2024
88.
Aslopovsky V R, Scherbinin A V, Bochenkova A V
Enhancing Two-Photon Absorption of Green Fluorescent Protein by Quantum Entanglement Journal Article
In: The Journal of Physical Chemistry B, 2024, (PMID: 39668340).
@article{doi:10.1021/acs.jpcb.4c07869b,
title = {Enhancing Two-Photon Absorption of Green Fluorescent Protein by Quantum Entanglement},
author = {Vladislav R. Aslopovsky and Andrei V. Scherbinin and Anastasia V. Bochenkova},
url = {https://doi.org/10.1021/acs.jpcb.4c07869},
doi = {10.1021/acs.jpcb.4c07869},
year = {2024},
date = {2024-12-13},
urldate = {2024-12-13},
journal = {The Journal of Physical Chemistry B},
abstract = {Exploring the electronic states of molecules through excitation with entangled and classical photon pairs offers new insights into the nature of light–matter interactions and stimulates the development of quantum spectroscopy. Here, we address the importance of temporal entanglement of light in two-photon absorption (TPA) upon the S0 → S1 transition by the green fluorescent protein (GFP)─a key molecular unit in the bioimaging of living cells. By invoking a two-level model applicable when permanent dipole pathways dominate the two-photon transition, we derive a convenient closed-form analytical expression for the entangled TPA strength. For the first time, we disclose specific molecular properties that cause classical and entangled two-photon absorptions to be qualitatively different when exciting the same state. We reveal a new nonclassical contribution to the TPA strength, which is defined by the magnitude and directional alignment of permanent dipole moments in the initial and final states. Using high-level electronic structure theory, we show that the nonclassical contribution is intrinsically larger than the classical counterpart in GFP, leading to an enhancement of the TPA strength due to quantum entanglement by several orders of magnitude. We also present evidence that the classical and quantum TPA strengths can be modulated differently by the protein environment and demonstrate how to control the outcome by alterations in the local electric field of the protein caused by a single amino acid replacement. Our findings establish physical grounds for enhancing TPA in photoactive proteins by quantum entanglement, facilitating the rational design of high-efficiency biomarkers for future applications that utilize quantum light.},
note = {PMID: 39668340},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Exploring the electronic states of molecules through excitation with entangled and classical photon pairs offers new insights into the nature of light–matter interactions and stimulates the development of quantum spectroscopy. Here, we address the importance of temporal entanglement of light in two-photon absorption (TPA) upon the S0 → S1 transition by the green fluorescent protein (GFP)─a key molecular unit in the bioimaging of living cells. By invoking a two-level model applicable when permanent dipole pathways dominate the two-photon transition, we derive a convenient closed-form analytical expression for the entangled TPA strength. For the first time, we disclose specific molecular properties that cause classical and entangled two-photon absorptions to be qualitatively different when exciting the same state. We reveal a new nonclassical contribution to the TPA strength, which is defined by the magnitude and directional alignment of permanent dipole moments in the initial and final states. Using high-level electronic structure theory, we show that the nonclassical contribution is intrinsically larger than the classical counterpart in GFP, leading to an enhancement of the TPA strength due to quantum entanglement by several orders of magnitude. We also present evidence that the classical and quantum TPA strengths can be modulated differently by the protein environment and demonstrate how to control the outcome by alterations in the local electric field of the protein caused by a single amino acid replacement. Our findings establish physical grounds for enhancing TPA in photoactive proteins by quantum entanglement, facilitating the rational design of high-efficiency biomarkers for future applications that utilize quantum light.
87.
Kusochek P A, Smitienko O A, Bochenkova A V
In: The Journal of Physical Chemistry B, vol. 128, no. 50, pp. 12471-12482, 2024, (PMID: 39641505).
@article{doi:10.1021/acs.jpcb.4c06832,
title = {Mode-Specific Photoresponse of Retinal Protonated Schiff Base Isomers in the Reversible Photochromic Reactions of Microbial and Animal Rhodopsins},
author = {Pavel A. Kusochek and Olga A. Smitienko and Anastasia V. Bochenkova},
url = {https://doi.org/10.1021/acs.jpcb.4c06832},
doi = {10.1021/acs.jpcb.4c06832},
year = {2024},
date = {2024-12-06},
urldate = {2024-12-06},
journal = {The Journal of Physical Chemistry B},
volume = {128},
number = {50},
pages = {12471-12482},
abstract = {The primary photoisomerization reactions of the all-trans to 13-cis and 11-cis to all-trans retinal protonated Schiff base (RPSB) in microbial and animal rhodopsins, respectively, occur on a subpicosecond time scale with high quantum yields. At the same time, the isolated RPSB exhibits slower excited-state decay, in particular, in its all-trans form, and hence the interaction with the protein environment is capable of changing the time scale as well as the specificity of the reaction. Here, by using the high-level QM/MM calculations, we provide a comparative study of the primary photoresponse of cis and trans RPSB isomers in both the initial forms and first photoproducts of microbial Krokinobacter eikastus rhodopsin 2 (KR2) and Halobacterium salinarum bacteriorhodopsin (BR), and animal Bos taurus visual rhodopsin (Rho). By simulating photoabsorption band shapes of RPSB inside the proteins, we show that its photoresponse is highly mode-specific for the forward reactions, resulting in excitation of those vibrational modes that facilitate particular double-bond isomerization. The reverse reaction shows specificity only for 13-cis isomers in microbial rhodopsins, whereas the specificity is lost for all-trans RPSB in visual rhodopsin. This indicates evolutionary highly tuned 11-cis chromophore–protein interactions in visual rhodopsin. We also highlight the differences in the photoresponse of RPSB in two microbial rhodopsins and discuss the implications to their excited-state dynamics.},
note = {PMID: 39641505},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The primary photoisomerization reactions of the all-trans to 13-cis and 11-cis to all-trans retinal protonated Schiff base (RPSB) in microbial and animal rhodopsins, respectively, occur on a subpicosecond time scale with high quantum yields. At the same time, the isolated RPSB exhibits slower excited-state decay, in particular, in its all-trans form, and hence the interaction with the protein environment is capable of changing the time scale as well as the specificity of the reaction. Here, by using the high-level QM/MM calculations, we provide a comparative study of the primary photoresponse of cis and trans RPSB isomers in both the initial forms and first photoproducts of microbial Krokinobacter eikastus rhodopsin 2 (KR2) and Halobacterium salinarum bacteriorhodopsin (BR), and animal Bos taurus visual rhodopsin (Rho). By simulating photoabsorption band shapes of RPSB inside the proteins, we show that its photoresponse is highly mode-specific for the forward reactions, resulting in excitation of those vibrational modes that facilitate particular double-bond isomerization. The reverse reaction shows specificity only for 13-cis isomers in microbial rhodopsins, whereas the specificity is lost for all-trans RPSB in visual rhodopsin. This indicates evolutionary highly tuned 11-cis chromophore–protein interactions in visual rhodopsin. We also highlight the differences in the photoresponse of RPSB in two microbial rhodopsins and discuss the implications to their excited-state dynamics.
86.
