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Chiodi D, Ishihara Y. The role of the methoxy group in approved drugs. Eur J Med Chem 2024; 273:116364. [PMID: 38781921 DOI: 10.1016/j.ejmech.2024.116364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/12/2024] [Accepted: 03/23/2024] [Indexed: 05/25/2024]
Abstract
The methoxy substituent is prevalent in natural products and, consequently, is present in many natural product-derived drugs. It has also been installed in modern drug molecules with no remnant of natural product features because medicinal chemists have been taking advantage of the benefits that this small functional group can bestow on ligand-target binding, physicochemical properties, and ADME parameters. Herein, over 230 methoxy-containing small-molecule drugs, as well as several fluoromethoxy-containing drugs, are presented from the vantage point of the methoxy group. Biochemical mechanisms of action, medicinal chemistry SAR studies, and numerous X-ray cocrystal structures are analyzed to identify the precise role of the methoxy group for many of the drugs and drug classes. Although the methoxy substituent can be considered as the hybridization of a hydroxy and a methyl group, the combination of these functionalities often results in unique effects that can amount to more than the sum of the individual parts.
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Affiliation(s)
- Debora Chiodi
- Department of Chemistry, Takeda Pharmaceuticals, 9625 Towne Centre Drive, San Diego, CA, 92121, USA
| | - Yoshihiro Ishihara
- Department of Chemistry, Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, CA, 92121, USA.
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2
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Drius G, Tarroni R, Birchmeier M, Parolin C, Boga C, Monari M, Bordoni S. Unpredictable Dynamic Behaviour of Ruthenium Chelate Pyrrole Derivatives. Molecules 2024; 29:3068. [PMID: 38999019 PMCID: PMC11242957 DOI: 10.3390/molecules29133068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 06/21/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024] Open
Abstract
Reaction of [Ru(H)2(CO)(PPh3)3] 1 with an equimolar amount of pyrrole-2-carboxylic acid (H2L1) leads to the homoleptic chelate derivative k2(O,O)-[RuH(CO)(HL1)(PPh3)2] 2. Prolonged acetonitrile refluxing promotes an unusual k2(O,O)- → k2(N,O)- dynamic chelate conversion, forming a neutral, stable, air- and moisture- insensitive, solvento-species k2(N,O)-[Ru(MeCN)(CO)(L1)(PPh3)2] 3. Analogously, reaction of 1 with the pyrrole-2-carboxyaldehyde (HL2) affords k2(N,O)-[RuH(CO)(HL2)(PPh3)2] 4, 5, as a couple of functional isomers. Optimized reaction conditions such as temperature and solvent polarity allow the isolation of dominant configurations. Structure 5 is a pyrrolide Ru-carbaldehyde, obtained from cyclization of the pendant CHO function, whereas species 4 can be viewed as an ethanoyl-conjugated Ru-pyrrole. Derivatives 3-5 were characterized by single crystal X-ray diffraction, ESI-Ms, IR, and NMR spectroscopy, indicating distinct features for the Ru-bonded pyrrolyl groups. DFT computational results, coplanarity, bond equalization, and electron delocalization along the fused five-membered rings support aromatic features. In accordance with the antisymbiotic trans-influence, both the isolated isomers 4 and 5 disclose CO ligands opposite to N- or O-anionic groups. The quantitative Mayer bond order evidences a stabilizing backbonding effect. Antibacterial and antifungal trials on Gram-positive (Staphylococcus aureus), Gram-negative (Escherichia coli), and Candida albicans were further carried out.
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Affiliation(s)
- Giacomo Drius
- Department of Industrial Chemistry 'Toso Montanari', Alma Mater Studiorum, Università di Bologna, Via Piero Gobetti, 85, 40129 Bologna, Italy
| | - Riccardo Tarroni
- Department of Industrial Chemistry 'Toso Montanari', Alma Mater Studiorum, Università di Bologna, Via Piero Gobetti, 85, 40129 Bologna, Italy
| | - Matteo Birchmeier
- Department of Industrial Chemistry 'Toso Montanari', Alma Mater Studiorum, Università di Bologna, Via Piero Gobetti, 85, 40129 Bologna, Italy
| | - Carola Parolin
- Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy
| | - Carla Boga
- Department of Industrial Chemistry 'Toso Montanari', Alma Mater Studiorum, Università di Bologna, Via Piero Gobetti, 85, 40129 Bologna, Italy
| | - Magda Monari
- Department of Chemistry 'Giacomo Ciamician', Alma Mater Studiorum, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Silvia Bordoni
- Department of Industrial Chemistry 'Toso Montanari', Alma Mater Studiorum, Università di Bologna, Via Piero Gobetti, 85, 40129 Bologna, Italy
- Health Sciences and Technologies Interdepartmental Centre for Industrial Research (CIRI SDV), University of Bologna, 40126 Bologna, Italy
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3
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Wang P, Zhang K, Li H, Hu J, Zheng M. Enhanced Ion Transport Through Mesopores Engineered with Additional Adsorption of Layered Double Hydroxides Array in Alkaline Flow Batteries. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308791. [PMID: 38096872 DOI: 10.1002/smll.202308791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/19/2023] [Indexed: 06/07/2024]
Abstract
Efficient mass transfer in electrodes is essential for the electrochemical processes of battery charge and discharge, especially at high rates and capacities. This study introduces a 3D electrode design featuring layered double hydroxides (LDHs) nanosheets array grown in situ on a carbon felt surface for flow batteries. The mesoporous structure and surface characteristic of LDH nanosheets, especially, the hydroxyl groups forming a unique "H-bonding-like" geometry with ferrous cyanide ions, facilitate efficient adsorption and ion transport. Thus, the designed LDHs electrode enables the alkaline zinc-iron flow battery to maintain a voltage efficiency of 81.6% at an ultra-high current density of 320 mA cm-2, surpassing the values reported in previous studies. The energy efficiency remains above 84% after 375 cycles at a current density of 240 mA cm-2. Molecular dynamics simulations verify the enhanced adsorption effect of LDH materials on active ions, thus facilitating ion transport in the battery. This study provides a novel approach to improve mass transport in electrodes for alkaline flow batteries and other energy storage devices.
