1
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Pichierri F. Tri-tert-butyl methane and its halogen analogues: a computational study of intramolecular interactions in a family of sterically crowded molecules. Struct Chem 2022. [DOI: 10.1007/s11224-022-02102-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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2
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Theoretical insights into the nature of the bonding between carbon monoxide and iron(II) phthalocyanine: How do QTAIM descriptors change as a function of the Fe–CO distance? Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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3
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Ziemniak M, Pawlędzio S, Zawadzka-Kaźmierczuk A, Dominiak PM, Trzybiński D, Koźmiński W, Zieliński R, Fokt I, Priebe W, Woźniak K, Pająk B. X-ray wavefunction refinement and comprehensive structural studies on bromo-substituted analogues of 2-deoxy-d-glucose in solid state and solution. RSC Adv 2022; 12:8345-8360. [PMID: 35424802 PMCID: PMC8985090 DOI: 10.1039/d1ra08312k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/01/2022] [Accepted: 03/05/2022] [Indexed: 11/21/2022] Open
Abstract
The structural studies on two bromo-substituted derivatives of 2-deoxy-d-glucose (2-DG), namely 2-deoxy-2-bromo-d-glucose (2-BG) and 2-deoxy-2-bromo-d-mannose (2-BM) are described. 2-DG itself is an inhibitor of hexokinase, the first enzyme in the glycolysis process, playing a vital role in both cancer cell metabolism and viral replication in host cells. Because of that, 2-DG derivatives are considered as potential anti-cancer and anti-viral drugs. An X-ray quantum crystallography approach allowed us to obtain more accurate positions of hydrogen atoms by applying Hirshfeld atom refinement, providing a better description of hydrogen bonding even in the case of data from routine X-ray experiments. Obtained structures showed that the introduction of bromine at the C2 position in the pyranose ring has a minor influence on its conformation but still, it has a noticeable effect on the crystal structure. Bromine imposes the formation of a layered supramolecular landscape containing hydrogen bonds, which involves the bromine atom. Periodic DFT calculations of cohesive and interaction energies (at the B3LYP level of theory) have supported these findings and highlighted energetic changes upon bromine substitution. Based on molecular wavefunction from the refinement, we calculated the electrostatic potential, Laplacian, and ELI-D, and applied them to charge-density studies, which confirmed the geometry of hydrogen bonding and involvement of the bromine atom with these intermolecular interactions. NMR studies in the solution show that both compounds do not display significant differences in their anomeric equilibria compared to 2-DG, and the pyranose ring puckering is similar in both aqueous and solid state.
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Affiliation(s)
- Marcin Ziemniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Sylwia Pawlędzio
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Anna Zawadzka-Kaźmierczuk
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Damian Trzybiński
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Wiktor Koźmiński
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Rafał Zieliński
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center 1901 East Rd. Houston TX 77054 USA
| | - Izabela Fokt
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center 1901 East Rd. Houston TX 77054 USA
| | - Waldemar Priebe
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center 1901 East Rd. Houston TX 77054 USA
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Beata Pająk
- Independent Laboratory of Genetics and Molecular Biology, Kaczkowski Military Institute of Hygiene and Epidemiology Kozielska 4 01-163 Warsaw Poland
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4
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Auride ion interaction with borane: A theoretical study of AuBH3−. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2021.139288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Lozada IB, Ortiz RJ, Braun JD, Williams JAG, Herbert DE. Donor-Acceptor Boron-Ketoiminate Complexes with Pendent N-Heterocyclic Arms: Switched-on Luminescence through N-Heterocycle Methylation. J Org Chem 2021; 87:184-196. [PMID: 34936362 DOI: 10.1021/acs.joc.1c02138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of intramolecular, donor-stabilized BF2 complexes supported by phenanthridinyl-decorated, β-ketoiminate chelating ligand scaffolds is described, along with their characterization by spectroscopy and X-ray diffraction. In solution, the relative orientation of the pendent phenanthridinyl arm is fixed despite not coordinating to the boron center, and a well-resolved through-space interaction between a phenanthridinyl C-H and a single fluorine atom can be observed by 19F-1H NOE NMR spectroscopy. The neutral compounds are nonetheless only weakly luminescent in fluid solution, ascribed to nonradiative decay pathways enabled by rotation of the N-heterocyclic unit. Methylation of the phenanthridinyl nitrogen restricts this rotation, "switching on" comparably strong emission in solution. Modeling by density functional theory (DFT) and time-dependent DFT (TDDFT) indicates that the character of the lowest energy excitation changes upon methylation, with shallow calculated potential energy surfaces of the neutral complexes consistent with their lack of significant radiative decay.