Isaev T, Oleynichenko A V, Makinskii D, Zaitsevskii A
Optical cycling in charged complexes with Ra–N bonds Journal Article
In: Chemical Physics Letters, vol. 845, pp. 141301, 2024, ISSN: 0009-2614.
@article{ISAEV2024141301,
title = {Optical cycling in charged complexes with Ra–N bonds},
author = {Timur Isaev and Alexander V. Oleynichenko and Dmitrii Makinskii and Andréi Zaitsevskii},
url = {https://www.sciencedirect.com/science/article/pii/S0009261424002380},
doi = {https://doi.org/10.1016/j.cplett.2024.141301},
issn = {0009-2614},
year = {2024},
date = {2024-06-16},
urldate = {2024-01-01},
journal = {Chemical Physics Letters},
volume = {845},
pages = {141301},
abstract = {The extension of laser cooling and trapping techniques to polyatomic molecular ions would have advanced scientific applications such as search of physics outside of the Standard Model, ultracold chemistry etc. We apply the Fock space relativistic coupled cluster method to study low-lying electronic states of molecular ions with Ra–N bonds, namely RaNCH+, RaNH3+ and RaNCCH3+. Prospects of laser cooling of these species are estimated, and the peculiarities of unpaired-electron distributions are analyzed from the point of view of the molecular electronic structure. RaNH3+ and RaNCCH3+ are the first symmetric top molecular ions expected to be suitable for direct laser cooling.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The extension of laser cooling and trapping techniques to polyatomic molecular ions would have advanced scientific applications such as search of physics outside of the Standard Model, ultracold chemistry etc. We apply the Fock space relativistic coupled cluster method to study low-lying electronic states of molecular ions with Ra–N bonds, namely RaNCH+, RaNH3+ and RaNCCH3+. Prospects of laser cooling of these species are estimated, and the peculiarities of unpaired-electron distributions are analyzed from the point of view of the molecular electronic structure. RaNH3+ and RaNCCH3+ are the first symmetric top molecular ions expected to be suitable for direct laser cooling.
85.
Petrov S V
Molecular Rotation and Generalized Euler Equations Journal Article
In: Russ. J. Phys. Chem., vol. 98, no. 5, pp. 837–846, 2024, ISSN: 1531-863X.
@article{Petrov2024,
title = {Molecular Rotation and Generalized Euler Equations},
author = {S. V. Petrov},
doi = {10.1134/s0036024424050212},
issn = {1531-863X},
year = {2024},
date = {2024-05-00},
urldate = {2024-05-00},
journal = {Russ. J. Phys. Chem.},
volume = {98},
number = {5},
pages = {837--846},
publisher = {Pleiades Publishing Ltd},
abstract = {The main equations of motion of a rigid body are transformed to describe molecular rotation with respect to intramolecular motion.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The main equations of motion of a rigid body are transformed to describe molecular rotation with respect to intramolecular motion.
84.
Ivanenkov Y A, Evteev S A, Malyshev A S, Terentiev V A, Bezrukov D S, Ereshchenko A V, Korzhenevskaya A A, Zagribelnyy B A, Shegay P V, Kaprin A D
AlphaFold for a medicinal chemist: tool or toy? Journal Article
In: Russian Chemical Reviews, vol. 93, no. 3, pp. RCR5107, 2024.
@article{2024_Ivanenkov,
title = {AlphaFold for a medicinal chemist: tool or toy?},
author = {Yan A. Ivanenkov and Sergei A. Evteev and Alexander S. Malyshev and Victor A. Terentiev and Dmitry S. Bezrukov and Alexey V. Ereshchenko and Anastasia A. Korzhenevskaya and Bogdan A. Zagribelnyy and Petr V. Shegay and Andrey D. Kaprin},
url = {AlphaFold for a medicinal chemist: tool or toy?},
doi = {10.59761/RCR5107},
year = {2024},
date = {2024-04-02},
urldate = {2024-04-01},
journal = {Russian Chemical Reviews},
volume = {93},
number = {3},
pages = {RCR5107},
publisher = {Autonomous Non-profit Organization Editorial Board of the journal Uspekhi Khimii},
abstract = {The development of novel small drug molecules is a complex and important cross-disciplinary task. In the early stages of development, chemoinformatics and bioinformatics methods are routinely used to reduce the cost of finding a lead compound. Among the tools of medicinal chemistry, docking and molecular dynamics occupy a special place. These methods are used to predict the possible mechanism of binding of a potential ligand to a protein target. However, in order to perform a docking study, it is necessary to know the spatial structure of the protein under investigation. Although databases of crystallographic structures are available, the three-dimensional representations of many protein molecules have not been reported. There is therefore a need to model such three-dimensional conformations. Several computer algorithms have been published to solve this problem. AlphaFold is considered by the scientific community to be the most effective approach to predicting the three-dimensional structure of proteins. However, the scope of its application in medicinal chemistry, especially for virtual screening, remains unclear. This review describes methods for predicting the three-dimensional structure of a protein and provides representative examples of the use of AlphaFold for the design and rational selection of potential ligands. Special attention is given to publications presenting the results of experimental validation of the approach. On the basis of performed analysis, the main problems in the field and possible ways to solve them are formulated.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The development of novel small drug molecules is a complex and important cross-disciplinary task. In the early stages of development, chemoinformatics and bioinformatics methods are routinely used to reduce the cost of finding a lead compound. Among the tools of medicinal chemistry, docking and molecular dynamics occupy a special place. These methods are used to predict the possible mechanism of binding of a potential ligand to a protein target. However, in order to perform a docking study, it is necessary to know the spatial structure of the protein under investigation. Although databases of crystallographic structures are available, the three-dimensional representations of many protein molecules have not been reported. There is therefore a need to model such three-dimensional conformations. Several computer algorithms have been published to solve this problem. AlphaFold is considered by the scientific community to be the most effective approach to predicting the three-dimensional structure of proteins. However, the scope of its application in medicinal chemistry, especially for virtual screening, remains unclear. This review describes methods for predicting the three-dimensional structure of a protein and provides representative examples of the use of AlphaFold for the design and rational selection of potential ligands. Special attention is given to publications presenting the results of experimental validation of the approach. On the basis of performed analysis, the main problems in the field and possible ways to solve them are formulated.
83.
Rutskoy B, Ozerov G, Bezrukov D
The Role of Bond Functions in Describing Intermolecular Electron Correlation for Van der Waals Dimers: A Study of (CH4)2 and Ne2 Journal Article
In: International Journal of Molecular Sciences, vol. 25, no. 3, 2024, ISSN: 1422-0067.
