Article
Biochemistry & Molecular Biology
Jinyu Wang, Yajun Liu
Summary: In this study, we used DFT and TD-DFT to calculate the pH-dependent absorption and fluorescence spectra of flavin in three redox states (quinone, semiquinone, and hydroquinone) in solvents. The chemical equilibrium of these states and the pH effect on the spectra were discussed. This conclusion helps identify the existing forms of flavin in solvents with different pH values.
Article
Spectroscopy
Gouri Deshpande, Jayashree Tonannavar, J. Tonannavar, Siddanagouda B. Patil, Vinay S. Kundargi, Santosh Patil, B. G. Mulimani, S. Narayana Kalkura, J. Ramana Ramya, K. Thanigai Arul
Summary: This study presents the detection of mineral constituents in human urinary calculi samples using Fourier Transform based IR and Raman spectral measurements. The identified mineral constituents can be deduced from the application of Lambert-Beer law of radiation absorption. The findings have the potential to contribute to the management of urolithiasis.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Chemistry, Multidisciplinary
Z. Liu, X. Zhang
Summary: A theoretical investigation of vanadium naphthalocyanine (VONc) was performed, including the molecular, electronic structures, and vibrational spectrum. The study compared VONc with other metal naphthalocyanines and found differences in symmetry and bond lengths. VONc exhibited the smallest HOMO-LUMO gap among the studied compounds. Accurate vibrational mode assignments were obtained using calculated potential energy distribution and animated pictures. A new symbol system was adopted to improve the clarity of the assignments, and corrections were made based on experimental comparisons.
MATERIALS TODAY CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Bella Grigorenko, Tatiana Domratcheva, Alexander Nemukhin
Summary: The oxygenase activity of the flavin-dependent enzyme RutA is associated with the formation of flavin-oxygen adducts in the enzyme active site. Using quantum mechanics/molecular mechanics (QM/MM) modeling, we investigated potential reaction pathways initiated by triplet state complexes of molecular oxygen with reduced flavin mononucleotide (FMN) in protein cavities. The results show that these complexes can be located at different positions on the isoalloxazine ring of flavin, and the activated dioxygen attacks specific positions in the ring, resulting in covalent adducts or direct oxidation of flavin.
Article
Multidisciplinary Sciences
Alexandra Yu. Ledneva, Mariia N. Ivanova, Pavel A. Poltarak, Spartak S. Yarovoy, Boris A. Kolesov, Vladimir E. Fedorov, Nikolay G. Naumov
Summary: A series of rhenium compounds with octahedral cluster core and molecular and polymeric structures were synthesized. The analysis of their vibrational spectra revealed that the composition and symmetry of the cluster core affected the main characteristic bands in both ionic and polymeric compounds.
Article
Chemistry, Physical
Veronica Macaluso, Shaima Hashem, Michele Nottoli, Filippo Lipparini, Lorenzo Cupellini, Benedetta Mennucci
Summary: A novel strategy was designed to compute TRIR spectra of photoreceptors by combining different types of molecular dynamics, revealing that the dynamic Stokes shift of flavin is ultrafast and mainly driven by the internal reorganization of the chromophore.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Physical
V. L. Furer, A. E. Vandyukov, Z. V. Ahkmetzyanova, V. A. Burilov, S. E. Solovieva, I. S. Antipin, V. I. Kovalenko
Summary: The vibrational spectra of calix[4]arenes and thiacalix[4]arenes with azobenzene units containing carboxylate groups were recorded and analyzed. The cone conformation with four intramolecular cooperative hydrogen bonds was found to be the most stable and polar. Significant changes in shape and polarity were observed upon isomerization of azobenzene groups in calixarene molecules, with differences in properties between thiacalixarenes and classical calixarenes.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Chemistry, Physical
V. L. Furer, A. E. Vandyukov, S. R. Kleshnina, S. E. Solovieva, I. S. Antipin, V. Kovalenko
Summary: The vibrational spectra of p-hexasulfonatocalix[6]arene hexasodium salt (SC6) and p-tert-butylcalix[6]arene (TB6) were studied, allowing to distinguish bands of tert-butyl and sulfonate groups. The structure and vibrational spectra of the SC6 molecule were calculated for different conformations, with the compressed cone conformation being the most stable. The replacement of tert-butyl groups with sulfonate groups resulted in an increase in the cavity size of calixarene molecules and changes in supramolecular properties.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Biochemistry & Molecular Biology
Victor L. Furer, Alexandr E. Vandyukov, Sofya R. Kleshnina, Svetlana E. Solovieva, Igor S. Antipin, Valery Kovalenko
Summary: The vibrational spectra of TCAS and BuTCA were studied to analyze their structures and characteristic bands. It was found that sodium ions in TCAS molecule influence the electron density distribution and supramolecular interactions.
JOURNAL OF MOLECULAR MODELING
(2021)
Article
Biochemistry & Molecular Biology
Victor L. Furer, Alexandr E. Vandyukov, Alexandr S. Ovsyannikov, Svetlana E. Solovieva, Igor S. Antipin
Summary: This study aims to investigate the structure and spectra of distally substituted para-tert-butylthiacalix[4]arene aliphatic (C1) and aromatic (C2) esters. Calculations showed that the most stable conformation for C1 and C2 molecules is a distorted cone 2 (DC2) with the same ester group orientation. Thiacalixarene molecules' cavities shrink when aromatic ester groups replace aliphatic ester groups. The replacement also leads to changes in ionization energy, electron affinity, chemical potential, softness, electrophilicity index, and dipole moment.