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Affiliation(s)
- Issiah B Lozada
- Department of Chemistry and the Manitoba Institute for Materials, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Robert J Ortiz
- Department of Chemistry and the Manitoba Institute for Materials, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Jason D Braun
- Department of Chemistry and the Manitoba Institute for Materials, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | | | - David E Herbert
- Department of Chemistry and the Manitoba Institute for Materials, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
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6
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Ośmiałowski B, Dziuk B, Ejsmont K, Chęcińska L, Dobrzańska L. Effect of conjugated system extension on structural features and electron-density distribution in charge-transfer difluoroborates. Acta Crystallogr C 2021; 77:807-813. [PMID: 34864724 DOI: 10.1107/s2053229621012249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/18/2021] [Indexed: 11/10/2022] Open
Abstract
A comparative structural study of two related donor-acceptor pyridine-based BF2 complexes, namely, 3-(dimethylamino)-1,1-difluoro-1H-pyrido[1,2-c][1,3,5,2]oxadiazaborinin-9-ium-1-uide, C8H10BF2N3O (1), and 3-{(1E,3E)-4-[4-(dimethylamino)phenyl]buta-1,3-dien-1-yl}-1,1-difluoro-1H-pyrido[1,2-c][1,3,5,2]oxadiazaborinin-9-ium-1-uide, C18H18BF2N3O (2), containing a dimethylamino group and either the shortest (in 1) or the longest (in 2) charge-transfer path known until now in this family of compounds, is presented. Single-crystal X-ray diffraction analysis supported by computational investigations shed more light on these systems, indicating, among other aspects, the predominance of C-H...F contacts in 1, the formation of antiparallel dimers held together by π-π interactions in both compounds, and the involvement of fused BF2-bearing rings in the charge-transfer process.
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Affiliation(s)
- Borys Ośmiałowski
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, Toruń 87-100, Poland
| | - Błażej Dziuk
- Faculty of Chemistry, Wrocław University of Science and Technology, Norwida 4/6, Wrocław 50-373, Poland
| | - Krzysztof Ejsmont
- Faculty of Chemistry, University of Opole, Oleska 48, Opole 45-052, Poland
| | - Lilianna Chęcińska
- Faculty of Chemistry, University of Łódź, Pomorska 163/165, Łódź 90-236, Poland
| | - Liliana Dobrzańska
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, Toruń 87-100, Poland
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7
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Adjieufack AI, Bake MM, Nguimkeu CN, Pilmé J, Ndassa IM. Exploring The Sequence of Electron Density Along The Chemical Reactions Between Carbonyl Oxides And Ammonia/Water Using Bond Evolution Theory. Chemphyschem 2021; 22:1792-1801. [PMID: 34197684 DOI: 10.1002/cphc.202100221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/16/2021] [Indexed: 11/10/2022]
Abstract
The molecular mechanism of the reactions between four carbonyl oxides and ammonia/water are investigated using the M06-2X functional together with 6-311++G(d,p) basis set. The analysis of activation and reaction enthalpy shows that the exothermicity of each process increased with the substitution of electron donating substituents (methyl and ethenyl). Along each reaction pathway, two new chemical bonds C-N/C-O and O-H are expected to form. A detailed analysis of the flow of the electron density during their formation have been characterized from the perspective of bonding evolution theory (BET). For all reaction pathways, BET revealed that the process of C-N and O-H bond formation takes place within four structural stability domains (SSD), which can be summarized as follows: the depopulation of V(N) basin with the formation of first C-N bond (appearance of V(C,N) basin), cleavage of N-H bond with the creation of V(N) and V(H) monosynaptic basin, and finally the V(H,O) disynaptic basin related to O-H bond. On the other hand, in the case of water, the cleavage of O-H bond with the formation of V(O) and V(H) basins is the first stage, followed by the formation of the O-H bond as a second stage, and finally the creation of C-O bond.