@article{ijms25031472,
title = {The Role of Bond Functions in Describing Intermolecular Electron Correlation for Van der Waals Dimers: A Study of (CH4)2 and Ne2},
author = {Bogdan Rutskoy and Georgiy Ozerov and Dmitry Bezrukov},
url = {https://www.mdpi.com/1422-0067/25/3/1472},
doi = {10.3390/ijms25031472},
issn = {1422-0067},
year = {2024},
date = {2024-01-25},
urldate = {2024-01-01},
journal = {International Journal of Molecular Sciences},
volume = {25},
number = {3},
abstract = {We present a study of the intermolecular interactions in van der Waals complexes of methane and neon dimers within the framework of the CCSD method. This approach was implemented and applied to calculate and examine the behavior of the contracted two-particle reduced density matrix (2-RDM). It was demonstrated that the region near the minimum of the two-particle density matrix correlation part, corresponding to the primary bulk of the Coulomb hole contribution, exerts a significant influence on the dispersion interaction energetics of the studied systems. As a result, the bond functions approach was applied to improve the convergence performance for the intermolecular correlation energy results with respect to the size of the atomic basis. For this, substantial acceleration was achieved by introducing an auxiliary basis of bond functions centered on the minima of the 2-RDM. For both methane and neon dimers, this general conclusion was confirmed with a series of CCSD calculations for the 2-RDM and the correlation energies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We present a study of the intermolecular interactions in van der Waals complexes of methane and neon dimers within the framework of the CCSD method. This approach was implemented and applied to calculate and examine the behavior of the contracted two-particle reduced density matrix (2-RDM). It was demonstrated that the region near the minimum of the two-particle density matrix correlation part, corresponding to the primary bulk of the Coulomb hole contribution, exerts a significant influence on the dispersion interaction energetics of the studied systems. As a result, the bond functions approach was applied to improve the convergence performance for the intermolecular correlation energy results with respect to the size of the atomic basis. For this, substantial acceleration was achieved by introducing an auxiliary basis of bond functions centered on the minima of the 2-RDM. For both methane and neon dimers, this general conclusion was confirmed with a series of CCSD calculations for the 2-RDM and the correlation energies.
82.
Bochenkova A V
Multiconfigurational Methods Including XMCQDPT2 Theory for Excited States of Light-Sensitive Biosystems Book Chapter
In: Yáñez, Manuel; Boyd, Russell J. (Ed.): Comprehensive Computational Chemistry (First Edition), vol. 4, pp. 141-157, Elsevier, Oxford, First Edition, 2024, ISBN: 978-0-12-823256-9.
@inbook{BOCHENKOVA2024141,
title = {Multiconfigurational Methods Including XMCQDPT2 Theory for Excited States of Light-Sensitive Biosystems},
author = {Anastasia V. Bochenkova},
editor = {Manuel Yáñez and Russell J. Boyd},
url = {https://www.sciencedirect.com/science/article/pii/B9780128219782001331},
doi = {10.1016/B978-0-12-821978-2.00133-1},
isbn = {978-0-12-823256-9},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
booktitle = {Comprehensive Computational Chemistry (First Edition)},
volume = {4},
pages = {141-157},
publisher = {Elsevier},
address = {Oxford},
edition = {First Edition},
series = {Comprehensive Computational Chemistry (First Edition)},
abstract = {Multiconfigurational methods are often required for treating extended regions of potential energy surfaces of excited and ground electronic states and their crossings. Among various multiconfigurational approaches, multireference perturbation theory (MR-PT) methods, which are based on multiconfigurational reference wave functions, are widely employed in the studies of photochemistry of large molecular systems. This is due to their favorable cost-to-performance ratio as compared to more accurate MR approaches. In this chapter, we discuss a hierarchy of MR-PT2 methods, which use both single-state (SS) and multi-state (MS) strategies with emphasis on their theoretical foundations, relations to each other and applicability to specific problems. Formulation of the MS-MR-PT2 methods are directly related to the theory of effective Hamiltonians, which is briefly described here. We underline the importance of invariance properties and discuss the XMCQDPT2 method in more detail. As a representative example, we also provide its application to the studies of the photoresponse of retinal protonated Schiff base – a chromophore of vision.},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
Multiconfigurational methods are often required for treating extended regions of potential energy surfaces of excited and ground electronic states and their crossings. Among various multiconfigurational approaches, multireference perturbation theory (MR-PT) methods, which are based on multiconfigurational reference wave functions, are widely employed in the studies of photochemistry of large molecular systems. This is due to their favorable cost-to-performance ratio as compared to more accurate MR approaches. In this chapter, we discuss a hierarchy of MR-PT2 methods, which use both single-state (SS) and multi-state (MS) strategies with emphasis on their theoretical foundations, relations to each other and applicability to specific problems. Formulation of the MS-MR-PT2 methods are directly related to the theory of effective Hamiltonians, which is briefly described here. We underline the importance of invariance properties and discuss the XMCQDPT2 method in more detail. As a representative example, we also provide its application to the studies of the photoresponse of retinal protonated Schiff base – a chromophore of vision.
81.
Leibin I V, Bezrukov D S, Buchachenko A A
Trapping and thermal migration of the first- and second-row atoms in Ar, Kr and Xe crystals Journal Article
In: Phys. Chem. Chem. Phys., vol. 26, iss. 2, pp. 958-973, 2024.
@article{D3CP04178F,
title = {Trapping and thermal migration of the first- and second-row atoms in Ar, Kr and Xe crystals},
author = {Iosif V. Leibin and Dmitry S. Bezrukov and Alexei A. Buchachenko},
url = {http://dx.doi.org/10.1039/D3CP04178F},
doi = {10.1039/D3CP04178F},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Phys. Chem. Chem. Phys.},
volume = {26},
issue = {2},
pages = {958-973},
publisher = {The Royal Society of Chemistry},
abstract = {Trapping and temperature-induced migration (TIM) of the first- and second-row atoms A from H to Ne in the face-centered cubic rare gas RG = Ar, Kr and Xe crystals are investigated within the classical crystal model parameterized by the empirically modified pairwise potentials. New ab initio coupled cluster A–RG potentials computed in a uniform way for all the atoms A are used to represent the atom–crystal interactions. Absolute and relative stabilities of the substitutional and interstitial trapping sites, their structures, interstitial migration pathways, related activation energies and rough estimates of the TIM rates are obtained. The isotropic model, which neglects non-zero atomic electronic orbital momentum, reveals that migration of interstitial atoms along the network of conjugated fcc octahedral voids is the generic case for atomic mobility. Anisotropic interactions with a crystal inherent to P-state atoms B, C, O and F are accounted for using the non-relativistic diatomics-in-molecule method. Depending on its sign, interaction anisotropy can alter the structures of interstitial trapping sites and transition states remarkably. This, in turn, can dramatically affect the TIM rates. Comparison with reliable experimental data available for oxygen and hydrogen indicates a systematic overestimation of the measured activation energies, by 30% at worst. A comprehensive literature review accomplished for other atoms reveals a lack of information on the TIM processes and rates, though makes it possible to verify a part of the present results on the trapping site energies and structures.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Trapping and temperature-induced migration (TIM) of the first- and second-row atoms A from H to Ne in the face-centered cubic rare gas RG = Ar, Kr and Xe crystals are investigated within the classical crystal model parameterized by the empirically modified pairwise potentials. New ab initio coupled cluster A–RG potentials computed in a uniform way for all the atoms A are used to represent the atom–crystal interactions. Absolute and relative stabilities of the substitutional and interstitial trapping sites, their structures, interstitial migration pathways, related activation energies and rough estimates of the TIM rates are obtained. The isotropic model, which neglects non-zero atomic electronic orbital momentum, reveals that migration of interstitial atoms along the network of conjugated fcc octahedral voids is the generic case for atomic mobility. Anisotropic interactions with a crystal inherent to P-state atoms B, C, O and F are accounted for using the non-relativistic diatomics-in-molecule method. Depending on its sign, interaction anisotropy can alter the structures of interstitial trapping sites and transition states remarkably. This, in turn, can dramatically affect the TIM rates. Comparison with reliable experimental data available for oxygen and hydrogen indicates a systematic overestimation of the measured activation energies, by 30% at worst. A comprehensive literature review accomplished for other atoms reveals a lack of information on the TIM processes and rates, though makes it possible to verify a part of the present results on the trapping site energies and structures.
