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Liebschner D, Afonine PV, Poon BK, Moriarty NW, Adams PD. Improved joint X-ray and neutron refinement procedure in Phenix. Acta Crystallogr D Struct Biol 2023; 79:1079-1093. [PMID: 37942718 PMCID: PMC10833352 DOI: 10.1107/s2059798323008914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023] Open
Abstract
Neutron diffraction is one of the three crystallographic techniques (X-ray, neutron and electron diffraction) used to determine the atomic structures of molecules. Its particular strengths derive from the fact that H (and D) atoms are strong neutron scatterers, meaning that their positions, and thus protonation states, can be derived from crystallographic maps. However, because of technical limitations and experimental obstacles, the quality of neutron diffraction data is typically much poorer (completeness, resolution and signal to noise) than that of X-ray diffraction data for the same sample. Further, refinement is more complex as it usually requires additional parameters to describe the H (and D) atoms. The increase in the number of parameters may be mitigated by using the `riding hydrogen' refinement strategy, in which the positions of H atoms without a rotational degree of freedom are inferred from their neighboring heavy atoms. However, this does not address the issues related to poor data quality. Therefore, neutron structure determination often relies on the presence of an X-ray data set for joint X-ray and neutron (XN) refinement. In this approach, the X-ray data serve to compensate for the deficiencies of the neutron diffraction data by refining one model simultaneously against the X-ray and neutron data sets. To be applicable, it is assumed that both data sets are highly isomorphous, and preferably collected from the same crystals and at the same temperature. However, the approach has a number of limitations that are discussed in this work by comparing four separately re-refined neutron models. To address the limitations, a new method for joint XN refinement is introduced that optimizes two different models against the different data sets. This approach is tested using neutron models and data deposited in the Protein Data Bank. The efficacy of refining models with H atoms as riding or as individual atoms is also investigated.
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Affiliation(s)
- Dorothee Liebschner
- Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Pavel V. Afonine
- Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Billy K. Poon
- Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nigel W. Moriarty
- Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Paul D. Adams
- Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
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2
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Catapano L, Long F, Yamashita K, Nicholls RA, Steiner RA, Murshudov GN. Neutron crystallographic refinement with REFMAC5 from the CCP4 suite. Acta Crystallogr D Struct Biol 2023; 79:1056-1070. [PMID: 37921806 PMCID: PMC7615533 DOI: 10.1107/s2059798323008793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023] Open
Abstract
Hydrogen (H) atoms are abundant in macromolecules and often play critical roles in enzyme catalysis, ligand-recognition processes and protein-protein interactions. However, their direct visualization by diffraction techniques is challenging. Macromolecular X-ray crystallography affords the localization of only the most ordered H atoms at (sub-)atomic resolution (around 1.2 Å or higher). However, many H atoms of biochemical significance remain undetectable by this method. In contrast, neutron diffraction methods enable the visualization of most H atoms, typically in the form of deuterium (2H) atoms, at much more common resolution values (better than 2.5 Å). Thus, neutron crystallography, although technically demanding, is often the method of choice when direct information on protonation states is sought. REFMAC5 from the Collaborative Computational Project No. 4 (CCP4) is a program for the refinement of macromolecular models against X-ray crystallographic and cryo-EM data. This contribution describes its extension to include the refinement of structural models obtained from neutron crystallographic data. Stereochemical restraints with accurate bond distances between H atoms and their parent atom nuclei are now part of the CCP4 Monomer Library, the source of prior chemical information used in the refinement. One new feature for neutron data analysis in REFMAC5 is refinement of the protium/deuterium (1H/2H) fraction. This parameter describes the relative 1H/2H contribution to neutron scattering for hydrogen isotopes. The newly developed REFMAC5 algorithms were tested by performing the (re-)refinement of several entries available in the PDB and of one novel structure (FutA) using either (i) neutron data only or (ii) neutron data supplemented by external restraints to a reference X-ray crystallographic structure. Re-refinement with REFMAC5 afforded models characterized by R-factor values that are consistent with, and in some cases better than, the originally deposited values. The use of external reference structure restraints during refinement has been observed to be a valuable strategy, especially for structures at medium-low resolution.
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Affiliation(s)
- Lucrezia Catapano
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, United Kingdom
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Fei Long
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Keitaro Yamashita
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Robert A. Nicholls
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Roberto A. Steiner
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, United Kingdom
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Garib N. Murshudov
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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3
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Sharma V, Sahu B, Kumar Das U, Kumar Patra G. A reversible fluorescent-colorimetric malononitrile based novel Schiff-base chemosensor for visual detection of bicarbonate ion in aqueous solution. Inorganica Chim Acta 2023. [DOI: 10.1016/j.ica.2023.121491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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4
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Simoncic P, Romeijn E, Hovestreydt E, Steinfeld G, Santiso-Quiñones G, Merkelbach J. Electron crystallography and dedicated electron-diffraction instrumentation. Acta Crystallogr E Crystallogr Commun 2023; 79:410-422. [PMID: 37151820 PMCID: PMC10162091 DOI: 10.1107/s2056989023003109] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/04/2023] [Indexed: 05/09/2023]
Abstract
Electron diffraction (known also as ED, 3D ED or microED) is gaining momentum in science and industry. The application of electron diffraction in performing nano-crystallography on crystals smaller than 1 µm is a disruptive technology that is opening up fascinating new perspectives for a wide variety of compounds required in the fields of chemical, pharmaceutical and advanced materials research. Electron diffraction enables the characterization of solid compounds complementary to neutron, powder X-ray and single-crystal X-ray diffraction, as it has the unique capability to measure nanometre-sized crystals. The recent introduction of dedicated instrumentation to perform ED experiments is a key aspect of the continued growth and success of this technology. In addition to the ultra-high-speed hybrid-pixel detectors enabling ED data collection in continuous rotation mode, a high-precision goniometer and horizontal layout have been determined as essential features of an electron diffractometer, both of which are embodied in the Eldico ED-1. Four examples of data collected on an Eldico ED-1 are showcased to demonstrate the potential and advantages of a dedicated electron diffractometer, covering selected applications and challenges of electron diffraction: (i) multiple reciprocal lattices, (ii) absolute structure of a chiral compound, and (iii) R-values achieved by kinematic refinement comparable to X-ray data.
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Affiliation(s)
- Petra Simoncic
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
- Correspondence e-mail:
| | - Eva Romeijn
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | - Eric Hovestreydt
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | - Gunther Steinfeld
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | | | - Johannes Merkelbach
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
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5
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Hegde V, O SC, Kulkarni NV, Mathew J. Synthesis and Characterization of Cobalt (II) Pincer Complexes and their Application as Dyes in Dye-Sensitized Solar Cells. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
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Yamada T, Yoshiya M, Kanno M, Takatsu H, Ikeda T, Nagai H, Yamane H, Kageyama H. Correlated Rattling of Sodium-Chains Suppressing Thermal Conduction in Thermoelectric Stannides. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2207646. [PMID: 36527352 DOI: 10.1002/adma.202207646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/18/2022] [Indexed: 06/17/2023]
Abstract
Tin-based intermetallics with tunnel frameworks containing zigzag Na chains that excite correlated rattling impinging on the framework phonons are attractive as thermoelectric materials owing to their low lattice thermal conductivity. The correlated rattling of Na atoms in the zigzag chains and the origin of the low thermal conductivity is uncovered via experimental and computational analyses. The Na atoms behave as oscillators along the tunnel, resulting in substantial interactions between Na atoms in the chain and between the chain and framework. In these intermetallic compounds, a shorter inter-rattler distance results in lower thermal conductivity, suggesting that phonon scattering by the correlated rattling Na-chains is enhanced. These results provide new insights into the behavior of thermoelectric materials with low thermal conductivity and suggest strategies for the development of such materials that utilize the correlated rattling.
