1
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Liu Y, Yu L, She Z, Li L, Ji T, Li Y, Wang Y. Rhodamine 6G-PAH probes for heavy metal: Fluorescence detection, bioimaging, and solid-phase sensing application. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 325:125070. [PMID: 39232313 DOI: 10.1016/j.saa.2024.125070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 08/24/2024] [Accepted: 08/27/2024] [Indexed: 09/06/2024]
Abstract
Four rhodamine 6G-PAH probes with pyrene (R6G-Pyr), anthracene (R6G-Ant), acenaphthene (R6G-Acp) or phenanthrene (R6G-PA) as fluorophore were designed and synthesized for Hg(II) detection. Probe R6G-PA, which had the lowest detection limit of 0.84 nmol/L, displayed the best fluorescence performance as compared to the other three probes. This type of probe had good anti-interference properties against most common metal ions except Cu(II). Metal Cu(II) had a certain quenching effect on the fluorescence generated by Hg(II), with a minimum detection limit of 0.31 nmol/L (for R6G-Acp), indicating its potential practicability for Cu(II) detection. The structure-fluorescence relationship was discussed based on density functional theory (DFT) calculations, and R6G-PA + Hg(II), which had the minimum dihedral angle between polycyclic aromatic rings and rhodamine spiro ring, produced the strongest π-π accumulation and provided the brightest fluorescence. Probe R6G-PA was successfully employed for fluorescence detection of Hg(II) in biological samples. Its solid-phase sensor PS@R6G-PA was developed by immobilizing R6G-PA on PS microspheres for the determination of Hg(II) in water and food samples, with excellent reproducibility and fluorescence "on/off" response. The relative error of the spiked recovery rate was less than 10 %.
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Affiliation(s)
- Yuanyuan Liu
- School of Pharmaceutical and Chemical Engineering, ChengXian College, Southeast University, Nanjing 210088, PR China
| | - Lili Yu
- School of Pharmaceutical and Chemical Engineering, ChengXian College, Southeast University, Nanjing 210088, PR China
| | - Zhuxin She
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
| | - Ling Li
- School of Pharmaceutical and Chemical Engineering, ChengXian College, Southeast University, Nanjing 210088, PR China
| | - Tailong Ji
- School of Pharmaceutical and Chemical Engineering, ChengXian College, Southeast University, Nanjing 210088, PR China
| | - Yi Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China.
| | - Yuqiao Wang
- Research Center for Nano Photoelectrochemistry and Devices, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China.
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2
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El Moutaouakil Ala Allah A, Kariuki BM, Alsubari A, Al-Sulami AI, Allehyani BH, Alsulami WO, Mague JT, Ramli Y. Synthesis, crystal structure and Hirshfeld surface of ethyl 2-[2-(methyl-sulfan-yl)-5-oxo-4,4-diphenyl-4,5-di-hydro-1 H-imidazol-1-yl]acetate (thio-phenytoin derivative). Acta Crystallogr E Crystallogr Commun 2024; 80:926-930. [PMID: 39267872 PMCID: PMC11389683 DOI: 10.1107/s2056989024007345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Accepted: 07/23/2024] [Indexed: 09/15/2024]
Abstract
The di-hydro-imidazole ring in the title mol-ecule, C20H20N2O3S, is slightly distorted and the lone pair on the tri-coordinate nitro-gen atom is involved in intra-ring π bonding. The methyl-sulfanyl substituent lies nearly in the plane of the five-membered ring while the ester substituent is rotated well out of that plane. In the crystal, C-H⋯O hydrogen bonds form inversion dimers, which are connected along the a- and c-axis directions by additional C-H⋯O hydrogen bonds, forming layers parallel to the ac plane. The major contributors to the Hirshfeld surface are C⋯H/H⋯C, O⋯H/H⋯O and S⋯H/H⋯S contacts at 20.5%, 14.7% and 4.9%, respectively.
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Affiliation(s)
| | - Benson M Kariuki
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Abdulsalam Alsubari
- Laboratory of Medicinal Chemistry, Faculty of Clinical Pharmacy, 21 September University, Yemen
| | - Ahlam I Al-Sulami
- University of Jeddah, College of Science, Department of Chemistry, Jeddah 21589, Saudi Arabia
| | - Basmah H Allehyani
- University of Jeddah, College of Science, Department of Chemistry, Jeddah 21589, Saudi Arabia
| | - Wafa O Alsulami
- University of Jeddah, College of Science, Department of Chemistry, Jeddah 21589, Saudi Arabia
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA
| | - Youssef Ramli
- Laboratory of Medicinal Chemistry Drug Sciences Research Center Faculty of Medicine and Pharmacy Mohammed V University in Rabat Morocco
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3
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Bakhite E, Mohamed SK, Lai CH, Subramani K, Marae IS, Abuelhassan S, Soliman AAE, Youssef MSK, Abuelizz HA, Mague JT, Al-Salahi R, El Bakri Y. Synthesis, Crystal Structure, Hirshfeld Surface Analysis, and Computational Approach of a New Pyrazolo[3,4- g]isoquinoline Derivative as Potent against Leucine-Rich Repeat Kinase 2 (LRRK2). ACS OMEGA 2024; 9:30751-30770. [PMID: 39035914 PMCID: PMC11256088 DOI: 10.1021/acsomega.4c03208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024]
Abstract
Ethyl-2-((8-cyano-3,5,9a-trimethyl-1-(4-oxo-4,5-dihydrothiazol-2-yl)-4-phenyl-3a,4,9,9a-tetrahydro-1H-pyrazolo[3,4-g]isoquinolin-7-yl)thio)acetate (5) was synthesized, and its structure was characterized by IR, MS, and NMR (1H and 13C) and verified by a single-crystal X-ray structure determination. Compound 5 adopts a "pincer" conformation. In the crystal, the hydrogen bonds of -H···O, C-H···O, and O-H···S form thick layers of molecules that are parallel to (101). The layers are linked by C-H···π(ring) interactions. The Hirshfeld surface analysis shows that intermolecular hydrogen bonding plays a more important role than both intramolecular hydrogen bonding and π···π stacking in the crystal. The intramolecular noncovalent interactions in 5 were studied by QTAIM, NCI, and DFT-NBO calculations. Based on structural activity relationship studies, leucine-rich repeat kinase 2 (LRRK2) was found to bind 5 and was further subjected to molecular docking studies, molecular dynamics, and ADMET analysis to probe potential drug candidacy.