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Affiliation(s)
- Pengfei Wang
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China
- Institute of Thermal Science and Power Systems, Zhejiang University, Hangzhou, 310027, China
| | - Kun Zhang
- Institute of Thermal Science and Power Systems, Zhejiang University, Hangzhou, 310027, China
- Institute of Wenzhou, Zhejiang University, Wenzhou, 325036, China
| | - Hao Li
- Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai, 980-8577, Japan
| | - Jing Hu
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C, 8000, Denmark
| | - Menglian Zheng
- State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China
- Institute of Thermal Science and Power Systems, Zhejiang University, Hangzhou, 310027, China
- Institute of Wenzhou, Zhejiang University, Wenzhou, 325036, China
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4
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Makarov AY, Buravlev AA, Romanenko GV, Bogomyakov AS, Zakharov BA, Morozov VA, Sukhikh AS, Shundrina IK, Shundrin LA, Irtegova IG, Cherepanova SV, Bagryanskaya IY, Nikulshin PV, Zibarev AV. Hysteretic Room-Temperature Magnetic Bistability of the Crystalline 4,7-Difluoro-1,3,2-Benzodithiazolyl Radical. Chempluschem 2024; 89:e202300736. [PMID: 38332534 DOI: 10.1002/cplu.202300736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 02/10/2024]
Abstract
The title radical R⋅, synthesized by reduction of the corresponding cation R+, is thermally stable up to ~380 K in the crystalline state under anaerobic conditions. With SQUID magnetometry, single-crystal and powder XRD, solid-state EPR and TG-DSC, reversible spin-Peierls transition between diamagnetic and paramagnetic states featuring ~10 K hysteretic loop is observed for R⋅ in the temperature range ~310-325 K; ΔH=~2.03 kJ mol-1 and ΔS=~6.23 J mol-1 K-1. The transition is accompanied by mechanical movement of the crystals, i. e., by thermosalient behavior. The low-temperature diamagnetic P-1 polymorph of R⋅ consists of R⋅2 π-dimers arranged in (…R⋅2…)n π-stacks; whereas the high-temperature paramagnetic P21/c polymorph, of uniform (…R⋅…)n π-stacks. With the XRD geometries, CASSCF and broken-symmetry DFT jointly suggest strong antiferromagnetic (AF) interactions within R⋅2 and weak between R⋅2 for the (…R⋅2…)n stacks; and moderate AF interactions between R⋅ for the (…R⋅…)n stacks. The fully hydrocarbon archetype of R⋅ does not reveal the aforementioned properties. Thus, the fluorinated 1,3,2-benzodithiazolyls pave a new pathway in the design and synthesis of metal-less magnetically-bistable materials.
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Affiliation(s)
- Alexander Yu Makarov
- Vorozhtsov Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Alexander A Buravlev
- Vorozhtsov Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Department of Natural Sciences National Research University, Novosibirsk State University, 630090, Novosibirsk, Russia
| | - Galina V Romanenko
- International Tomography Center, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Artem S Bogomyakov
- International Tomography Center, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Boris A Zakharov
- Boreskov Institute of Catalysis, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Department of Natural Sciences National Research University, Novosibirsk State University, 630090, Novosibirsk, Russia
| | - Vitaly A Morozov
- International Tomography Center, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Alexander S Sukhikh
- Nikolaev Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Department of Physics, National Research University - Novosibirsk State University, 630090, Novosibirsk, Russia
| | - Inna K Shundrina
- Vorozhtsov Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Leonid A Shundrin
- Vorozhtsov Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Irina G Irtegova
- Vorozhtsov Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Svetlana V Cherepanova
- Boreskov Institute of Catalysis, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Irina Yu Bagryanskaya
- Vorozhtsov Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Pavel V Nikulshin
- Vorozhtsov Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Current address: Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Andrey V Zibarev
- Vorozhtsov Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
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Gusak MY, Kinzhalov MA, Frontera A, Bokach NA, Kukushkin VY. Metal-Induced Enhancement of Tetrel Bonding. The Case of C⋅⋅⋅X-Ir III (X=Cl, Br) Tetrel Bond Involving a Methyl Group. Chem Asian J 2024:e202400421. [PMID: 38788128 DOI: 10.1002/asia.202400421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/16/2024] [Accepted: 05/24/2024] [Indexed: 05/26/2024]
Abstract
In X-ray structures of the isomorphic mer-[IrX3(THT)(CNXyl)2] (X=Cl 1, Br 2; THT=tetrahydrothiophene; Xyl=2,6-Me2C6H3-) complexes, we revealed short intermolecular contacts between the C-atom of an isocyanide methyl group and halide ligands of another molecule. Geometrical consideration of the X-ray data and analysis of appropriate DFT studies allowed the attribution of these contacts to CMe⋅⋅⋅X-IrIII (X=Cl, Br) tetrel bond. Specifically, through the application of DFT calculations and various theoretical models, the presence of tetrel bonding interactions was validated, and the contribution of the CMe⋅⋅⋅X-IrIII interaction was assessed. The reinforcement of the tetrel bond upon the isocyanide coordination to iridium(III) is substantiated by molecular electrostatic potential (MEP) surface calculations. To distinguish the tetrel bonding characteristics of CMe⋅⋅⋅X-IrIII (X=Cl, Br) interactions from conventional hydrogen bonding, we employed multiple computational methodologies, including Natural Bond Orbital (NBO) analysis and Electron Localization Function (ELF) analysis. Additionally, Energy Decomposition Analysis (EDA) was applied to selected model systems to explore the underlying physical nature of these interactions.
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Affiliation(s)
- Mikhail Yu Gusak
- Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg, 199034, Russian Federation
| | - Mikhail A Kinzhalov
- Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg, 199034, Russian Federation
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta de Valldemossa km 7.5., 07122, Palma de Mallorca (Baleares), Spain
| | - Nadezhda A Bokach
- Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg, 199034, Russian Federation
| | - Vadim Yu Kukushkin
- Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg, 199034, Russian Federation
- Institute of Chemistry and Pharmaceutical Technologies, Altai State University, 656049, Barnaul, Russian Federation
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6
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Nikulshin PV, Makarov AY, Koskin IP, Becker CS, Kazantsev MS, Beckmann J, Balmohammadi Y, Grabowsky S, Mebs S, Naumova OV, Protasov DY, Svit KA, Irtegova IG, Radiush EA, Bagryanskaya IY, Shundrin LA, Zibarev AV. 1,2,3,4-Tetrafluorobiphenylene: A Prototype Janus-Headed Scaffold for Ambipolar Materials. Chempluschem 2024; 89:e202300692. [PMID: 38052725 DOI: 10.1002/cplu.202300692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023]
Abstract
The title compound was synthesized by Ullmann cross-coupling in low yield as the first representative of [n]phenylene containing hydrocarbon and fluorocarbon rings. Stille/Suzuki-Miyaura cross-coupling reactions, as well as substitution of fluorine in suitable starting compounds, failed to give the same product. The geometric and electronic structures of the title compound were studied by X-ray diffraction, cyclic voltammetry and density functional theory calculations, together with Hirshfeld surface and reduced density gradient analyses. The crystal structure features head-to-tail π-stacking and other fluorine-related secondary bonding interactions. From the nucleus-independent chemical shifts descriptor, the four-membered ring of the title compound is antiaromatic, and the six-membered rings are aromatic. The Janus molecule is highly polarized; and the six-membered fluoro- and hydrocarbon rings are Lewis π-acidic and π-basic, respectively. The electrochemically-generated radical cation of the title compound is long-lived as characterized by electron paramagnetic resonance, whereas the radical anion is unstable in solution. The title compound reveals electrical properties of an insulator. On expanding its molecular scaffold towards partially fluorinated [n]phenylenes (n≥2), the properties presumably can be transformed into those of semiconductors. In this context, the title compound is suggested as a prototype scaffold for ambipolar materials for organic electronics and spintronics.
