectroscopy techniques and supported by quantum-chemical DFT/TD-DFT calculations. The initially excited 4T2 state undergoes intersystem crossing to the vibrationally hot 2E state with time constants of 1.1±0.2 and 1.8±0.1 ps in DMSO and DMF, respectively. Vibrational relaxation occurs in the same timescale and takes 1-5 ps. A major part of [Cr(NCS)6]3- complex in the 2E state undergoes intersystem crossing to the ground state with time constants 65±5 and 85±5 ns in DMSO and DMF, respectively. A minor part of electronically excited [Cr(NCS)6]3- undergoes irreversible photochemical decomposition. In DMSO, the photolysis of [Cr(NCS)6]3- complex results in single or double thiocyanate ion release followed by the coordination of the solvent molecules with time constant of 1±0.2 ms.
Biophysical Journal, Feb 1, 2023
![Research paper thumbnail of A highly diastereoselective one-pot three-component 1,3-dipolar cycloaddition of cyclopropenes with azomethine ylides generated from 11<i>H</i>-indeno[1,2-<i>b</i>]-quinoxalin-11-ones](https://attachments.academia-assets.com/120191442/thumbnails/1.jpg)
](Organic chemistry frontiers, 2018
S2 1. Experimental data Table S1. Optimization of the reaction conditions a Entry Solvent T [°C] ... more S2 1. Experimental data Table S1. Optimization of the reaction conditions a Entry Solvent T [°C] Time, h Yield 4aaa ,% b 1 methanol reflux 12 80 2 ethanol reflux 12 76 3 THF reflux 12 49 c 4 acetonitrile reflux 12 61 c 5 DMF 80 10 73 6 1,4-dioxane 80 12 43 c 7 DMSO 80 12 67 8 ethanol RT 72 54 c 9 methanol RT 72 51 c a Reaction conditions: 1a (1 equiv.), 2a (1 equiv.), 3a (2 equiv.), solvent. b Isolated yield. c Unreacted 1a and 2a are present in the reaction mixture. General procedure A for the one-pot three-component reaction of cyclopropenes, 11Hindeno[1,2-b]quinoxalin-11-ones, and secondary α-amino acids: A mixture of corresponding cyclopropene 1 (0.3 mmol), 11H-indeno[1,2-b]quinoxalin-11-one 2 (0.3 mmol), and secondary αamino acid 3 (0.6 mmol) was refluxed in methanol (6 mL) for 12 h until complete consumption of 1 as monitored by TLC. After cooling, the solvent was evaporated under reduced pressure. The residue was transferred into a separatory funnel using CH2Cl2 (5 mL), washed twice with water and brine. The washed organic phase was dried over anhydrous Na2SO4, filtered and concentrated on the rotary evaporator. The resulting crude product 4 was purified by recrystallization from MeOH or by preparative thin layer chromatography (PTLC) on alumina using a mixture of hexane-CH2Cl2 (2:1, 4haa, 4aac).
Nanomaterials
Two series of β-NaYF4:Ln3+ nanoparticles (Ln = La–Nd, Sm–Lu) containing 20 at. % and 40 at. % of ... more Two series of β-NaYF4:Ln3+ nanoparticles (Ln = La–Nd, Sm–Lu) containing 20 at. % and 40 at. % of Ln3+ with well-defined morphology and size were synthesized via a facile citric-acid-assisted hydrothermal method using rare-earth chlorides as the precursors. The materials were composed from the particles that have a shape of uniform hexagonal prisms with an approximate size of 80–1100 nm. The mean diameter of NaYF4:Ln3+ crystals non-monotonically depended on the lanthanide atomic number and the minimum size was observed for Gd3+-doped materials. At the same time, the unit cell parameters decreased from La to Lu according to XRD data analysis. The diameter-to-length ratio increased from La to Lu in both studied series. The effect of the doping lanthanide(III) ion nature on particle size and shape was explained in terms of crystal growth dynamics. This study reports the correlation between the nanoparticle morphologies and the type and content of doping lanthanide ions. The obtained res...