2023
80.
Ostrovsky M A, Smitienko O A, Bochenkova A V, Feldman T B
Similarities and Differences in Photochemistry of Type I and Type II Rhodopsins Journal Article
In: Biochemistry (Moscow), vol. 88, no. 10, pp. 1528–1543, 2023, ISSN: 16083040.
@article{Ostrovsky2023b,
title = {Similarities and Differences in Photochemistry of Type I and Type II Rhodopsins},
author = {Mikhail A. Ostrovsky and Olga A. Smitienko and Anastasia V. Bochenkova and Tatiana B. Feldman},
url = {https://link.springer.com/article/10.1134/S0006297923100097},
doi = {10.1134/S0006297923100097},
issn = {16083040},
year = {2023},
date = {2023-10-01},
urldate = {2023-10-01},
journal = {Biochemistry (Moscow)},
volume = {88},
number = {10},
pages = {1528–1543},
publisher = {Springer},
abstract = {Abstract: The diversity of the retinal-containing proteins (rhodopsins) in nature is extremely large. Fundamental similarity of the structure and photochemical properties unites them into one family. However, there is still a debate about the origin of retinal-containing proteins: divergent or convergent evolution? In this review, based on the results of our own and literature data, a comparative analysis of the similarities and differences in the photoconversion of the rhodopsin of types I and II is carried out. The results of experimental studies of the forward and reverse photoreactions of the bacteriorhodopsin (type I) and visual rhodopsin (type II) rhodopsins in the femto- and picosecond time scale, photo-reversible reaction of the octopus rhodopsin (type II), photovoltaic reactions, as well as quantum chemical calculations of the forward photoreactions of bacteriorhodopsin and visual rhodopsin are presented. The issue of probable convergent evolution of type I and type II rhodopsins is discussed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract: The diversity of the retinal-containing proteins (rhodopsins) in nature is extremely large. Fundamental similarity of the structure and photochemical properties unites them into one family. However, there is still a debate about the origin of retinal-containing proteins: divergent or convergent evolution? In this review, based on the results of our own and literature data, a comparative analysis of the similarities and differences in the photoconversion of the rhodopsin of types I and II is carried out. The results of experimental studies of the forward and reverse photoreactions of the bacteriorhodopsin (type I) and visual rhodopsin (type II) rhodopsins in the femto- and picosecond time scale, photo-reversible reaction of the octopus rhodopsin (type II), photovoltaic reactions, as well as quantum chemical calculations of the forward photoreactions of bacteriorhodopsin and visual rhodopsin are presented. The issue of probable convergent evolution of type I and type II rhodopsins is discussed.
79.
Ozerov G K, Bodunov A A, Bezrukov D S
In: Russ. J. Phys. Chem., vol. 97, no. 7, pp. 1509–1514, 2023, ISSN: 1531-863X.
@article{Ozerov2023,
title = {Theoretical Description of Relativistic Terms of a Hydrogen Atom in a Magnetic Field: A Variational Approach in the Basis of Hydrogen-Like Spinors},
author = {G. K. Ozerov and A. A. Bodunov and D. S. Bezrukov},
doi = {10.1134/s0036024423070208},
issn = {1531-863X},
year = {2023},
date = {2023-07-01},
urldate = {2023-07-00},
journal = {Russ. J. Phys. Chem.},
volume = {97},
number = {7},
pages = {1509--1514},
publisher = {Pleiades Publishing Ltd},
abstract = {The incomplete diagonalization of a Dirac Hamiltonian in the basis of the states of an unperturbed atom is used to obtain solutions to the Dirac equation for a hydrogen atom in a constant uniform magnetic field and a wide range of changes in strength. The resulting finite expressions for the matrix elements of the perturbation operator of an arbitrary hydrogen-like atom are used to estimate the action of operators in minimizing the energy dispersion functional. The approach allows precise estimates of the energy of the ground state and values of the energies of transition that are in good agreement with results from earlier studies. It is shown that the proposed technique for minimizing the energy dispersion functional allows the incomplete diagonalization of operators for an arbitrarily chosen block of target states, provided that the initial approximation is correct.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The incomplete diagonalization of a Dirac Hamiltonian in the basis of the states of an unperturbed atom is used to obtain solutions to the Dirac equation for a hydrogen atom in a constant uniform magnetic field and a wide range of changes in strength. The resulting finite expressions for the matrix elements of the perturbation operator of an arbitrary hydrogen-like atom are used to estimate the action of operators in minimizing the energy dispersion functional. The approach allows precise estimates of the energy of the ground state and values of the energies of transition that are in good agreement with results from earlier studies. It is shown that the proposed technique for minimizing the energy dispersion functional allows the incomplete diagonalization of operators for an arbitrarily chosen block of target states, provided that the initial approximation is correct.
78.
Boichenko A N, Bochenkova A V
Calculating Vertical Ionization Energies of Hydrated Biological Chromophores Based on Multiconfigurational Perturbation Theory Journal Article
In: Russian Journal of Physical Chemistry A 2023 97:4, vol. 97, no. 4, pp. 763–767, 2023, ISSN: 1531-863X.
@article{Boichenko2023,
title = {Calculating Vertical Ionization Energies of Hydrated Biological Chromophores Based on Multiconfigurational Perturbation Theory},
author = {A. N. Boichenko and A. V. Bochenkova},
url = {https://link.springer.com/article/10.1134/S0036024423040088},
doi = {10.1134/S0036024423040088},
issn = {1531-863X},
year = {2023},
date = {2023-04-01},
journal = {Russian Journal of Physical Chemistry A 2023 97:4},
volume = {97},
number = {4},
pages = {763–767},
publisher = {Springer},
abstract = {Here we introduce a methodology for calculating vertical detachment energies (VDE) and vertical ionization energies (VIE) of anionic and neutral chromophores in aqueous environment. The proposed method is based on the extended multiconfigurational quasidegenerate perturbation theory coupled to the explicit treatment of solvent effects in the frame of the effective fragment potential method. We show that the solvent polarization contribution must be considered for getting accurate quantitative estimations of VDEs and VIEs. The calculated values of VDE for phenolate (7.3 eV) and VIE for phenol (7.9 eV) in aqueous environment are in good agreement with the experimental results obtained using X-ray and multiphoton UV photoelectron spectroscopy. Our approach will be useful for studying processes of photoinduced electron transfer from anionic as well as neutral biological chromophores in aqueous solution.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Here we introduce a methodology for calculating vertical detachment energies (VDE) and vertical ionization energies (VIE) of anionic and neutral chromophores in aqueous environment. The proposed method is based on the extended multiconfigurational quasidegenerate perturbation theory coupled to the explicit treatment of solvent effects in the frame of the effective fragment potential method. We show that the solvent polarization contribution must be considered for getting accurate quantitative estimations of VDEs and VIEs. The calculated values of VDE for phenolate (7.3 eV) and VIE for phenol (7.9 eV) in aqueous environment are in good agreement with the experimental results obtained using X-ray and multiphoton UV photoelectron spectroscopy. Our approach will be useful for studying processes of photoinduced electron transfer from anionic as well as neutral biological chromophores in aqueous solution.