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Affiliation(s)
- Takahiro Yamada
- Institute of Multidisciplinary Research for Advanced Material, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, 332-0012, Japan
| | - Masato Yoshiya
- Division of Materials and Manufacturing Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masahiro Kanno
- Institute of Multidisciplinary Research for Advanced Material, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
- Department of Metallurgy, Materials Science and Materials Processing, Graduate School of Engineering, Tohoku University, 6-6-04 Aramaki Aza Aoba, Aoba-ku, Sendai, 980-8579, Japan
| | - Hiroshi Takatsu
- Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Takuji Ikeda
- Research Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology (AIST Tohoku), 4-2-1 Nigatake, Miyagino-ku, Sendai, 983-8551, Japan
| | - Hideaki Nagai
- Research Institute for Energy Conservation, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Hisanori Yamane
- Institute of Multidisciplinary Research for Advanced Material, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Hiroshi Kageyama
- Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto, 615-8510, Japan
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7
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Silalahi RPB, Liao JH, Tseng YF, Chiu TH, Kahlal S, Saillard JY, Liu CW. Unusual core engineering on a copper hydride nanoball. Dalton Trans 2023; 52:2106-2114. [PMID: 36722491 DOI: 10.1039/d2dt03449b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A neutral polyhydrido copper cluster, [Cu27H15{S2CNnBu2}12] (abbreviated as [Cu27H15]), was prepared by the reaction of dithiocarbamates (dtc), Cu(I) salts and NaBH4. The isolated cluster provides insights into core engineering, demonstrating its novel ability to reversibly add or remove one copper atom from the cluster core. Single-crystal X-ray analysis reveals that the new core-shell structure exhibits a Cu24 rhombicuboctahedral outer cage and an inner Cu3 triangular kernel. The two core-shell clusters, [Cu27H15{S2CNnBu2}12] and previously published [Cu28H15(S2CNnBu2)12]+ (abbreviated as [Cu28H15]+), are only differentiated by one copper atom in their inner core. Importantly, we demonstrate core engineering with the controllable reversible transition between an irregular Cu4 tetrahedron and a Cu3 triangle, whilst maintaining their outer Cu24 shell intact. The 15 hydride atoms in [Cu27H15], coordinated in three different modes, are co-incident with the hydride positions in [Cu28H15]+. The degradation of [Cu27H15] in solution or the addition of one eq. of Cu(I) ions leads to the conversion of [Cu27H15] into [Cu28H15]+, while the reverse transformation can be achieved by the addition of either formic acid or a reducing agent to [Cu28H15]+. A dicationic species was observed in the ESI mass spectrum, and the composition is formulated as [Cu56H30(S2CNnBu2)24]2+, a dimer of [Cu27H15(S2CNnBu2)12 + Cu+]22+. The dimeric species was further explored by DFT calculations, suggesting that the lowest energy structure consists of a [Cu28H15]+ and a [Cu27H15] cluster connected through one Cu+ atom bridge. As a result, [Cu27H15] is considered an intermediate species in the formation of the more stable [Cu28H15]+ nanoball.
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Affiliation(s)
- Rhone P Brocha Silalahi
- Department of Chemistry, National Dong Hwa University, Hualien 974301, Taiwan, Republic of China.
| | - Jian-Hong Liao
- Department of Chemistry, National Dong Hwa University, Hualien 974301, Taiwan, Republic of China.
| | - Yu-Fang Tseng
- Department of Chemistry, National Dong Hwa University, Hualien 974301, Taiwan, Republic of China.
| | - Tzu-Hao Chiu
- Department of Chemistry, National Dong Hwa University, Hualien 974301, Taiwan, Republic of China.
| | - Samia Kahlal
- Univ Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France.
| | | | - C W Liu
- Department of Chemistry, National Dong Hwa University, Hualien 974301, Taiwan, Republic of China.
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8
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Latonduine-1-Amino-Hydantoin Hybrid, Triazole-Fused Latonduine Schiff Bases and Their Metal Complexes: Synthesis, X-ray and Electron Diffraction, Molecular Docking Studies and Antiproliferative Activity. INORGANICS 2023. [DOI: 10.3390/inorganics11010030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A series of latonduine derivatives, namely 11-nitro-indolo[2,3-d]benzazepine-7-(1-amino-hydantoin) (B), triazole-fused indolo[2,3-d]benzazepine-based Schiff bases HL1 and HL2 and metal complexes [M(p-cymene)(HL1)Cl]Cl, where M = Ru (1), Os (2), and [Cu(HL2)Cl2] (3) were synthesized and characterized by spectroscopic techniques (UV–vis, 1H, 13C, 15N–1H HSQC NMR) and ESI mass spectrometry. The molecular structures of B and HL1 were confirmed by single-crystal X-ray diffraction, while that of 3 by electron diffraction of nanometer size crystalline sample. Molecular docking calculations of species B in the binding pocket of PIM-1 enzyme revealed that the 1-amino-hydantoin moiety is not involved in any hydrogen-bonding interactions, even though a good accommodation of the host molecule in the ATP binding pocket of the enzyme was found. The antiproliferative activity of organic compounds B, HL1 and HL2, as well as complexes 1–3 was investigated in lung adenocarcinoma A549, colon adenocarcinoma LS-174 and triple-negative breast adenocarcinoma MDA-MB-231 cells and normal human lung fibroblast cells MRC-5 by MTT assays; then, the results are discussed.
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Ganguly S, Bhunia P, Mayans J, Ghosh A. Trinuclear heterometallic CuII–MII (M = Mn and Co) complexes of N,O donor ligands with o-nitro benzoate anion: structures, magnetic properties and catalytic oxidase activities. Inorganica Chim Acta 2023. [DOI: 10.1016/j.ica.2023.121404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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10
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Sharma V, Sahu M, Manna AK, De D, Patra GK. A quinazolin-based Schiff-base chemosensor for colorimetric detection of Ni 2+ and Zn 2+ ions and ' turn-on' fluorometric detection of Zn 2+ ion. RSC Adv 2022; 12:34226-34235. [PMID: 36545589 PMCID: PMC9709804 DOI: 10.1039/d2ra05564c] [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: 09/04/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
Herein, we have reported a novel quinazolin-based Schiff base chemosensor (E)-2-benzamido-N'-(1-(pyridin-2-yl)ethylidene)benzohydrazide (L). L has been designed, synthesised and characterised by 1H-NMR, IR spectroscopy, ESI-MS spectrometry and theoretical studies. The receptor showed appreciable colorimetric λ max shift for both Ni2+ and Zn2+ ions and fluorometric "turn on" response in presence of only Zn2+ ion. The Jobs plot analysis revealed that receptor forms 2 : 1 complex with both the ions Ni2+ and Zn2+, further confirmed by ESI-MS analysis. The single crystal structure of L-Ni2+ complex (1) has also been determined. The colorimetric detection limits were calculated to 7.9 nM and 7.5 nM respectively for Ni2+ and Zn2+ in methanol-Tris-HCl buffer medium (10 mM, pH 7.2, 1 : 1 v/v). The chemosensor L can be applied for the recovery of contaminated water samples.
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Affiliation(s)
- Vanshika Sharma
- Department of Chemistry, Guru Ghasidas VishwavidyalayaBilaspur (C. G)India+91 7587312992
| | - Meman Sahu
- Department of Chemistry, Guru Ghasidas VishwavidyalayaBilaspur (C. G)India+91 7587312992
| | - Amit Kumar Manna
- Department of Chemistry, Guru Ghasidas VishwavidyalayaBilaspur (C. G)India+91 7587312992
| | - Dinesh De
- Department of Chemistry, Guru Ghasidas VishwavidyalayaBilaspur (C. G)India+91 7587312992
| | - Goutam Kumar Patra
- Department of Chemistry, Guru Ghasidas VishwavidyalayaBilaspur (C. G)India+91 7587312992
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11
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Surface modifications of eight-electron palladium silver superatomic alloys. Commun Chem 2022; 5:151. [PMID: 36697889 PMCID: PMC9814913 DOI: 10.1038/s42004-022-00769-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/03/2022] [Indexed: 11/21/2022] Open
Abstract
Atomically precise thiolate-protected coinage metal nanoclusters and their alloys are far more numerous than their selenium congeners, the synthesis of which remains extremely challenging. Herein, we report the synthesis of a series of atomically defined dithiophosph(in)ate protected eight-electron superatomic palladium silver nanoalloys [PdAg20{S2PR2}12], 2a-c (where R = OiPr, a; OiBu, b; Ph, c) via ligand exchange and/or co-reduction methods. The ligand exchange reaction on [PdAg20{S2P(OnPr)2}12], 1, with [NH4{Se2PR2}12] (where R = OiPr, or OnPr) leads to the formation of [PdAg20{Se2P(OiPr)2}12] (3) and [PdAg20{Se2P(OnPr)2}12] (4), respectively. Solid state structures of 2a, 2b, 3 and 4 unravel different PdAg20 metal frameworks from their parent cluster, originating from the different distributions of the eight-capping silver(I) atoms around a Pd@Ag12 centered icosahedron with C2, D3, Th and Th symmetries, respectively. Surprisingly ambient temperature crystallization of the reaction product 3 obtained by the ligand exchange reaction on 1 has resulted in the co-crystallization of two isomers in the unit cell with overall T (3a) and C3 (3b) symmetries, respectively. To our knowledge, this is the first ever characterized isomeric pair among the selenolate-protected NCs. Density functional theory (DFT) studies further rationalize the preferred geometrical isomerism of the PdAg20 core.