JOURNAL OF MOLECULAR MODELING
(2023)
Article
Chemistry, Physical
V. L. Furer, L. Potapova, D. Chachkov, I. M. Vatsouro, V. V. Kovalev, E. A. Shokova, V. Kovalenko
Summary: The IR spectra of calix[6]arenes with adamantylacetic acid and adamantyl substituents were studied, showing that formation of intramolecular H-bonds does not weaken cyclic cooperative H-bonds. Heating a sample to 180 degrees C destroys some H-bonds, but they can be restored upon cooling. Heating up to 355 degrees C leads to irreversible changes in the H-bonding system.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Chemistry, Physical
V. L. Furer, L. I. Potapova, A. E. Vandyukov, D. V. Chachkov, I. M. Vatsouro, V. V. Kovalev, E. A. Shokova, V. I. Kovalenko
Summary: The IR and Raman spectra of two calixarene compounds were studied, showing that the dimerization of carboxyl groups is more favorable than tetramerization and with significant energy differences. The molecular calculations indicated a unique cone conformation in both dimeric and tetrameric complexes of the compounds.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Environmental Sciences
Xiuying Zhang, Xin Shi, Ming Deng, Yue Wang, Ping Ning, Lihong Tang, Zhiyuan Ning
Summary: This study investigated the structures and mechanisms of arsenic(V) adsorbed on Fe(III)-oxyhydroxide adsorption complexes using hybrid density functional theory calculations and experimental FT-IR spectroscopy. Experimental results showed higher removal rates of arsenic(V) in the pH range of 5.0-10.0. Additionally, the stabilities of different As(V)-Fe(III)-oxyhydroxide complexes were revealed and found to be interconvertible.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Review
Biochemistry & Molecular Biology
Yusuke Nakasone, Masahide Terazima
Summary: This review describes the reactions of three BLUF proteins with similar EAL functional groups or with a separated target protein using time-resolved diffusion technique.
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES
(2022)
Article
Spectroscopy
Andrey Morozov, Tatiana Nazdracheva, Andrei Kochur, Victor Yavna
Summary: This study aims to investigate the influence of solvate shells interaction on the profiles of infrared spectra of sodium chloride solutions. Experimental measurements of infrared spectra were conducted on distilled water and sodium chloride solutions at limit and half-limit concentrations. Theoretical calculations using the DFT approach with the XLYP exchange-correlation potential were employed to compute the infrared spectra profiles for clusters containing 9 water molecules and one NaCl molecule. The results showed that the infrared spectrum is mainly influenced by the interaction of Na+ and Cl- solvation shells, each consisting of 4 water molecules, with the 9th water molecule providing bonding between the solvated ions.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2023)
Article
Chemistry, Physical
Martin Zachmann, Gerald Mathias, Iris Antes
Article
Chemistry, Physical
Konstantin Lorenzen, Gerald Mathias, Paul Tavan
JOURNAL OF CHEMICAL PHYSICS
(2015)
Article
Chemistry, Physical
Magnus Schwoerer, Konstantin Lorenzen, Gerald Mathias, Paul Tavan
JOURNAL OF CHEMICAL PHYSICS
(2015)
Article
Chemistry, Physical
Nicolas Lenner, Gerald Mathias
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2016)
Article
Chemistry, Physical
Magnus Schwoerer, Christoph Wichmann, Erik Gawehn, Gerald Mathias
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2016)
Article
Chemistry, Physical
Sebastian Bauer, Paul Tavan, Gerald Mathias
CHEMICAL PHYSICS LETTERS
(2014)
Article
Chemistry, Physical
Magnus Schwoerer, Benedikt Breitenfeld, Philipp Troester, Sebastian Bauer, Konstantin Lorenzen, Paul Tavan, Gerald Mathias
JOURNAL OF CHEMICAL PHYSICS
(2013)
Article
Chemistry, Physical
Sebastian Bauer, Gerald Mathias, Paul Tavan
JOURNAL OF CHEMICAL PHYSICS
(2014)
Article
Chemistry, Physical
Sebastian Bauer, Paul Tavan, Gerald Mathias
JOURNAL OF CHEMICAL PHYSICS
(2014)
Article
Chemistry, Physical
Gerald Mathias, Sergei D. Ivanov, Alexander Witt, Marcel D. Baer, Dominik Marx
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2012)
Article
Chemistry, Physical
Joost VandeVondele, Philipp Troester, Paul Tavan, Gerald Mathias
JOURNAL OF PHYSICAL CHEMISTRY A
(2012)
Article
Chemistry, Physical
Alexander Witt, Sergei D. Ivanov, Gerald Mathias, Dominik Marx
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2011)
Article
Chemistry, Physical
Matthias Heyden, Jian Sun, Harald Forbert, Gerald Mathias, Martina Havenith, Dominik Marx
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2012)
Article
Chemistry, Multidisciplinary
Rachel Glaves, Gerald Mathias, Dominik Marx
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2012)
Article
Computer Science, Interdisciplinary Applications
Tobias Kloeffel, Gerald Mathias, Bernd Meyer
Summary: The compute power of individual nodes in today's supercomputer hardware is growing faster than the speed of interconnects, posing a challenge for modernizing simulation software to increase computational load on nodes while reducing inter-node communication. This study demonstrates a strategy for plane-wave based electronic structure methods and AIMD simulations to achieve this goal, focusing on USPP and optimizing workload partitioning and communication-intensive routines for enhanced performance and scalability. The new algorithms have been successfully implemented in the CPMD program, showing improved simulation efficiency for systems like liquid water with hundreds of molecules.
COMPUTER PHYSICS COMMUNICATIONS
(2021)