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Affiliation(s)
- Pavel V Nikulshin
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Current address: Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Alexander Yu Makarov
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Igor P Koskin
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Christina S Becker
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Maxim S Kazantsev
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Jens Beckmann
- Institute for Inorganic Chemistry and Crystallography, University of Bremen, 28359, Bremen, Germany
| | - Yaser Balmohammadi
- Department of Chemistry, Biochemistry and Pharmaceutical Science, University of Bern, 3012, Bern, Switzerland
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Science, University of Bern, 3012, Bern, Switzerland
| | - Stefan Mebs
- Institute for Experimental Physics, Free University of Berlin, 14195, Berlin, Germany
| | - Olga V Naumova
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Dmitry Yu Protasov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Kirill A Svit
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Irina G Irtegova
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Ekaterina A Radiush
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Irina Yu Bagryanskaya
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Leonid A Shundrin
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - Andrey V Zibarev
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
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Grineva OV. Comparison of Intermolecular Halogen...Halogen Distances in Organic and Organometallic Crystals. Int J Mol Sci 2023; 24:11911. [PMID: 37569289 PMCID: PMC10419058 DOI: 10.3390/ijms241511911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/15/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Statistical analysis of halogen...halogen intermolecular distances was performed for three sets of homomolecular crystals under normal conditions: C-Hal1...Hal2-C distances in crystals consisting of: (i) organic compounds (set Org); (ii) organometallic compounds (set Orgmet); and (iii) distances M1-Hal1...Hal2-M2 (set MHal) (in all cases Hal1 = Hal2, and in MHal M1 = M2, M is any metal). When analyzing C-Hal...Hal-C distances, a new method for estimating the values of van der Waals radii is proposed, based on the use of two subsets of distances: (i) the shortest distances from each substance less than a threshold; and (ii) all C-Hal...Hal-C distances less than the same threshold. As initial approximations for these thresholds for different Hal, the Ragg values previously introduced in investigations with the participation of the author were used (Ragg values make it possible to perform a statistical assessment of the presence of halogen aggregates in crystals). The following values are recommended in this work to be used as universal values for crystals of organic and organometallic compounds: RF = 1.57, RCl = 1.90, RBr = 1.99, and RI = 2.15 Å. They are in excellent agreement with the results of some other works but significantly (by 0.10-0.17 Å) greater than the commonly used values. For the Orgmet set, slightly lower values for RI (2.11-2.09 Å) were obtained, but number of the C-I...I-C distances available for analysis was significantly smaller than in the other subgroups, which may be the reason for the discrepancy with value for the Org set (2.15 Å). Statistical analysis of the M-Hal...Hal-M distances was performed for the first time. A Hal-aggregation coefficient for M-Hal bonds is proposed, which allows one to estimate the propensity of M-Hal groups with certain M and Hal to participate in Hal-aggregates formed by M-Hal...Hal-M contacts. In particular, it was found that, for the Hg-Hal groups (Hal = Cl, Br, I), there is a high probability that the crystals have Hg-Hal...Hal-Hg distances with length ≤ Ragg.
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Affiliation(s)
- Olga V Grineva
- Chemistry Department, Moscow M. V. Lomonosov State University, 119991 Moscow, Russia
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Bravetti F, Tapmeyer L, Skorodumov K, Alig E, Habermehl S, Hühn R, Bordignon S, Gallo A, Nervi C, Chierotti MR, Schmidt MU. Leucopterin, the white pigment in butterfly wings: structural analysis by PDF fit, FIDEL fit, Rietveld refinement, solid-state NMR and DFT-D. IUCRJ 2023; 10:448-463. [PMID: 37335768 PMCID: PMC10324491 DOI: 10.1107/s2052252523004281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/16/2023] [Indexed: 06/21/2023]
Abstract
Leucopterin (C6H5N5O3) is the white pigment in the wings of Pieris brassicae butterflies, and other butterflies; it can also be found in wasps and other insects. Its crystal structure and its tautomeric form in the solid state were hitherto unknown. Leucopterin turned out to be a variable hydrate, with 0.5 to about 0.1 molecules of water per leucopterin molecule. Under ambient conditions, the preferred state is the hemihydrate. Initially, all attempts to grow single crystals suitable for X-ray diffraction were to no avail. Attempts to determine the crystal structure by powder diffraction using the direct-space method failed, because the trials did not include the correct, but rare, space group P2/c. Attempts were made to solve the crystal structure by a global fit to the pair distribution function (PDF-Global-Fit), as described by Prill and co-workers [Schlesinger et al. (2021). J. Appl. Cryst. 54, 776-786]. The approach worked well, but the correct structure was not found, because again the correct space group was not included. Finally, tiny single crystals of the hemihydrate could be obtained, which allowed at least the determination of the crystal symmetry and the positions of the C, N and O atoms. The tautomeric state of the hemihydrate was assessed by multinuclear solid-state NMR spectroscopy. 15N CPMAS spectra showed the presence of one NH2 and three NH groups, and one unprotonated N atom, which agreed with the 1H MAS and 13C CPMAS spectra. Independently, the tautomeric state was investigated by lattice-energy minimizations with dispersion-corrected density functional theory (DFT-D) on 17 different possible tautomers, which also included the prediction of the corresponding 1H, 13C and 15N chemical shifts in the solid. All methods showed the presence of the 2-amino-3,5,8-H tautomer. The DFT-D calculations also confirmed the crystal structure. Heating of the hemihydrate results in a slow release of water between 130 and 250 °C, as shown by differential thermal analysis and thermogravimetry (DTA-TG). Temperature-dependent powder X-ray diffraction (PXRD) showed an irreversible continuous shift of the reflections upon heating, which reveals that leucopterin is a variable hydrate. This observation was also confirmed by PXRD of samples obtained under various synthetic and drying conditions. The crystal structure of a sample with about 0.2 molecules of water per leucopterin was solved by a fit with deviating lattice parameters (FIDEL), as described by Habermehl et al. [Acta Cryst. (2022), B78, 195-213]. A local fit, starting from the structure of the hemihydrate, as well as a global fit, starting from random structures, were performed, followed by Rietveld refinements. Despite dehydration, the space group remains P2/c. In both structures (hemihydrate and variable hydrate), the leucopterin molecules are connected by 2-4 hydrogen bonds into chains, which are connected by further hydrogen bonds to neighbouring chains. The molecular packing is very efficient. The density of leucopterin hemihydrate is as high as 1.909 kg dm-3, which is one of the highest densities for organic compounds consisting of C, H, N and O only. The high density might explain the good light-scattering and opacity properties of the wings of Pieris brassicae and other butterflies.
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Affiliation(s)
- Federica Bravetti
- Dipartimento di Chimica e Centro di Eccellenza NIS, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Lukas Tapmeyer
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
- F.K.M. Buster Altöl- und Reststoff-Entsorgung GmbH, Holländerstrasse 18, 68219 Mannheim, Germany
| | - Kathrin Skorodumov
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
- Institut für Organische Chemie und Chemische Biologie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Edith Alig
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Stefan Habermehl
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Robert Hühn
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Simone Bordignon
- Dipartimento di Chimica e Centro di Eccellenza NIS, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Angelo Gallo
- Dipartimento di Chimica e Centro di Eccellenza NIS, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Carlo Nervi
- Dipartimento di Chimica e Centro di Eccellenza NIS, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Michele R. Chierotti
- Dipartimento di Chimica e Centro di Eccellenza NIS, Università degli Studi di Torino, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Martin U. Schmidt
- Institut für Anorganische und Analytische Chemie, Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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9
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Anipa V, Tarzia A, Jelfs KE, Alexandrov EV, Addicoat MA. Pore topology analysis in porous molecular systems. ROYAL SOCIETY OPEN SCIENCE 2023; 10:220813. [PMID: 36778946 PMCID: PMC9905991 DOI: 10.1098/rsos.220813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/05/2022] [Indexed: 06/18/2023]
Abstract
Porous molecular materials are constructed from molecules that assemble in the solid-state such that there are cavities or an interconnected pore network. It is challenging to control the assembly of these systems, as the interactions between the molecules are generally weak, and subtle changes in the molecular structure can lead to vastly different intermolecular interactions and subsequently different crystal packing arrangements. Similarly, the use of different solvents for crystallization, or the introduction of solvent vapour, can result in different polymorphs and pore networks being formed. It is difficult to uniquely describe the pore networks formed, and thus we analyse 1033 crystal structures of porous molecular systems to determine the underlying topology of their void spaces and potential guest diffusion networks. Material-agnostic topology definitions are applied. We use the underlying topological nets to examine whether it is possible to apply isoreticular design principles to porous molecular materials. Overall, our automatic analysis of a large dataset gives a general insight into the relationships between molecular topologies and the topological nets of their pore network. We show that while porous molecular systems tend to pack similarly to non-porous molecules, the topologies of their pore distributions resemble those of more prominent porous materials, such as metal-organic frameworks and covalent organic frameworks.