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12
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Clabbers MT, Martynowycz MW, Hattne J, Gonen T. Hydrogens and hydrogen-bond networks in macromolecular MicroED data. J Struct Biol X 2022; 6:100078. [PMID: 36507068 PMCID: PMC9731847 DOI: 10.1016/j.yjsbx.2022.100078] [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: 08/18/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Microcrystal electron diffraction (MicroED) is a powerful technique utilizing electron cryo-microscopy (cryo-EM) for protein structure determination of crystalline samples too small for X-ray crystallography. Electrons interact with the electrostatic potential of the sample, which means that the scattered electrons carry information about the charged state of atoms and provide relatively stronger contrast for visualizing hydrogen atoms. Accurately identifying the positions of hydrogen atoms, and by extension the hydrogen bonding networks, is of importance for understanding protein structure and function, in particular for drug discovery. However, identification of individual hydrogen atom positions typically requires atomic resolution data, and has thus far remained elusive for macromolecular MicroED. Recently, we presented the ab initio structure of triclinic hen egg-white lysozyme at 0.87 Å resolution. The corresponding data were recorded under low exposure conditions using an electron-counting detector from thin crystalline lamellae. Here, using these subatomic resolution MicroED data, we identified over a third of all hydrogen atom positions based on strong difference peaks, and directly visualize hydrogen bonding interactions and the charged states of residues. Furthermore, we find that the hydrogen bond lengths are more accurately described by the inter-nuclei distances than the centers of mass of the corresponding electron clouds. We anticipate that MicroED, coupled with ongoing advances in data collection and refinement, can open further avenues for structural biology by uncovering the hydrogen atoms and hydrogen bonding interactions underlying protein structure and function.
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Affiliation(s)
- Max T.B. Clabbers
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, United States
| | - Michael W. Martynowycz
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, United States
| | - Johan Hattne
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, United States
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, United States,Department of Physiology, University of California, Los Angeles, CA 90095, United States,Corresponding author at: Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States.
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Sodium β-Diketonate Glyme Adducts as Precursors for Fluoride Phases: Synthesis, Characterization and Functional Validation. Molecules 2022; 27:molecules27196282. [PMID: 36234815 PMCID: PMC9571527 DOI: 10.3390/molecules27196282] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/12/2022] [Accepted: 09/19/2022] [Indexed: 11/29/2022] Open
Abstract
Very few sodium complexes are available as precursors for the syntheses of sodium-based nanostructured materials. Herein, the diglyme, triglyme, and tetraglyme (CH3O(CH2CH2O)nCH3, n = 2–4) adducts of sodium hexafluoroacetylacetonate were synthesized in a single-step reaction and characterized by IR spectroscopy, 1H, and 13C NMR. Single-crystal X-ray diffraction studies provide evidence of the formation of the ionic oligomeric structure [Na4(hfa)6]2−•2[Na(diglyme2]+ when the diglyme is coordinated, while a mononuclear seven-coordinated complex Na(hfa)•tetraglyme is formed with the tetraglyme. Reaction with the monoglyme (CH3OCH2CH2OCH3) does not occur, and the unadducted polymeric structure [Na(hfa)]n forms, while the triglyme gives rise to a liquid adduct, Na(hfa)•triglyme•H2O. Thermal analysis data reveal great potentialities for their applications as precursors in metalorganic chemical vapor deposition (MOCVD) and sol-gel processes. As a proof-of-concept, the Na(hfa)•tetraglyme adduct was successfully applied to both the low-pressure MOCVD and the sol-gel/spin-coating synthesis of NaF films.
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14
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Luo Y, Clabbers MTB, Qiao J, Yuan Z, Yang W, Zou X. Visualizing the Entire Range of Noncovalent Interactions in Nanocrystalline Hybrid Materials Using 3D Electron Diffraction. J Am Chem Soc 2022; 144:10817-10824. [PMID: 35678508 PMCID: PMC9490833 DOI: 10.1021/jacs.2c02426] [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] [Indexed: 01/20/2023]
Abstract
![]()
Noncovalent interactions
are essential in the formation and properties
of a diverse range of hybrid materials. However, reliably identifying
the noncovalent interactions in nanocrystalline materials remains
challenging using conventional methods such as X-ray diffraction and
spectroscopy. Here, we demonstrate that accurate atomic positions
including hydrogen atoms can be determined using three-dimensional
electron diffraction (3D ED), from which the entire range of noncovalent
interactions in a nanocrystalline aluminophosphate hybrid material
SCM-34 are directly visualized. The protonation states of both the
inorganic and organic components in SCM-34 are determined from the
hydrogen positions. All noncovalent interactions, including hydrogen-bonding,
electrostatic, π–π stacking, and van der Waals
interactions, are unambiguously identified, which provides detailed
insights into the formation of the material. The 3D ED data also allow
us to distinguish different types of covalent bonds based on their
bond lengths and to identify an elongated terminal P=O π-bond
caused by noncovalent interactions. Our results show that 3D ED can
be a powerful tool for resolving detailed noncovalent interactions
in nanocrystalline materials. This can improve our understanding of
hybrid systems and guide the development of novel functional materials.
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Affiliation(s)
- Yi Luo
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Max T B Clabbers
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jian Qiao
- State Key Laboratory of Green Chemical Engineering and Industrial Catalysis, Sinopec Shanghai Research Institute of Petrochemical Technology, 1658 Pudong Beilu, Shanghai 201208, China
| | - Zhiqing Yuan
- State Key Laboratory of Green Chemical Engineering and Industrial Catalysis, Sinopec Shanghai Research Institute of Petrochemical Technology, 1658 Pudong Beilu, Shanghai 201208, China
| | - Weimin Yang
- State Key Laboratory of Green Chemical Engineering and Industrial Catalysis, Sinopec Shanghai Research Institute of Petrochemical Technology, 1658 Pudong Beilu, Shanghai 201208, China
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden
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15
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Matsubara K, Tomomatsu K, Tajiri A, Watanabe A, Koga Y, Ishikawa R, Yamada Y. Pincer‐type Mesoionic Carbene Nickel(II) Complexes: Synthesis, Properties, Reactions, and Catalytic Application to the Suzuki–Miyaura Coupling Reaction of Aryl Bromides. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202100870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kouki Matsubara
- Fukuoka University Department of Chemistry 8-19-1 NanakumaJonan-Ku 814-0180 Fukuoka JAPAN
| | | | - Ayame Tajiri
- Fukuoka University: Fukuoka Daigaku Chemistry JAPAN
| | | | - Yuji Koga
- Fukuoka University: Fukuoka Daigaku Chemistry JAPAN
| | | | - Yuji Yamada
- Fukuoka University: Fukuoka Daigaku Chemistry JAPAN
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16
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Ganguly S, Bhunia P, Mayans J, Ghosh A. Pentanuclear M II–Mn II (M = Ni and Cu) complexes of N 2O 2 donor ligands with a variation of carboxylate anions: syntheses, structures, magnetic properties and catecholase-like activities. NEW J CHEM 2022. [DOI: 10.1039/d2nj02215j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One NiII2MnII3 and two CuII2MnII3 complexes have been synthesized using N2O2 donor ligands. The former complex exhibits spin crossover at 2 K temperature. All the complexes exhibit catecholase-like activities.