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Affiliation(s)
- Etify
A. Bakhite
- Department
of Chemistry, Faculty of Science, Assiut
University, Assiut 71516, Egypt
| | - Shaaban Kamel Mohamed
- Chemistry
and Environmental Division, Manchester Metropolitan
University, Manchester M1 5GD, England
- Chemistry
Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Chin-Hung Lai
- Department
of Medical Applied Chemistry, Chung Shan
Medical University, Taichung 40241, Taiwan
- Department
of Medical Education, Chung Shan Medical
University Hospital, Taichung 40201, Taiwan
| | - Karthikeyan Subramani
- Center
for
Healthcare Advancement, Innovation and Research, Vellore Institute of Technology University, Chennai Campus, Chennai 600127, India
| | - Islam S. Marae
- Department
of Chemistry, Faculty of Science, Assiut
University, Assiut 71516, Egypt
| | - Suzan Abuelhassan
- Department
of Chemistry, Faculty of Science, Assiut
University, Assiut 71516, Egypt
| | | | | | - Hatem A. Abuelizz
- Department
of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Joel T. Mague
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Rashad Al-Salahi
- Department
of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Youness El Bakri
- Department
of Theoretical and Applied Chemistry, South
Ural State University, Lenin prospect 76, Chelyabinsk 454080, Russian Federation
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4
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Cui Y, Cao J, Lin J, Li C, Yao J, Liu K, Hou A, Guo Z, Zhao J, Liu Q. Advancing nonlinear optics: discovery and characterization of new non-centrosymmetric phenazine-based halides. Dalton Trans 2024; 53:10235-10243. [PMID: 38828765 DOI: 10.1039/d4dt01096e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Organic-inorganic metal halides (OIMHs) have drawn considerable attention due to their remarkable optoelectronic properties and substantial promise for nonlinear optical applications. In this research, phenazine has been selected as the organic cation because of its π-conjugated feature. Three compounds, (C12H9N2)PbCl3, (C12H9N2)SbCl4, and (C12H9N2)2InBr4·Br, were synthesized. Initial space group assignments were centrosymmetric for (C12H9N2)PbCl3 and (C12H9N2)SbCl4. However, under 1550 nm laser excitation, (C12H9N2)PbCl3 and (C12H9N2)SbCl4 exhibited second harmonic generation intensities ∼1.7 times greater than that of the benchmark KH2PO4. Structural reevaluation ultimately confirmed non-centrosymmetric P1 and P21 space groups for (C12H9N2)PbCl3 and (C12H9N2)SbCl4, respectively. Upon excitation at 335 nm and 470 nm, (C12H9N2)PbCl3, (C12H9N2)SbCl4, and (C12H9N2)2InBr4·Br emit fluorescence at room temperature. (C12H9N2)2InBr4·Br exhibits reversible phase transitions, showing potential for phase change energy storage. Our research underscores the critical role of comprehensive experimental validation in determining the precise crystallographic space groups and reveals the extensive potential of OIMHs as versatile candidates for advanced optoelectronic applications.
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Affiliation(s)
- Yibo Cui
- The Beijing Municipal Key Laboratory of New Energy Materials and Technologies, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China.
| | - Jindong Cao
- The Beijing Municipal Key Laboratory of New Energy Materials and Technologies, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China.
| | - Jiawei Lin
- The Beijing Municipal Key Laboratory of New Energy Materials and Technologies, School of Materials Sciences and Engineering and Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Chunxiao Li
- Center for Crystal Research and Development, Key Laboratory of Functional Crystals and Laser Technology, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jiyong Yao
- Center for Crystal Research and Development, Key Laboratory of Functional Crystals and Laser Technology, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Kunjie Liu
- The Beijing Municipal Key Laboratory of New Energy Materials and Technologies, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China.
| | - An Hou
- The Beijing Municipal Key Laboratory of New Energy Materials and Technologies, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China.
| | - Zhongnan Guo
- The Beijing Municipal Key Laboratory of New Energy Materials and Technologies, School of Materials Sciences and Engineering and Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Jing Zhao
- The Beijing Municipal Key Laboratory of New Energy Materials and Technologies, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China.
| | - Quanlin Liu
- The Beijing Municipal Key Laboratory of New Energy Materials and Technologies, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China.
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5
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Thompson AL, White NG. Hydrogen atoms in supramolecular chemistry: a structural perspective. Where are they, and why does it matter? Chem Soc Rev 2023; 52:6254-6269. [PMID: 37599586 DOI: 10.1039/d3cs00516j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Hydrogen bonding interactions are ubiquitous across the biochemical and chemical sciences, and are of particular interest to supramolecular chemists. They have been used to assemble hydrogen bonded polymers, cages and frameworks, and are the functional motif in many host-guest systems. Single crystal X-ray diffraction studies are often used as a key support for proposed structures, although this presents challenges as hydrogen atoms interact only weakly with X-rays. In this Tutorial Review, we discuss the information that can be gleaned about hydrogen bonding interactions through crystallographic experiments, key limitations of the data, and emerging techniques to overcome these limitations.
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Affiliation(s)
- Amber L Thompson
- Chemical Crystallography, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK.
| | - Nicholas G White
- Research School of Chemistry, The Australian National University, Canberra 2601, ACT, Australia.
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6
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Faris A, Edder Y, Hdoufane I, Ait Lahcen I, Saadi M, El Ammari L, Berraho M, Cherqaoui D, Boualy B, Karim A. Syntheses, characterization and DFT studies of two new (π-allyl) palladium(II) complexes of β-8,9-dihydrohimachalene. J COORD CHEM 2023. [DOI: 10.1080/00958972.2023.2194013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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7
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Jha KK, Kleemiss F, Chodkiewicz ML, Dominiak PM. Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time-accuracy trade-off. J Appl Crystallogr 2023; 56:116-127. [PMID: 36777135 PMCID: PMC9901929 DOI: 10.1107/s1600576722010883] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/13/2022] [Indexed: 12/24/2022] Open
Abstract
Aspherical atom refinement is the key to achieving accurate structure models, displacement parameters, hydrogen-bond lengths and analysis of weak interactions, amongst other examples. There are various quantum crystallographic methods to perform aspherical atom refinement, including Hirshfeld atom refinement (HAR) and transferable aspherical atom model (TAAM) refinement. Both HAR and TAAM have their limitations and advantages, the former being more accurate and the latter being faster. With the advent of non-spherical atoms in Olex2 (NoSpherA2), it is now possible to overcome some limitations, like treating disorder, twinning and network structures, in aspherical refinements using HAR, TAAM or both together. TAAM refinement in NoSpherA2 showed significant improvement in refinement statistics compared with independent atom model (IAM) refinements on a diverse set of X-ray diffraction data. The sensitivity of TAAM towards poor data quality and disorder was observed in terms of higher refinement statistics for such structures. A comparison of IAM with TAAM and HAR in NoSpherA2 indicated that the time taken by TAAM refinements was of the same order of magnitude as that taken by IAM, while in HAR the time taken using a minimal basis set was 50 times higher than for IAM and rapidly increased with increasing size of the basis sets used. The displacement parameters for hydrogen and non-hydrogen atoms were very similar in both HAR and TAAM refinements. The hydrogen-bond lengths were slightly closer to neutron reference values in the case of HAR with higher basis sets than in TAAM. To benefit from the advantages of each method, a new hybrid refinement approach has been introduced, allowing a combination of IAM, HAR and TAAM in one structure refinement. Refinement of coordination complexes involving metal-organic compounds and network structures such as covalent organic frameworks and metal-organic frameworks is now possible in a hybrid mode such as IAM-TAAM or HAR-TAAM, where the metal atoms are treated via either the IAM or HAR method and the organic part via TAAM, thus reducing the computational costs without compromising the accuracy. Formal charges on the metal and ligand can also be introduced in hybrid-mode refinement.