This is supplementary data for F1000Research article: A voltage-dependent fluorescent indicator f... more This is supplementary data for F1000Research article: A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling. Here are files for modeling archaerhodopsin-3 with I-TASSER, Medeller and RosettaCM algorithms, structure postprocessing and spectra calculations.
Fluorescence of the vast majority of natural opsin-based photoactive proteins is extremely low in... more Fluorescence of the vast majority of natural opsin-based photoactive proteins is extremely low in accordance with their functions that depend on efficient transduction of absorbed light energy. However, recently proposed several classes of engineered rhodopsins with enhanced fluorescence along with the discovery of a new natural highly fluorescent rhodopsin, NeoR, opened a way to exploit these transmembrane proteins as fluorescent sensors and draw more attention to studies on this untypical rhodopsins property. Here we review available data on the fluorescence of the retinal chromophore in microbial and animal rhodopsins and their photocycle intermediates as well as different isomers of the protonated retinal Schiff base in different solvents and the gas phase.
ACS Physical Chemistry Au, 2014
Genetically encoded voltage indicators (GEVIs) have found wide applications as molecular tools fo... more Genetically encoded voltage indicators (GEVIs) have found wide applications as molecular tools for visualization of changes in cell membrane potential. Among others, several classes of archaerhodopsin-3-based GEVIs have been developed and have proved themselves promising in various molecular imaging studies. To expand the application range for this type of GEVIs, new variants with absorption band maxima shifted toward the first biological window and enhanced fluorescence signal are required. Here, we integrate computational and experimental strategies to reveal structural factors that distinguish far-red bright archaerhodopsin-3-based GEVIs, Archers, obtained by directed evolution in a previous study (McIsaac et al., PNAS, 2014) and the wild-type archaerhodopsin-3 with an extremely dim fluorescence signal, aiming to use the obtained information in subsequent rational design. We found that the fluorescence can be enhanced by stabilization of a certain conformation of the protein, which, in turn, can be achieved by tuning the pKa value of two titratable residues. These findings were supported further by introducing mutations into wild-type archeorhodopsin-3 and detecting the enhancement of the fluorescence signal. Finally, we came up with a rational design and proposed previously unknown Archers variants with red-shifted absorption bands (λmax up to 640 nm) and potential-dependent bright fluorescence (quantum yield up to 0.97%).
International Journal of Molecular Sciences
A typical feature of proteins from the rhodopsin family is the sensitivity of their absorption ba... more A typical feature of proteins from the rhodopsin family is the sensitivity of their absorption band maximum to protein amino acid composition. For this reason, studies of these proteins often require methodologies that determine spectral shift caused by amino acid substitutions. Generally, quantum mechanics/molecular mechanics models allow for the calculation of a substitution-induced spectral shift with high accuracy, but their application is not always easy and requires special knowledge. In the present study, we propose simple models that allow us to estimate the direct effect of a charged or polar residue substitution without extensive calculations using only rhodopsin three-dimensional structure and plots or tables that are provided in this article. The models are based on absorption maximum values calculated at the SORCI+Q level of theory for cis- and trans-forms of retinal protonated Schiff base in an external electrostatic field of charges and dipoles. Each value corresponds...
International Journal of Molecular Sciences
Membrane potential is a fundamental property of biological cells. Changes in membrane potential c... more Membrane potential is a fundamental property of biological cells. Changes in membrane potential characterize a vast number of vital biological processes, such as the activity of neurons and cardiomyocytes, tumorogenesis, cell-cycle progression, etc. A common strategy to record membrane potential changes that occur in the process of interest is to utilize organic dyes or genetically-encoded voltage indicators with voltage-dependent fluorescence. Sensors are introduced into target cells, and alterations of fluorescence intensity are recorded with optical methods. Techniques that allow recording relative changes of membrane potential and do not take into account fluorescence alterations due to factors other than membrane voltage are already widely used in modern biological and biomedical studies. Such techniques have been reviewed previously in many works. However, in order to investigate a number of processes, especially long-term processes, the measured signal must be corrected to ex...