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Affiliation(s)
- Sayantan Ganguly
- Department of Chemistry, University College of Science, University of Calcutta, 92, A. P. C. Road, Kolkata 700 009, India
- Department of Chemistry, Taki Government College, Taki, Hasnabad, West Bengal 743429, India
| | - Pradip Bhunia
- Department of Chemistry, University College of Science, University of Calcutta, 92, A. P. C. Road, Kolkata 700 009, India
| | - Júlia Mayans
- Departament de Química Inorgànica i Orgànica and Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona (UB), Martí iFranqués 1-11, Barcelona 08028, Spain
| | - Ashutosh Ghosh
- Department of Chemistry, University College of Science, University of Calcutta, 92, A. P. C. Road, Kolkata 700 009, India
- Rani Rashmoni Green University, Tarakeswar, Hooghly 712410, West Bengal, India
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17
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Manas Bandyopadhyay, Sengupta U, Periyasamy M, Mukhopadhyay S, Hasija A, Chopra D, Özdemir N, Said MA, Bera MK. Cu(II)(PhOMe-Salophen) Complex: Greener Pasture Biological Study, XRD/HAS Interactions, and MEP. RUSS J INORG CHEM+ 2022; 67. [PMCID: PMC10028762 DOI: 10.1134/s0036023623700274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
PhOMe-salophen (1b) (salophen is N,N-bis(salycilidene)-1,2-phenylenediamine with two tert-butyl on each ring) and Cu(II) complex with PhOMe-salophen (1c) have been synthesized and characterized using various tools, including X-ray diffraction for the Cu(II)-complex (1c, C43H52CuN2O3)). The copper complex has been obtained by Cu2+ templated approach using 1b. PhOMe-salophen (1b) has been obtained in reasonably high yield using a mixture of the Schiff-base, 1a, Pd(OAc)2, PPh3, Na2CO3, 4-methoxyphenylboronic acid in benzene. We focus in this research work on the electronic and structural properties of the Cu–Schiff base complex. The tetra-coordinate τ4 index was calculated, indicating almost a perfect square planner in agreement with X-ray diffraction results. MEP reveals the maximum positive regions in 1/-associated with the azomethine and methoxyphenyl C–H bonds with an average value of 0.03 a.u. Hirshfeld surface analysis (HSA) was also studied to highlight the significant inter-atomic contacts and their percentage contribution through 2D Fingerprint plot. In a fair comparative molecular docking study, 1b and 1c were docked together with N-[{(5-methylisoxazol-3-yl)-carbonyl}alanyl}-l-valyl]-N1-((1R,2Z)-4-(benzyloxy)-4-oxo-1-[{(3R)-2-oxopyrrolidin-3-yl}methyl]but-2-enyl)-l-leucinamide, N3 against main protease Mpro, (PDB code 7BQY) using the same parameters and conditions. Interesting here to use the free energy, in silico, molecular docking approach, which aims to rank our molecules with respect to the well-known inhibitor, N3. The binding scores of 1b, 1c, N3 are –7.8, –9.0, and –8.4 kcal/mol, respectively. These preliminary results propose that ligands deserve additional study in the context of possible remedial agents for COVID-19.
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Affiliation(s)
- Manas Bandyopadhyay
- Department of Chemistry, Indian Institute of Engineering Science and Technology (IIEST), Shibpur P.O. Botanic Garden, 7111103 Howrah, India
| | - Utsav Sengupta
- Department of Chemistry, Indian Institute of Engineering Science and Technology (IIEST), Shibpur P.O. Botanic Garden, 7111103 Howrah, India
| | - Muthaimanoj Periyasamy
- Department of Mining Engineering, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, P.O. Botanic Garden, 7111103 Howrah, India
| | - Sudipta Mukhopadhyay
- Department of Mining Engineering, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, P.O. Botanic Garden, 7111103 Howrah, India
| | - Avantika Hasija
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Bhopal Bypass Rd, Bhauri, 462066 Bhopal, Madhya Pradesh India
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Bhopal Bypass Rd, Bhauri, 462066 Bhopal, Madhya Pradesh India
| | - Namık Özdemir
- Department of Mathematics and Science Education, Faculty of Education, Ondokuz Mayıs University, 55139 Samsun, Turkey
| | - Musa A. Said
- Department of Chemistry, Faculty of Science, Taibah University, 30002 Al-Madinah Al-Munawarah, Saudi Arabia
- Institut fuer Anorganische Chemie, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Mrinal K. Bera
- Department of Chemistry, Indian Institute of Engineering Science and Technology (IIEST), Shibpur P.O. Botanic Garden, 7111103 Howrah, India
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18
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Gam F, Chantrenne I, Kahlal S, Chiu TH, Liao JH, Liu CW, Saillard JY. Alloying dichalcogenolate-protected Ag 21 eight-electron nanoclusters: a DFT investigation. NANOSCALE 2021; 14:196-203. [PMID: 34908067 DOI: 10.1039/d1nr06019h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The isoelectronic doping of dichalcogenolato nanoclusters of the type [Ag21{E2P(OR)2}12]+ (E = S, Se) by any heteroatom belonging to groups 9-12 was systematically investigated using DFT calculations. Although they can differ in their global structure, all of these species have the same M@M12-centered icosahedral core. In any case, the different structure types are all very close in energy. In all of them, three different alloying sites can be identified (central, icosahedral, peripheral) and calculations allowed the trends in heteroatom site occupation preference across the group 9-12 family to be revealed. These trends are supported by complementary experimental results. They were rationalized on the basis of electronegativity, potential involvement in the bonding of valence d-orbitals and atom size. TD-DFT calculations showed that the effect of doping on optical properties is sizable and this should stimulate research on the modulation of luminescence properties in the dithiolato and diseleno families of complexes.
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Affiliation(s)
- Franck Gam
- Université de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France.
| | - Isaac Chantrenne
- Université de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France.
| | - Samia Kahlal
- Université de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France.
| | - Tzu-Hao Chiu
- Department of Chemistry, National Dong Hwa University, Hualien 974301, Taiwan, Republic of China.
| | - Jian-Hong Liao
- Department of Chemistry, National Dong Hwa University, Hualien 974301, Taiwan, Republic of China.
| | - C W Liu
- Department of Chemistry, National Dong Hwa University, Hualien 974301, Taiwan, Republic of China.
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19
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Microcrystal electron diffraction in macromolecular and pharmaceutical structure determination. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 37:93-105. [PMID: 34895659 DOI: 10.1016/j.ddtec.2020.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 02/05/2023]
Abstract
Microcrystal electron diffraction (MicroED) has recently shown to be a promising technique for structure determination in structural biology and pharmaceutical chemistry. Here, we discuss the unique properties of electrons and motivate its use for diffraction experiments. We review the latest developments in MicroED, and illustrate its applications in macromolecular crystallography, fragment screening and structure guided drug discovery. We discuss the perspectives of MicroED in synthetic chemistry and pharmaceutical development. We anticipate that the rapid advances MicroED showcased here will promote further development of electron crystallography and open up new opportunities for drug discovery.
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20
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Hu W, Liao T, Deng L, Sun H, Zhou Z, Chai H, Zhao C. Synthesis, crystal structure, and
density functional theory
study of a
new compound
4‐(2‐chlorobenzyl)‐1‐(5‐fluoro‐2‐hydroxy‐3‐(thiomorpholinomethyl)phenyl [1,2,4]triazolo[4,3‐a]quinazolin‐5(
4H
)‐one. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Weiyin Hu
- School of Pharmaceutical Sciences Guizhou University Guiyang China
- Guizhou Engineering Laboratory for Synthetic Drugs, Guizhou university Guiyang China
- Key Laboratory of Guizhou for Fermentation Engineering and Biomedicine, Guizhou university Guiyang China
| | - Tianhui Liao
- School of Pharmaceutical Sciences Guizhou University Guiyang China
- Key Laboratory of Guizhou for Fermentation Engineering and Biomedicine, Guizhou university Guiyang China
| | - Liyuan Deng
- Guizhou Engineering Laboratory for Synthetic Drugs, Guizhou university Guiyang China
- Key Laboratory of Guizhou for Fermentation Engineering and Biomedicine, Guizhou university Guiyang China
| | - Hong Sun
- School of Pharmaceutical Sciences Guizhou University Guiyang China
- Key Laboratory of Guizhou for Fermentation Engineering and Biomedicine, Guizhou university Guiyang China
| | - Zhixu Zhou
- School of Pharmaceutical Sciences Guizhou University Guiyang China
- Guizhou Engineering Laboratory for Synthetic Drugs, Guizhou university Guiyang China
| | - Huifang Chai
- Department of Pharmacy Guiyang College of Traditional Chinese Medicine Guiyang China
| | - Chunshen Zhao
- School of Pharmaceutical Sciences Guizhou University Guiyang China
- Guizhou Engineering Laboratory for Synthetic Drugs, Guizhou university Guiyang China
- Department of Pharmacy Guiyang College of Traditional Chinese Medicine Guiyang China
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21
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Ren Q, Huang PY, Liu Y, Liao WK, Zhou ZX, Zhao CS. SYNTHESIS, CRYSTAL STRUCTURE, AND DFT STUDY OF 4-(2-CHLOROBENZYL)-1-(5-NITRO-2-(PYRROLIDIN-1-YL)PHENYL)- [1,2,4]TRIAZOLO[4,3-a]QUINAZOLIN-5(4H)-ONE. J STRUCT CHEM+ 2021. [DOI: 10.1134/s0022476621090171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Electrochemical sensing of hydrogen peroxide on a carbon paste electrode modified by a silver complex based on the 1,3-bis(1H-benzimidazole-2-yl)propane ligand. ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2021. [DOI: 10.1515/znb-2021-0089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
A new carbon paste electrode (Ag-CPE) modified with a nitrogen heterocyclic silver(I) complex, [Ag2(BBP)2](pic)2·CH3OH (BBP = 1,3-bis(1H-benzimidazol-2-yl)propane, pic = picrate), was developed as a highly sensitive and simple electrochemical sensor for the determination of hydrogen peroxide. The Ag(I) complex was prepared by an interface reaction and characterized by elemental analysis, IR and UV/Vis spectra and single crystal X-ray diffraction. The Ag(I) complex shows a dinuclear cluster structure, which is formed by two BBP ligands bridging two Ag (I) centers and an Ag–Ag interaction (d
Ag–Ag = 3.0875 Å). Cyclic voltammetry and chronoamperometry studies showed that the electrochemical sensing performance of Ag-CPE for H2O2 was improved in 0.2 m phosphate buffer solution (PBS, pH = 6). The electrochemical H2O2 sensor Ag-CPE exhibits a wide linear detection range from 0.5 to 4.0 mm and a lower detection limit of 0.39 μm with a relatively high sensitivity of 6.77 μA mm
−1. Moreover, the sensor also shows good anti-interference properties and stability. The results prove that the Ag(I) complex based on the bis(benzimidazole) ligand may be an efficient component of electrode materials.