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Affiliation(s)
- Kunal Kumar Jha
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
| | - Florian Kleemiss
- Fakultät für Chemie und Pharmazie, Universität Regensburg, Universitätstrasse 31, Regensburg, Bayern 93053, Germany
| | - Michał Leszek Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
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8
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Shi PC, Xiao JL, Deng WF, Guo Q, Jin L, Zhou ZX, Ji C. Synthesis, Crystal Structure, and DFT Study of (5-Bromo-2-fluorophenyl)-2-pyrazinylmethanone. RUSS J GEN CHEM+ 2023. [DOI: 10.1134/s1070363223010139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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9
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Ivanov SM, Koltun DS. Crystal Structure Analysis of 4-Oxo, 4-hydroxy- and 4-alkyl-7-bromopyrazolo[5,1- c][1,2,4]triazines. JOURNAL OF CHEMICAL CRYSTALLOGRAPHY 2022; 53:1-12. [PMID: 36567741 PMCID: PMC9759054 DOI: 10.1007/s10870-022-00973-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
The crystal structures of 8-R1-7-bromo-3-tert-butyl-1-R2-pyrazolo[5,1-c][1,2,4]triazin-4(1H)-ones 1a-c, 2a,c (R1 = CN, CO2Et, NO2, R2 = H, 1:1 and 3:1 solvates with DMSO; R1 = CN, CO2Et, R2 = CH2Boc), 8-R1-7-bromo-3-tert-butyl-1-R2-1,4-dihydropyrazolo[5,1-c][1,2,4]triazin-4-ols 3a,b (R1 = CN, R2 = n-Bu; R1 = Br, R2 = CH2Boc), 1,4-dihydro- and aromatic 7-R3-3-tert-butyl-4-R4-8-methylpyrazolo[5,1-c][1,2,4]triazines 5a,b, 6 (R3 = H, R4 = n-Pr; R3 = Br, R4 = n-Bu) were investigated by X-ray diffraction analysis. The structural preferences and different packing modes based on the intermolecular interactions were analyzed by the Hirshfeld surface and energy framework analysis. Graphical Abstract The crystal structures of ten 3-tert-butyl-4-oxo, 4-hydroxy- and 4-alkyl-7-bromopyrazolo[5,1-c][1,2,4]triazines including non-solvated, 1:1 and 3:1 solvates with DMSO were investigated by single crystal X-ray diffraction, Hirshfeld surface and energy framework analyses. Supplementary Information The online version contains supplementary material available at 10.1007/s10870-022-00973-x.
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Affiliation(s)
- Sergey M. Ivanov
- N.D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, Leninsky Prospekt, 47., Moscow, Russia 119991
| | - Denis S. Koltun
- N.D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, Leninsky Prospekt, 47., Moscow, Russia 119991
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10
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Electron density is not spherical: the many applications of the transferable aspherical atom model. Comput Struct Biotechnol J 2022; 20:6237-6243. [DOI: 10.1016/j.csbj.2022.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/20/2022] Open
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11
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Selmi A, Said K, Nasri S, Tachoua W. Crystal Structure, Magnetic Study, and Antidiabetic Activity of Ni(II) Complex with N,O‐Donors Ligands. CRYSTAL RESEARCH AND TECHNOLOGY 2022. [DOI: 10.1002/crat.202200102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ahmed Selmi
- Laboratory of Physical Chemistry of Materials Faculty of Sciences of Monastir University of Monastir Monastir 5019 Tunisia
| | - Khemais Said
- Organic Chemistry Laboratory (LR17/ES08) Department of Chemistry Faculty of Sciences of Sfax University of Sfax Sfax 3018 Tunisia
| | - Saber Nasri
- Laboratory of Spectroscopic Characterization and Optical Materials, Physics Department Faculty of Science of Sfax University of Sfax Sfax 3018 Tunisia
| | - Wafa Tachoua
- Laboratory Nature and Life Sciences Department Benyoucef Benkhedda University Didouche Mourad Algiers 16000 Algeria
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Jha KK, Gruza B, Sypko A, Kumar P, Chodkiewicz ML, Dominiak PM. Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB. J Chem Inf Model 2022; 62:3752-3765. [PMID: 35943747 PMCID: PMC9400107 DOI: 10.1021/acs.jcim.2c00144] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
A fast and accurate operational model of electron density
is crucial
in many scientific disciplines including crystallography, molecular
biology, pharmaceutical, and structural chemistry. In quantum crystallography,
the aspherical refinement of crystal structures is becoming increasingly
popular because of its accurate description in terms of physically
meaningful properties. The transferable aspherical atom model (TAAM)
is quick and precise, though it requires a robust algorithm for atom
typing and coverage of the most popular atom types present in small
organic molecules. Thus, the University at Buffalo Databank (UBDB)
has been renamed to the Multipolar Atom Types from Theory and Statistical
clustering (MATTS) data bank, broadened, restructured, and implemented
into the software DiSCaMB with 651 atom types obtained from 2316 small-molecule
crystal structures containing C, H, N, O, P, S, F, Cl, and Br atoms.
MATTS2021 data bank now covers most of the small molecules, peptides,
RNA, DNA, and some frequently occurring cations and anions in biological,
pharmaceutical, and organic materials, including the majority of known
crystal structures composed of the above elements. The multipole model
parameters (Pval, κ, κ′, Plm) obtained for different
atom types were greatly influenced by neighboring atom types, hybridization,
geometrical strain in the ring system, and charges on the molecule.
Contrary to previous findings, the atoms showing variable oxidation
states and ions deviate from the linear dependence of monopole-derived
charges on the expansion–contraction κ parameter.
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Affiliation(s)
- Kunal Kumar Jha
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Barbara Gruza
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Aleksandra Sypko
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Prashant Kumar
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Michał Leszek Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
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Byrne NM, Schofield MH, Cahill CL. A novel symmetric pyrazine (pyz)-bridged uranyl dimer [UO 2Cl 3(H 2O)(Pyz) 0.5] 22-: synthesis, structure and computational analysis. Dalton Trans 2022; 51:11013-11020. [PMID: 35791868 DOI: 10.1039/d2dt01486f] [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
Herein we report on the synthesis of (HPyz+)2[UO2Cl3(H2O)(Pyz)0.5]2·2H2O which features a novel pyrazine-bridged uranyl dimer, [UO2Cl3(H2O)(Pyz)0.5]22-. A rigorous computational and experimental analysis of this compound was performed to fully explore the influence of coordination on the electronic structure and potential charge-transfer characteristics of this dimer, revealing a delocalized π-system across the bridging pyrazine and the axial components of both uranyl centers. Electrostatic surface potentials, used to rationalize the observed assembly, indicate a decreased basicity of the uranyl oxo versus [UO2Cl4]2-, and signify a lessened capacity for the terminal -yl oxos of the [UO2Cl3(H2O)(Pyz)0.5]22- dimer to participate in supramolecular assembly. A combined density functional theory (DFT) and quantum theory of atoms in molecules (QTAIM) analysis further evidenced an increase in UO bond strengths within the dimer, which is supported by a blue shift in the characteristic Raman-active uranyl symmetric stretch (ν1) with respect to the more typically observed [UO2Cl4]2-.
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Affiliation(s)
- Nicole M Byrne
- Department of Chemistry, The George Washington University, 800 22nd St NW, Suite 4000, Washington, D.C., 20052, USA.
| | - Mark H Schofield
- Department of Chemistry, The George Washington University, 800 22nd St NW, Suite 4000, Washington, D.C., 20052, USA.
| | - Christopher L Cahill
- Department of Chemistry, The George Washington University, 800 22nd St NW, Suite 4000, Washington, D.C., 20052, USA.