77.
Sinenka H, Bruyakin Y, Zaitsevskii A, Isaev T, Bochenkova A V
Zwitterions Functionalized by Optical Cycling Centers: Toward Laser-Coolable Polyatomic Molecular Cations Journal Article
In: Journal of Physical Chemistry Letters, vol. 14, pp. 5784–5790, 2023, ISSN: 1948-7185.
@article{sinenka2023zwitterions568824647,
title = {Zwitterions Functionalized by Optical Cycling Centers: Toward Laser-Coolable Polyatomic Molecular Cations},
author = {Hryhory Sinenka and Yurii Bruyakin and Andrei Zaitsevskii and Timur Isaev and Anastasia V. Bochenkova},
doi = {10.1021/acs.jpclett.3c00904},
issn = {1948-7185},
year = {2023},
date = {2023-01-01},
journal = {Journal of Physical Chemistry Letters},
volume = {14},
pages = {5784–5790},
publisher = {United States},
address = {United States},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
76.
Boichenko A N, Bochenkova A V
Accurate Vertical Electron Detachment Energies and Multiphoton Resonant Photoelectron Spectra of Biochromophore Anions in Aqueous Solution Journal Article
In: Journal of Chemical Theory and Computation, vol. 19, no. 13, pp. 4088-4099, 2023, (PMID: 37146177).
@article{doi:10.1021/acs.jctc.2c01082,
title = {Accurate Vertical Electron Detachment Energies and Multiphoton Resonant Photoelectron Spectra of Biochromophore Anions in Aqueous Solution},
author = {Anton N. Boichenko and Anastasia V. Bochenkova},
url = {https://doi.org/10.1021/acs.jctc.2c01082},
doi = {10.1021/acs.jctc.2c01082},
year = {2023},
date = {2023-01-01},
journal = {Journal of Chemical Theory and Computation},
volume = {19},
number = {13},
pages = {4088-4099},
note = {PMID: 37146177},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
75.
Robertson K, Fortune W G, Davies J A, Boichenko A, Scholz M S, Tau O, Bochenkova A V, Fielding H H
Wavelength dependent mechanism of phenolate photooxidation in aqueous solution Journal Article
In: Chemical Science, vol. 14, iss. 12, pp. 3257-3264, 2023.
@article{D3SC00016H,
title = {Wavelength dependent mechanism of phenolate photooxidation in aqueous solution},
author = {Kate Robertson and William G. Fortune and Julia A. Davies and Anton N. Boichenko and Michael S. Scholz and Omri Tau and Anastasia V. Bochenkova and Helen H. Fielding},
url = {http://dx.doi.org/10.1039/D3SC00016H},
doi = {10.1039/D3SC00016H},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Chemical Science},
volume = {14},
issue = {12},
pages = {3257-3264},
publisher = {The Royal Society of Chemistry},
abstract = {Phenolate photooxidation is integral to a range of biological processes, yet the mechanism of electron ejection has been disputed. Here, we combine femtosecond transient absorption spectroscopy, liquid-microjet photoelectron spectroscopy and high-level quantum chemistry calculations to investigate the photooxidation dynamics of aqueous phenolate following excitation at a range of wavelengths, from the onset of the S0–S1 absorption band to the peak of the S0–S2 band. We find that for λ ≥ 266 nm, electron ejection occurs from the S1 state into the continuum associated with the contact pair in which the PhO˙ radical is in its ground electronic state. In contrast, we find that for λ ≤ 257 nm, electron ejection also occurs into continua associated with contact pairs containing electronically excited PhO˙ radicals and that these contact pairs have faster recombination times than those containing PhO˙ radicals in their ground electronic state.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Phenolate photooxidation is integral to a range of biological processes, yet the mechanism of electron ejection has been disputed. Here, we combine femtosecond transient absorption spectroscopy, liquid-microjet photoelectron spectroscopy and high-level quantum chemistry calculations to investigate the photooxidation dynamics of aqueous phenolate following excitation at a range of wavelengths, from the onset of the S0–S1 absorption band to the peak of the S0–S2 band. We find that for λ ≥ 266 nm, electron ejection occurs from the S1 state into the continuum associated with the contact pair in which the PhO˙ radical is in its ground electronic state. In contrast, we find that for λ ≤ 257 nm, electron ejection also occurs into continua associated with contact pairs containing electronically excited PhO˙ radicals and that these contact pairs have faster recombination times than those containing PhO˙ radicals in their ground electronic state.
74.
Aslopovsky V R, Scherbinin A V, Kleshchina N N, Bochenkova A V
Impact of the Protein Environment on Two-Photon Absorption Cross-Sections of the GFP Chromophore Anion Resolved at the XMCQDPT2 Level of Theory Journal Article
In: International Journal of Molecular Sciences, vol. 24, no. 14, 2023, ISSN: 1422-0067.
@article{ijms241411266,
title = {Impact of the Protein Environment on Two-Photon Absorption Cross-Sections of the GFP Chromophore Anion Resolved at the XMCQDPT2 Level of Theory},
author = {Vladislav R. Aslopovsky and Andrei V. Scherbinin and Nadezhda N. Kleshchina and Anastasia V. Bochenkova},
url = {https://www.mdpi.com/1422-0067/24/14/11266},
doi = {10.3390/ijms241411266},
issn = {1422-0067},
year = {2023},
date = {2023-01-01},
journal = {International Journal of Molecular Sciences},
volume = {24},
number = {14},
abstract = {The search for fluorescent proteins with large two-photon absorption (TPA) cross-sections and improved brightness is required for their efficient use in bioimaging. Here, we explored the impact of a single-point mutation close to the anionic form of the GFP chromophore on its TPA activity. We considered the lowest-energy transition of EGFP and its modification EGFP T203I. We focused on a methodology for obtaining reliable TPA cross-sections for mutated proteins, based on conformational sampling using molecular dynamics simulations and a high-level XMCQDPT2-based QM/MM approach. We also studied the numerical convergence of the sum-over-states formalism and provide direct evidence for the applicability of the two-level model for calculating TPA cross-sections in EGFP. The calculated values were found to be very sensitive to changes in the permanent dipole moments between the ground and excited states and highly tunable by internal electric field of the protein environment. In the case of the GFP chromophore anion, even a single hydrogen bond was shown to be capable of drastically increasing the TPA cross-section. Such high tunability of the nonlinear photophysical properties of the chromophore anions can be used for the rational design of brighter fluorescent proteins for bioimaging using two-photon laser scanning microscopy.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The search for fluorescent proteins with large two-photon absorption (TPA) cross-sections and improved brightness is required for their efficient use in bioimaging. Here, we explored the impact of a single-point mutation close to the anionic form of the GFP chromophore on its TPA activity. We considered the lowest-energy transition of EGFP and its modification EGFP T203I. We focused on a methodology for obtaining reliable TPA cross-sections for mutated proteins, based on conformational sampling using molecular dynamics simulations and a high-level XMCQDPT2-based QM/MM approach. We also studied the numerical convergence of the sum-over-states formalism and provide direct evidence for the applicability of the two-level model for calculating TPA cross-sections in EGFP. The calculated values were found to be very sensitive to changes in the permanent dipole moments between the ground and excited states and highly tunable by internal electric field of the protein environment. In the case of the GFP chromophore anion, even a single hydrogen bond was shown to be capable of drastically increasing the TPA cross-section. Such high tunability of the nonlinear photophysical properties of the chromophore anions can be used for the rational design of brighter fluorescent proteins for bioimaging using two-photon laser scanning microscopy.