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23
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Bairagi KM, Ingle KS, Bhowal R, Mohurle SA, Hasija A, Alwassil OI, Venugopala KN, Chopra D, Nayak SK. Interplay of Halogen and Hydrogen Bonding through Co-Crystallization in Pharmacologically Active Dihydropyrimidines: Insights from Crystal Structure and Energy Framework. Chempluschem 2021; 86:1167-1176. [PMID: 34409757 DOI: 10.1002/cplu.202100259] [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: 06/05/2021] [Revised: 07/31/2021] [Indexed: 11/05/2022]
Abstract
A solvent-assisted grinding method has been used to prepare co-crystals in substituted dihydropyrimidines (DHPM) that constitutes pharmacologically active compounds. These were characterized using FT-IR, PXRD, and single-crystal X-ray diffraction. In order to explore the possibility of formation of halogen (XB) and hydrogen bonding (HB) synthons in the solid state, co-crystallization attempts of differently substituted DHPM molecules, containing nitro, hydoxy, and chloro substituents, with different co-formers, such as 1,4-diiodo tetrafluorobenzene (1,4 DITFB) and 3-nitrobenzoic acid (3 NBA) were performed. The XB co-crystals (C2aXB, C2bXB, and C2cXB) prefer the formation of C-I⋅⋅⋅O/C-I⋅⋅⋅S XB synthon, whereas the HB co-crystal (C2dHB) is stabilized by N-H⋅⋅⋅O H-bond formation. Hirshfeld surface analysis revealed that the percentage contribution of intermolecular interactions for XB co-crystals prefer equal contribution of XB synthon along with HB synthon. Furthermore, the interaction energy was analyzed using energy frameworks, which suggests that their stability, a combination of electrostatics and dispersion, is enhanced through XB/HB in comparison to the parent DHPMs.
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Affiliation(s)
- Keshab M Bairagi
- Department of Chemistry, Institution Visvesvaraya National Institute of Technology, Nagpur Address Nagpur, 440010, Maharashtra, India
| | - Kapil S Ingle
- Department of Chemistry, Institution Visvesvaraya National Institute of Technology, Nagpur Address Nagpur, 440010, Maharashtra, India
| | - Rohit Bhowal
- Department of Chemistry, Institution Indian Institute of Science Education and Research Bhopal Address Bhopal, Bhauri, Bhopal 462023, India
| | - Smital A Mohurle
- Department of Chemistry, Institution Visvesvaraya National Institute of Technology, Nagpur Address Nagpur, 440010, Maharashtra, India
| | - Avantika Hasija
- Department of Chemistry, Institution Indian Institute of Science Education and Research Bhopal Address Bhopal, Bhauri, Bhopal 462023, India
| | - Osama I Alwassil
- Department of Pharmaceutical Sciences, King Saud bin Abdulaziz University for health sciences, Riyadh, 11481, Kingdom of Saudi Arabia
| | - Katharigatta N Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, 31982, Kingdom of Saudi Arabia.,Department of Biotechnology and Food Technology, Durban University of Technology, Durban, Durban, 4001, South Africa.,Department of Pharmaceutical Sciences College of Clinical Pharmacy King Faisal University, Al-Ahsa, 31982, Kingdom of Saudi Arabia.,Department of Biotechnology and Food Technology, Durban University of Technology, Durban, Durban, 4001, South Africa
| | - Deepak Chopra
- Department of Chemistry, Institution Indian Institute of Science Education and Research Bhopal Address Bhopal, Bhauri, Bhopal 462023, India
| | - Susanta K Nayak
- Department of Chemistry, Institution Visvesvaraya National Institute of Technology, Nagpur Address Nagpur, 440010, Maharashtra, India
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25
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Li JQ, Li RN, Li MX, Shao M, He X. Enhancing water stability in Co(II) coordination polymers from their structural transformation by temperature-controlling and their dye degradation property. J SOLID STATE CHEM 2021. [DOI: 10.1016/j.jssc.2021.122110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Investigation of intermolecular interactions in fluoro/trifluoromethyl derivatives of benzoylferrocene. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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27
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Sahu M, Manna AK, Chowdhury S, Patra GK. A novel dihydro phenylquinazolinone-based two-in-one colourimetric chemosensor for nickel(ii), copper(ii) and its copper complex for the fluorescent colourimetric nanomolar detection of the cyanide anion. RSC Adv 2020; 10:44860-44875. [PMID: 35516234 PMCID: PMC9058604 DOI: 10.1039/d0ra09023a] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
Currently, considerable efforts have been devoted to the detection and quantification of hazardous multi-analytes using a single probe. Herein, we have developed a simple, environment-friendly colourimetric sensor for the sensitive, selective and rapid detection of Ni2+ and Cu2+ ions using a simple organic Schiff base ligand L in methanol-Tris-HCl buffer (1 : 1 v/v, 10 mM, pH = 7.2). The probe L exhibited a binding-induced colour change from colourless to yellow and fluorescence quenching in the presence of both Ni2+ and Cu2+ ions. The interactions between L and the respective metal ions were studied by Job's plot, electrospray ionisation-mass spectrometry (ESI-MS), Fourier-transform infrared spectroscopy (FT-IR), density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations. The limit of detection (LOD) of L towards Ni2+ and Cu2+ was calculated to be 7.4 × 10-7 M and 4.9 × 10-7 M, respectively. Furthermore, the L-Cu2+ complex could be used as a new cascade fluorescent-colourimetric sensor to detect CN- ions with a very low level of detection (40 nM). Additionally, L could operate in a wide pH range, and thus was successfully applied for the detection and quantification of Ni2+ and Cu2+ in environmental samples, and for building OR- and IMPLICATION-type logic gates.
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Affiliation(s)
- Meman Sahu
- Department of Chemistry, Guru Ghasidas Vishwavidyalaya Bilaspur (C.G) India +917587312992
| | - Amit Kumar Manna
- Department of Chemistry, Guru Ghasidas Vishwavidyalaya Bilaspur (C.G) India +917587312992
| | - Shubhamoy Chowdhury
- Department of Chemistry, Gour Banga University Malda West Bengal 732 103 India
| | - Goutam Kumar Patra
- Department of Chemistry, Guru Ghasidas Vishwavidyalaya Bilaspur (C.G) India +917587312992
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28
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Isolation of a Nitromethane Anion in the Calix-Shaped Inorganic Cage. Molecules 2020; 25:molecules25235670. [PMID: 33271966 PMCID: PMC7729913 DOI: 10.3390/molecules25235670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/03/2022] Open
Abstract
A calix-shaped polyoxometalate, [V12O32]4− (V12), stabilizes an anion moiety in its central cavity. This molecule-sized container has the potential to control the reactivity of an anion. The highly-reactive cyanate is smoothly trapped by V12 to form [V12O32(CN)]5−. In the CH3NO2 solution, cyanate abstracts protons from CH3NO2, and the resultant CH2NO2− is stabilized in V12 to form [V12O32(CH2NO2)]5− (V12(CH2NO2)). A crystallographic analysis revealed the double-bond characteristic short bond distance of 1.248 Å between the carbon and nitrogen atoms in the nitromethane anion in V12. 1H and 13C NMR studies showed that the nitromethane anion in V12 must not be exchanged with the nitromethane solvent. Thus, the V12 container restrains the reactivity of anionic species.