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14
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Duneş G, Soran A, Silvestru C. Organopnictogen(III) bis(arylthiolates) containing NCN-aryl pincer ligands: from synthesis and characterization to reactivity. Dalton Trans 2022; 51:10406-10419. [PMID: 35762306 DOI: 10.1039/d2dt01436j] [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
Salt elimination reactions between organopnictogen(III) dichlorides, RPnCl2 [R1 = 2,6-(Me2NCH2)2C6H3, Pn = Sb (1), Bi (2); R2 = 2,6-{MeN(CH2CH2)2NCH2}2C6H3, Pn = Sb (3), Bi (4); R3 = 2,6-{O(CH2CH2)2NCH2}2C6H3, Pn = Sb (5), Bi (6)] and 2 equivalents of KSC6H3Me2-2,6 afforded the isolation of a series of new NCN-chelated monoorganopnictogen(III) bis(arylthiolates), RPn(SC6H3Me2-2,6)2 [R1, Pn = Sb (7), Bi (8); R2, Pn = Sb (9), Bi (10); R3, Pn = Sb (11), Bi (12)]. Compounds 7 and 8 are unstable upon exposure to a dry O2 atmosphere and their aerobic decomposition yields the monoorganopnictogen(III) oxides, cyclo-[2,6-(Me2NCH2)2C6H3Pn(μ-O)]2 [Pn = Sb (13), Bi (14)] with concomitant formation of the corresponding disulfide, ArS-SAr (Ar = C6H3Me2-2,6). The oxidative addition of elemental sulfur or selenium to 7 undergoes a similar reaction path and gives stable heterocyclic species cyclo-[2,6-(Me2NCH2)2C6H3Sb(μ-E)]2 [E = S (15), Se (16)]. The reaction of 12 with I2 (1 : 1 molar ratio) gives the diiodide [2,6-{O(CH2CH2)2NCH2}2C6H3]BiI2 (17), along with the S-S oxidative coupling by-product, ArS-SAr. The use of an excess of iodine affords the crystallization of a 2 : 1 iodine adduct of 17 (17·0.5I2), built through halogen bonding. All new compounds were characterized by multinuclear NMR spectroscopy and ESI-MS as well as single crystal X-ray diffraction (except compounds 9 and 10).
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Affiliation(s)
- Gabriel Duneş
- Department of Chemistry, Supramolecular Organic and Organometallic Chemistry Centre (SOOMCC), Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, 11 Arany Janos, 400028 Cluj-Napoca, Romania.
| | - Albert Soran
- Department of Chemistry, Supramolecular Organic and Organometallic Chemistry Centre (SOOMCC), Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, 11 Arany Janos, 400028 Cluj-Napoca, Romania.
| | - Cristian Silvestru
- Department of Chemistry, Supramolecular Organic and Organometallic Chemistry Centre (SOOMCC), Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, 11 Arany Janos, 400028 Cluj-Napoca, Romania.
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15
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Akyeva AY, Kansuzyan AV, Vukich KS, Kuhn L, Saverina EA, Minyaev ME, Pechennikov VM, Egorov MP, Alabugin IV, Vorobyev SV, Syroeshkin MA. Remote Stereoelectronic Effects in Pyrrolidone- and Caprolactam-Substituted Phenols: Discrepancies in Antioxidant Properties Evaluated by Electrochemical Oxidation and H-Atom Transfer Reactivity. J Org Chem 2022; 87:5371-5384. [PMID: 35363496 DOI: 10.1021/acs.joc.2c00207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New antioxidants are commonly evaluated via two main approaches, i.e., the ability to donate an electron and the ability to intercept free radicals. We compared these approaches by evaluating the properties of 11 compounds containing both antioxidant moieties (mono- and polyphenols) and auxiliary pharmacophores (pyrrolidone and caprolactam). Several common antioxidants, such as butylated hydroxytoluene (BHT), 2,3,5-trimethylphenol (TMP), quercetin, and dihydroquercetin, were added for comparison. The antioxidant properties of these compounds were determined by their rates of reaction with 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical and their oxidation potentials from cyclic voltammetry. Although these methods test different chemical properties, their results correlate reasonably well. However, several exceptions exist where the two methods give opposite predictions! One of them is the different behavior of mono- and polyphenols: polyphenols can react with DPPH more than an order of magnitude faster than monophenols of a similar oxidation potential. The second exception stems from the size of a "bystander" lactam ring at the benzylic position. Although the phenols with a seven-membered lactam ring are harder to oxidize, the sterically nonhindered compounds react with DPPH about 2× faster than the analogous five-membered lactams. The limitations of computational methods, especially those based on a single parameter, are also evaluated and discussed.
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Affiliation(s)
- Anna Ya Akyeva
- N.D. Zelinsky Institute of Organic Chemistry, 119991 Moscow Russia
| | | | - Katarina S Vukich
- N.D. Zelinsky Institute of Organic Chemistry, 119991 Moscow Russia.,I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Leah Kuhn
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | | | | | | | - Mikhail P Egorov
- N.D. Zelinsky Institute of Organic Chemistry, 119991 Moscow Russia
| | - Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Stepan V Vorobyev
- Gubkin Russian State University of Oil and Gas, 65 Leninsky Prospect, 119991 Moscow, Russia
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16
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Fodor A, Gualtieri M, Zeller M, Tarasco E, Klein MG, Fodor AM, Haynes L, Lengyel K, Forst SA, Furgani GM, Karaffa L, Vellai T. Type Strains of Entomopathogenic Nematode-Symbiotic Bacterium Species, Xenorhabdus szentirmaii (EMC) and X. budapestensis (EMA), Are Exceptional Sources of Non-Ribosomal Templated, Large-Target-Spectral, Thermotolerant-Antimicrobial Peptides (by Both), and Iodinin (by EMC). Pathogens 2022; 11:pathogens11030342. [PMID: 35335666 PMCID: PMC8950435 DOI: 10.3390/pathogens11030342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 01/26/2023] Open
Abstract
Antimicrobial multidrug resistance (MDR) is a global challenge, not only for public health, but also for sustainable agriculture. Antibiotics used in humans should be ruled out for use in veterinary or agricultural settings. Applying antimicrobial peptide (AMP) molecules, produced by soil-born organisms for protecting (soil-born) plants, seems a preferable alternative. The natural role of peptide-antimicrobials, produced by the prokaryotic partner of entomopathogenic-nematode/bacterium (EPN/EPB) symbiotic associations, is to sustain monoxenic conditions for the EPB in the gut of the semi-anabiotic infective dauer juvenile (IJ) EPN. They keep pathobiome conditions balanced for the EPN/EPB complex in polyxenic (soil, vanquished insect cadaver) niches. Xenorhabdus szentirmaii DSM16338(T) (EMC), and X. budapestensis DSM16342(T) (EMA), are the respective natural symbionts of EPN species Steinernema rarum and S. bicornutum. We identified and characterized both of these 15 years ago. The functional annotation of the draft genome of EMC revealed 71 genes encoding non-ribosomal peptide synthases, and polyketide synthases. The large spatial Xenorhabdus AMP (fabclavine), was discovered in EMA, and its biosynthetic pathway in EMC. The AMPs produced by EMA and EMC are promising candidates for controlling MDR prokaryotic and eukaryotic pathogens (bacteria, oomycetes, fungi, protozoa). EMC releases large quantity of iodinin (1,6-dihydroxyphenazine 5,10-dioxide) in a water-soluble form into the media, where it condenses to form spectacular water-insoluble, macroscopic crystals. This review evaluates the scientific impact of international research on EMA and EMC.
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Affiliation(s)
- András Fodor
- Department of Genetics, Eötvös University, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary; (A.M.F.); (K.L.); or (G.M.F.); or (T.V.)