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Affiliation(s)
- Abel Idrice Adjieufack
- Physical and Theoretical Chemistry Laboratory, University of Yaoundé 1, P.O. Box 812, Yaoundé, Cameroon.,Computational Chemistry Laboratory, High Teacher Training College, University of Yaoundé 1, P.O. Box 47, Yaoundé, Cameroon
| | - Maraf Mbah Bake
- Physical and Theoretical Chemistry Laboratory, University of Yaoundé 1, P.O. Box 812, Yaoundé, Cameroon.,Computational Chemistry Laboratory, High Teacher Training College, University of Yaoundé 1, P.O. Box 47, Yaoundé, Cameroon
| | - Charnel Nguemo Nguimkeu
- Physical and Theoretical Chemistry Laboratory, University of Yaoundé 1, P.O. Box 812, Yaoundé, Cameroon.,Computational Chemistry Laboratory, High Teacher Training College, University of Yaoundé 1, P.O. Box 47, Yaoundé, Cameroon
| | - Julien Pilmé
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, CC 137-4, place Jussieu, 75252, Paris CEDEX 05, France
| | - Ibrahim Mbouombouo Ndassa
- Computational Chemistry Laboratory, High Teacher Training College, University of Yaoundé 1, P.O. Box 47, Yaoundé, Cameroon
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8
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Ernst M, Genoni A, Macchi P. Analysis of crystal field effects and interactions using X-ray restrained ELMOs. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127975] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Symmetric Fluoroborate and its Boron Modification: Crystal and Electronic Structures. CRYSTALS 2019. [DOI: 10.3390/cryst9120662] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Four boron-carrying molecules were synthesized and purified. These were found to be (a) relatively neutral with respect to the parent BF derivative and (b) functionalized by donor–acceptor groups resulting in a charge transfer within the molecule. The study discusses the steric effect and the influence of the substitution of the side rings on the surroundings of the boron atom. Electronic structures were characterized by real-space bonding indicators. Hirshfeld surface and energy frameworks tools were applied to examine the crystal packing features.
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10
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Meyer B, Barthel S, Mace A, Vannay L, Guillot B, Smit B, Corminboeuf C. DORI Reveals the Influence of Noncovalent Interactions on Covalent Bonding Patterns in Molecular Crystals Under Pressure. J Phys Chem Lett 2019; 10:1482-1488. [PMID: 30865472 PMCID: PMC6452419 DOI: 10.1021/acs.jpclett.9b00220] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The study of organic molecular crystals under high pressure provides fundamental insight into crystal packing distortions and reveals mechanisms of phase transitions and the crystallization of polymorphs. These solid-state transformations can be monitored directly by analyzing electron charge densities that are experimentally obtained at high pressure. However, restricting the analysis to the featureless electron density does not reveal the chemical bonding nature and the existence of intermolecular interactions. This shortcoming can be resolved by the use of the DORI (density overlap region indicator) descriptor, which is capable of simultaneously detecting both covalent patterns and noncovalent interactions from electron density and its derivatives. Using the biscarbonyl[14]annulene crystal under pressure as an example, we demonstrate how DORI can be exploited on experimental electron densities to reveal and monitor changes in electronic structure patterns resulting from molecular compression. A novel approach based on a flood-fill-type algorithm is proposed for analyzing the topology of the DORI isosurface. This approach avoids the arbitrary selection of DORI isovalues and provides an intuitive way to assess how compression packing affects covalent bonding in organic solids.
