1
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Sosulin IS, Ryan DH, Lisouskaya A. Radicals from tributyl phosphate decomposition: a combined electron paramagnetic resonance spectroscopic and computational chemistry investigation. Phys Chem Chem Phys 2023; 25:29350-29357. [PMID: 37877227 DOI: 10.1039/d3cp03584k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
The radiation- and chemically-induced radicals from tributyl phosphate (TBP) have been characterized by EPR spectroscopy and theoretical calculations. The yield of X-ray-generated TBP radicals measured by a PBN spin trap is 0.22 μmol J-1 (2.1 radicals/100 eV) at room temperature (298 K). The EPR spectra obtained by irradiating TBP with an electron beam at 77 K are in close agreement with literature data for samples irradiated with gamma- and X-rays [https://doi.org/10.1007/BF02165504, https://doi.org/10.1016/1359-0197(89)90319-6]. Possible conformers of alkyl-type, TBP-derived radicals were analyzed by Density Functional Theory calculations. The main contribution to the experimental spectrum at 77 K is shown to be made by a conformer of the CH3˙CHCH2-radical, which contains all carbon atoms of the butyl group in the same plane. The EPR spectra of TBP radicals induced by the OH radical in aqueous solution were measured for the first time using a continuous flow system. The formation of the alkyl-type TBP radicals CH3˙CHCH2-, ˙CH2CH2-, and -CH2˙CHO- in the ratio of 5/4/1 was detected; their spectral assignment was based on quantum chemical calculations with rotational averaging of HFC constants for the corresponding beta- and alpha-protons.
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Affiliation(s)
- Ilya S Sosulin
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Delaney H Ryan
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA.
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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2
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Khatmullina KG, Slesarenko NA, Chernyak AV, Baymuratova GR, Yudina AV, Berezin MP, Tulibaeva GZ, Slesarenko AA, Shestakov AF, Yarmolenko OV. New Network Polymer Electrolytes Based on Ionic Liquid and SiO 2 Nanoparticles for Energy Storage Systems. MEMBRANES 2023; 13:548. [PMID: 37367752 DOI: 10.3390/membranes13060548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023]
Abstract
Elementary processes of electro mass transfer in the nanocomposite polymer electrolyte system by pulse field gradient, spin echo NMR spectroscopy and the high-resolution NMR method together with electrochemical impedance spectroscopy are examined. The new nanocomposite polymer gel electrolytes consisted of polyethylene glycol diacrylate (PEGDA), salt LiBF4 and 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIBF4) and SiO2 nanoparticles. Kinetics of the PEGDA matrix formation was studied by isothermal calorimetry. The flexible polymer-ionic liquid films were studied by IRFT spectroscopy, differential scanning calorimetry and temperature gravimetric analysis. The total conductivity in these systems was about 10-4 S cm-1 (-40 °C), 10-3 S cm-1 (25 °C) and 10-2 S cm-1 (100 °C). The method of quantum-chemical modeling of the interaction of SiO2 nanoparticles with ions showed the advantage of the mixed adsorption process, in which a negatively charged surface layer is formed from Li+ BF4- ions on silicon dioxide particles and then from ions of the ionic liquid EMI+ BF4-. These electrolytes are promising for use both in lithium power sources and in supercapacitors. The paper shows preliminary tests of a lithium cell with an organic electrode based on a pentaazapentacene derivative for 110 charge-discharge cycles.
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Affiliation(s)
- Kyunsylu G Khatmullina
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
- Department of Chemistry and Electrochemical Energy, Institute of Energy Efficiency and Hydrogen Technologies (IEEHT), Moscow Power Engineering Institute, National Research University, 111250 Moscow, Russia
| | - Nikita A Slesarenko
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
| | - Alexander V Chernyak
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
- Scientific Center in Chernogolovka of the Institute of Solid State Physics Named Yu.A. Osipyan RAS, 142432 Chernogolovka, Russia
| | - Guzaliya R Baymuratova
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
| | - Alena V Yudina
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
| | - Mikhail P Berezin
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
| | - Galiya Z Tulibaeva
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
| | - Anna A Slesarenko
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
| | - Alexander F Shestakov
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
- Faculty of Fundamental Physical and Chemical Engineering, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olga V Yarmolenko
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
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3
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Wang Z, Neese F. Development of NOTCH, an all-electron, beyond-NDDO semiempirical method: Application to diatomic molecules. J Chem Phys 2023; 158:2889026. [PMID: 37154284 DOI: 10.1063/5.0141686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
In this work, we develop a new semiempirical method, dubbed NOTCH (Natural Orbital Tied Constructed Hamiltonian). Compared to existing semiempirical methods, NOTCH is less empirical in its functional form as well as parameterization. Specifically, in NOTCH, (1) the core electrons are treated explicitly; (2) the nuclear-nuclear repulsion term is calculated analytically, without any empirical parameterization; (3) the contraction coefficients of the atomic orbital (AO) basis depend on the coordinates of the neighboring atoms, which allows the size of AOs to depend on the molecular environment, despite the fact that a minimal basis set is used; (4) the one-center integrals of free atoms are derived from scalar relativistic multireference equation-of-motion coupled cluster calculations instead of empirical fitting, drastically reducing the number of necessary empirical parameters; (5) the (AA|AB) and (AB|AB)-type two-center integrals are explicitly included, going beyond the neglect of differential diatomic overlap approximation; and (6) the integrals depend on the atomic charges, effectively mimicking the "breathing" of AOs when the atomic charge varies. For this preliminary report, the model has been parameterized for the elements H-Ne, giving only 8 empirical global parameters. Preliminary results on the ionization potentials, electron affinities, and excitation energies of atoms and diatomic molecules, as well as the equilibrium geometries, vibrational frequencies dipole moments, and bond dissociation energies of diatomic molecules, show that the accuracy of NOTCH rivals or exceeds those of popular semiempirical methods (including PM3, PM7, OM2, OM3, GFN-xTB, and GFN2-xTB) as well as the cost-effective ab initio method Hartree-Fock-3c.
