Theoretical modelling of structure, vibrational and UV–vis absorbance spectra of rubrofusarin molecule

Pankin, Dmitrii; Povolotckaia, Anastasia; Borisov, E. N.; Belyakov, Mikhail V.; Borzenko, Sergey; Gulyaev, Anatoly; Moskovskiy, Maksim

doi:10.1016/j.saa.2023.122469

Cited by 7 publications

(7 citation statements)

References 39 publications

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“…The B3LYP hybrid functional with the Pople type triple‐zeta split valence basis with polarization functions 6–311G(2d,p) was chosen as a calculation method. As shown earlier in a number of papers, [44–46] this approach allows us to predict accurately the vibrational properties of aromatic and polycyclic molecules. For the studied molecules, at the initial stage, the geometry optimization of the molecule was performed until the convergence conditions for the maximum and RMS values of atomic displacements and forces were met.…”

Section: Methodsmentioning

confidence: 83%

Vinyl Phosphonates as Photopharmacological Agents: Laser‐Induced Cis‐Trans Isomerization and Butyrylcholinesterase Activity

Bikbaeva,

Egorova,

Sonin

et al. 2023

ChemPhotoChem

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Photoswitchable molecules are highly requested compounds in various fields and, in particular, biomedicine. The urgent modern task of photopharmacology (an emerging approach in medicine) is the design of molecules that have both photoswitchable and bioactive properties. In this study, we present vinyl phosphonates – diene compounds with ethyl and isopropyl substituents on the phosphonate group. Both compounds demonstrated laser‐induced cis‐trans isomerization via a C=C bond after irradiation at 266 nm. The photoisomerization quantum yield was 17 % and 20 % for compounds with ethyl and isopropyl groups, respectively. The main advantage of the presented vinyl phosphonates is their bioactivity, unlike other photoswitchable molecules. Rather efficient butyrylcholinesterase inhibition by both presented compounds was demonstrated by IPC‐Micro analysis. The notable butyrylcholinesterase inhibition increase by 5 and 9 times was found for the vinyl phosphonates after laser irradiation. Such a sizeable difference in inhibition values for different isomeric states is a critical factor, which opens the way toward promising applications of vinyl phosphonates as photopharmacological agents.

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Section: Methodsmentioning

confidence: 83%

Vinyl Phosphonates as Photopharmacological Agents: Laser‐Induced Cis‐Trans Isomerization and Butyrylcholinesterase Activity

Bikbaeva,

Egorova,

Sonin

et al. 2023

ChemPhotoChem

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“…Thus, the idea of detecting the plant pathogens using optical methods [ 47 ] looks promising. Naturally, quantum chemistry calculations applying the TD-DFT approach have been used for many carotenoids and other photosynthetic pigments [ 48 , 49 ]; moreover, some studies have recently been published on the simulation of the vibrational spectrum of rubrofusarin [ 50 ]. It is worth noting that these methods can estimate the vibrational structures of the ground state quite well; however, for modeling excited states, complicating the calculations is necessary.…”

Section: Discussionmentioning

confidence: 99%

A Prototype Method for the Detection and Recognition of Pigments in the Environment Based on Optical Property Simulation

Pishchalnikov,

Chesalin,

Kurkov

et al. 2023

Plants

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The possibility of pigment detection and recognition in different environments such as solvents or proteins is a challenging, and at the same time demanding, task. It may be needed in very different situations: from the nondestructive in situ identification of pigments in paintings to the early detection of fungal infection in major agro-industrial crops and products. So, we propose a prototype method, the key feature of which is a procedure analyzing the lineshape of a spectrum. The shape of the absorption spectrum corresponding to this transition strongly depends on the immediate environment of a pigment and can serve as a marker to detect the presence of a particular pigment molecule in a sample. Considering carotenoids as an object of study, we demonstrate that the combined operation of the differential evolution algorithm and semiclassical quantum modeling of the optical response based on a generalized spectral density (the number of vibronic modes is arbitrary) allows us to distinguish quantum models of the pigment for different solvents. Moreover, it is determined that to predict the optical properties of monomeric pigments in protein, it is necessary to create a database containing, for each pigment, in addition to the absorption spectra measured in a predefined set of solvents, the parameters of the quantum model found using differential evolution.