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Affiliation(s)
- Benjamin Meyer
- Laboratory
for Computational Molecular Design (LCMD), Institute of Chemical Sciences
and Engineering (ISIC), École Polytechnique
Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- National
Center for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Senja Barthel
- National
Center for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Laboratory
of Molecular Simulation (LSMO), Institute of Chemical Sciences and
Engineering (ISIC), École Polytechnique
Fédérale de Lausanne (EPFL Valais), CH-1951 Sion, Switzerland
| | - Amber Mace
- National
Center for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Laboratory
of Molecular Simulation (LSMO), Institute of Chemical Sciences and
Engineering (ISIC), École Polytechnique
Fédérale de Lausanne (EPFL Valais), CH-1951 Sion, Switzerland
- Department
of Materials and Environmental Chemistry, Stockholm University, SE-10691 Stockholm, Sweden
| | - Laurent Vannay
- Laboratory
for Computational Molecular Design (LCMD), Institute of Chemical Sciences
and Engineering (ISIC), École Polytechnique
Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Benoit Guillot
- Laboratoire
CRM2, UMR 7036, Université de Lorraine, F-54506 Vandoeuvre-lès-Nancy, France
| | - Berend Smit
- National
Center for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Laboratory
of Molecular Simulation (LSMO), Institute of Chemical Sciences and
Engineering (ISIC), École Polytechnique
Fédérale de Lausanne (EPFL Valais), CH-1951 Sion, Switzerland
| | - Clémence Corminboeuf
- Laboratory
for Computational Molecular Design (LCMD), Institute of Chemical Sciences
and Engineering (ISIC), École Polytechnique
Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- National
Center for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- E-mail: . Tel: +41 (0)21 693 93 57. Fax: +41 (0)21 693
97 00
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11
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Jarzembska KN, Kamiński R, Durka K, Woźniak K. Ground-State Charge-Density Distribution in a Crystal of the Luminescent ortho-Phenylenediboronic Acid Complex with 8-Hydroxyquinoline. J Phys Chem A 2018; 122:4508-4520. [PMID: 29672046 DOI: 10.1021/acs.jpca.8b00832] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This contribution is devoted to the first electron density studies of a luminescent oxyquinolinato boron complex in the solid state. ortho-Phenylenediboronic acid mixed with 8-hydroxyquinoline in dioxane forms high-quality single crystals via slow solvent evaporation, which allows successful high resolution data collection (sin θ/λ = 1.2 Å-1) and charge density distribution modeling. Particular attention has been paid to the boron-oxygen fragment connecting the two parts of the complex, and to the solvent species exhibiting anharmonic thermal motion. The experiment and theory compared rather well in terms of atomic charges and volumes, except for the boron centers. Boron atoms, as expected, constitute the most electron-deficient species in the complex molecule, whereas the neighboring oxygen and carbon atoms are the most significantly negatively charged ones. This part of the molecule appears to be very much involved in the charge transfer occurring between the acid fragment and oxyquinoline moiety leading to the observed fluorescence, as supported by the time-dependent density functional theory (TDDFT) results and the generated transition density maps. TDDFT calculations indicated that p-type atomic orbitals contributing to the HOMO-1, HOMO, and LUMO play the major role in the lowest energy transitions, and enabled further comparison with the charge density features, which is discussed in details. Furthermore, the results confirmed the known fact the Q ligand character is most important for the spectroscopic properties of this class of complexes.
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Affiliation(s)
- Katarzyna N Jarzembska
- Department of Chemistry , University of Warsaw , Żwirki i Wigury 101 , 02-089 Warsaw , Poland
| | - Radosław Kamiński
- Department of Chemistry , University of Warsaw , Żwirki i Wigury 101 , 02-089 Warsaw , Poland
| | - Krzysztof Durka
- Department of Chemistry , Warsaw University of Technology , Noakowskiego 3 , 00-664 Warsaw , Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry , University of Warsaw , Żwirki i Wigury 101 , 02-089 Warsaw , Poland
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