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29
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Suresh A, Gonde S, Mondal PK, Sahoo J, Chopra D. Improving solubility and intrinsic dissolution rate of ofloxacin API through salt formation via mechanochemical synthesis with diphenic acid. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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30
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Ganguly S, Mayans J, Ghosh A. Modulation of Nuclearity in Cu II -Mn II Complexes of a N 2 O 2 Donor Ligand Depending upon Carboxylate Anions: Structures, Magnetic Properties and Catalytic Oxidase Activities. Chem Asian J 2020; 15:4055-4069. [PMID: 32722886 DOI: 10.1002/asia.202000706] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/24/2020] [Indexed: 12/12/2022]
Abstract
Three new hetero-metallic copper(II)-manganese(II) complexes, [(CuL)2 Mn3 (C6 H5 CO2 )6 ] (1), [(CuL)2 Mn(CH3 CO2 )2 ] (2), and {[(CuL)2 Mn(C6 H5 CH2 CO2 )2 ] ⋅ 2CH3 CN} (3), have been synthesized using [CuL] as ''metalloligand'' (where H2 L=N,N'-bis(2-hydroxynaphthyl-methylidene)-1,3-propanediamine). Single-crystal structural analyses show an almost linear penta-nuclear structure for complex 1 where a square planar [CuL] unit is connected to each of the two terminal MnII ions of a linear, centrosymmetric [Mn3 (benzoate)6 ] unit through the double phenoxido bridges. Both complexes 2 and 3 possess a linear tri-nuclear structure where two terminal square-pyramidal [CuL] units are bonded to the central MnII ion through double phenoxido oxygen atoms along with a syn-syn bridging acetate (for 2)/phenyl acetate (for 3). All three complexes exhibit catecholase, and phenoxazinone synthase-like activities under aerial conditions. For catecholase like activity, the turnover numbers (kcat ) are 595, 40, and 205 h-1 whereas, for phenoxazinone synthase like activity, the turnover numbers are 25, 4, and 11 h-1 for complexes 1-3, respectively. The mechanism of both catalytic oxidase activities is proposed on the basis of mass spectral evidences. Variable-temperature (2-300 K) dc molar magnetic susceptibility measurements of 1 reveal antiferromagnetic interactions between the Cu-Mn centres (J1 =-29.3 cm-1 ), and also between the Mn-Mn centres of the [Mn3 (benzoate)6 ] unit (J2 =-0.68 cm-1 ). On increasing the magnetic field at 2 K, its ground spin state changes from S=3/2 to S=5/2 at 4 T, attributable to the low value of J2 which makes the excited spin states close in energy with the ground spin state. Complexes 2 and 3 show antiferromagnetic coupling interactions between the Cu-Mn pairs with J values of -9.51, and -5.32 cm-1 , respectively.
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Affiliation(s)
- Sayantan Ganguly
- Department of Chemistry, University College of Science, University of Calcutta, 92, A. P. C. Road, Kolkata, 700 009, India.,Department of Chemistry, Taki Government College, Taki, Hasnabad, West Bengal, 743429, India
| | - Júlia Mayans
- Instituto de Ciencia Molecular (ICMol), Universitat de València, c/ Catedrático José Beltrán 2, 46980 Paterna, València, Spain
| | - Ashutosh Ghosh
- Department of Chemistry, University College of Science, University of Calcutta, 92, A. P. C. Road, Kolkata, 700 009, India.,Rani Rashmoni Green University, Tarakeswar, Hooghly, 712419, West Bengal, India
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31
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Dutta S, Ghosh TK, Mahapatra P, Ghosh A. Joining of Trinuclear Heterometallic Cu II2-M II (M = Mn, Cd) Nodes by Nicotinate to Form 1D Chains: Magnetic Properties and Catalytic Activities. Inorg Chem 2020; 59:14989-15003. [PMID: 33001631 DOI: 10.1021/acs.inorgchem.0c01733] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the present work, four new heterometallic coordination complexes, {[(CuL)2Mn(nic)(H2O)2](ClO4)(0.5H2O)}n (1), {[(CuL)2Cd(nic)(H2O)2](ClO4)(H2O)}n (2), [(CuL)2Mn(nic)2]·2CH3OH (3), and [(CuL)2Cd(nic)2]·2CH3OH (4) (where H2L = N,N'-bis(α-methylsalicylidene)-1,3-propanediamine and nic = nicotinate ion), have been synthesized and characterized by single-crystal X-ray crystallography. In complexes 1 and 2, the nicotinate ion acts as a bifunctional linker (N,O donor) and joins the linear trinuclear nodes to form 1D polymeric chains. However, in complexes 3 and 4, the nicotinate ion uses only the oxygen atoms of the carboxylic acid (O donor) to bind to the metal centers, forming discrete linear trinuclear units, while the pyridyl nitrogen (N donor atom) remains free. The dc magnetic susceptibility measurements show that the CuII and MnII ions are antiferromagnetically coupled in both 1 and 3, with exchange coupling constants (JMn-Cu) of -20.57 ± 0.08 and -9.38 ± 0.08 cm-1, respectively. Among the four complexes, 1 and 3 show catechol oxidase and phenoxazinone synthase like catalytic activities. The turnover numbers (kcat) of complexes 1 and 3 for catecholase activity are 1121 and 720 h-1, respectively, at an optimum pH of 8.0 and for phenoxazinone synthase activity are 429 and 398 h-1, respectively, at an optimum pH of 9.7. The higher kcat values of 1 for both reactions are attributable to a water molecule coordinated to the central MnII atom that facilitates the substrate-catalyst binding. An ESI-mass spectral analysis indicates that trinuclear heterometallic species, e.g., [(CuL)2Mn(nic)(H2O)]+ for 1 and [(CuL)2Mn(nic)]+ for 3, are the active species that bind to the substrate, and on that basis, probable mechanisms through the formation of radical intermediates have been proposed.
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Affiliation(s)
- Sabarni Dutta
- Department of Chemistry, University College of Science, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Tanmoy Kumar Ghosh
- Department of Chemistry, University College of Science, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Prithwish Mahapatra
- Department of Chemistry, University College of Science, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Ashutosh Ghosh
- Department of Chemistry, University College of Science, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India.,Rani Rashmoni Green University, Tarakeswar, Hooghly 712410, West Bengal, India
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Ivanov SA, Stash AI, Riekehr L, Chen YS, Ye ZG. Structure of Pb(Fe 2/3W 1/3)O 3 single crystals with partial cation order. Sci Rep 2020; 10:14567. [PMID: 32884049 PMCID: PMC7471969 DOI: 10.1038/s41598-020-71438-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 07/30/2020] [Indexed: 11/09/2022] Open
Abstract
Despite intensive studies on the complex perovskite Pb(Fe2/3W1/3)O3 (PFWO) relaxor, understanding the exact nature of its multifunctional properties has remained a challenge for decades. In this work we report a comprehensive structural study of the PFWO single crystals using a combination of synchrotron X-ray diffraction and high-resolution electron microscopy. The set of {h + ½, k + ½, l + ½} superlattice reflections was observed for the first time based on single-crystal synchrotron X-ray experiments (100-450 K) and transmission electron microscopy investigations, which indicates some kind of B-cation ordering in PFWO which had been thought to be totally disordered. It was found that (1) the crystal structure of PFWO should be described by a partly ordered cubic perovskite (i.e. Fm - 3m), (2) the weak ferromagnetic properties and excess magnetic moment of PFWO can be understood based on non-random distribution of Fe cations between the 4a and 4b sites, and (3) the Pb displacement disorder is present in this material and the cations are probably displaced along the <100> directions. The X-ray diffraction results of this investigation show that partial cation ordering indeed exists in PFWO, which makes it necessary to revisit the generally accepted interpretations of the results obtained up to date. In agreement with X-ray diffraction study the main results of TEM study include: (1) a long range order that can be described with the Fm - 3m symmetry is reliably detected, (2) the coherence length of that long range order is in the order of 1-2 nm and (3) no remarkable chemical inhomogeneity is found in the tested PFWO crystal, excluding the possibility of a compositional ordering arising from substitutional defects in the perovskite structure.
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Affiliation(s)
- S A Ivanov
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, Russia, 119991.