Journal of the American Chemical Society, 2012
Detailed knowledge of the molecular mechanisms that control the spectral properties in the rhodop... more Detailed knowledge of the molecular mechanisms that control the spectral properties in the rhodopsin protein family is important for understanding the functions of these photoreceptors and for the rational design of artificial photosensitive proteins. Here we used a high-level ab initio QM/MM method to investigate the mechanism of spectral tuning in the chloride-bound and anion-free forms of halorhodopsin from Natronobacterium pharaonis (phR) and the interprotein spectral shift between them. We demonstrate that the chloride ion tunes the spectral properties of phR via two distinct mechanisms: (i) electrostatic interaction with the chromophore, which results in a 95 nm difference between the absorption maxima of the two forms, and (ii) induction of a structural reorganization in the protein, which changes the positions of charged and polar residues and reduces this difference to 29 nm. The present study expands our knowledge concerning the role of the reorganization of the internal H-bond network for color tuning in general and provides a detailed investigation of the tuning mechanism in phR in particular.
Physical Chemistry Chemical Physics, 2020
Accurate prediction of water molecules in protein cavities is an important factor for obtaining h... more Accurate prediction of water molecules in protein cavities is an important factor for obtaining high-quality rhodopsin QM/MM models.
ACS omega, Jan 31, 2018
Rhodopsins are seven α-helical membrane proteins that are of great importance in chemistry, biolo... more Rhodopsins are seven α-helical membrane proteins that are of great importance in chemistry, biology, and modern biotechnology. Any in silico study on rhodopsin properties and functioning requires a high-quality three-dimensional structure. Due to particular difficulties with obtaining membrane protein structures from the experiment, in silico prediction of the three-dimensional rhodopsin structure based only on its primary sequence is an especially important task. For the last few years, significant progress was made in the field of protein structure prediction, especially for methods based on comparative modeling. However, the majority of this progress was made for soluble proteins and further investigations are needed to achieve similar progress for membrane proteins. In this paper, we evaluate the performance of modern protein structure prediction methodologies (implemented in the Medeller, I-TASSER, and Rosetta packages) for their ability to predict rhodopsin structures. Three w...
Journal of Chemical Theory and Computation
Journal of the American Chemical Society, 2011
The molecular dynamics (MD) trajectories were calculated using the velocity Verlet algorithm 1 ac... more The molecular dynamics (MD) trajectories were calculated using the velocity Verlet algorithm 1 accordingtotheclassical Newton'sequa?ons whichweresolvednumerically.At ?me(t)thealgorithmrequirescoordinates,veloci?esandforces asinput.Inthefirststepof thealgorithmthecoordinatesforthenew?mestep(t+dt)aredetermined:
Physical Chemistry Chemical Physics, 2009
Acceleration of the Z to E photoisomerization of penta-2,4-dieniminium by hydrogen out-of-plane m... more Acceleration of the Z to E photoisomerization of penta-2,4-dieniminium by hydrogen out-of-plane motion: Theoretical study on a model system of retinal protonated Schiff base submitted by: Masato Sumita, Mikhail N. Ryazantsev, and Kazuya Saito contents: Potential energy surfaces with the interpolated point at θ 1 = 50 • The Cartesian coordinates of the stationary points in the S 1 and S 0 states and the S 1 /S 0 degeneracy points (inÅ).