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Affiliation(s)
- Zikuan Wang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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4
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Morozov B, Oshchepkov AS, Klemt I, Agafontsev AM, Krishna S, Hampel F, Xu HG, Mokhir A, Guldi D, Kataev E. Supramolecular Recognition of Cytidine Phosphate in Nucleotides and RNA Sequences. JACS AU 2023; 3:964-977. [PMID: 37006770 PMCID: PMC10052242 DOI: 10.1021/jacsau.2c00658] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 06/19/2023]
Abstract
Supramolecular recognition of nucleotides would enable manipulating crucial biochemical pathways like transcription and translation directly and with high precision. Therefore, it offers great promise in medicinal applications, not least in treating cancer or viral infections. This work presents a universal supramolecular approach to target nucleoside phosphates in nucleotides and RNA. The artificial active site in new receptors simultaneously realizes several binding and sensing mechanisms: encapsulation of a nucleobase via dispersion and hydrogen bonding interactions, recognition of the phosphate residue, and a self-reporting feature-"turn-on" fluorescence. Key to the high selectivity is the conscious separation of phosphate- and nucleobase-binding sites by introducing specific spacers in the receptor structure. We have tuned the spacers to achieve high binding affinity and selectivity for cytidine 5' triphosphate coupled to a record 60-fold fluorescence enhancement. The resulting structures are also the first functional models of poly(rC)-binding protein coordinating specifically to C-rich RNA oligomers, e.g., the 5'-AUCCC(C/U) sequence present in poliovirus type 1 and the human transcriptome. The receptors bind to RNA in human ovarian cells A2780, causing strong cytotoxicity at 800 nM. The performance, self-reporting property, and tunability of our approach open up a promising and unique avenue for sequence-specific RNA binding in cells by using low-molecular-weight artificial receptors.
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Affiliation(s)
- Boris
S. Morozov
- Department
of Chemistry and Pharmacy, Friedrich-Alexander-Universität
Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, Erlangen 91058, Germany
| | | | - Insa Klemt
- Department
of Chemistry and Pharmacy, Friedrich-Alexander-Universität
Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, Erlangen 91058, Germany
| | - Aleksandr M. Agafontsev
- Department
of Chemistry and Pharmacy, Friedrich-Alexander-Universität
Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, Erlangen 91058, Germany
| | - Swathi Krishna
- Department
of Chemistry and Pharmacy, Interdisciplinary Center for Molecular
Materials (ICMM), Friedrich-Alexander-Universität
Erlangen-Nürnberg, Egerlandstr. 3, Erlangen 91058, Germany
| | - Frank Hampel
- Department
of Chemistry and Pharmacy, Friedrich-Alexander-Universität
Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, Erlangen 91058, Germany
| | - Hong-Gui Xu
- Department
of Chemistry and Pharmacy, Friedrich-Alexander-Universität
Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, Erlangen 91058, Germany
| | - Andriy Mokhir
- Department
of Chemistry and Pharmacy, Friedrich-Alexander-Universität
Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, Erlangen 91058, Germany
| | - Dirk Guldi
- Department
of Chemistry and Pharmacy, Interdisciplinary Center for Molecular
Materials (ICMM), Friedrich-Alexander-Universität
Erlangen-Nürnberg, Egerlandstr. 3, Erlangen 91058, Germany
| | - Evgeny Kataev
- Department
of Chemistry and Pharmacy, Friedrich-Alexander-Universität
Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, Erlangen 91058, Germany
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Synthesis of Synthetic Musks: A Theoretical Study Based on the Relationships between Structure and Properties at Molecular Scale. Int J Mol Sci 2023; 24:ijms24032768. [PMID: 36769089 PMCID: PMC9917709 DOI: 10.3390/ijms24032768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Synthetic musks (SMs), as an indispensable odor additive, are widely used in various personal care products. However, due to their physico-chemical properties, SMs were detected in various environmental media, even in samples from arctic regions, leading to severe threats to human health (e.g., abortion risk). Environmentally friendly and functionally improved SMs have been theoretically designed in previous studies. However, the synthesizability of these derivatives has barely been proven. Thus, this study developed a method to verify the synthesizability of previously designed SM derivatives using machine learning, 2D-QSAR, 3D-QSAR, and high-throughput density functional theory in order to screen for synthesizable, high-performance (odor sensitivity), and environmentally friendly SM derivatives. In this study, three SM derivatives (i.e., D52, D37, and D25) were screened and recommended due to their good performances (i.e., high synthesizability and odor sensitivity; low abortion risk; and bioaccumulation ability in skin keratin). In addition, the synthesizability mechanism of SM derivatives was also analyzed. Results revealed that high intramolecular hydrogen bond strength, electrostatic interaction, qH+ value, energy gap, and low EHOMO would lead to a higher synthesizability of SMs and their derivatives. This study broke the synthesizability bottleneck of theoretically designed environment-friendly SM derivatives and advanced the mechanism of screening functional derivatives.
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Chernyak AV, Slesarenko NA, Slesarenko AA, Baymuratova GR, Tulibaeva GZ, Yudina AV, Volkov VI, Shestakov AF, Yarmolenko OV. Effect of the Solvate Environment of Lithium Cations on the Resistance of the Polymer Electrolyte/Electrode Interface in a Solid-State Lithium Battery. MEMBRANES 2022; 12:1111. [PMID: 36363666 PMCID: PMC9694555 DOI: 10.3390/membranes12111111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
The effect of the composition of liquid electrolytes in the bulk and at the interface with the LiFePO4 cathode on the operation of a solid-state lithium battery with a nanocomposite polymer gel electrolyte based on polyethylene glycol diacrylate and SiO2 was studied. The self-diffusion coefficients on the 7Li, 1H, and 19F nuclei in electrolytes based on LiBF4 and LiTFSI salts in solvents (gamma-butyrolactone, dioxolane, dimethoxyethane) were measured by nuclear magnetic resonance (NMR) with a magnetic field gradient. Four compositions of the complex electrolyte system were studied by high-resolution NMR. The experimentally obtained 1H chemical shifts are compared with those theoretically calculated by quantum chemical modeling. This made it possible to suggest the solvate shell compositions that facilitate the rapid transfer of the Li+ cation at the nanocomposite electrolyte/LiFePO4 interface and ensure the stable operation of a solid-state lithium battery.