73.
Chaliy V A, Kelbysheva E S, Ezernitskaya M G, Strelkova T V, Bochenkova A V, Medvedev M G, Telegina L N
CO-Preserving Photoinduced Transfer of Cymantrenyl Moiety: a Tandem Experimental and Computational Investigation Journal Article
In: Chemistry – A European Journal, vol. 29, no. 29, pp. e202203949, 2023.
@article{https://doi.org/10.1002/chem.202203949,
title = {CO-Preserving Photoinduced Transfer of Cymantrenyl Moiety: a Tandem Experimental and Computational Investigation},
author = {Vasiliy A. Chaliy and Elena S. Kelbysheva and Mariam G. Ezernitskaya and Tatyana V. Strelkova and Anastasia V. Bochenkova and Michael G. Medvedev and Lyudmila N. Telegina},
url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/chem.202203949},
doi = {https://doi.org/10.1002/chem.202203949},
year = {2023},
date = {2023-01-01},
journal = {Chemistry – A European Journal},
volume = {29},
number = {29},
pages = {e202203949},
abstract = {Abstract Cyclopentadienyl manganese tricarbonyl (cymantrene) is known to undergo photochemical reactions by releasing one of its CO ligands. Here we present the first example of a photorearrangement of a cymantrenylmethyl fragment, where it retains all its three CO ligands. A tandem experimental and DFT (density functional theory)-based computational investigation allows us to explain this unexpected behavior: the rearrangement, indeed, begins with the release of one CO ligand, but cage effect of the solvent captures this CO molecule, allowing it to rapidly reattach once the rearrangement takes place.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract Cyclopentadienyl manganese tricarbonyl (cymantrene) is known to undergo photochemical reactions by releasing one of its CO ligands. Here we present the first example of a photorearrangement of a cymantrenylmethyl fragment, where it retains all its three CO ligands. A tandem experimental and DFT (density functional theory)-based computational investigation allows us to explain this unexpected behavior: the rearrangement, indeed, begins with the release of one CO ligand, but cage effect of the solvent captures this CO molecule, allowing it to rapidly reattach once the rearrangement takes place.
72.
Andersen L H, Rasmussen A P, Pedersen H B, Beletsan O B, Bochenkova A V
High-Resolution Spectroscopy and Selective Photoresponse of Cryogenically Cooled Green Fluorescent Protein Chromophore Anions Journal Article
In: The Journal of Physical Chemistry Letters, vol. 14, no. 28, pp. 6395-6401, 2023, (PMID: 37428615).
@article{doi:10.1021/acs.jpclett.3c01452,
title = {High-Resolution Spectroscopy and Selective Photoresponse of Cryogenically Cooled Green Fluorescent Protein Chromophore Anions},
author = {Lars H. Andersen and Anne P. Rasmussen and Henrik B. Pedersen and Oleg B. Beletsan and Anastasia V. Bochenkova},
url = {https://doi.org/10.1021/acs.jpclett.3c01452},
doi = {10.1021/acs.jpclett.3c01452},
year = {2023},
date = {2023-01-01},
journal = {The Journal of Physical Chemistry Letters},
volume = {14},
number = {28},
pages = {6395-6401},
note = {PMID: 37428615},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2022
71.
Bochenkova A V, Andersen L H
Action-Absorption Spectroscopy at the Band Origin of the Deprotonated Green Fluorescent Protein Chromophore In Vacuo Journal Article
In: J Phys Chem Lett, vol. 13, no. 29, pp. 6683–6685, 2022, ISSN: 1948-7185.
@article{pmid35848550,
title = {Action-Absorption Spectroscopy at the Band Origin of the Deprotonated Green Fluorescent Protein Chromophore In Vacuo},
author = {Anastasia V Bochenkova and Lars H Andersen},
doi = {10.1021/acs.jpclett.2c01791},
issn = {1948-7185},
year = {2022},
date = {2022-07-01},
journal = {J Phys Chem Lett},
volume = {13},
number = {29},
pages = {6683--6685},
abstract = {The application of action spectroscopy in connection with determination of the S to S band origin in the GFP anion model chromophore (deprotonated HBDI) is discussed. We specifically address the consequences of the lowest vibrational levels in S being located behind a potential-energy barrier that inhibits internal conversion to the S electronic ground state. Action spectroscopy based on consecutive absorption of two photons together with internal conversion will as a consequence reveal an apparent band origin that is significantly blue-shifted.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The application of action spectroscopy in connection with determination of the S to S band origin in the GFP anion model chromophore (deprotonated HBDI) is discussed. We specifically address the consequences of the lowest vibrational levels in S being located behind a potential-energy barrier that inhibits internal conversion to the S electronic ground state. Action spectroscopy based on consecutive absorption of two photons together with internal conversion will as a consequence reveal an apparent band origin that is significantly blue-shifted.
70.
Bochenkov V E, Sopova N S, Shakhov A M, Astafiev A A, Bochenkova A V
Protein Mobility Measurements through Oxidative Green-to-Red Photoconversion of EGFP Journal Article
In: The Journal of Physical Chemistry B, vol. 126, iss. 23, pp. 4184–4188, 2022.