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
European Journal of Pharmacology, 2023
ACS Chemical Neuroscience
Azobenzene-based quaternary ammonium compounds provide optical control of ion channels and are co... more Azobenzene-based quaternary ammonium compounds provide optical control of ion channels and are considered promising agents for regulation of neuronal excitability and for restoration of the photosensitivity of retinal cells. However, the selectivity of the action of these compounds remains insufficiently known. We studied the action of DENAQ (diethylamine-azobenzene-quaternary ammonium) and DMNAQ (dimethylamine-azobenzene-quaternary ammonium) on ionotropic glutamate receptors in rat brain neurons. In the dark, both compounds applied extracellularly caused fast and reversible inhibition of NMDA (N-methyl-d-aspartate) receptor-mediated currents with IC50 values of 10 and 5 μM, respectively. Light-induced transformation of DENAQ and DMNAQ to their cis forms caused the IC50 values to increase to 30 and 27 μM, respectively. Detailed analysis of this action revealed a complex nature consisting of fast inhibitory and slower potentiating effects. The AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptors were only weakly affected independently on illumination. We conclude that, in addition to their long-lasting intracellular action, which persists after washout, azobenzene-based quaternary ammonium compounds should affect glutamatergic transmission and synaptic plasticity during treatment. Our findings also extend the list of soluble photoswitchable inhibitors of NMDA receptors. While the site(s) and mechanisms of action are unclear, the effect of DENAQ demonstrates strong pH dependence. At acidic pH values, DENAQ potentiates both NMDA and AMPA receptors.
ACS Physical Chemistry Au, Apr 29, 2024
Genetically encoded voltage indicators (GEVIs) have found wide applications as molecular tools fo... more Genetically encoded voltage indicators (GEVIs) have found wide applications as molecular tools for visualization of changes in cell membrane potential. Among others, several classes of archaerhodopsin-3-based GEVIs have been developed and have proved themselves promising in various molecular imaging studies. To expand the application range for this type of GEVIs, new variants with absorption band maxima shifted toward the first biological window and enhanced fluorescence signal are required. Here, we integrate computational and experimental strategies to reveal structural factors that distinguish far-red bright archaerhodopsin-3-based GEVIs, Archers, obtained by directed evolution in a previous study (McIsaac et al., PNAS, 2014) and the wild-type archaerhodopsin-3 with an extremely dim fluorescence signal, aiming to use the obtained information in subsequent rational design. We found that the fluorescence can be enhanced by stabilization of a certain conformation of the protein, which, in turn, can be achieved by tuning the pKa value of two titratable residues. These findings were supported further by introducing mutations into wild-type archeorhodopsin-3 and detecting the enhancement of the fluorescence signal. Finally, we came up with a rational design and proposed previously unknown Archers variants with red-shifted absorption bands (λmax up to 640 nm) and potential-dependent bright fluorescence (quantum yield up to 0.97%).
Journal of Physical Chemistry B, Apr 13, 2020
The ultrafast photochemistry of the [Cr(NCS)6]3- complex upon excitation to the 4T2 ligand-field ... more The ultrafast photochemistry of the [Cr(NCS)6]3- complex upon excitation to the 4T2 ligand-field (LF) state was studied in dimethylsulfoxide (DMSO) and N,N-dimethylformamide (DMF) in a wide temporal range (100 fs - 9 ms) by a combination of femtosecond and nanosecond transient absorption spectroscopy techniques and supported by quantum-chemical DFT/TD-DFT calculations. The initially excited 4T2 state undergoes intersystem crossing to the vibrationally hot 2E state with time constants of 1.1±0.2 and 1.8±0.1 ps in DMSO and DMF, respectively. Vibrational relaxation occurs in the same timescale and takes 1-5 ps. A major part of [Cr(NCS)6]3- complex in the 2E state undergoes intersystem crossing to the ground state with time constants 65±5 and 85±5 ns in DMSO and DMF, respectively. A minor part of electronically excited [Cr(NCS)6]3- undergoes irreversible photochemical decomposition. In DMSO, the photolysis of [Cr(NCS)6]3- complex results in single or double thiocyanate ion release followed by the coordination of the solvent molecules with time constant of 1±0.2 ms.