- Department of Engineering Sciences, Solid State Physics, Angstrom Laboratory, Uppsala University, Box 534, 751 21, Uppsala, Sweden.
| | - A I Stash
- A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Science, Vavilov St., 28, Moscow, Russia, 119991
| | - L Riekehr
- Department of Engineering Sciences, Solid State Electronics, Angstrom Laboratory, Uppsala University, Box 534, 751 21, Uppsala, Sweden
| | - Y-S Chen
- NSF's ChemMatCARS Beamline@APS, The University of Chicago, Argonne, IL, 60439, USA
| | - Z-G Ye
- Department of Chemistry and 4D LABS, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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A highly selective novel multiple amide based Schiff base optical chemosensor for rapid detection of Cu2+ and its applications in real sample analysis, molecular logic gate and smart phone. Microchem J 2020. [DOI: 10.1016/j.microc.2020.104860] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Hydrogen and Halogen Bond Mediated Coordination Polymers of Chloro-Substituted Pyrazin-2-Amine Copper(I) Bromide Complexes. CHEMISTRY 2020. [DOI: 10.3390/chemistry2030045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A new class of six mono- (1; 3-Cl-, 2; 5-Cl-, 3; 6-Cl-) and di-(4; 3,6-Cl, 5; 5,6-Cl-, 6; 3,5-Cl-) chloro-substituted pyrazin-2-amine ligands (1–6) form complexes with copper (I) bromide, to give 1D and 2D coordination polymers through a combination of halogen and hydrogen bonding that were characterized by X-ray diffraction analysis. These Cu(I) complexes were prepared indirectly from the ligands and CuBr2 via an in situ redox process in moderate to high yields. Four of the pyrazine ligands, 1, 4–6 were found to favor a monodentate mode of coordination to one CuI ion. The absence of a C6-chloro substituent in ligands 1, 2 and 6 supported N1–Cu coordination over the alternative N4–Cu coordination mode evidenced for ligands 4 and 5. These monodentate systems afforded predominantly hydrogen bond (HB) networks containing a catenated (μ3-bromo)-CuI ‘staircase’ motif, with a network of ‘cooperative’ halogen bonds (XB), leading to infinite polymeric structures. Alternatively, ligands 2 and 3 preferred a μ2-N,N’ bridging mode leading to three different polymeric structures. These adopt the (μ3-bromo)-CuI ‘staircase’ motif observed in the monodentate ligands, a unique single (μ2-bromo)-CuI chain, or a discrete Cu2Br2 rhomboid (μ2-bromo)-CuI dimer. Two main HB patterns afforded by self-complimentary dimerization of the amino pyrazines described by the graph set notation R22(8) and non-cyclic intermolecular N–H∙∙∙N’ or N–H∙∙∙Br–Cu leading to infinite polymeric structures are discussed. The cooperative halogen bonding between C–Cl∙∙∙Cl–C and the C–Cl∙∙∙Br–Cu XB contacts are less than the sum of the van der Waals radii of participating atoms, with the latter ranging from 3.4178(14) to 3.582(15) Å. In all cases, the mode of coordination and pyrazine ring substituents affect the pattern of HBs and XBs in these supramolecular structures.
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Hasegawa M, Sakurai S, Yamaguchi MA, Iwasawa D, Yajima N, Ogata S, Inazuka Y, Ishii A, Suzuki K. Aspects of lanthanide complexes for selectivity, intensity and sharpness in luminescence bands from twenty-four praseodymium, europium and gadolinium complexes with differently distorted-hexadentate ligands. Photochem Photobiol Sci 2020; 19:1054-1062. [PMID: 32609140 DOI: 10.1039/d0pp00069h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We structurally and spectroscopically investigated a series of praseodymium (Pr) complexes with eight ligands that form helicate molecular structures. The mother ligand skeleton (L) has two bipyridine moieties bridged with ethylenediamine. The bridged skeleton of PrL was changed to diamines 1-methyl-ethylenediamine, trimethylenediamine and 2,2'-dimethyl-trimethylenediamine, and the corresponding ligands were designated as Lme, Lpr and Ldmpr, for each Pr in these complexes upon UV-excitation. The luminescence quantum yields of PrL and PrLpr in the visible and near infrared (NIR) regions indicate that PrL is excited by both the electronic state of the ligand and the ff absorption band, whereas PrLpr is excited through the ligand. The addition of a methyl group to PrL and PrLpr has a different effect on the Pr emission intensity with the intensity of PrLme decreasing more than that of PrL and PrLdmpr and increasing more than that of PrLpr. Thus, the coordination of Pr and the increased rigidity of the ligand upon methylation enhance luminescence. The azomethine moieties on Lme, Lpr and Ldmpr were reduced and formed the corresponding PrLH, PrLmeH, PrLprH and PrLdmprH complexes. The luminescence of the non-methylated series is due to transitions related to the 1D2 level and thus the methylated series luminesces due to high energy levels such as 3PJ arising from the shortened π electronic systems. We also discuss the strong red emission of a series of Eu complexes with eight ligands from the viewpoint of their molecular structures and luminescence efficiencies and evaluate the Judd-Ofelt parameters from the luminescence spectra of Eu complexes.
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Affiliation(s)
- Miki Hasegawa
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, 252-5258, Chuo-ku, Sagamihara, Kanagawa, Japan. .,Mirai Molecular Materials Design Institute, Aoyama Gakuin University, 5-10-1 Fuchinobe, 252-5258, Chuo-ku, Sagamihara, Kanagawa, Japan.
| | - Shoya Sakurai
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, 252-5258, Chuo-ku, Sagamihara, Kanagawa, Japan
| | - Masafumi Andrew Yamaguchi
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, 252-5258, Chuo-ku, Sagamihara, Kanagawa, Japan
| | - Daichi Iwasawa
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, 252-5258, Chuo-ku, Sagamihara, Kanagawa, Japan
| | - Naho Yajima
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, 252-5258, Chuo-ku, Sagamihara, Kanagawa, Japan
| | - Shuhei Ogata
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, 252-5258, Chuo-ku, Sagamihara, Kanagawa, Japan
| | - Yudai Inazuka
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, 252-5258, Chuo-ku, Sagamihara, Kanagawa, Japan
| | - Ayumi Ishii
- Mirai Molecular Materials Design Institute, Aoyama Gakuin University, 5-10-1 Fuchinobe, 252-5258, Chuo-ku, Sagamihara, Kanagawa, Japan.,JST, PRESTO, 4-1-8 Moncho, 332-0012, Kawaguchi, Saitama, Japan.,Graduate School of Engineering, Toin University of Yokohama, 225-8503, Kurogane-cho, Aoba-ku, Yokohama, Kanagawa, Japan
| | - Kengo Suzuki
- Hamamatsu Photonics K. K, 812 Joko-cho, 341-3196, Higashi-ku, Hamamatsu, Shizuoka, Japan
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Crystal structures and Full Interaction Maps of proton transfer coordination compounds, templated via Schiff base hydrolysis in situ. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114628] [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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37
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Sahu M, Kumar Manna A, Rout K, Mondal J, Patra GK. A highly selective thiosemicarbazone based Schiff base chemosensor for colorimetric detection of Cu2+ and Ag+ ions and turn-on fluorometric detection of Ag+ ions. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119633] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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38
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Abstract
Neutron and X-ray crystallography are complementary to each other. While X-ray scattering is directly proportional to the number of electrons of an atom, neutrons interact with the atomic nuclei themselves. Neutron crystallography therefore provides an excellent alternative in determining the positions of hydrogens in a biological molecule. In particular, since highly polarized hydrogen atoms (H+) do not have electrons, they cannot be observed by X-rays. Neutron crystallography has its own limitations, mainly due to inherent low flux of neutrons sources, and as a consequence, the need for much larger crystals and for different data collection and analysis strategies. These technical challenges can however be overcome to yield crucial structural insights about protonation states in enzyme catalysis, ligand recognition, as well as the presence of unusual hydrogen bonds in proteins.