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Affiliation(s)
- Alexander V. Chernyak
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
- Scientific Center in Chernogolovka RAS, 142432 Chernogolovka, Russia
| | - Nikita A. Slesarenko
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
| | - Anna A. Slesarenko
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
| | - Guzaliya R. Baymuratova
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
| | - Galiya Z. Tulibaeva
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
| | - Alena V. Yudina
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
| | - Vitaly I. Volkov
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
- Scientific Center in Chernogolovka RAS, 142432 Chernogolovka, Russia
| | - Alexander F. Shestakov
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
- Faculty of Fundamental Physical and Chemical Engineering, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olga V. Yarmolenko
- Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
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Fabrizio A, Briling KR, Corminboeuf C. SPA HM: the spectrum of approximated Hamiltonian matrices representations. DIGITAL DISCOVERY 2022; 1:286-294. [PMID: 35769206 PMCID: PMC9189859 DOI: 10.1039/d1dd00050k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/04/2022] [Indexed: 11/21/2022]
Abstract
Physics-inspired molecular representations are the cornerstone of similarity-based learning applied to solve chemical problems. Despite their conceptual and mathematical diversity, this class of descriptors shares a common underlying philosophy: they all rely on the molecular information that determines the form of the electronic Schrödinger equation. Existing representations take the most varied forms, from non-linear functions of atom types and positions to atom densities and potential, up to complex quantum chemical objects directly injected into the ML architecture. In this work, we present the spectrum of approximated Hamiltonian matrices (SPAHM) as an alternative pathway to construct quantum machine learning representations through leveraging the foundation of the electronic Schrödinger equation itself: the electronic Hamiltonian. As the Hamiltonian encodes all quantum chemical information at once, SPAHM representations not only distinguish different molecules and conformations, but also different spin, charge, and electronic states. As a proof of concept, we focus here on efficient SPAHM representations built from the eigenvalues of a hierarchy of well-established and readily-evaluated "guess" Hamiltonians. These SPAHM representations are particularly compact and efficient for kernel evaluation and their complexity is independent of the number of different atom types in the database.
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Affiliation(s)
- Alberto Fabrizio
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
| | - Ksenia R Briling
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
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8
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Oshchepkov AS, Reznichenko O, Xu D, Morozov BS, Granzhan A, Kataev EA. Dye-functionalized phosphate-binding macrocycles: from nucleotide to G-quadruplex recognition and "turn-on" fluorescence sensing. Chem Commun (Camb) 2021; 57:10632-10635. [PMID: 34581337 DOI: 10.1039/d1cc04096k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A novel strategy to design "turn-on" fluorescent receptors for G-quadruplexes of DNA is presented, which relies on the connection of phosphate binding macrocycles (PBM) with naphthalimide dyes. A new PBM-dye family was synthesized and evaluated in terms of binding and detection of nucleotides and DNA G-quadruplexes of different topologies.
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Affiliation(s)
- Aleksandr S Oshchepkov
- Department of Chemistry and Pharmacy, University Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany. .,Institute of Chemistry, Technische Universität Chemnitz, 09107 Chemnitz, Germany
| | - Oksana Reznichenko
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, Bât. 110, Centre Universitaire Paris Sud, F-91405 Orsay, France
| | - Dan Xu
- Institute of Chemistry, Technische Universität Chemnitz, 09107 Chemnitz, Germany
| | - Boris S Morozov
- Department of Chemistry and Pharmacy, University Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany. .,Institute of Chemistry, Technische Universität Chemnitz, 09107 Chemnitz, Germany
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, Bât. 110, Centre Universitaire Paris Sud, F-91405 Orsay, France
| | - Evgeny A Kataev
- Department of Chemistry and Pharmacy, University Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany. .,CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, Bât. 110, Centre Universitaire Paris Sud, F-91405 Orsay, France
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9
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Briling KR, Fabrizio A, Corminboeuf C. Impact of quantum-chemical metrics on the machine learning prediction of electron density. J Chem Phys 2021; 155:024107. [PMID: 34266253 DOI: 10.1063/5.0055393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Machine learning (ML) algorithms have undergone an explosive development impacting every aspect of computational chemistry. To obtain reliable predictions, one needs to maintain a proper balance between the black-box nature of ML frameworks and the physics of the target properties. One of the most appealing quantum-chemical properties for regression models is the electron density, and some of us recently proposed a transferable and scalable model based on the decomposition of the density onto an atom-centered basis set. The decomposition, as well as the training of the model, is at its core a minimization of some loss function, which can be arbitrarily chosen and may lead to results of different quality. Well-studied in the context of density fitting (DF), the impact of the metric on the performance of ML models has not been analyzed yet. In this work, we compare predictions obtained using the overlap and the Coulomb-repulsion metrics for both decomposition and training. As expected, the Coulomb metric used as both the DF and ML loss functions leads to the best results for the electrostatic potential and dipole moments. The origin of this difference lies in the fact that the model is not constrained to predict densities that integrate to the exact number of electrons N. Since an a posteriori correction for the number of electrons decreases the errors, we proposed a modification of the model, where N is included directly into the kernel function, which allowed lowering of the errors on the test and out-of-sample sets.
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Affiliation(s)
- Ksenia R Briling
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Alberto Fabrizio
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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10
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Makarova TM, Makarov GI. Investigation of Allosteric Effect of 2,8-Dimethylation of A2503 in E. coli 23S rRNA by Molecular-Dynamics Simulations. BIOCHEMISTRY (MOSCOW) 2021; 85:1458-1467. [PMID: 33280585 DOI: 10.1134/s0006297920110139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ribosome is a molecular machine that synthesizes all cellular proteins. It also is a target of about half of the clinically used antibiotics. Adaptive chemical modification of ribosomal RNAs residues is one of the ways to provide resistance to certain antibiotics. A curious example of such modification is 2,8-dimethylation of A2503 in 23S rRNA, which induces resistance to phenols, linkosamides, oxazolidinones, pleuromutilins, and certain macrolides. In this article the effect of 2,8-dimethylation of A2503 on conformation and mobility of RNA residues of the 70S E. coli ribosome was investigated employing molecular dynamics simulations method. Significant alterations were detected both in the immediate environment of the 2503 23S rRNA residue and in the nucleotides located deeper in the nascent peptide exit tunnel (NPET), which are known to be involved in signal transmission from the antibiotics bound in the NPET to the peptidyl transferase center. These alterations shift the ribosome towards the A/A, P/P-state from the conformationally different state - P/P, E/E one in our case. The obtained results allow us to conclude that the effect of m2m8A2503 modification involves additional stabilization of the A/A, P/P-state favoring the peptidyl transferase reaction (PTR) contrary to antibiotics that inhibit PTR.