Biophysical Journal, Feb 1, 2023
Organic chemistry frontiers, 2018
S2 1. Experimental data Table S1. Optimization of the reaction conditions a Entry Solvent T [°C] ... more S2 1. Experimental data Table S1. Optimization of the reaction conditions a Entry Solvent T [°C] Time, h Yield 4aaa ,% b 1 methanol reflux 12 80 2 ethanol reflux 12 76 3 THF reflux 12 49 c 4 acetonitrile reflux 12 61 c 5 DMF 80 10 73 6 1,4-dioxane 80 12 43 c 7 DMSO 80 12 67 8 ethanol RT 72 54 c 9 methanol RT 72 51 c a Reaction conditions: 1a (1 equiv.), 2a (1 equiv.), 3a (2 equiv.), solvent. b Isolated yield. c Unreacted 1a and 2a are present in the reaction mixture. General procedure A for the one-pot three-component reaction of cyclopropenes, 11Hindeno[1,2-b]quinoxalin-11-ones, and secondary α-amino acids: A mixture of corresponding cyclopropene 1 (0.3 mmol), 11H-indeno[1,2-b]quinoxalin-11-one 2 (0.3 mmol), and secondary αamino acid 3 (0.6 mmol) was refluxed in methanol (6 mL) for 12 h until complete consumption of 1 as monitored by TLC. After cooling, the solvent was evaporated under reduced pressure. The residue was transferred into a separatory funnel using CH2Cl2 (5 mL), washed twice with water and brine. The washed organic phase was dried over anhydrous Na2SO4, filtered and concentrated on the rotary evaporator. The resulting crude product 4 was purified by recrystallization from MeOH or by preparative thin layer chromatography (PTLC) on alumina using a mixture of hexane-CH2Cl2 (2:1, 4haa, 4aac).
Nanomaterials
Two series of β-NaYF4:Ln3+ nanoparticles (Ln = La–Nd, Sm–Lu) containing 20 at. % and 40 at. % of ... more Two series of β-NaYF4:Ln3+ nanoparticles (Ln = La–Nd, Sm–Lu) containing 20 at. % and 40 at. % of Ln3+ with well-defined morphology and size were synthesized via a facile citric-acid-assisted hydrothermal method using rare-earth chlorides as the precursors. The materials were composed from the particles that have a shape of uniform hexagonal prisms with an approximate size of 80–1100 nm. The mean diameter of NaYF4:Ln3+ crystals non-monotonically depended on the lanthanide atomic number and the minimum size was observed for Gd3+-doped materials. At the same time, the unit cell parameters decreased from La to Lu according to XRD data analysis. The diameter-to-length ratio increased from La to Lu in both studied series. The effect of the doping lanthanide(III) ion nature on particle size and shape was explained in terms of crystal growth dynamics. This study reports the correlation between the nanoparticle morphologies and the type and content of doping lanthanide ions. The obtained res...
This is supplementary data for F1000Research article: A voltage-dependent fluorescent indicator f... more This is supplementary data for F1000Research article: A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling. Here are files for modeling archaerhodopsin-3 with I-TASSER, Medeller and RosettaCM algorithms, structure postprocessing and spectra calculations.
Fluorescence of the vast majority of natural opsin-based photoactive proteins is extremely low in... more Fluorescence of the vast majority of natural opsin-based photoactive proteins is extremely low in accordance with their functions that depend on efficient transduction of absorbed light energy. However, recently proposed several classes of engineered rhodopsins with enhanced fluorescence along with the discovery of a new natural highly fluorescent rhodopsin, NeoR, opened a way to exploit these transmembrane proteins as fluorescent sensors and draw more attention to studies on this untypical rhodopsins property. Here we review available data on the fluorescence of the retinal chromophore in microbial and animal rhodopsins and their photocycle intermediates as well as different isomers of the protonated retinal Schiff base in different solvents and the gas phase.