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Affiliation(s)
- Verity Anipa
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Andrew Tarzia
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, UK
| | - Kim E. Jelfs
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, UK
| | - Eugeny V. Alexandrov
- Samara Center for Theoretical Materials Science (SCTMS), Samara University, Ac. Pavlov Street 1, Samara 443011, Russia
- Samara Center for Theoretical Materials Science (SCTMS), Samara State Technical University, Molodogvardeyskaya Street 244, Samara 443100, Russia
- Laboratory of Coherent Optics, Samara Branch of P. N. Lebedev Physical Institute of the Russian Academy of Sciences, Novo-Sadovaya Street 221, Samara 443011, Russia
- Institute of Experimental Medicine and Biotechnology, Samara State Medical University, Chapayevskaya Street 89, Samara 443099, Russia
| | - Matthew A. Addicoat
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
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10
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Chulanova EA, Radiush EA, Semenov NA, Hupf E, Irtegova IG, Kosenkova YS, Bagryanskaya IY, Shundrin LA, Beckmann J, Zibarev AV. Tuning Molecular Electron Affinities against Atomic Electronegativities by Spatial Expansion of a π-System. Chemphyschem 2023; 24:e202200876. [PMID: 36661050 DOI: 10.1002/cphc.202200876] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 01/21/2023]
Abstract
2,1,3-Benzochalcogenadiazoles C6 R4 N2 E (E/R; E=S, Se, Te; R=H, F, Cl, Br, I) and C6 H2 R2 N2 E (E/R'; E=S, Se, Te; R=Br, I) are 10π-electron hetarenes. By CV/EPR measurements, DFT calculations, and QTAIM and ELI-D analyses, it is shown that their molecular electron affinities (EAs) increase with decreasing Allen electronegativities and electron affinities of the E and non-hydrogen R (except Cl) atoms. DFT calculations for E/R+e⋅- →[E/R]⋅- electron capture reveal negative ΔG values numerically increasing with increasing atomic numbers of the E and R atoms; positive ΔS has a minor influence. It is suggested that the EA increase is caused by more effective charge/spin delocalization in the radical anions of heavier derivatives due to contributions from diffuse (a real-space expanded) p-AOs of the heavier E and R atoms; and that this counterintuitive effect might be of the general character.
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Affiliation(s)
- Elena A Chulanova
- Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russian Federation.,Current address: Institute for Applied Physics, University of Tübingen, 72076, Tübingen, Germany
| | - Ekaterina A Radiush
- Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russian Federation
| | - Nikolay A Semenov
- Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russian Federation
| | - Emanuel Hupf
- Institute for Inorganic Chemistry and Crystallography, University of Bremen, 28359, Bremen, Germany
| | - Irina G Irtegova
- Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russian Federation
| | - Yulia S Kosenkova
- Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russian Federation
| | - Irina Yu Bagryanskaya
- Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russian Federation
| | - Leonid A Shundrin
- Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russian Federation
| | - Jens Beckmann
- Institute for Inorganic Chemistry and Crystallography, University of Bremen, 28359, Bremen, Germany
| | - Andrey V Zibarev
- Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russian Federation
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11
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Zanetti RD, da Cunha GA, Moreira MB, Farias RL, de Souza RF, de Godoy PR, Brassesco MS, Rocha FV, Lima MA, Mauro AE, Netto AV. Orthopalladated N,N-Dimethyl-1-Phenethylamine Compounds Containing 2,6-Lutidine: Synthesis, Dna Binding Studies and Cytotoxicity Evaluation. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.116185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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12
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Peluso P, Chankvetadze B. Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers. Chem Rev 2022; 122:13235-13400. [PMID: 35917234 DOI: 10.1021/acs.chemrev.1c00846] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, I-07100 Sassari, Italy
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Avenue 3, 0179 Tbilisi, Georgia
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13
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Korobeinikov NA, Usoltsev AN, Shentseva IA, Abramov PA, Korolkov IV, Plusnin PE, Kolesov BA, Sokolov MN, Adonin SA. TRIIODIDE SALTS OF 4-DIMETHYLAMINO- AND 3-BROMO-1-METHYLPYRIDINIUM: CRYSTAL STRUCTURES AND FEATURES OF NON-COVALENT I⋯I INTERACTIONS IN SOLIDS. J STRUCT CHEM+ 2022. [DOI: 10.1134/s0022476622060178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Varadwaj A, Varadwaj PR, Marques HM, Yamashita K. The Pnictogen Bond: The Covalently Bound Arsenic Atom in Molecular Entities in Crystals as a Pnictogen Bond Donor. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113421. [PMID: 35684359 PMCID: PMC9181914 DOI: 10.3390/molecules27113421] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/08/2022] [Accepted: 05/17/2022] [Indexed: 12/04/2022]
Abstract
In chemical systems, the arsenic-centered pnictogen bond, or simply the arsenic bond, occurs when there is evidence of a net attractive interaction between the electrophilic region associated with a covalently or coordinately bound arsenic atom in a molecular entity and a nucleophile in another or the same molecular entity. It is the third member of the family of pnictogen bonds formed by the third atom of the pnictogen family, Group 15 of the periodic table, and is an inter- or intramolecular noncovalent interaction. In this overview, we present several illustrative crystal structures deposited into the Cambridge Structure Database (CSD) and the Inorganic Chemistry Structural Database (ICSD) during the last and current centuries to demonstrate that the arsenic atom in molecular entities has a significant ability to act as an electrophilic agent to make an attractive engagement with nucleophiles when in close vicinity, thereby forming σ-hole or π-hole interactions, and hence driving (in part, at least) the overall stability of the system’s crystalline phase. This overview does not include results from theoretical simulations reported by others as none of them address the signatory details of As-centered pnictogen bonds. Rather, we aimed at highlighting the interaction modes of arsenic-centered σ- and π-holes in the rationale design of crystal lattices to demonstrate that such interactions are abundant in crystalline materials, but care has to be taken to identify them as is usually done with the much more widely known noncovalent interactions in chemical systems, halogen bonding and hydrogen bonding. We also demonstrate that As-centered pnictogen bonds are usually accompanied by other primary and secondary interactions, which reinforce their occurrence and strength in most of the crystal structures illustrated. A statistical analysis of structures deposited into the CSD was performed for each interaction type As···D (D = N, O, S, Se, Te, F, Cl, Br, I, arene’s π system), thus providing insight into the typical nature of As···D interaction distances and ∠R–As···D bond angles of these interactions in crystals, where R is the remainder of the molecular entity.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Tokyo 113-8656, Japan;
- Correspondence: (A.V.); (P.R.V.)
| | - Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Tokyo 113-8656, Japan;
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
- Correspondence: (A.V.); (P.R.V.)
| | - Helder M. Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Tokyo 113-8656, Japan;
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15
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Baillargeon P, Robidas R, Toulgoat O, Michaud Z, Legault CY, Rahem T. Crystal Structures of Lignocellulosic Furfuryl Biobased Polydiacetylenes with Hydrogen-Bond Networks: Influencing the Direction of Solid-State Polymerization through Modification of the Spacer Length. CRYSTAL GROWTH & DESIGN 2022; 22:2812-2823. [PMID: 35529068 PMCID: PMC9073937 DOI: 10.1021/acs.cgd.2c00307] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/05/2022] [Indexed: 05/02/2023]
Abstract
We present the topochemical polymerization of two lignocellulosic biobased diacetylenes (DAs) that only differ by an alkyl spacer length of 1 methylene (n = 1) or 3 methylene units (n = 3) between the diyne and carbamate functionalities. Their crystalline molecular organizations have the distinctive feature of being suitable for polymerization in two potential directions, either parallel or skewed to the hydrogen-bonded (HB) network. However, single-crystal structures of the final polydiacetylenes (PDAs) demonstrate that the resulting orientation of the conjugated backbones is different for these two derivatives, which lead to HB supramolecular polymer networks (2D nanosheets) for n = 1 and to independent linear PDA chains with intramolecular HBs for n = 3. Thus, spacer length modification can be considered a new strategy to influence the molecular orientation of conjugated polymer chains, which is crucial for developing the next generation of materials with optimal mechanical and optoelectronic properties. Calculations were performed on model oligodiacetylenes to evaluate the cooperativity effect of HBs in the different crystalline supramolecular packing motifs and the energy profile related to the torsion of the conjugated backbone of a PDA chain (i.e., its ability to adopt planar or helical conformations).
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Affiliation(s)
- Pierre Baillargeon
- Département
de chimie, Cégep de Sherbrooke, 475 rue du Cégep, Sherbrooke, Québec J1E 4K1, Canada
| | - Raphaël Robidas
- Département
de chimie, Université de Sherbrooke, 2500 boul. de l’Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Olivier Toulgoat
- Département
de chimie, Cégep de Sherbrooke, 475 rue du Cégep, Sherbrooke, Québec J1E 4K1, Canada
| | - Zacharie Michaud
- Département
de chimie, Cégep de Sherbrooke, 475 rue du Cégep, Sherbrooke, Québec J1E 4K1, Canada
| | - Claude Y. Legault
- Département
de chimie, Université de Sherbrooke, 2500 boul. de l’Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Tarik Rahem
- Département
de chimie, Cégep de Sherbrooke, 475 rue du Cégep, Sherbrooke, Québec J1E 4K1, Canada
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16
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Miller DK, Chernyshov IY, Torubaev YV, Rosokha SV. From weak to strong interactions: structural and electron topology analysis of the continuum from the supramolecular chalcogen bonding to covalent bonds. Phys Chem Chem Phys 2022; 24:8251-8259. [PMID: 35320823 DOI: 10.1039/d1cp05441d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The relationship between covalent and supramolecular bonding, and the criteria of the assignments of different interactions were explored via the review of selenium and tellurium containing structures in the Cambridge Structural Database and their computational analysis using Quantum Theory of Atoms in Molecules (QTAIM). This combined study revealed continuums of the interatomic Se⋯Br and Te⋯I distances, dCh⋯X, in the series of associations from the sums of the van der Waals radii of these atoms (rCh + rX) to their covalent bond lengths. The electron densities, ρ(r), at Bond Critical Points (BCPs) along the chalcogen bond paths increased gradually from about 0.01 a.u. common for the non-covalent interactions to about 0.1 a.u. typical for the covalent bonds. The log ρ(r) values fell on the same linear trend line when plotted against normalized interatomic distances, RXY = dCh⋯X/(rCh + rX). The transition from the positive to negative values of the energy densities, H(r), at the BCPs (related to a changeover of essentially non-covalent into partially covalent interactions) were observed at RXY ≈ 0.80. Synchronous changes of bonding characteristics with RXY (similar to that found earlier in the halogen-bonded systems) designated normalized interatomic separation as a critical factor determining the nature of these bondings. The uninterrupted continuums of Te⋯I and Se⋯Br bond lengths and BCPs' characteristics signified an intrinsic link between limiting types of bonding involving chalcogen atoms and between covalent and supramolecular bonding in general.
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Affiliation(s)
- Daniel K Miller
- Chemistry Department, Ball State University, Muncie, IN, 47306, USA.
| | - Ivan Yu Chernyshov
- TheoMat group, ChemBio Cluster, ITMO University, Lomonosova 9, St. Petersburg, 191002, Russia
| | - Yury V Torubaev
- N.S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, GSP-1, L eninsky prospect, 31, Moscow, 119991, Russia
| | - Sergiy V Rosokha
- Chemistry Department, Ball State University, Muncie, IN, 47306, USA.
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17
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Kolganov AA, Gabrienko AA, Chernyshov IY, Stepanov AG, Pidko EA. Property-activity relations of multifunctional reactive ensembles in cation-exchanged zeolites: a case study of methane activation on Zn 2+-modified zeolite BEA. Phys Chem Chem Phys 2022; 24:6492-6504. [PMID: 35254352 DOI: 10.1039/d1cp05854a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The reactivity theories and characterization studies for metal-containing zeolites are often focused on probing the metal sites. We present a detailed computational study of the reactivity of Zn-modified BEA zeolite towards C-H bond activation of the methane molecule as a model system that highlights the importance of representing the active site as the whole reactive ensemble integrating the extra-framework ZnEF2+ cations, framework oxygens (OF2-), and the confined space of the zeolite pores. We demonstrate that for our model system the relationship between the Lewis acidity, defined by the probe molecule adsorption energy, and the activation energy for methane C-H bond cleavage performs with a determination coefficient R2 = 0.55. This suggests that the acid properties of the localized extra-framework cations can be used only for a rough assessment of the reactivity of the cations in the metal-containing zeolites. In turn, studying the relationship between the activation energy and pyrrole adsorption energy revealed a correlation, with R2 = 0.80. This observation was accounted for by the similarity between the local geometries of the pyrrole adsorption complexes and the transition states for methane C-H bond cleavage. The inclusion of a simple descriptor for zeolite local confinement allows transferability of the obtained property-activity relations to other zeolite topologies. Our results demonstrate that the representation of the metal cationic species as a synergistically cooperating active site ensembles allows reliable detection of the relationship between the acid properties and reactivity of the metal cation in zeolite materials.