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Affiliation(s)
- T M Makarova
- South Ural State University, Chelyabinsk, 454080, Russia.
| | - G I Makarov
- South Ural State University, Chelyabinsk, 454080, Russia
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11
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Binding and Sensing Properties of a Hybrid Naphthalimide-Pyrene Aza-Cyclophane towards Nucleotides in an Aqueous Solution. Molecules 2021; 26:molecules26040980. [PMID: 33673272 PMCID: PMC7918853 DOI: 10.3390/molecules26040980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/20/2022] Open
Abstract
Selective recognition of nucleotides with synthetic receptors is an emerging direction to solve a series of nucleic acid-related challenges in biochemistry. Towards this goal, a new aza-cyclophane with two different dyes, naphthalimide and pyrene, connected through a triamine linker has been synthesized and studied for the ability to bind and detect nucleoside triphosphates in an aqueous solution. The receptor shows Foerster resonance energy transfer (FRET) in fluorescence spectra upon excitation in DMSO, which is diminished dramatically in the presence of water. According to binding studies, the receptor has a preference to bind ATP (adenosine triphosphate) and CTP (cytidine triphosphate) with a “turn-on” fluorescence response. Two separate emission bands of dyes allow one to detect nucleotides in a ratiometric manner in a broad concentration range of 10−5–10−3 M. Spectroscopic measurements and quantum chemical calculations suggest the formation of receptor–nucleotide complexes, which are stabilized by dispersion interactions between a nucleobase and dyes, while hydrogen bonding interactions of nucleobases with the amine linkers are responsible for selectivity.
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12
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Agafontsev AM, Shumilova TA, Oshchepkov AS, Hampel F, Kataev EA. Ratiometric Detection of ATP by Fluorescent Cyclophanes with Bellows-Type Sensing Mechanism. Chemistry 2020; 26:9991-9997. [PMID: 32497327 PMCID: PMC7496914 DOI: 10.1002/chem.202001523] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/01/2020] [Indexed: 12/13/2022]
Abstract
Pyrene-based cyclophanes have been synthesized with the aim to realize a bellows-type sensing mechanism for the ratiometric detection of nucleotide concentrations in a buffered aqueous solution. The sensing mechanism involves the encapsulation of a nucleobase between two pyrene rings, which affects the monomer-excimer equilibrium of the receptor in the excited state. The nature of the spacer and its connection pattern to pyrene rings have been varied to achieve high selectivity for ATP. The 1,8-substituted pyrene-based cyclophane with the 2,2'-diaminodiethylamine spacer demonstrates the best selectivity for ATP showing a 50-fold increase in the monomer-excimer emission ratio upon saturation with the nucleotide. The receptor can detect ATP within the biological concentrations range over a wide pH range. NMR and spectroscopic studies have revealed the importance of hydrogen bonding and stacking interactions for achieving a required receptor selectivity. The probe has been successfully applied for the real-time monitoring of creatine kinase activity.
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Affiliation(s)
- Aleksandr M. Agafontsev
- N. N. Vorozhtsov Institute of Organic Chemistry SB RAS9 Lavrentiev Avenue630090NovosibirskRussian Federation
- Institute of ChemistryTechnische Universität Chemnitz09107ChemnitzGermany
| | | | | | - Frank Hampel
- Department of Chemistry and PharmacyUniversity of Erlangen-NürnbergNikolaus-Fiebiger-Str. 1091058ErlangenGermany
| | - Evgeny A. Kataev
- Department of Chemistry and PharmacyUniversity of Erlangen-NürnbergNikolaus-Fiebiger-Str. 1091058ErlangenGermany
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13
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Yudina AV, Baymuratova GR, Tulibaeva GZ, Litvinov AL, Shestakov AF, Yarmolenko OV. Conductivity increase effect in nanocomposite polymer gel electrolytes: manifestation in the IR spectra. Russ Chem Bull 2020. [DOI: 10.1007/s11172-020-2923-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Oshchepkov AS, Namashivaya SSR, Khrustalev VN, Hampel F, Laikov DN, Kataev EA. Control of Photoisomerization of an Azoazacryptand by Anion Binding and Cucurbit[8]uril Encapsulation in an Aqueous Solution. J Org Chem 2020; 85:9255-9263. [PMID: 32584036 DOI: 10.1021/acs.joc.0c01260] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Control of isomerization of a receptor bearing multiple light-switchable subunits in a confined space is critical for the design of synthetic molecular machines. Toward this goal, a new azacryptand containing three azobenzene subunits has been developed, and its photoisomerization in an aqueous solution has been studied depending on anion coordination and recognition by a larger host-cucurbit[8]uril (CB[8]). The cryptand in its hexaprotonated form shows considerable affinity for fluoride and perchlorate, which in turn affects the isomer distribution of the receptor under UV-light irradiation, stabilizing the isomers of the cryptand with Z-configurations. CB[8] was found to be able to encapsulate the isomers of the cryptand by forming a Matryoshka-type complex. The irradiation of a 10:1 CB[8]-cryptand mixture has led to a selective conversion of the cryptand to the E,E,Z isomer inside CB[8]. It has been demonstrated that the addition of fluoride to the resulted complex induces the release of the cryptand as a major E,E,E isomer, while other studied anions were ineffective in this reaction. To our knowledge, this work presents a first example of a host-controlled photoisomerization of an anion receptor bearing multiple switching azobenzenes that model the function of naturally occurring chaperones.