@article{doi:10.1021/acs.jpcb.2c00643,
title = {Protein Mobility Measurements through Oxidative Green-to-Red Photoconversion of EGFP},
author = {Vladimir E. Bochenkov and Nina S. Sopova and Aleksander M. Shakhov and Artyom A. Astafiev and Anastasia V. Bochenkova},
url = {https://doi.org/10.1021/acs.jpcb.2c00643},
doi = {10.1021/acs.jpcb.2c00643},
year = {2022},
date = {2022-06-03},
urldate = {2022-06-03},
journal = {The Journal of Physical Chemistry B},
volume = {126},
issue = {23},
pages = {4184–4188},
abstract = {Protein dynamics plays a key role in live cell functioning, stimulating the development of new experimental techniques for studying protein transport phenomena. Here, we introduce a relaxation method that is based on the rapid formation of a nonequilibrium concentration profile of the enhanced green fluorescent protein (EGFP) across a sample by its oxidative green-to-red photoconversion. Following the blue-light irradiation of a part of a sample containing EGFP and an oxidant, the diffusion-controlled response of a system is monitored. Changes in the concentration of the initial green-emitting and oxidized red-emitting forms are simultaneously tracked by fluorescence lifetime measurements using the time-correlated single photon counting. We show that the diffusion coefficient of EGFP in water, determined by this method, is in good agreement with previously published data. This approach opens a way for the studies of intracellular viscosity changes combined with sensing of elevated levels of reactive oxygen species.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Protein dynamics plays a key role in live cell functioning, stimulating the development of new experimental techniques for studying protein transport phenomena. Here, we introduce a relaxation method that is based on the rapid formation of a nonequilibrium concentration profile of the enhanced green fluorescent protein (EGFP) across a sample by its oxidative green-to-red photoconversion. Following the blue-light irradiation of a part of a sample containing EGFP and an oxidant, the diffusion-controlled response of a system is monitored. Changes in the concentration of the initial green-emitting and oxidized red-emitting forms are simultaneously tracked by fluorescence lifetime measurements using the time-correlated single photon counting. We show that the diffusion coefficient of EGFP in water, determined by this method, is in good agreement with previously published data. This approach opens a way for the studies of intracellular viscosity changes combined with sensing of elevated levels of reactive oxygen species.
69.
Rasmussen A P, Teiwes R, Farkhutdinova D A, Bochenkova A V, Andersen L H
On the temperature of large biomolecules in ion-storage rings Journal Article
In: The European Physical Journal D, vol. 76, no. 5, pp. 76, 2022.
@article{Rasmussen2022,
title = {On the temperature of large biomolecules in ion-storage rings},
author = {Anne P. Rasmussen and Ricky Teiwes and Dilara A. Farkhutdinova and Anastasia V. Bochenkova and Lars H. Andersen},
url = {https://link.springer.com/article/10.1140/epjd/s10053-022-00400-y https://link.springer.com/10.1140/epjd/s10053-022-00400-y},
doi = {10.1140/epjd/s10053-022-00400-y},
year = {2022},
date = {2022-05-01},
journal = {The European Physical Journal D},
volume = {76},
number = {5},
pages = {76},
publisher = {Springer},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
68.
Gruber E, Kabylda A M, Nielsen M B, Rasmussen A P, Teiwes R, Kusochek P A, Bochenkova A V, Andersen L H
Light Driven Ultrafast Bioinspired Molecular Motors: Steering and Accelerating Photoisomerization Dynamics of Retinal Journal Article
In: Journal of the American Chemical Society, vol. 144, no. 1, pp. 69–73, 2022.
@article{Gruber2021,
title = {Light Driven Ultrafast Bioinspired Molecular Motors: Steering and Accelerating Photoisomerization Dynamics of Retinal},
author = {E. Gruber and A. M. Kabylda and M. B. Nielsen and A. P. Rasmussen and R. Teiwes and P. A. Kusochek and A. V. Bochenkova and L. H. Andersen},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85122207922&doi=10.1021%2fjacs.1c10752&partnerID=40&md5=3a578161de96a630322dcf7146d53bbf},
doi = {10.1021/jacs.1c10752},
year = {2022},
date = {2022-01-01},
urldate = {2021-01-01},
journal = {Journal of the American Chemical Society},
volume = {144},
number = {1},
pages = {69–73},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
67.
Tau O, Henley A, Boichenko A N, Kleshchina N N, Riley R, Wang B, Winning D, Lewin R, Parkin I P, Ward J M, Hailes H C, Bochenkova A V, Fielding H H
Liquid-microjet photoelectron spectroscopy of the green fluorescent protein chromophore Journal Article
In: Nature communications, vol. 13, no. 1, pp. 507, 2022, ISSN: 2041-1723.
@article{fielding2022liquid-microjet429253392,
title = {Liquid-microjet photoelectron spectroscopy of the green fluorescent protein chromophore},
author = {Omri Tau and Alice Henley and Anton N. Boichenko and Nadezhda N. Kleshchina and River Riley and Bingxing Wang and Danielle Winning and Ross Lewin and Ivan P. Parkin and John M. Ward and Helen C. Hailes and Anastasia V. Bochenkova and Helen H. Fielding},
doi = {10.1038/s41467-022-28155-5},
issn = {2041-1723},
year = {2022},
date = {2022-01-01},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {507},
publisher = {United Kingdom},
address = {United Kingdom},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
66.
Finenko A A, Bézard B, Gordon I E, Chistikov D N, Lokshtanov S E, Petrov S V, Vigasin A A
Trajectory-based Simulation of Far-infrared Collision-induced Absorption Profiles of CH4–N2 for Modeling Titan’s Atmosphere Journal Article
In: The Astrophysical Journal Supplement Series, vol. 258, no. 2, pp. 33, 2022.
@article{Finenko_2022,
title = {Trajectory-based Simulation of Far-infrared Collision-induced Absorption Profiles of CH4–N2 for Modeling Titan's Atmosphere},
author = {Artem A. Finenko and Bruno Bézard and Iouli E. Gordon and Daniil N. Chistikov and Sergei E. Lokshtanov and Sergey V. Petrov and Andrey A. Vigasin},
url = {https://doi.org/10.3847/1538-4365/ac36d3},
doi = {10.3847/1538-4365/ac36d3},
year = {2022},
date = {2022-01-01},
journal = {The Astrophysical Journal Supplement Series},
volume = {258},
number = {2},
pages = {33},
publisher = {American Astronomical Society},
abstract = {We report the results of the trajectory-based simulation of far-infrared collision-induced absorption (CIA) due to CH4–N2 pairs at temperatures between 70 and 400 K. Our analysis utilizes recently calculated high-level potential energy and induced dipole surfaces. Treating collision partners as rigid rotors, the time evolution of interaction-induced dipole is accumulated over a vast ensemble of classical trajectories and subsequently transformed into a CIA spectrum via Fourier transform. In our calculations, both bound and unbound states are properly accounted for, and the rigorous theory of lower-order spectral moments is addressed to check the accuracy of simulated profiles. Classically derived trajectory-based profiles are subject to two approximate desymmetrization procedures so that resulting profiles conform to the quantum principle of detailed balance. The simulated profiles are compared to laboratory measurements and employed for modeling Titan’s spectra in the 50–500 cm−1 range. Based on the desymmetrized simulated profiles, a new semiempirical model for CH4–N2 CIA is proposed for modeling Titan’s infrared spectra. Synthetic spectra derived using this model yield an excellent agreement with the data recorded by the Composite Infrared Spectrometer aboard the Cassini spacecraft at low and high emission angles.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We report the results of the trajectory-based simulation of far-infrared collision-induced absorption (CIA) due to CH4–N2 pairs at temperatures between 70 and 400 K. Our analysis utilizes recently calculated high-level potential energy and induced dipole surfaces. Treating collision partners as rigid rotors, the time evolution of interaction-induced dipole is accumulated over a vast ensemble of classical trajectories and subsequently transformed into a CIA spectrum via Fourier transform. In our calculations, both bound and unbound states are properly accounted for, and the rigorous theory of lower-order spectral moments is addressed to check the accuracy of simulated profiles. Classically derived trajectory-based profiles are subject to two approximate desymmetrization procedures so that resulting profiles conform to the quantum principle of detailed balance. The simulated profiles are compared to laboratory measurements and employed for modeling Titan’s spectra in the 50–500 cm−1 range. Based on the desymmetrized simulated profiles, a new semiempirical model for CH4–N2 CIA is proposed for modeling Titan’s infrared spectra. Synthetic spectra derived using this model yield an excellent agreement with the data recorded by the Composite Infrared Spectrometer aboard the Cassini spacecraft at low and high emission angles.