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Affiliation(s)
- Alexander A Kolganov
- Boreskov Institute of Catalysis, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 5, Novosibirsk 630090, Russia
| | - Anton A Gabrienko
- Boreskov Institute of Catalysis, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 5, Novosibirsk 630090, Russia
| | - Ivan Yu Chernyshov
- TheoMAT Group, ChemBio Cluster, ITMO University, Lomonosova Street 9, Saint Petersburg, 191002, Russia
| | - Alexander G Stepanov
- Boreskov Institute of Catalysis, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 5, Novosibirsk 630090, Russia
| | - Evgeny A Pidko
- Inorganic Systems Engineering group, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands. .,TsyfroCatLab Group, University of Tyumen, Volodarskogo St. 6, Tyumen 625003, Russia
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18
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Shestimerova TA, Bykov AV, Kuznetsov AN, Grishko AY, Wei Z, Dikarev EV, Shevelkov AV. Pattern of covalent and non‐covalent interactions within the pentaiodide anion in the structure of (3‐HOC5H9NH2)I5. Z Anorg Allg Chem 2022. [DOI: 10.1002/zaac.202200039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Tatiana A. Shestimerova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia RUSSIAN FEDERATION
| | - Andrey V. Bykov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia RUSSIAN FEDERATION
| | - Alexey N. Kuznetsov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia. N. S. Kurnakov Institute of General and Inorganic Chemistry RAS, 119991 Moscow, Russia RUSSIAN FEDERATION
| | - Alexey Y. Grishko
- Department of Materials Sciences, Lomonosov Moscow State University, 119991 Moscow, Russia RUSSIAN FEDERATION
| | - Zheng Wei
- Department of Chemistry, University at Albany, SUNY, Albany New York 12222, United States RUSSIAN FEDERATION
| | - Evgeny V. Dikarev
- Department of Chemistry, University at Albany, SUNY, Albany New York 12222, United States RUSSIAN FEDERATION
| | - Andrei V. Shevelkov
- Lomonosov Moscow State University Chemistry Leninskie Gory 1/3 119991 Moscow RUSSIAN FEDERATION
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19
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Afonin AV, Semenov VA, Vashchenko AV. Digitization of the electron shell via the localized orbital locator formalism: trends in the size and electronegativity changes of atoms across the periodic table. Phys Chem Chem Phys 2022; 24:28127-28133. [DOI: 10.1039/d2cp04203g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The parameters of the (3,−3) critical point in the topology of the localized orbital locator inside the electron shell reflect regularity in the change of basic atom properties across the periodic table.
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Affiliation(s)
- Andrei V. Afonin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of Russian Academy of Sciences, 1 Favorsky St., 664033 Irkutsk, Russian Federation
| | - Valentin A. Semenov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of Russian Academy of Sciences, 1 Favorsky St., 664033 Irkutsk, Russian Federation
| | - Alexander V. Vashchenko
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of Russian Academy of Sciences, 1 Favorsky St., 664033 Irkutsk, Russian Federation
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20
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Garau A, Aragoni MC, Arca M, Caltagirone C, Demartin F, Isaia F, Lippolis V, Pivetta T. A new assembly of diiodine molecules at the 1,3-dimethylimidazole-2-thione (Me 2ImS) template: crystal structure of (Me 2ImS) 2·(I 2) 5. NEW J CHEM 2022. [DOI: 10.1039/d2nj00526c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The poly(I2) adduct [(Me2ImS)2·(I2)5] has been synthesised using a two-step process. The FT-Raman spectrum and MEP maps are discussed.
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Affiliation(s)
- Alessandra Garau
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - M. Carla Aragoni
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Massimiliano Arca
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Claudia Caltagirone
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Francesco Demartin
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133, Milano, Italy
| | - Francesco Isaia
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Vito Lippolis
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Tiziana Pivetta
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy
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21
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Torubaev YV, Rozhkov AV, Skabitsky IV, Gomila RM, Frontera A, Kukushkin VY. Heterovalent chalcogen bonding: supramolecular assembly driven by the occurrence of a tellurium( ii)⋯Ch( i) (Ch = S, Se, Te) linkage. Inorg Chem Front 2022. [DOI: 10.1039/d2qi01420c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The revealed heterovalent TeII⋯ChI (Ch = S, Se, Te) chalcogen bonding was used for targeted noncovalent integration of two Ch centers in different oxidation states.
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Affiliation(s)
- Yury V. Torubaev
- N. S. Kurnakov Institute of General and Inorganic Chemistry of Russian Academy of Sciences, Moscow, 119991, Russian Federation
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anton V. Rozhkov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg, 199034, Russian Federation
| | - Ivan V. Skabitsky
- N. S. Kurnakov Institute of General and Inorganic Chemistry of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Rosa M. Gomila
- Department of Chemistry, Universitat de les Illes Balears, 07122 Palma de Mallorca, Baleares, Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, 07122 Palma de Mallorca, Baleares, Spain
| | - Vadim Yu. Kukushkin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg, 199034, Russian Federation
- Institute of Chemistry and Pharmaceutical Technologies, Altai State University, 656049 Barnaul, Russian Federation
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22
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El Alouani Dahmouni N, Switlicka A, Machura B, Moliner N, Rabelo R, Ruiz-García R, Stiriba SE, Cano J, Julve M. Bulky countercation effects on the crystal packing of anionic dithiooxalato-containing Ni( ii), Pd( ii) and Pt( ii) complexes: spectroscopic–redox correlations. CrystEngComm 2022. [DOI: 10.1039/d2ce00489e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The metal ion, countercation and crystallization solvent control the packing of bis(dithiooxalato-k2S,S′)metallate(ii) complex anions in the solid state.
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Affiliation(s)
- Nadia El Alouani Dahmouni
- Departament de Química Inorgànica/Instituto de Ciencia Molecular (ICMol), Facultat de Química de la Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, València, Spain
| | - Anna Switlicka
- Department of Crystallography, Institute of Chemistry, University of Silesia, 9th Szkolna St., 40-006 Katowice, Poland
| | - Barbara Machura
- Department of Crystallography, Institute of Chemistry, University of Silesia, 9th Szkolna St., 40-006 Katowice, Poland
| | - Nicolás Moliner
- Departament de Química Inorgànica/Instituto de Ciencia Molecular (ICMol), Facultat de Química de la Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, València, Spain
| | - Renato Rabelo
- Departament de Química Inorgànica/Instituto de Ciencia Molecular (ICMol), Facultat de Química de la Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, València, Spain
| | - Rafael Ruiz-García
- Departament de Química Inorgànica/Instituto de Ciencia Molecular (ICMol), Facultat de Química de la Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, València, Spain
| | - Salah-Eddine Stiriba
- Departament de Química Inorgànica/Instituto de Ciencia Molecular (ICMol), Facultat de Química de la Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, València, Spain
| | - Joan Cano
- Departament de Química Inorgànica/Instituto de Ciencia Molecular (ICMol), Facultat de Química de la Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, València, Spain
| | - Miguel Julve
- Departament de Química Inorgànica/Instituto de Ciencia Molecular (ICMol), Facultat de Química de la Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna, València, Spain
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23
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Posavec L, Nemec V, Stilinović V, Cinčić D. Halogen and Hydrogen Bond Motifs in Ionic Cocrystals Derived from 3-Halopyridinium Halogenides and Perfluorinated Iodobenzenes. CRYSTAL GROWTH & DESIGN 2021; 21:6044-6050. [PMID: 34759783 PMCID: PMC8569900 DOI: 10.1021/acs.cgd.1c00755] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Four halopyridinium salts, 3-chloro- and 3-bromopyridinium chlorides and bromides, have been successfully cocrystallized with two ditopic perfluorinated iodobenzenes, 1,4-diiodotetrafluorobenzene and 1,2-diiodotetrafluorobenzene. These halogen bond donor molecules were chosen because the different positionings of halogen bond donor atoms can lead to different supramolecular architectures. In this work, we present insight into the halogen bond acceptor potential of chloride and bromide ions, as well as the halogen bond donor potential of chlorine and bromine atoms substituted on the pyridinium ring when combined with the expectedly very strong hydrogen bonds between halopyridinium ions and free halogenide anions. A series of eight cocrystals were obtained in which three pairs of isostructural cocrystals were formed. Dominant interactions in the obtained cocrystals were charge-assisted hydrogen bonds between halopyridinium cations and halogenide ions as well as halogen bonds between halogen atoms on the pyridinium ring and halogenide ions.