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Affiliation(s)
| | - Siva S R Namashivaya
- Faculty of Natural Sciences, Technische Universität Chemnitz, 09107 Chemnitz, Germany
| | - Victor N Khrustalev
- Peoples' Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Frank Hampel
- Department of Chemistry and Pharmacy, University Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Dimitri N Laikov
- Chemistry Department, Moscow State University, Leninskie Gory, Building 1/3, GSP-1, Moscow 119991, Russia
| | - Evgeny A Kataev
- Department of Chemistry and Pharmacy, University Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
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15
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Briling KR, Laikov DN. Heptalene Synthesis by Addition of Aryl Acetylenes to
Azulenes. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1070428020040028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Khatymov RV, Shchukin PV, Muftakhov MV, Yakushchenko IK, Yarmolenko OV, Pankratyev EY. A unified statistical RRKM approach to the fragmentation and autoneutralization of metastable molecular negative ions of hexaazatrinaphthylenes. Phys Chem Chem Phys 2020; 22:3073-3088. [PMID: 31965122 DOI: 10.1039/c9cp05397b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For the compounds promising for use as n-type semiconductors in organic electronics and energy storage devices, hexaazatrinaphthylene (HATNA) and its derivative hexamethoxy-hexaazatrinaphthylene (HMHATA), the monomolecular processes occurring under the exposure of molecules to low-energy (0-15 eV) free electrons were studied by means of resonant electron capture negative ion mass spectrometry. Resonant electron attachment results in the formation of eminently long-lived molecular negative ions (MNIs) in an abnormally wide range of incident electron energy (Ee) from 0 to 5-7 eV. For both compounds, this observation serves as an indication of the strong electron-accepting properties and high stability of MNIs against electron autodetachment. A weak yield of the only fragment NIs, dehydrogenated anions, was detected for HATNA at Ee > 6 eV. MNIs of HMHATA are less stable to dissociative decay because of the presence of weakly bound terminal substituents. This is evidenced by the mass spectral observation of intense fragmentation occurring above Ee≈ 1 eV and leading to a loss of up to 3 methyl groups as the Ee increases. A series of metastable NI peaks observed in the mass spectra testify to the delayed and sequential nature of fragmentation. Based on the principles of statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theory, the theoretical model of dissociative decay of NIs was developed and then adopted to quantify the rates of ground-state anion decay via electron autodetachment. The experimentally measured electron autodetachment lifetimes and fragmentation rates were best reproduced by the model at molecular adiabatic electron affinities preset to 2.15 eV for HATNA and 1.88 eV for HMHATA, in reasonable agreement with the quantum chemical DFT PBE/3ζ predictions.
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Affiliation(s)
- Rustem V Khatymov
- Institute of Molecule and Crystal Physics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450075, Russia.
| | - Pavel V Shchukin
- Institute of Molecule and Crystal Physics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450075, Russia.
| | - Mars V Muftakhov
- Institute of Molecule and Crystal Physics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450075, Russia.
| | - Igor K Yakushchenko
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow Region 142432, Russia
| | - Ol'ga V Yarmolenko
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow Region 142432, Russia
| | - Evgeniy Yu Pankratyev
- Institute of Molecule and Crystal Physics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450075, Russia.
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17
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Morozov BS, Namashivaya SSR, Zakharko MA, Oshchepkov AS, Kataev EA. Anthracene-Based Amido-Amine Cage Receptor for Anion Recognition under Neutral Aqueous Conditions. ChemistryOpen 2020; 9:171-175. [PMID: 32025461 PMCID: PMC6996565 DOI: 10.1002/open.201900309] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/08/2019] [Indexed: 12/13/2022] Open
Abstract
A new amido-amine cage receptor, which combines 1,8-anthracene diacarboxamide subunit and a polyammonium azamacrocycle, is reported. Bearing both the hydrogen bond donor and the acceptor binding sites, the receptor is able to bind phosphate selectively under neutral (pH 7.2) aqueous conditions. The recognition events for phosphate and dicarboxylates are accomplished by a fluorescence enhancement in the anthracene emission. As revealed by experimental and theoretical studies, phosphate and oxalate show different recognition modes. Phosphate demonstrates hydrogen bond acceptor properties, while the coordination of oxalate favours the protonation of the receptor.
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Affiliation(s)
- Boris S. Morozov
- Faculty of Natural SciencesTechnische Universität ChemnitzStr. der Nationen 6209107ChemnitzGermany
| | - Siva S. R. Namashivaya
- Faculty of Natural SciencesTechnische Universität ChemnitzStr. der Nationen 6209107ChemnitzGermany
| | - Marina A. Zakharko
- A. N. Nesmeyanov Institute of Organoelement compounds of RASVavilova Str., 28Moscow119991Russia
| | - Aleksandr S. Oshchepkov
- Faculty of Natural SciencesTechnische Universität ChemnitzStr. der Nationen 6209107ChemnitzGermany
- Peoples' Friendship University of Russia (RUDN University)6 Miklukho-Maklay St117198MoscowRussia
| | - Evgeny A. Kataev
- Faculty of Natural SciencesTechnische Universität ChemnitzStr. der Nationen 6209107ChemnitzGermany
- Department of Chemistry and PharmacyUniversity Erlangen-NürnbergNikolaus-Fiebiger-Str. 1091058ErlangenGermany
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18
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Laikov DN, Briling KR. Atomic effective potentials for starting molecular electronic structure calculations. Theor Chem Acc 2020. [DOI: 10.1007/s00214-019-2521-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Fizer M, Slivka M, Baumer V, Slivka M, Fizer O. Alkylation of 2-oxo(thioxo)-thieno[2,3-d]pyrimidine-4-ones: Experimental and theoretical study. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.07.105] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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20
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Yarzhemsky VG, D’yakov YA, Izotov AD, Izotova VO. Chemical Properties of Gold Clusters as Dependent on the Structure and Doping by 5d Elements. RUSS J INORG CHEM+ 2019. [DOI: 10.1134/s0036023619100188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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21
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Scutelnic V, Rizzo TR. Cryogenic Ion Spectroscopy for Identification of Monosaccharide Anomers. J Phys Chem A 2019; 123:2815-2819. [PMID: 30829486 DOI: 10.1021/acs.jpca.9b00527] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We combine conformer-selective, cryogenic infrared spectroscopy, quantum mechanical computations, and 18O substitution at the reducing end to determine the structural preferences of protonated glucosamine in the gas phase. Cryogenic infrared-infrared (IR-IR) double resonance spectroscopy of helium-tagged, protonated glucosamine provides vibrational fingerprints of individual conformers, and 18O isotopic labeling facilitates the match with computed structures and provides a selective probe of the anomeric hydroxyl. This is key for using vibrational spectroscopy for glycan analysis and determining the generality of anomeric memory during glycosidic bond cleavage.