Chemosensors
We report the synthesis and investigation of Au–Ru composite with highly developed specific surfa... more We report the synthesis and investigation of Au–Ru composite with highly developed specific surface area exhibiting excellent electrocatalytic performance suitable for detection of such hydrophobic metabolites as epinephrine in the physiological environment. This electrode material was fabricated using two-stage laser-assisted metal deposition technique. The morphological and structural studies of Au–Ru were performed using methods of scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX) and X-ray diffraction spectroscopy (XRD). The voltammetric methods, including cyclic voltammetry (CV), differential pulse voltammetry (DPV) and direct amperometry, were used to analyze the composite’s electrochemical properties. The Au–Ru sensor exhibited two linear ranges of the non-enzymatic epinephrine detection: 0.01–10 μM and 10–1000 μM. The calculated sensitivities within these two ranges were 32.8 and 3.3 μA μM−1 cm−2, whereas the corresponding limits of detection wer...
Biosensors
Copper is an inexpensive material that has found wide application in electronics due to its remar... more Copper is an inexpensive material that has found wide application in electronics due to its remarkable electric properties. However, the high toxicity of both copper and copper oxide imposes restrictions on the application of this metal as a material for bioelectronics. One way to increase the biocompatibility of pure copper while keeping its remarkable properties is to use copper-based composites. In the present study, we explored a new copper–ruthenium composite as a potential biocompatible material for bioelectrodes. Sample electrodes were obtained by subsequent laser deposition of copper and ruthenium on glass plates from a solution containing salts of these metals. The fabricated Cu–Ru electrodes exhibit high effective area and their impedance properties can be described by simple R-CPE equivalent circuits that make them perspective for sensing applications. Finally, we designed a simple impedance cell-based biosensor using this material that allows us to distinguish between de...
Chemistry – A European Journal
Journal of the American Chemical Society, 2021
In the search for fundamentally new, active, stable, and readily synthetically accessible cycloal... more In the search for fundamentally new, active, stable, and readily synthetically accessible cycloalkynes as strain-promoted azide-alkyne cycloaddition (SPAAC) reagents for bioorthogonal bioconjugation, we integrated two common approaches: the reagent destabilization by the increase of a ring strain and the transition state stabilization through electronic effects. As a result new SPAAC reagents, heterocyclononynes fused to a heterocyclic core, were created. These compounds can be obtained through a general synthetic route based on four crucial steps: the electrophile-promoted cyclization, Sonogashira coupling, Nicholas reaction, and final deprotection of Co-complexes of cycloalkynes from cobalt. Varying the natures of the heterocycle and heteroatom allows for reaching the optimal stability-reactivity balance for new strained systems. Computational and experimental studies revealed similar SPAAC reactivities for stable 9-membered isocoumarin- and benzothiophene-fused heterocycloalkynes and their unstable 8-membered homologues. We discovered that close reactivity is a result of the interplay of two electronic effects, which stabilize SPAAC transition states (πin* → σ* and π* → πin*) with structural effects such as conformational changes from eclipsed to staggered conformations in the cycloalkyne scaffold, that noticeably impact alkyne bending and reactivity. The concerted influence of a heterocycle and a heteroatom on the polarization of a triple bond in highly strained cycles along with a low HOMO-LUMO gap was assumed to be the reason for the unpredictable kinetic instability of all the cyclooctynes and the benzothiophene-fused oxacyclononyne. The applicability of stable isocoumarin-fused azacyclononyne IC9N-BDP-FL for in vitro bioconjugation was exemplified by labeling and visualization of HEK293 cells carrying azido-DNA and azido-glycans.
European Journal of Organic Chemistry
Materials, 2020
A simple approach for in situ laser-induced modification of iridium-based materials to increase t... more A simple approach for in situ laser-induced modification of iridium-based materials to increase their electrocatalytic activity towards enzyme-free glucose sensing was proposed. For this purpose, we deposited gold and platinum separately and as a mixture on the surface of pre-synthesized iridium microstructures upon laser irradiation at a wavelength of 532 nm. Then, we carried out the comparative investigation of their morphology, elemental and phase composition as well as their electrochemical properties. The best morphology and, as a result, the highest sensitivity (~9960 µA/mM cm2) with respect to non-enzymatic determination of D-glucose were demonstrated by iridium-gold-platinum microstructures also showing low limit of detection (~0.12 µM), a wide linear range (0.5 µM–1 mM) along with good selectivity, reproducibility and stability.