- Department of Genetics, University of Szeged, Középfasor 52, H-6726 Szeged, Hungary
- Correspondence: ; Tel.: +36-(30)-490-9294
| | - Maxime Gualtieri
- Nosopharm, 110 Allée Charles Babbage, Espace Innovation 2, 30000 Nîmes, France;
| | - Matthias Zeller
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA;
| | - Eustachio Tarasco
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy;
- Institute for Sustainable Plant Protection of CNR, Via Amendola 122/D, 70126 Bari, Italy
| | - Michael G. Klein
- USDA-ARS & Department of Entomology, The Ohio State University, 13416 Claremont Ave, Cleveland, OH 44130, USA;
| | - Andrea M. Fodor
- Department of Genetics, Eötvös University, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary; (A.M.F.); (K.L.); or (G.M.F.); or (T.V.)
| | - Leroy Haynes
- Department of Chemistry, The College of Wooster, Wooster, OH 44691, USA;
| | - Katalin Lengyel
- Department of Genetics, Eötvös University, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary; (A.M.F.); (K.L.); or (G.M.F.); or (T.V.)
- National Institute of Pharmacy and Nutrition (NIPN), Zrinyi utca 3, H-1051 Budapest, Hungary
| | - Steven A. Forst
- Department of Biological Sciences, University of Wisconsin-Milwaukee, P.O. Box 413, Milwaukee, WI 53201, USA;
| | - Ghazala M. Furgani
- Department of Genetics, Eötvös University, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary; (A.M.F.); (K.L.); or (G.M.F.); or (T.V.)
- Department of Plant Protection, Faculty of Agriculture, University of Tripoli, Tripoli P.O. Box 13793, Libya
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem Tér 1, H-4032 Debrecen, Hungary;
- Institute of Metagenomics, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Tibor Vellai
- Department of Genetics, Eötvös University, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary; (A.M.F.); (K.L.); or (G.M.F.); or (T.V.)
- MTA-ELTE Genetics Research Group, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary
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17
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Uhrmacher F, Elbert SM, Rominger F, Mastalerz M. Synthesis of Large [2+3] Salicylimine Cages with Embedded Metal‐Salphen Units. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202100864] [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)
- Fabian Uhrmacher
- Organisch-Chemisches Institut Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Sven M. Elbert
- Organisch-Chemisches Institut Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Frank Rominger
- Organisch-Chemisches Institut Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Michael Mastalerz
- Organisch-Chemisches Institut Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Germany
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18
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Haj Hassani Sohi T, Maass F, Czekelius C, Suta M, Vasylyeva V. Co-crystallization of organic chromophore roseolumiflavin and effect on its optical characteristics. CrystEngComm 2022. [DOI: 10.1039/d2ce00589a] [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
Three roseolumiflavin co-crystals are designed to elucidate the accessibility of flavins for the targeted tuning of luminescence in the solid state.
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Affiliation(s)
- Takin Haj Hassani Sohi
- Laboratory for Molecular Crystal Engineering, Department of Inorganic Chemistry and Structural Chemistry I, Heinrich-Heine-University Duesseldorf, Universitaetstr. 1, 40225 Duesseldorf, Germany
| | - Felix Maass
- Laboratory for Molecular Crystal Engineering, Department of Inorganic Chemistry and Structural Chemistry I, Heinrich-Heine-University Duesseldorf, Universitaetstr. 1, 40225 Duesseldorf, Germany
| | - Constantin Czekelius
- Laboratory for Asymmetric Synthesis and Catalysis, Department of Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-University Duesseldorf, Universitaetstr. 1, 40225 Duesseldorf, Germany
| | - Markus Suta
- Laboratory for Inorganic Photoactive Materials, Department of Inorganic Chemistry and Structural Chemistry II, Heinrich-Heine-University Duesseldorf, Universitaetstr. 1, 40225 Duesseldorf, Germany
| | - Vera Vasylyeva
- Laboratory for Molecular Crystal Engineering, Department of Inorganic Chemistry and Structural Chemistry I, Heinrich-Heine-University Duesseldorf, Universitaetstr. 1, 40225 Duesseldorf, Germany
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19
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Saito S, Katamura T, Tsukazaki R, Fujisawa A, Yoshigoe Y, Mutoh Y. The Aza-Prins Reaction of 1,2-Dicarbonyl Compounds with 3-Vinyltetrahydroquinolines: Application to the Synthesis of Polycyclic Spirooxindole Derivatives. J Org Chem 2021; 86:16425-16433. [PMID: 34792347 PMCID: PMC8650011 DOI: 10.1021/acs.joc.1c01785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Indexed: 11/28/2022]
Abstract
The aza-Prins reaction of 6,7-dimethoxy-3-vinyl-1,2,3,4-tetrahydroquinoline (1) with 1,2-dicarbonyl compounds proceeded smoothly in the presence of HCl, and the corresponding tricyclic benzazocines were isolated in yields of 20-86%. The reaction proceeded in a stereoselective manner, and the formation of the 2,4-trans isomer was observed. The reaction of 1 with an enantiopure ketoester gave the corresponding tricyclic benzazocine as a mixture of diastereomers. The diastereomers were easily separated and converted to enantiopure tricyclic benzazocines. The synthesis of spirooxindole derivatives was achieved by the reaction of 1 with isatin derivatives.
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Affiliation(s)
- Shinichi Saito
- Department of Chemistry,
Faculty of Science, Tokyo University of
Science, 1-3 Kagurazaka, Shinjuku, Tokyo 162-8601, Japan
| | - Tomohiro Katamura
- Department of Chemistry,
Faculty of Science, Tokyo University of
Science, 1-3 Kagurazaka, Shinjuku, Tokyo 162-8601, Japan
| | - Rei Tsukazaki
- Department of Chemistry,
Faculty of Science, Tokyo University of
Science, 1-3 Kagurazaka, Shinjuku, Tokyo 162-8601, Japan
| | - Akito Fujisawa
- Department of Chemistry,
Faculty of Science, Tokyo University of
Science, 1-3 Kagurazaka, Shinjuku, Tokyo 162-8601, Japan
| | - Yusuke Yoshigoe
- Department of Chemistry,
Faculty of Science, Tokyo University of
Science, 1-3 Kagurazaka, Shinjuku, Tokyo 162-8601, Japan
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20
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Yang WQ, Tang W, Huang XJ, Song JG, Li YY, Xiong Y, Fan CL, Wu ZL, Wang Y, Ye WC. Quassinoids from the Roots of Eurycoma longifolia and Their Anti-Proliferation Activities. Molecules 2021; 26:molecules26195939. [PMID: 34641483 PMCID: PMC8512324 DOI: 10.3390/molecules26195939] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 11/23/2022] Open
Abstract
A phytochemical investigation on the roots of medicinal plant Eurycoma longifolia resulted in the isolation of 10 new highly oxygenated C20 quassinoids longifolactones G‒P (1–10), along with four known ones (11–14). Their chemical structures and absolute configurations were unambiguously elucidated on the basis of comprehensive spectroscopic analysis and X-ray crystallographic data. Notably, compound 1 is a rare pentacyclic C20 quassinoid featuring a densely functionalized 2,5-dioxatricyclo[5.2.2.04,8]undecane core. Compound 4 represents the first example of quassinoids containing a 14,15-epoxy functionality, and 7 features an unusual α-oriented hydroxyl group at C-14. All isolated compounds were evaluated for their anti-proliferation activities on human leukemia cells. Among the isolates, compounds 5, 12, 13, and 14 potently inhibited the in vitro proliferation of K562 and HL-60 cells with IC50 values ranging from 2.90 to 8.20 μM.