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Affiliation(s)
- Valeriu Scutelnic
- Laboratory of Molecular Physical Chemistry , École Polytechnique Fédérale de Lausanne , Station 6 , CH-1015 Lausanne , Switzerland
| | - Thomas R Rizzo
- Laboratory of Molecular Physical Chemistry , École Polytechnique Fédérale de Lausanne , Station 6 , CH-1015 Lausanne , Switzerland
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22
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23
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Kim IP, Martynenko VM, Chernyak AV, Shestakova AF, Benderskii VA. Fluorinated Organosilicon Oligomers with End Groups Capable of Further Polycondensation. HIGH ENERGY CHEMISTRY 2019. [DOI: 10.1134/s0018143919020073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Shestakov AF, Romanyuk OE, Mumyatov AV, Luchkin SY, Slesarenko AA, Yarmolenko OV, Stevenson KJ, Troshin PA. Theoretical and experimental evidence for irreversible lithiation of the conformationally flexible polyimide: Impact on battery performance. J Electroanal Chem (Lausanne) 2019. [DOI: 10.1016/j.jelechem.2019.01.063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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25
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Wu X, Dral PO, Koslowski A, Thiel W. Big data analysis of ab Initio molecular integrals in the neglect of diatomic differential overlap approximation. J Comput Chem 2019; 40:638-649. [PMID: 30549072 DOI: 10.1002/jcc.25748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 12/14/2022]
Abstract
Most modern semiempirical quantum-chemical (SQC) methods are based on the neglect of diatomic differential overlap (NDDO) approximation to ab initio molecular integrals. Here, we check the validity of this approximation by computing all relevant integrals for 32 typical organic molecules using Gaussian-type orbitals and various basis sets (from valence-only minimal to all-electron triple-ζ basis sets) covering in total more than 15.6 million one-electron (1-e) and 10.3 billion two-electron (2-e) integrals. The integrals are calculated in the nonorthogonal atomic basis and then transformed by symmetric orthogonalization to the Löwdin basis. In the case of the 1-e integrals, we find strong orthogonalization effects that need to be included in SQC models, for example, by strategies such as those adopted in the available OMx methods. For the valence-only minimal basis, we confirm that the 2-e Coulomb integrals in the Löwdin basis are quantitatively close to their counterparts in the atomic basis and that the 2-e exchange integrals can be safely neglected in line with the NDDO approximation. For larger all-electron basis sets, there are strong multishell orthogonalization effects that lead to more irregular patterns in the transformed 2-e integrals and thus cast doubt on the validity of the NDDO approximation for extended basis sets. Focusing on the valence-only minimal basis, we find that some of the NDDO-neglected integrals are reduced but remain sizable after the transformation to the Löwdin basis; this is true for the two-center 2-e hybrid integrals, the three-center 1-e nuclear attraction integrals, and the corresponding three-center 2-e hybrid integrals. We consider a scheme with a valence-only minimal basis that includes such terms as a possible strategy to go beyond the NDDO integral approximation in attempts to improve SQC methods. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Xin Wu
- Max-Planck-Institut für Kohlenforschung, 45470, Mülheim an der Ruhr, Germany
| | - Pavlo O Dral
- Max-Planck-Institut für Kohlenforschung, 45470, Mülheim an der Ruhr, Germany
| | - Axel Koslowski
- Max-Planck-Institut für Kohlenforschung, 45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, 45470, Mülheim an der Ruhr, Germany
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26
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Ryazantsev SV, Tyurin DA, Nuzhdin KB, Feldman VI, Khriachtchev L. The HKrCCH⋯CO2 complex: an ab initio and matrix-isolation study. Phys Chem Chem Phys 2019; 21:3656-3661. [DOI: 10.1039/c8cp04327b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structure of the HKrCCH⋯CO2 complex prepared in a low-temperature krypton matrix.
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Affiliation(s)
- Sergey V. Ryazantsev
- Department of Chemistry
- University of Helsinki
- FI-00014 Helsinki
- Finland
- Department of Chemistry
| | - Daniil A. Tyurin
- Department of Chemistry
- Lomonosov Moscow State University
- 119991 Moscow
- Russia
| | - Kirill B. Nuzhdin
- Department of Chemistry
- Lomonosov Moscow State University
- 119991 Moscow
- Russia
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27
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Sharapa DI, Genaev A, Cavallo L, Minenkov Y. A Robust and Cost‐Efficient Scheme for Accurate Conformational Energies of Organic Molecules. Chemphyschem 2018; 20:92-102. [DOI: 10.1002/cphc.201801063] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Dmitry I. Sharapa
- Institute of Catalysis Research and TechnologyKarlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz Platz 1 Eggenstein-Leopoldshafen D-76344 Germany
| | - Alexander Genaev
- Vorozhtsov Novosibirsk Institute of Organic Chemistry Academician Lavrent'ev Ave., 9 Novosibirsk 630090 Russian Federation
| | - Luigi Cavallo
- KAUST Catalysis Center (KCC)King Abdullah University of Science and Technology Thuwal- 23955-6900 Saudi Arabia
| | - Yury Minenkov
- Moscow Institute of Physics and Technology Institutskiy Pereulok 9, Dolgoprudny Moscow Region 141700 Russia
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28
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29
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Briling KR. Comment on "A new parametrizable model of molecular electronic structure" [J. Chem. Phys. 135, 134120 (2011)]. J Chem Phys 2018; 147:157101. [PMID: 29055299 DOI: 10.1063/1.5000525] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ksenia R Briling
- Chemistry Department, Moscow State University, 119991 Moscow, Russia
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30
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Smith DGA, Burns LA, Sirianni DA, Nascimento DR, Kumar A, James AM, Schriber JB, Zhang T, Zhang B, Abbott AS, Berquist EJ, Lechner MH, Cunha LA, Heide AG, Waldrop JM, Takeshita TY, Alenaizan A, Neuhauser D, King RA, Simmonett AC, Turney JM, Schaefer HF, Evangelista FA, DePrince AE, Crawford TD, Patkowski K, Sherrill CD. Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development. J Chem Theory Comput 2018; 14:3504-3511. [DOI: 10.1021/acs.jctc.8b00286] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel G. A. Smith
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Lori A. Burns
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Dominic A. Sirianni
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Daniel R. Nascimento
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Ashutosh Kumar
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Andrew M. James
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Jeffrey B. Schriber
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Tianyuan Zhang