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24
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Shestimerova TA, Golubev NA, Bykov MA, Mironov AV, Fateev SA, Tarasov AB, Turkevych I, Wei Z, Dikarev EV, Shevelkov AV. Molecular and Supramolecular Structures of Triiodides and Polyiodobismuthates of Phenylenediammonium and Its N,N-dimethyl Derivative. Molecules 2021; 26:molecules26185712. [PMID: 34577182 PMCID: PMC8470886 DOI: 10.3390/molecules26185712] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 11/29/2022] Open
Abstract
Despite remarkable progress in photoconversion efficiency, the toxicity of lead-based hybrid perovskites remains an important issue hindering their applications in consumer optoelectronic devices, such as solar cells, LED displays, and photodetectors. For that reason, lead-free metal halide complexes have attracted great attention as alternative optoelectronic materials. In this work, we demonstrate that reactions of two aromatic diamines with iodine in hydroiodic acid produced phenylenediammonium (PDA) and N,N-dimethyl-phenylenediammonium (DMPDA) triiodides, PDA(I3)2⋅2H2O and DMPDA(I3)I, respectively. If the source of bismuth was added, they were converted into previously reported PDA(BiI4)2⋅I2 and new (DMPDA)2(BiI6)(I3)⋅2H2O, having band gaps of 1.45 and 1.7 eV, respectively, which are in the optimal range for efficient solar light absorbers. All four compounds presented organic–inorganic hybrids, whose supramolecular structures were based on a variety of intermolecular forces, including (N)H⋅⋅⋅I and (N)H⋅⋅⋅O hydrogen bonds as well as I⋅⋅⋅I secondary and weak interactions. Details of their molecular and supramolecular structures are discussed based on single-crystal X-ray diffraction data, thermal analysis, and Raman and optical spectroscopy.
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Affiliation(s)
- Tatiana A. Shestimerova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (T.A.S.); (N.A.G.); (M.A.B.); (A.V.M.); (A.B.T.)
| | - Nikita A. Golubev
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (T.A.S.); (N.A.G.); (M.A.B.); (A.V.M.); (A.B.T.)
| | - Mikhail A. Bykov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (T.A.S.); (N.A.G.); (M.A.B.); (A.V.M.); (A.B.T.)
| | - Andrei V. Mironov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (T.A.S.); (N.A.G.); (M.A.B.); (A.V.M.); (A.B.T.)
| | - Sergey A. Fateev
- Department of Materials Science, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Alexey B. Tarasov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (T.A.S.); (N.A.G.); (M.A.B.); (A.V.M.); (A.B.T.)
- Department of Materials Science, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Ivan Turkevych
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8565, Japan;
| | - Zheng Wei
- Department of Chemistry, University at Albany, SUNY, Albany, NY 12222, USA; (Z.W.); (E.V.D.)
| | - Evgeny V. Dikarev
- Department of Chemistry, University at Albany, SUNY, Albany, NY 12222, USA; (Z.W.); (E.V.D.)
| | - Andrei V. Shevelkov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (T.A.S.); (N.A.G.); (M.A.B.); (A.V.M.); (A.B.T.)
- Correspondence:
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25
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Anisimov AA, Ananyev IV. Revisiting the energy treatment of the density of molecular crystals: an interrelation between intermolecular interaction energies and changes of molecular volume. Russ Chem Bull 2021. [DOI: 10.1007/s11172-021-3236-x] [Citation(s) in RCA: 2] [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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26
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Mezentsev-Cherkes IA, Shestimerova TA, Medved'ko AV, Kalinin MA, Kuznetsov AN, Wei Z, Dikarev EV, Vatsadze SZ, Shevelkov AV. Synthesis and supramolecular organization of the iodide and triiodides of a polycyclic adamantane-based diammonium cation: the effects of hydrogen bonds and weak I⋯I interactions. CrystEngComm 2021. [DOI: 10.1039/d0ce01730b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Adamantane-like divalent building blocks and iodide or polyiodide anions combine into supramolecular architectures with the help of various noncovalent forces ranging from strong hydrogen bonds to secondary and weak I⋯I interactions.
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Affiliation(s)
| | | | | | - Mikhail A. Kalinin
- Department of Chemistry
- Lomonosov Moscow State University
- 119991 Moscow
- Russia
| | - Alexey N. Kuznetsov
- Department of Chemistry
- Lomonosov Moscow State University
- 119991 Moscow
- Russia
- N. S. Kurnakov Institute of General and Inorganic Chemistry RAS
| | - Zheng Wei
- Department of Chemistry
- University at Albany
- Albany
- USA
| | | | - Sergey Z. Vatsadze
- Department of Chemistry
- Lomonosov Moscow State University
- 119991 Moscow
- Russia
- N.D. Zelinsky Institute of Organic Chemistry RAS
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27
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Halogen vs. ionic bonding: an unusual isomorphism between the neutral (C5Me5)2Fe/C2I2 cocrystal and ionic [(C5Me5)2Fe]Br3 crystal. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.01.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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28
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Asgarpour Khansary M, Walker G, Shirazian S. Incomplete cocrystalization of ibuprofen and nicotinamide and its interplay with formation of ibuprofen dimer and/or nicotinamide dimer: A thermodynamic analysis based on DFT data. Int J Pharm 2020; 591:119992. [DOI: 10.1016/j.ijpharm.2020.119992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 12/20/2022]
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29
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Chong-Canto S, García-Báez EV, Martínez-Martínez FJ, Ramos-Organillo AA, Padilla-Martínez II. Mechanochemical Synthesis and Structure of the Tetrahydrate and Mesoporous Anhydrous Metforminium(2+)- N, N'-1,4-Phenylenedioxalamic Acid (1:2) Salt: The Role of Hydrogen Bonding and n→π * Charge Assisted Interactions. Pharmaceutics 2020; 12:E998. [PMID: 33096739 PMCID: PMC7594043 DOI: 10.3390/pharmaceutics12100998] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/13/2020] [Accepted: 10/18/2020] [Indexed: 11/20/2022] Open
Abstract
A new organic salt of metformin, an antidiabetic drug, and N,N'-(1,4-phenylene)dioxalamic acid, was mechanochemically synthesized, purified by crystallization from solution and characterized by single X-ray crystallography. The structure revealed a salt-type crystal hydrate composed of one dicationic metformin unit, two monoanionic units of the acid and four water molecules, namely H2Mf(HpOXA)2∙4H2O. X-ray powder, IR, 13C-CPMAS, thermal and BET adsorption-desorption analyses were performed to elucidate the structure of the molecular and supramolecular structure of the anhydrous microcrystalline mesoporous solid H2Mf(HpOXA)2. The results suggest that their structures, conformation and hydrogen bonding schemes are very similar. To the best of our knowledge, the selective formation of the monoanion HpOXA-, as well as its structure in the solid, is herein reported for the first time. Regular O(δ-)∙∙∙C(δ), O(δ-)∙∙∙N+ and bifacial O(δ-)∙∙∙C(δ)∙∙∙O(δ-) of n→π * charge-assisted interactions are herein described in H2MfA organic salts which could be responsible of the interactions of metformin in biologic systems. The results support the participation of n→π * charge-assisted interactions independently, and not just as a short contact imposed by the geometric constraint due to the hydrogen bonding patterns.