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Affiliation(s)
- Wei-Qun Yang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China;
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China; (W.T.); (X.-J.H.); (J.-G.S.); (Y.-Y.L.); (Y.X.); (C.-L.F.); (W.-C.Y.)
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Wei Tang
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China; (W.T.); (X.-J.H.); (J.-G.S.); (Y.-Y.L.); (Y.X.); (C.-L.F.); (W.-C.Y.)
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Xiao-Jun Huang
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China; (W.T.); (X.-J.H.); (J.-G.S.); (Y.-Y.L.); (Y.X.); (C.-L.F.); (W.-C.Y.)
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Jian-Guo Song
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China; (W.T.); (X.-J.H.); (J.-G.S.); (Y.-Y.L.); (Y.X.); (C.-L.F.); (W.-C.Y.)
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Yue-Yue Li
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China; (W.T.); (X.-J.H.); (J.-G.S.); (Y.-Y.L.); (Y.X.); (C.-L.F.); (W.-C.Y.)
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Yu Xiong
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China; (W.T.); (X.-J.H.); (J.-G.S.); (Y.-Y.L.); (Y.X.); (C.-L.F.); (W.-C.Y.)
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Chun-Lin Fan
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China; (W.T.); (X.-J.H.); (J.-G.S.); (Y.-Y.L.); (Y.X.); (C.-L.F.); (W.-C.Y.)
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Zhen-Long Wu
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China; (W.T.); (X.-J.H.); (J.-G.S.); (Y.-Y.L.); (Y.X.); (C.-L.F.); (W.-C.Y.)
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China
- Correspondence: (Z.-L.W.); (Y.W.); Tel.: +86-20-8522-1559 (Y.W.)
| | - Ying Wang
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China; (W.T.); (X.-J.H.); (J.-G.S.); (Y.-Y.L.); (Y.X.); (C.-L.F.); (W.-C.Y.)
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China
- Correspondence: (Z.-L.W.); (Y.W.); Tel.: +86-20-8522-1559 (Y.W.)
| | - Wen-Cai Ye
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China; (W.T.); (X.-J.H.); (J.-G.S.); (Y.-Y.L.); (Y.X.); (C.-L.F.); (W.-C.Y.)
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China
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21
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Byrne NM, Schofield MH, Nicholas AD, Cahill CL. Bimetallic uranyl/cobalt(II) isothiocyanates: structure, property and spectroscopic analysis of homo- and heterometallic phases. Dalton Trans 2021; 50:9158-9172. [PMID: 34115090 DOI: 10.1039/d1dt01464a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the synthesis and characterization of a family of UO22+/Co2+ isothiocyanate materials containing [UO2(NCS)5]3- and/or [Co(NCS)4]2- building units charged balanced by tetramethylammonium cations and assembled via SS or SOyl non-covalent interactions (NCIs), namely (C4H12N)3[UO2(NCS)5], (C4H12N)2[Co(NCS)4], and (C4H12N)5[Co(NCS)4][UO2(NCS)5]. The homometallic uranyl phase preferentially assembles via SS interactions, whereas in the heterometallic phase SOyl interactions are predominant. The variation in assembly mode is explored using electrostatic surfaces potentials, revealing that the pendant -NCS ligands of the [Co(NCS)4]2- anion is capable of outcompeting those of the [UO2(NCS)5]3- anion. Notably, the heterometallic phase displays atypical blue shifting of the uranyl symmetric stretch in the Raman spectra, which is in contrast to many other compounds featuring non-covalent interactions at uranyl oxygen atoms. A combined experimental and computational (density functional theory and natural bond orbital analyses) approach revealed that coupling of the uranyl symmetric stretch with isothiocyanate modes of equatorial -NCS ligands was responsible for the atypical blue shift in the heterometallic phase.
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Affiliation(s)
- Nicole M Byrne
- Department of Chemistry, The George Washington University, 800 22nd St NW, Suite 4000, Washington, D.C. 20052, USA.
| | - Mark H Schofield
- Department of Chemistry, The George Washington University, 800 22nd St NW, Suite 4000, Washington, D.C. 20052, USA.
| | - Aaron D Nicholas
- Department of Chemistry, The George Washington University, 800 22nd St NW, Suite 4000, Washington, D.C. 20052, USA.
| | - Christopher L Cahill
- Department of Chemistry, The George Washington University, 800 22nd St NW, Suite 4000, Washington, D.C. 20052, USA.
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22
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Synthesis, structural characterization and antimycobacterial evaluation of several halogenated non-nitro benzothiazinones. Med Chem Res 2021; 30:1523-1533. [PMID: 34131377 PMCID: PMC8192043 DOI: 10.1007/s00044-021-02735-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/28/2021] [Indexed: 10/25/2022]
Abstract
8-Nitro-1,3-benzothiazin-4-ones (BTZs), with BTZ043 and PBTZ169 as the most advanced compounds, represent a new class of potent antitubercular agents, which irreversibly inhibit decaprenylphosphoryl-β-d-ribose-2'-epimerase (DprE1), an enzyme crucial for cell wall synthesis in the pathogen Mycobacterium tuberculosis. Synthesis, structural characterization and in vitro testing against Mycobacterium aurum DSM 43999 and M. tuberculosis H37Rv of halogenated 2-(4-ethoxycarbonylpiperazin-1-yl)-1,3-benzothiazin-4-ones lacking a nitro group are reported. X-ray crystallography reveals that the structure of the BTZ scaffold can significantly deviate from planarity. In contrast to recent reports, the results of the present study indicate that further investigation of halogenated non-nitro BTZs for antitubercular activity is less than a promising approach.
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23
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Dittrich B. On modelling disordered crystal structures through restraints from molecule-in-cluster computations, and distinguishing static and dynamic disorder. IUCRJ 2021; 8:305-318. [PMID: 33708406 PMCID: PMC7924241 DOI: 10.1107/s2052252521000531] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
Distinguishing disorder into static and dynamic based on multi-temperature X-ray or neutron diffraction experiments is the current state of the art, but is only descriptive, not predictive. Here, several disordered structures are revisited from the Cambridge Crystallographic Data Center 'drug subset', the Cambridge Structural Database and own earlier work, where experimental intensities of Bragg diffraction data were available. Using the molecule-in-cluster approach, structures with distinguishable conformations were optimized separately, as extracted from available or generated disorder models of the respective disordered crystal structures. Re-combining these 'archetype structures' by restraining positional and constraining displacement parameters for conventional least-squares refinement, based on the optimized geometries, then often achieves a superior fit to the experimental diffraction data compared with relying on experimental information alone. It also simplifies and standardizes disorder refinement. Ten example structures were analysed. It is observed that energy differences between separate disorder conformations are usually within a small energy window of RT (T = crystallization temperature). Further computations classify disorder into static or dynamic, using single experiments performed at one single temperature, and this was achieved for propionamide.