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Boyi Zhang
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Adam S. Abbott
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Eric J. Berquist
- University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Marvin H. Lechner
- Department of Chemistry, Technical University of Munich, 80333 Munich, Germany
| | - Leonardo A. Cunha
- The Technical Institute of Aeronautics, São José dos Campos, 12228-900, Brazil
| | - Alexander G. Heide
- Department of Chemistry, Bethel University, St. Paul, Minnesota 55112, United States
| | - Jonathan M. Waldrop
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Tyler Y. Takeshita
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Asem Alenaizan
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Daniel Neuhauser
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Rollin A. King
- Department of Chemistry, Bethel University, St. Paul, Minnesota 55112, United States
| | - Andrew C. Simmonett
- National Institutes of Health - National Heart, Lung and Blood Institute, Laboratory of Computational Biology, 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Justin M. Turney
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | | | - A. Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - T. Daniel Crawford
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Konrad Patkowski
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - C. David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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31
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Orel VB, Vitkovskaya NM, Kobychev VB, Trofimov BA. Transition-Metal-Free C-Vinylation of Ketones with Acetylenes: A Quantum-Chemical Rationalization of Similarities and Differences in Catalysis by Superbases MOH/DMSO and tBuOM/DMSO (M = Na, K). J Org Chem 2018; 83:3719-3726. [PMID: 29505724 DOI: 10.1021/acs.joc.8b00071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transition-metal-free C-vinylation of acetone with phenylacetylene catalyzed by superbases MOH/DMSO and tBuOM/DMSO (M = Na, K) has been theoretically evaluated in the B3LYP/6-311++G**//B3LYP/6-31+G* approach to rationalize similarities and differences in activity of the above catalytic systems. The close solvate surroundings of sodium and potassium tert-butoxides have been studied. Formation of tBuOM· nDMSO complexes and their structure and thermodynamic stability are discussed in comparison with similar complexes of alkali-metal hydroxides MOH· nDMSO. Activation barriers of the title reaction in the presence of tBuOM· nDMSO complexes are found to be less than those with MOH· nDMSO complexes participating.
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Affiliation(s)
- Vladimir B Orel
- Laboratory of Quantum Chemistry , Irkutsk State University , 1 K. Marks Street , 664003 Irkutsk , Russian Federation.,A. E. Favorsky Irkutsk Institute of Chemistry , Siberian Branch of the Russian Academy of Sciences , 1 Favorsky Street , 664033 Irkutsk , Russian Federation
| | - Nadezhda M Vitkovskaya
- Laboratory of Quantum Chemistry , Irkutsk State University , 1 K. Marks Street , 664003 Irkutsk , Russian Federation
| | - Vladimir B Kobychev
- Laboratory of Quantum Chemistry , Irkutsk State University , 1 K. Marks Street , 664003 Irkutsk , Russian Federation
| | - Boris A Trofimov
- A. E. Favorsky Irkutsk Institute of Chemistry , Siberian Branch of the Russian Academy of Sciences , 1 Favorsky Street , 664033 Irkutsk , Russian Federation
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32
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Self-assembly through hydrogen bonding and photochemical properties of supramolecular complexes of bis(18-crown-6)stilbene with alkanediammonium ions. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2017.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Peraza A, Hernández R, Ruette F. Fundamental relationships between elementary functionals in quantum chemistry. An application for H2 and H2+. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2016.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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34
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Vitkovskaya NM, Orel VB, Kobychev VB, Bobkov AS, Larionova EY, Trofimov BA. Exploring acetylene chemistry in superbasic media: A theoretical study of the effect of water on vinylation and ethynylation reactions with acetylene in KOH/DMSO and NaOH/DMSO systems. J PHYS ORG CHEM 2016. [DOI: 10.1002/poc.3669] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | | | | | - Elena Yu. Larionova
- East-Siberian Institute of Ministry of Internal Affairs of Russian Federation; Irkutsk Russian Federation
| | - Boris A. Trofimov
- A.E. Favorsky Irkutsk Institute of Chemistry SB RAS; Irkutsk Russian Federation
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35
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Ushakov EN, Vedernikov AI, Lobova NA, Dmitrieva SN, Kuz'mina LG, Moiseeva AA, Howard JAK, Alfimov MV, Gromov SP. Supramolecular Dimerization and [2 + 2] Photocycloaddition Reactions of Crown Ether Styryl Dyes Containing a Tethered Ammonium Group: Structure-Property Relationships. J Phys Chem A 2015; 119:13025-37. [PMID: 26650887 DOI: 10.1021/acs.jpca.5b10758] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular self-assembly is an effective strategy for controlling the [2 + 2] photocycloaddition reaction of olefins. The geometrical properties of supramolecular assemblies are proven to have a critical effect on the efficiency and selectivity of this photoreaction both in the solid state and in solution, but the role of other factors remains poorly understood. Convenient supramolecular systems to study the structure-property relationships are pseudocyclic dimers spontaneously formed by styryl dyes containing a crown ether moiety and a remote ammonium group. New dyes of this type were synthesized to investigate the effects of structural and electronic factors on the quantitative characteristics of supramolecular dimerization and [2 + 2] photocycloaddition in solution. Variable structural parameters for the styryl dyes were the size and structure of macrocyclic moiety, the nature of heteroaromatic residue, and the length of the ammonioalkyl group attached to this residue. Quantum chemical calculations of the pseudocyclic dimers were performed in order to interpret the relationships between the structure of the ammonium dyes and the efficiency of the supramolecular photoreaction. One of the dimeric complexes was obtained in the crystalline state and studied by X-ray diffraction. The results obtained demonstrate that the photocycloaddition in the pseudocyclic dimers can be dramatically affected by the electronic structure of the styryl moieties, as dependent on the electron-donating ability of the substituents on the benzene ring, and by the conformational flexibility of the pseudocycle, which determines the mobility of the olefinic bonds. The significance of electronic factors is highlighted by the fact that the photocycloaddition quantum yield in geometrically similar dimeric structures varies from ≤10(-4) to 0.38. The latter value is unusually high for olefins in solution.