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“…For the optimized structure, the phonon frequencies were calculated by the linear response method (density-functional-perturbation theory, DFPT). 59,60 The theoretical Raman intensities were obtained from the Raman activities using the following Equation (1) 61,62 in order to compare the experimental spectrum with the theoretical one:…”

Section: Methodsmentioning

confidence: 99%

“…For the optimized structure, the phonon frequencies were calculated by the linear response method (density‐functional‐perturbation theory, DFPT) 59,60 . The theoretical Raman intensities were obtained from the Raman activities using the following Equation () 61,62 in order to compare the experimental spectrum with the theoretical one:

\begin{equation}{\mathrm{I\ }} = \ \frac{{{\mathrm{N}}{{\left( {{{\mathrm{v}}_0} - {{\mathrm{v}}_i}} \right)}^4}{{\mathrm{R}}_a}}}{{{{\mathrm{v}}_i}\left( {1 - {e^{\left( { - \frac{{{\mathrm{hc}}{{\mathrm{v}}_{\mathrm{i}}}}}{{{{\mathrm{k}}_{\mathrm{B}}}{\mathrm{T}}}}} \right)}}} \right)}},\end{equation}

…”

Section: Methodsmentioning

confidence: 99%

Topotactic transformation of gadolinite‐ to melilite‐type structure revisited

Gorelova,

Vereshchagin,

Shagova

et al. 2024

J Am Ceram Soc.

Self Cite

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Topotactic reactions can lead to the formation of new phases, which cannot be obtained via classical synthesis methods. The high‐temperature topotactic transformation of gadolinite‐type compounds, homilite Ca2Fe2+B2Si2O8O2 and datolite Ca2□B2Si2O8(OH)2, into a melilite‐type compound, okayamalite Ca2B2SiO7, was studied by in situ high‐temperature single‐crystal X‐ray diffraction and ex situ Raman spectroscopy. Furthermore, the density functional theory was used to calculate the electronic structures and Raman spectra of datolite, homilite, and okayamalite. At low temperatures (250–500°C), homilite undergoes the Fe oxidation process, whereas at high temperatures, both homilite and datolite transform into okayamalite (750 and 780°C, respectively). The transformation of datolite into okayamalite is a conversion of a single crystal to a polycrystalline aggregate, while the transformation of homilite into okayamalite is a transformation of a single crystal to a single crystal. Datolite derived from okayamalite is similar to natural okayamalite, whereas homilite derived from okayamalite shows Fe3+ for Si/B substitution. The existence of tetrahedrally coordinated Fe3+ leads to a stabilizing effect, resulting in the formation of a single crystal of okayamalite. In addition, the incorporation of iron into the structure of okaymalite leads to a change in the thermal behavior of the compound (α11 = 22 and 15×10−6°C–1 for datolite‐derived and homilite‐derived okayamalites, respectively). However, the thermal expansion of okayamalites is almost isotropic, which is typical for melilite‐type compounds.datolite, high‐temperature, homilite, okayamalite, topotactic reaction

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Theoretical modelling of structure, vibrational and UV–vis absorbance spectra of rubrofusarin molecule

Cited by 7 publications

References 39 publications

Vinyl Phosphonates as Photopharmacological Agents: Laser‐Induced Cis‐Trans Isomerization and Butyrylcholinesterase Activity

Vinyl Phosphonates as Photopharmacological Agents: Laser‐Induced Cis‐Trans Isomerization and Butyrylcholinesterase Activity

A Prototype Method for the Detection and Recognition of Pigments in the Environment Based on Optical Property Simulation

Topotactic transformation of gadolinite‐ to melilite‐type structure revisited

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