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Affiliation(s)
- Birger Dittrich
- Novartis Campus, Novartis Pharma AG, Postfach, Basel, CH-4002, Switzerland
- Mathematisch-Naturwissenschaftliche Fakultät, Universität Zürich, Winterthurerstrasse 190, Zürich, CH-8057, Switzerland
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Kleemiss F, Dolomanov OV, Bodensteiner M, Peyerimhoff N, Midgley L, Bourhis LJ, Genoni A, Malaspina LA, Jayatilaka D, Spencer JL, White F, Grundkötter-Stock B, Steinhauer S, Lentz D, Puschmann H, Grabowsky S. Accurate crystal structures and chemical properties from NoSpherA2. Chem Sci 2020; 12:1675-1692. [PMID: 34163928 PMCID: PMC8179328 DOI: 10.1039/d0sc05526c] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/06/2020] [Indexed: 12/21/2022] Open
Abstract
The relationship between the structure and the properties of a drug or material is a key concept of chemistry. Knowledge of the three-dimensional structure is considered to be of such importance that almost every report of a new chemical compound is accompanied by an X-ray crystal structure - at least since the 1970s when diffraction equipment became widely available. Crystallographic software of that time was restricted to very limited computing power, and therefore drastic simplifications had to be made. It is these simplifications that make the determination of the correct structure, especially when it comes to hydrogen atoms, virtually impossible. We have devised a robust and fast system where modern chemical structure models replace the old assumptions, leading to correct structures from the model refinement against standard in-house diffraction data using no more than widely available software and desktop computing power. We call this system NoSpherA2 (Non-Spherical Atoms in Olex2). We explain the theoretical background of this technique and demonstrate the far-reaching effects that the improved structure quality that is now routinely available can have on the interpretation of chemical problems exemplified by five selected examples.
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Affiliation(s)
- Florian Kleemiss
- Universität Bern, Departement für Chemie und Biochemie Freiestrasse 3 3012 Bern Switzerland
| | | | - Michael Bodensteiner
- Universität Regensburg, Fakultät für Chemie und Pharmazie, Universitätsstr. 31 93053 Regensburg Germany
| | - Norbert Peyerimhoff
- Durham University, Department of Mathematical Sciences South Road Durham DH1 3LE UK
| | - Laura Midgley
- Durham University, Department of Mathematical Sciences South Road Durham DH1 3LE UK
| | - Luc J Bourhis
- Bruker France 4 Allée Lorentz, Champs-sur-Marne 77447 Marne-la-Vallée cedex 2 France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019 1 Boulevard Arago 57078 Metz France
| | - Lorraine A Malaspina
- Universität Bern, Departement für Chemie und Biochemie Freiestrasse 3 3012 Bern Switzerland
| | - Dylan Jayatilaka
- University of Western Australia, School of Molecular Sciences 35 Stirling Highway WA 6009 Perth Australia
| | - John L Spencer
- Victoria University of Wellington, School of Chemical and Physical Sciences Wellington 6012 New Zealand
| | - Fraser White
- Rigaku Europe SE Hugenottenallee 167 63263 Neu-Isenburg Germany
| | - Bernhard Grundkötter-Stock
- Freie Universität Berlin, Institut für Chemie und Biochemie Anorganische Chemie, Fabeckstr. 34/36 14195 Berlin Germany
| | - Simon Steinhauer
- Freie Universität Berlin, Institut für Chemie und Biochemie Anorganische Chemie, Fabeckstr. 34/36 14195 Berlin Germany
| | - Dieter Lentz
- Freie Universität Berlin, Institut für Chemie und Biochemie Anorganische Chemie, Fabeckstr. 34/36 14195 Berlin Germany
| | | | - Simon Grabowsky
- Universität Bern, Departement für Chemie und Biochemie Freiestrasse 3 3012 Bern Switzerland
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25
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Jha KK, Gruza B, Kumar P, Chodkiewicz ML, Dominiak PM. TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:296-306. [PMID: 32831250 DOI: 10.1107/s2052520620002917] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X-H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X-H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (dmin ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.
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Affiliation(s)
- Kunal Kumar Jha
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Barbara Gruza
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Prashant Kumar
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Michal Leszek Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
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26
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Zhao YJ, Ma JP, Fan J, Geng Y, Dong YB. Syntheses and structures of two novel fluorescent metal-organic frameworks generated from a tridentate donor-acceptor motif ligand. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2020; 76:605-615. [PMID: 32499459 DOI: 10.1107/s2053229620006488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/14/2020] [Indexed: 11/10/2022]
Abstract
The tridentate organic ligand 4,4',4''-(4,4,8,8,12,12-hexamethyl-8,12-dihydro-4H-benzo[9,1]quinolizino[3,4,5,6,7-defg]acridine-2,6,10-triyl)tribenzoic acid (H3L) has been synthesized (as the methanol 1.25-solvate, C48H39NO6·1.25CH3OH). As a donor-acceptor motif molecule, H3L possess strong intramolecular charge transfer (ICT) fluorescence. Through hydrogen bonds, H3L molecules construct a two-dimensional (2D) network, which pack together into three-dimensional (3D) networks with an ABC stacking pattern in the crystalline state. Based on H3L and M(NO3)2 salts (M = Cd and Zn) under solvothermal conditions, two metal-organic frameworks (MOFs), namely, catena-poly[[triaquacadmium(II)]-μ-10-(4-carboxyphenyl)-4,4'-(4,4,8,8,12,12-hexamethyl-8,12-dihydro-4H-benzo[9,1]quinolizino[3,4,5,6,7-defg]acridine-2,6-diyl)dibenzoato], [Cd(C48H37NO6)(H2O)3]n, I, and poly[[μ3-4,4',4''-(4,4,8,8,12,12-hexamethyl-8,12-dihydro-4H-benzo[9,1]quinolizino[3,4,5,6,7-defg]acridine-2,6,10-triyl)tribenzoato](μ3-hydroxido)zinc(II)], [Zn2(C48H36NO6)(OH)]n, II, were synthesized. Single-crystal analysis revealed that both MOFs adopt a 3D structure. In I, partly deprotonated HL2- behaves as a bidentate ligand to link a CdII ion to form a one-dimensional chain. In the solid state of I, the existence of weak interactions, such as O-H...O hydrogen bonds and π-π interactions, plays an essential role in aligning 2D nets and 3D networks with AB packing patterns for I. The deprotonated ligand L3- in II is utilized as a tridentate building block to bind ZnII ions to construct 3D networks, where unusual Zn4O14 clusters act as connection nodes. As a donor-acceptor molecule, H3L exhibits fluorescence with a photoluminescence quantum yield (PLQY) of 70% in the solid state. In comparison, the PL of both MOFs is red-shifted with even higher PLQYs of 79 and 85% for I and II, respectively.
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Affiliation(s)
- Yong Jin Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Jian Ping Ma
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Jianzhong Fan
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Yan Geng
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Yu Bin Dong
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
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27
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Falvello LR. What is a crystal to the new chemical crystallographer, after that first, automated structure analysis? CRYSTALLOGR REV 2020. [DOI: 10.1080/0889311x.2020.1760856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Larry R. Falvello
- Department of Inorganic Chemistry and Aragón Materials Science Institute, University of Zaragoza - CSIC Zaragoza, Spain
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28
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Suzuki A, Mutoh Y, Tsuchida N, Fung CW, Kikkawa S, Azumaya I, Saito S. Synthesis and Systematic Structural Analysis of Cationic Half-Sandwich Ruthenium Chalcogenocarbonyl Complexes. Chemistry 2020; 26:3795-3802. [PMID: 31925839 DOI: 10.1002/chem.201904600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Indexed: 11/07/2022]
Abstract
Although the chemistry of transition-metal complexes with carbonyl (CO) and thiocarbonyl (CS) ligands has been well developed, their heavier analogues, namely selenocarbonyl (CSe) and tellurocarbonyl (CTe) complexes remain scarce. The limited availability of such CSe and CTe complexes has so far hampered our understanding of the differences between such chalcogenocarbonyl (CE: E=O, S, Se, Te) ligands. Herein, we report the synthesis and properties of a series of cationic half-sandwich ruthenium CE complexes of the type [CpRu(CE)(H2 IMes)(CNCH2 Ts)][BArF 4 ] (Cp=η5 -C5 H5 - ; H2 IMes=1,3-dimesitylimidazolin-2-ylidene; ArF =3,5-(CF3 )2 C6 H3 ). A combination of X-ray diffraction analyses, NMR spectroscopic analyses, and DFT calculations revealed an increasing π-accepting ability of the CE ligands in the order O<S<Se<Te. A variable-temperature NMR analysis of the thus obtained chiral-at-metal CE complexes indicated high stereochemical stability.