The Journal of Physical Chemistry B
Ultrafast excited-state dynamics of CuBr3- complex was studied in acetonitrile and dichloromethan... more Ultrafast excited-state dynamics of CuBr3- complex was studied in acetonitrile and dichloromethane solutions using femtosecond transient absorption spectroscopy with 18 fs temporal resolution and quantum-chemical DFT calculations. Upon 640 nm excitation, the CuBr3- complex is promoted to the ligand-to-metal charge transfer (LMCT) state, which then shortly undergoes internal conversion into the vibrationally hot ligand field (LF) excited state with time constants of 30 and 40 fs in acetonitrile and dichloromethane, respectively. The LF state nonradiatively relaxes into the ground state in 2.6 and 7.3 ps in acetonitrile and dichloromethane, respectively. Internal conversion of the LF state is accompanied by vibrational relaxation that occurs on the same time scale. Based on the analysis of coherent oscillations and quantum-chemical calculations, the predominant forms of the CuBr3- complex in acetonitrile and dichloromethane solutions were revealed. In acetonitrile, the CuBr3- complex exists as [CuBr3(CH3CN)2]-, whereas three forms of this complex, [CuBr3CH2Cl2]-, [CuBr3(CH2Cl2)2]-, and [CuBr3(CH2Cl2)3]-, are present in equilibrium in dichloromethane.
Materials
In this paper, we propose a fast and simple approach for the fabrication of the electrocatalytica... more In this paper, we propose a fast and simple approach for the fabrication of the electrocatalytically active ruthenium-containing microstructures using a laser-induced metal deposition technique. The results of scanning electron microscopy and electrical impedance spectroscopy (EIS) demonstrate that the fabricated ruthenium-based microelectrode had a highly developed surface composed of 10 μm pores and 10 nm zigzag cracks. The fabricated material exhibited excellent electrochemical properties toward non-enzymatic dopamine sensing, including high sensitivity (858.5 and 509.1 μA mM−1 cm−2), a low detection limit (0.13 and 0.15 μM), as well as good selectivity and stability.
ACS Biomaterials Science & Engineering
In this review, we aim to introduce the reader to the technique of electrical impedance spectrosc... more In this review, we aim to introduce the reader to the technique of electrical impedance spectroscopy (EIS) with a focus on its biological and medical applications. We explain the theoretical and experimental aspects of the EIS with the details essential for biological studies, i.e. interaction of metal electrodes with biological matter and liquids, strategies of increasing measurement rate and noise reduction in bio-EIS experiments etc. We give various examples of successful bio-EIS practical implementations in science and technology: from the whole-body health monitoring and sensors for vision prosthetic care to single living cell examination platforms and virus diseases research. Present review can be used as a bio-EIS tutorial for students as well as a handbook for scientists and engineers due to extensive references covering the contemporary research papers in the field.
Nanomaterials
The luminescent coarse-, micro- and nanocrystalline europium(III) terephthalate tetrahydrate (Eu2... more The luminescent coarse-, micro- and nanocrystalline europium(III) terephthalate tetrahydrate (Eu2bdc3‧4H2O) metal-organic frameworks were synthesized by the ultrasound-assisted wet-chemical method. Electron micrographs show that the europium(III) terephthalate microparticles are 7 μm long leaf-like plates. According to the dynamic light scattering technique, the average size of the Eu2bdc3‧4H2O nanoparticles is equal to about 8 ± 2 nm. Thereby, the reported Eu2bdc3‧4H2O nanoparticles are the smallest nanosized rare-earth-based MOF crystals, to the best of our knowledge. The synthesized materials demonstrate red emission due to the 5D0–7FJ transitions of Eu3+ upon 250 nm excitation into 1ππ* state of the terephthalate ion. Size reduction results in broadened emission bands, an increase in the non-radiative rate constants and a decrease in both the quantum efficiency of the 5D0 level and Eu3+ and the luminescence quantum yields. Cu2+, Cr3+, and Fe3+ ions efficiently and selectively qu...