65.
Sokolov A I, Sycheva M A, Farkhutdinova D A, Myasnyanko I N, Mikhaylov A A, Baleeva N S, Bochenkova A V, Baranov M S
Fluorescent 2-Hydroxy-3-(pyridin-2-yl)-4H-quinolizin-4-ones through Dimerization of Pyridineacetic Acids Journal Article
In: European Journal of Organic Chemistry, vol. 2022, no. 30, pp. e202200680, 2022.
@article{https://doi.org/10.1002/ejoc.202200680,
title = {Fluorescent 2-Hydroxy-3-(pyridin-2-yl)-4H-quinolizin-4-ones through Dimerization of Pyridineacetic Acids},
author = {Anatolii I. Sokolov and Maria A. Sycheva and Dilara A. Farkhutdinova and Ivan N. Myasnyanko and Andrey A. Mikhaylov and Nadezhda S. Baleeva and Anastasia V. Bochenkova and Mikhail S. Baranov},
url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/ejoc.202200680},
doi = {https://doi.org/10.1002/ejoc.202200680},
year = {2022},
date = {2022-01-01},
journal = {European Journal of Organic Chemistry},
volume = {2022},
number = {30},
pages = {e202200680},
abstract = {Abstract Pyridineacetic acids undergo dimerization under action of the activating agents, giving rise to 2-hydroxy-3-(pyridin-2-yl)-4H-quinolizin-4-ones. The introduction of a difluoroboryl bridge into such derivatives leads to novel highly fluorescent compounds.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract Pyridineacetic acids undergo dimerization under action of the activating agents, giving rise to 2-hydroxy-3-(pyridin-2-yl)-4H-quinolizin-4-ones. The introduction of a difluoroboryl bridge into such derivatives leads to novel highly fluorescent compounds.
2021
64.
Lambo R, Xu C -Y, Pratt S T, Xu H, Zappala J C, Bailey K G, Lu Z -T, Mueller P, O’Connor T P, Kamorzin B B, Bezrukov D S, Xie Y -Q, Buchachenko A A, Singh J T
High-resolution spectroscopy of neutral Yb atoms in a solid Ne matrix Journal Article
In: Phys. Rev. A, vol. 104, iss. 6, pp. 062809, 2021.
@article{PhysRevA.104.062809,
title = {High-resolution spectroscopy of neutral Yb atoms in a solid Ne matrix},
author = {R. Lambo and C. -Y. Xu and S. T. Pratt and H. Xu and J. C. Zappala and K. G. Bailey and Z. -T. Lu and P. Mueller and T. P. O'Connor and B. B. Kamorzin and D. S. Bezrukov and Y. -Q. Xie and A. A. Buchachenko and J. T. Singh},
url = {https://link.aps.org/doi/10.1103/PhysRevA.104.062809},
doi = {10.1103/PhysRevA.104.062809},
year = {2021},
date = {2021-12-01},
journal = {Phys. Rev. A},
volume = {104},
issue = {6},
pages = {062809},
publisher = {American Physical Society},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
63.
Sinenko G D, Farkhutdinova D A, Myasnyanko I N, Baleeva N S, Baranov M S, Bochenkova A V
Designing red-shifted molecular emitters based on the annulated locked GFPchromophore derivatives Journal Article
In: International Journal of Molecular Sciences, vol. 22, no. 24, pp. 13645, 2021.
@article{Sinenko2021,
title = {Designing red-shifted molecular emitters based on the annulated locked GFPchromophore derivatives},
author = {G. D. Sinenko and D. A. Farkhutdinova and I. N. Myasnyanko and N. S. Baleeva and M. S. Baranov and A. V. Bochenkova},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85121343375&doi=10.3390%2fijms222413645&partnerID=40&md5=3538db985b54d3e96fac059fa8c047d4},
doi = {10.3390/ijms222413645},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {International Journal of Molecular Sciences},
volume = {22},
number = {24},
pages = {13645},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
62.
Kusochek P A, Logvinov V V, Bochenkova A V
Role of the Protein Environment in Photoisomerization of Type I and Type II Rhodopsins: a Theoretical Perspective Journal Article
In: Moscow University Chemistry Bulletin, vol. 76, no. 6, pp. 407-416, 2021.
@article{Kusochek2021407,
title = {Role of the Protein Environment in Photoisomerization of Type I and Type II Rhodopsins: a Theoretical Perspective},
author = {P. A. Kusochek and V. V. Logvinov and A. V. Bochenkova},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85120800108&doi=10.3103%2fS0027131421060110&partnerID=40&md5=9aa76018ed468350c52c3a510602ec38},
doi = {10.3103/S0027131421060110},
year = {2021},
date = {2021-01-01},
journal = {Moscow University Chemistry Bulletin},
volume = {76},
number = {6},
pages = {407-416},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
61.
Woodhouse J L, Henley A, Lewin R, Ward J M, Hailes H C, Bochenkova A V, Fielding H H
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title = {Controlling Light-Induced Proton Transfer from the GFP Chromophore},
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Kusochek P A, Scherbinin A V, Bochenkova A V
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Ivanenkov Y A, Filyaeva K Y, Matniyazov R T, Baymiev A K, Vladimirova A A, Yamidanov R S, Mavzyutov A R, Zileeva Z R, Zainullina L F, Vakhitova J V, Marina V I, Terentiev V A, Osterman I A, Kartsev V G, Bezrukov D S, Dontsova O A
Antibacterial activity of noscapine analogs Journal Article
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title = {Antibacterial activity of noscapine analogs},
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Ozerov G K, Bezrukov D S, Buchachenko A A
Generic accommodations of an atom in the Lennard-Jones fcc and hcp rare-gas solids: A computational study Journal Article
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title = {Modeling of the thermal migration mechanisms of atomic oxygen in Ar, Kr, and Xe crystals},
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Molecular dynamics simulations of the Ba+ ion mobility in liquid xenon Journal Article
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title = {Molecular dynamics simulations of the Ba+ ion mobility in liquid xenon},
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Is Solid Copper Oxalate a Spin Chain or a Mixture of Entangled Spin Pairs? Journal Article
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Trapping and migration of P-state atoms in rare gas solids: effect of angular momentum anisotropy for model O(3P) and C(3P) atoms Journal Article
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Tetrahydrocarbazoles as Novel Class of DNA Biosynthesis Inhibitors in Bacteria Journal Article
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