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Affiliation(s)
- Evgeny N Ushakov
- Institute of Problems of Chemical Physics, Russian Academy of Sciences , Chernogolovka 142432, Moscow Region, Russian Federation.,Photochemistry Center, Russian Academy of Sciences , ul. Novatorov 7A-1, Moscow 119421, Russian Federation
| | - Artem I Vedernikov
- Photochemistry Center, Russian Academy of Sciences , ul. Novatorov 7A-1, Moscow 119421, Russian Federation
| | - Natalia A Lobova
- Photochemistry Center, Russian Academy of Sciences , ul. Novatorov 7A-1, Moscow 119421, Russian Federation
| | - Svetlana N Dmitrieva
- Photochemistry Center, Russian Academy of Sciences , ul. Novatorov 7A-1, Moscow 119421, Russian Federation
| | - Lyudmila G Kuz'mina
- N. S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences , Leninskiy prosp. 31, Moscow 119991, Russian Federation
| | - Anna A Moiseeva
- Department of Chemistry, M. V. Lomonosov Moscow State University , Leninskie Gory 1, Moscow 119991, Russian Federation
| | - Judith A K Howard
- Department of Chemistry, Durham University , South Road, Durham DH1 3LE, United Kingdom
| | - Michael V Alfimov
- Photochemistry Center, Russian Academy of Sciences , ul. Novatorov 7A-1, Moscow 119421, Russian Federation
| | - Sergey P Gromov
- Photochemistry Center, Russian Academy of Sciences , ul. Novatorov 7A-1, Moscow 119421, Russian Federation.,Department of Chemistry, M. V. Lomonosov Moscow State University , Leninskie Gory 1, Moscow 119991, Russian Federation
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36
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Ushakov EN, Vedernikov AI, Sazonov SK, Kuz´mina LG, Alfimov MV, Howard JAK, Gromov SP. Synthesis and photochemical study of a supramolecular pseudodimeric complex of 4-styrylpyridinium derivatives. Russ Chem Bull 2015. [DOI: 10.1007/s11172-015-0901-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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37
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Yilmazer ND, Korth M. Enhanced semiempirical QM methods for biomolecular interactions. Comput Struct Biotechnol J 2015; 13:169-75. [PMID: 25848495 PMCID: PMC4372622 DOI: 10.1016/j.csbj.2015.02.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 12/21/2022] Open
Abstract
Recent successes and failures of the application of 'enhanced' semiempirical QM (SQM) methods are reviewed in the light of the benefits and backdraws of adding dispersion (D) and hydrogen-bond (H) correction terms. We find that the accuracy of SQM-DH methods for non-covalent interactions is very often reported to be comparable to dispersion-corrected density functional theory (DFT-D), while computation times are about three orders of magnitude lower. SQM-DH methods thus open up a possibility to simulate realistically large model systems for problems both in life and materials science with comparably high accuracy.
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Affiliation(s)
| | - Martin Korth
- Institute of Theoretical Chemistry, Ulm University, D-89069 Ulm, Germany
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38
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Kataev EA, Shumilova TA. Investigation of structural mimetics of natural phosphate ion binding motifs. Molecules 2015; 20:3354-70. [PMID: 25690293 PMCID: PMC6272573 DOI: 10.3390/molecules20023354] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 01/19/2015] [Accepted: 02/12/2015] [Indexed: 11/20/2022] Open
Abstract
Phosphates are ubiquitous in biology and nearly half of all proteins interact with their partners by means of recognition of phosphate residues. Therefore, a better understanding of the phosphate ion binding by peptidic structures is highly desirable. Two new receptors have been designed and synthesized and their anion binding properties in an acetonitrile solution have been determined. The structure of hosts mimics a part of the kinase active site that is responsible for the recognition of the phosphate residue. New hosts contain additional free amino groups with the aim to facilitate coordination of protonated anions, such as dihydrogen phosphate. According to spectrophotometric measurements, stepwise 1:1 and 1:2 binding modes have been observed for both receptors in the presence of acetate, hydrogen sulfate and dihydrogen phosphate. Compared with the acyclic receptor, the macrocyclic receptor has demonstrated a remarkably enhanced selectivity for dihydrogen phosphate over other anions. Fluorometric measurements have revealed different responses of the acyclic and macrocyclic receptors towards anions. However, in both cases, a 5–8 nm hypsochromic shift of fluorescence maximum has been observed upon interaction of acetate and dihydrogen phosphate with receptors.
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Affiliation(s)
- Evgeny A Kataev
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz, 09107 Chemnitz, Germany.
| | - Tatiana A Shumilova
- Institute of Chemistry, Faculty of Natural Sciences, Technische Universität Chemnitz, 09107 Chemnitz, Germany.
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39
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Laikov DN. Penrose nanotiles: design of the thin and thick rhomb molecules to self-assemble into a quasicrystal. RSC Adv 2014. [DOI: 10.1039/c4ra01354a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
New organic molecules are designed, with synthesis in mind, to fit the shape of the thin and thick rhombs of the Penrose tiling and self-assemble by hydrogen bonding into nearly flat sheets (that may stack face-to-face) following the matching rules.
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40
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Kataev E, Arnold R, Rüffer T, Lang H. Fluorescence detection of adenosine triphosphate in an aqueous solution using a combination of copper(II) complexes. Inorg Chem 2012; 51:7948-50. [PMID: 22789028 DOI: 10.1021/ic300805q] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescent ligands have been designed to form ternary complexes with a Cu(II) cation and phosphates in a buffer solution at physiological pH 7.4. It has been shown that a combination of two different ligands and CuCl(2) allows one to achieve high adenosine triphosphate/adenosine diphosphate, adenosine 5'-monophosphate selectivity, and ratiometric fluorescence sensing, while separately each ligand complex does not have such properties.
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Affiliation(s)
- Evgeny Kataev
- Fakultät für Naturwissenschaften, Institut für Chemie, Technische Universität Chemnitz, Straße der Nationen 62, 09111 Chemnitz, Germany.
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