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Affiliation(s)
- Ayumi Suzuki
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3, Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Yuichiro Mutoh
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3, Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Noriko Tsuchida
- Department of Liberal Arts, Faculty of Medicine, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Chi-Wai Fung
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3, Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Shoko Kikkawa
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-3 Miyama, Funabashi-shi, Chiba, 274-8510, Japan
| | - Isao Azumaya
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-3 Miyama, Funabashi-shi, Chiba, 274-8510, Japan
| | - Shinichi Saito
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3, Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
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29
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Fung CW, Fukada G, Mutoh Y, Tsuchida N, Saito S. Synthesis and properties of anionic ruthenium thionitrosyl and selenonitrosyl complexes that contain tetraanionic 2-hydroxybenzamidobenzene ligands. Dalton Trans 2020; 49:613-624. [PMID: 31833532 DOI: 10.1039/c9dt04219a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Although transition-metal complexes that contain thiocarbonyl (CS) and selenocarbonyl (CSe) ligands have been well studied, only three neutral or cationic selenonitrosyl (NSe) complexes have been reported, while anionic NSe complexes remain elusive. Herein, we report the first examples of anionic NSe-ligated ruthenium complexes, which were obtained from the reaction of anionic ruthenium nitrido complexes, elemental selenium, and 4-(N,N-dimethylamino)pyridine (DMAP). The structures of one of these ruthenium NSe complexes, as well as of the corresponding thionitrosyl (NS) and nitrosyl (NO) complexes, were systematically examined by X-ray diffraction analyses and theoretical calculations. In contrast to previous reportes, the NSe ligand in these complexes is a better π-acceptor than the NO and NS ligands and exhibits a stronger trans influence.
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Affiliation(s)
- Chi-Wai Fung
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
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30
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Spek AL. checkCIF validation ALERTS: what they mean and how to respond. Acta Crystallogr E Crystallogr Commun 2020; 76:1-11. [PMID: 31921444 PMCID: PMC6944088 DOI: 10.1107/s2056989019016244] [Citation(s) in RCA: 666] [Impact Index Per Article: 166.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 12/02/2019] [Indexed: 11/23/2022]
Abstract
Authors of a paper that includes a new crystal-structure determination are expected to not only report the structural results of inter-est and their inter-pretation, but are also expected to archive in computer-readable CIF format the experimental data on which the crystal-structure analysis is based. Additionally, an IUCr/checkCIF validation report will be required for the review of a submitted paper. Such a validation report, automatically created from the deposited CIF file, lists as ALERTS not only potential errors or unusual findings, but also suggestions for improvement along with inter-esting information on the structure at hand. Major ALERTS for issues are expected to have been acted on already before the submission for publication or discussed in the associated paper and/or commented on in the CIF file. In addition, referees, readers and users of the data should be able to make their own judgment and inter-pretation of the underlying experimental data or perform their own calculations with the archived data. All the above is consistent with the FAIR (findable, accessible, inter-operable, and reusable) initiative [Helliwell (2019 ▸). Struct. Dyn. 6, 05430]. Validation can also be helpful for less experienced authors in pointing to and avoiding of crystal-structure determination and inter-pretation pitfalls. The IUCr web-based checkCIF server provides such a validation report, based on data uploaded in CIF format. Alternatively, a locally installable checkCIF version is available to be used iteratively during the structure-determination process. ALERTS come mostly as short single-line messages. There is also a short explanation of the ALERTS available through the IUCr web server or with the locally installed PLATON/checkCIF version. This paper provides additional background information on the checkCIF procedure and additional details for a number of ALERTS along with options for how to act on them.
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Affiliation(s)
- Anthony L. Spek
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
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31
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Dittrich B, Chan S, Wiggin S, Stevens JS, Pidcock E. Fast energy minimization of the CCDC drug-subset structures by molecule-in-cluster computations allows independent structure validation and model completion. CrystEngComm 2020. [DOI: 10.1039/d0ce00488j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Optimizing structures with computations on clusters of molecules permits generation of structure-specific restraints for refinement and structure validation.
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Affiliation(s)
| | | | - Seth Wiggin
- The Cambridge Crystallographic Data Center
- Cambridge
- UK
| | | | - Elna Pidcock
- The Cambridge Crystallographic Data Center
- Cambridge
- UK
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32
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Abstract
Disorder in crystal structures can disappear, depending on the circumstances, as shown by multi-temperature measurements, aspherical-atom refinement and computational analyses.
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Affiliation(s)
- Birger Dittrich
- Novartis Campus
- Novartis Pharma AG
- Basel CH-4002
- Switzerland
- Institut für Anorganische Chemie und Strukturchemie
| | - Christoph Sever
- Institut für Anorganische Chemie und Strukturchemie
- Heinrich-Heine Universität Düsseldorf
- 40225 Düsseldorf
- Germany
| | - Jens Lübben
- Institut für Anorganische Chemie und Strukturchemie
- Heinrich-Heine Universität Düsseldorf
- 40225 Düsseldorf
- Germany
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33
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Urzhumtsev AG, Lunin VY. Introduction to crystallographic refinement of macromolecular atomic models. Addendum. CRYSTALLOGR REV 2019. [DOI: 10.1080/0889311x.2019.1698032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Alexandre G. Urzhumtsev
- Centre for Integrative Biology, IGBMC, CNRS–INSERM–UdS, Illkirch, France
- Département de Physique, Faculté des Sciences et des Technologies, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Vladimir Y. Lunin
- Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Moscow Region, Russia
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34
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Cachau RE, Zhu J, Nicklaus MC. The upcoming subatomic resolution revolution. Curr Opin Struct Biol 2019; 58:53-58. [PMID: 31233975 DOI: 10.1016/j.sbi.2019.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/12/2019] [Accepted: 05/13/2019] [Indexed: 10/26/2022]
Abstract
Subatomic resolution macromolecular crystallography has been revealing the most fascinating details of macromolecular structures for many years. This most extreme form of macromolecular crystallography is going through rapid changes. A new generation of superbrilliant X-ray sources and detectors is facilitating the rapid acquisition of high-quality datasets. Equally important, a new breed of methods and highly integrated advanced computational tools for structure refinement and analysis is poised to change the way we use subatomic resolution data and reposition high-resolution macromolecular crystallography in medicinal chemistry studies. Subatomic resolution macromolecular crystallography may soon be a routine source of detailed molecular information besides precise geometries, including binding energies and other chemical descriptors, opening new possibilities of application.
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Affiliation(s)
- Raul E Cachau
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Inc., Frederick, MD 21702, USA.
| | - Jianghai Zhu
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Inc., Frederick, MD 21702, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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