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Affiliation(s)
- Sayuri Chong-Canto
- Laboratorio de Química Supramolecular y Nanociencias, Instituto Politécnico Nacional-UPIBI, Av. Acueducto s/n Barrio la Laguna Ticomán, Ciudad de México C.P. 07340, Mexico; (S.C.-C.); (E.V.G.-B.)
| | - Efrén V. García-Báez
- Laboratorio de Química Supramolecular y Nanociencias, Instituto Politécnico Nacional-UPIBI, Av. Acueducto s/n Barrio la Laguna Ticomán, Ciudad de México C.P. 07340, Mexico; (S.C.-C.); (E.V.G.-B.)
| | - Francisco J. Martínez-Martínez
- Facultad de Ciencias Químicas, Universidad de Colima, Km. 9 Carretera Colima-Coquimatlán, Coquimatlán C.P. 28400, Colima, Mexico; (F.J.M.-M.); (A.A.R.-O.)
| | - Angel A. Ramos-Organillo
- Facultad de Ciencias Químicas, Universidad de Colima, Km. 9 Carretera Colima-Coquimatlán, Coquimatlán C.P. 28400, Colima, Mexico; (F.J.M.-M.); (A.A.R.-O.)
| | - Itzia I. Padilla-Martínez
- Laboratorio de Química Supramolecular y Nanociencias, Instituto Politécnico Nacional-UPIBI, Av. Acueducto s/n Barrio la Laguna Ticomán, Ciudad de México C.P. 07340, Mexico; (S.C.-C.); (E.V.G.-B.)
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30
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Rahm M, Ångqvist M, Rahm JM, Erhart P, Cammi R. Non-Bonded Radii of the Atoms Under Compression. Chemphyschem 2020; 21:2441-2453. [PMID: 32896974 DOI: 10.1002/cphc.202000624] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/07/2020] [Indexed: 12/19/2022]
Abstract
We present quantum mechanical estimates for non-bonded, van der Waals-like, radii of 93 atoms in a pressure range from 0 to 300 gigapascal. Trends in radii are largely maintained under pressure, but atoms also change place in their relative size ordering. Multiple isobaric contractions of radii are predicted and are explained by pressure-induced changes to the electronic ground state configurations of the atoms. The presented radii are predictive of drastically different chemistry under high pressure and permit an extension of chemical thinking to different thermodynamic regimes. For example, they can aid in assignment of bonded and non-bonded contacts, for distinguishing molecular entities, and for estimating available space inside compressed materials. All data has been made available in an interactive web application.
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Affiliation(s)
- Martin Rahm
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Mattias Ångqvist
- Department of Physics, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - J Magnus Rahm
- Department of Physics, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Paul Erhart
- Department of Physics, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Roberto Cammi
- Department of Chemical Science, Life Science and Environmental Sustainability, University of Parma, Parma, Italy
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31
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Chernyshov IY, Ananyev IV, Pidko EA. Revisiting van der Waals Radii: From Comprehensive Structural Analysis to Knowledge-Based Classification of Interatomic Contacts. Chemphyschem 2020; 21:370-376. [PMID: 31912957 PMCID: PMC7079509 DOI: 10.1002/cphc.201901083] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/06/2020] [Indexed: 11/25/2022]
Abstract
Weak noncovalent interactions are responsible for structure and properties of almost all supramolecular systems, such as nucleic acids, enzymes, and pharmaceutical crystals. However, the analysis of their significance and structural role is not straightforward and commonly requires model studies. Herein, we describe an efficient and universal approach for the analysis of noncovalent interactions and determination of van der Waals radii using the line-of-sight (LoS) concept. The LoS allows to unambiguously identify and classify the "direct" interatomic contacts in complex molecular systems. This approach not only provides an improved theoretical base to molecular "sizes" but also enables the quantitative analysis of specificity, anisotropy, and steric effects of intermolecular interactions.
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Affiliation(s)
- Ivan Yu. Chernyshov
- TheoMAT Group, ChemBio clusterITMO UniversityLomonosova 9St. Petersburg191002Russia
| | - Ivan V. Ananyev
- Faculty of ChemistryNational Research University Higher School of EconomicsMoscow101000Russia
| | - Evgeny A. Pidko
- TheoMAT Group, ChemBio clusterITMO UniversityLomonosova 9St. Petersburg191002Russia
- Inorganic Systems Engineering GroupDelft University of TechnologyVan der Maasweg 92629 HZDelft (TheNetherlands
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32
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Balmohammadi Y, Khavasi HR, Naghavi SS. Existence of untypical halogen-involving interactions in crystal packings: a statistical and first-principles study. CrystEngComm 2020. [DOI: 10.1039/c9ce01885a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
There is a common perception by the scientific community that a halogen-involving interaction forms when the distance between the donor atom and the acceptor atom is less than the sum of their van der Waals (vdW) radii.
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Affiliation(s)
- Yaser Balmohammadi
- Department of Inorganic Chemistry and Catalysis
- Shahid Beheshti University
- Tehran 1983963113
- Iran
| | - Hamid Reza Khavasi
- Department of Inorganic Chemistry and Catalysis
- Shahid Beheshti University
- Tehran 1983963113
- Iran
| | - S. Shahab Naghavi
- Department of Physical and Computational Chemistry
- Shahid Beheshti University
- 1983963113 Tehran
- Iran
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33
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Torubaev YV, Skabitsky IV. A new supramolecular heterosynthon [C–I⋯OC(carboxylate)] at work: engineering copper acetate cocrystals. CrystEngComm 2020. [DOI: 10.1039/d0ce01093f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Carboxylate–iodine supramolecular heterosynthons in combination with energy frameworks can be reliably applied in engineering hybrid metal-carboxylate cocrystals.
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Affiliation(s)
- Yury V. Torubaev
- N.S. Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow
- Russia
| | - Ivan V. Skabitsky
- N.S. Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow
- Russia
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34
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Vologzhanina AV, Buikin PA, Korlyukov AA. Peculiarities of Br⋯Br bonding in crystal structures of polybromides and bromine solvates. CrystEngComm 2020. [DOI: 10.1039/d0ce00288g] [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
Analysis of supramolecular associates formed by Br⋯Br interactions in crystals of 204 polybromide and bromine-containing compounds has been carried out.
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Affiliation(s)
- Anna V. Vologzhanina
- A.N. Nesmeyanov Institute of Organoelement Compounds RAS
- 119991 Moscow
- Russian Federation
| | - Petr A. Buikin
- A.N. Nesmeyanov Institute of Organoelement Compounds RAS
- 119991 Moscow
- Russian Federation
- D.M. Mendeleev University of Chemical Technology of Russia
- 125047 Moscow
| | - Alexander A. Korlyukov
- A.N. Nesmeyanov Institute of Organoelement Compounds RAS
- 119991 Moscow
- Russian Federation
- D.M. Mendeleev University of Chemical Technology of Russia
- 125047 Moscow
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