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Raghavendra S, Chandra Shekhara Shetty T, Chidan Kumar CS, Naveen S, Chandraju S, Maidur SR, Shankaragouda Patil P, Ananthnag GS, Dharmaprakash SM. Novel acentric D-π-A-π-D nonlinear optical (2E, 4E)-[dimethylamino) phenyl]-1-(4methylphenyl)penta-2,4-dien-1-one crystal for second and third order nonlinear applications. J CHEM SCI 2020. [DOI: 10.1007/s12039-020-01764-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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40
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Liao J, Chang H, Fang C, Liu CW. T‐symmetric 40‐nucleus silver clusters assembled by hetero‐anions. J CHIN CHEM SOC-TAIP 2020. [DOI: 10.1002/jccs.202000071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jian‐Hong Liao
- Department of Chemistry National Dong Hwa University Hualien Taiwan R.O.C
| | - Hao‐Wei Chang
- Department of Chemistry National Dong Hwa University Hualien Taiwan R.O.C
| | - Ching‐Shiang Fang
- Department of Chemistry National Dong Hwa University Hualien Taiwan R.O.C
| | - C. W. Liu
- Department of Chemistry National Dong Hwa University Hualien Taiwan R.O.C
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Abstract
This chapter aims to give an overview of the process of interactive model building in macromolecular neutron crystallography for the researcher transitioning from X-ray crystallography alone. The two most popular programs for refinement and model building, phenix.refine and Coot, respectively, are used as examples, and familiarity with the programs is assumed. Some work-arounds currently required for proper communication between the programs are described. We also discuss the appearance of nuclear density maps and how this differs from that of electron density maps. Advice is given to facilitate deposition of jointly refined neutron/X-ray structures in the Protein Data Bank.
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42
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Dynamic nuclear polarization enhanced neutron crystallography: Amplifying hydrogen in biological crystals. Methods Enzymol 2020. [PMID: 32093831 DOI: 10.1016/bs.mie.2019.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Dynamic nuclear polarization (DNP) can provide a powerful means to amplify neutron diffraction from biological crystals by 10-100-fold, while simultaneously enhancing the visibility of hydrogen by an order of magnitude. Polarizing the neutron beam and aligning the proton spins in a polarized sample modulates the coherent and incoherent neutron scattering cross-sections of hydrogen, in ideal cases amplifying the coherent scattering by almost an order of magnitude and suppressing the incoherent background to zero. This chapter describes current efforts to develop and apply DNP techniques for spin polarized neutron protein crystallography, highlighting concepts, experimental design, labeling strategies and recent results, as well as considering new strategies for data collection and analysis that these techniques could enable.
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43
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Liebschner D, Afonine PV, Moriarty NW, Adams PD. What are the current limits on determination of protonation state using neutron macromolecular crystallography? Methods Enzymol 2020; 634:225-255. [PMID: 32093835 PMCID: PMC7571246 DOI: 10.1016/bs.mie.2020.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2024]
Abstract
The rate of deposition of models determined by neutron diffraction, or a hybrid approach that combines X-ray and neutron diffraction, has increased in recent years. The benefit of neutron diffraction is that hydrogen atom (H) positions are detectable, allowing for the determination of protonation state and water molecule orientation. This study analyses all neutron models deposited in the Protein Data Bank to date, focusing on protonation state and properties of H (or deuterium, D) atoms as well as the details of water molecules. In particular, clashes and hydrogen bonds involving H or D atoms are investigated. As water molecules are typically the least reproducible part of a structural model, their positions in neutron models were compared to those in homologous high-resolution X-ray structures. For models determined by joint refinement against X-ray and neutron data, the water structure comparison was also carried out for models re-refined against the X-ray data alone. The homologues have generally fewer conserved water molecules where X-ray only was used and the positions of equivalent waters vary more than in the case of the hybrid X-ray model. As neutron diffraction data are generally less complete than X-ray data, the influence of neutron data completeness on nuclear density maps was also analyzed. We observe and discuss systematic map quality deterioration as result of data incompleteness.
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Affiliation(s)
- Dorothee Liebschner
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States.
| | - Pavel V Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States; Department of Bioengineering, University of California Berkeley, Berkeley, CA, United States
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Abstract
This chapter introduces this topic for the whole volume. It is not a review, rather it presents the basics, the key considerations and forward references to the other chapters. This starts by setting the scene of principles and overall strategy, moves onto planning an experiment including its feasibility and then outlines practicalities with options for the experiment. The crystal structure that results will lead to publication and associated with it, Protein Data Bank deposition.
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Dutta S, Mayans J, Ghosh A. Facile synthesis of a new Cu(ii) complex with an unsymmetrical ligand and its use as an O 3 donor metalloligand in the synthesis of Cu(ii)-Mn(ii) complexes: structures, magnetic properties, and catalytic oxidase activities. Dalton Trans 2020; 49:1276-1291. [PMID: 31909778 DOI: 10.1039/c9dt04315b] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new, facile Cu(ii) template method has been employed for the unsymmetrical dicondensation of 1,2-ethylenediamine with salicylaldehyde and o-vanillin. The mononuclear complex, [CuL] (1), thus obtained, has been used as an O3 donor metalloligand for the synthesis of four new Cu(ii)-Mn(ii) complexes, [(CuL)MnCl2] (2), [(CuL)Mn(NO3)2(CH3OH)]n (3), {[(CuL)Mn(benz)(H2O)]2·(CuL)2(ClO4)2} (4) and [(CuL)Mn(benz)Cl]2 (5) (where benz = benzoate). Single-crystal structural analyses reveal that 2 is a dinuclear complex while complex 3 is polymeric with a repeating dinuclear [(CuL)Mn(NO3)2(CH3OH)] unit, linked via the nitrate ion. Both 4 and 5 are discrete tetranuclear complexes, where the dinuclear units [(CuL)Mn(benz)(H2O)] and [(CuL)Mn(benz)Cl] are connected by double benzoate and double chloride bridges, respectively. In complex 4, two monomeric [CuL] units are cocrystallized with the tetranuclear complex. An important difference in the structure of 4 from the other three complexes is that one solvent water molecule is coordinated to each Mn(ii) ion, which makes complex 4 catalytically very active towards mimicking catecholase and phenoxazinone synthase-like oxidation reactions. The turnover numbers (kcat) for the aerial oxidation of 3,5-di-tert-butylcatechol and o-aminophenol are 399 h-1 and 230 h-1, respectively. The evidence of the intermediate species in the mass spectra indicates possible heterometallic cooperation where the Mn(ii) center helps in substrate binding and Cu(ii) participates in the oxidation reactions with molecular oxygen. Cyclic voltammetry measurements suggest the reduction of Cu(ii) to Cu(i) during the catalytic process. Temperature-dependent dc molar magnetic susceptibility measurements reveal that complexes 2-5 are antiferromagnetically coupled with the exchange coupling constants (J) of J = -13.5 cm-1 and J = -13.5 cm-1 for 2 and 3, respectively, J1 = -12.6 cm-1 and J2 = -1.20 cm-1 for complex 4 and J1 = -13.24 cm-1 and J2 = 0.36 cm-1 for complex 5 as is expected from the Cu-O-Mn bridging angles.
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Affiliation(s)
- Sabarni Dutta
- Department of Chemistry, University College of Science, University of Calcutta, 92, A.P.C. Road, Kolkata 700 009, India.
| | - Júlia Mayans
- Departament de Química Inorgànica I Orgànica, Secció Inorgànica and Institut de Nanosciència I Nanotecnologia (IN2UB), Martíi Franqués 1-11, 08028, Barcelona, Spain
| | - Ashutosh Ghosh
- Department of Chemistry, University College of Science, University of Calcutta, 92, A.P.C. Road, Kolkata 700 009, India.
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Brocha Silalahi RP, Huang GR, Liao JH, Chiu TH, Chakrahari KK, Wang X, Cartron J, Kahlal S, Saillard JY, Liu CW. Copper Clusters Containing Hydrides in Trigonal Pyramidal Geometry. Inorg Chem 2020; 59:2536-2547. [DOI: 10.1021/acs.inorgchem.9b03501] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rhone P. Brocha Silalahi
- Department of Chemistry, National Dong Hwa University, No. 1, Sec. 2, Da Hsueh Rd, Shoufeng, Hualien 97401, Taiwan, R.O.C
| | - Guan-Rong Huang
- Department of Chemistry, National Dong Hwa University, No. 1, Sec. 2, Da Hsueh Rd, Shoufeng, Hualien 97401, Taiwan, R.O.C
| | - Jian-Hong Liao
- Department of Chemistry, National Dong Hwa University, No. 1, Sec. 2, Da Hsueh Rd, Shoufeng, Hualien 97401, Taiwan, R.O.C
| | - Tzu-Hao Chiu
- Department of Chemistry, National Dong Hwa University, No. 1, Sec. 2, Da Hsueh Rd, Shoufeng, Hualien 97401, Taiwan, R.O.C
| | | | - Xiaoping Wang
- Neutron Scattering Division, Neutron Sciences Directorate Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Julien Cartron
- Univ. Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France
| | - Samia Kahlal
- Univ. Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France
| | | | - C. W. Liu
- Department of Chemistry, National Dong Hwa University, No. 1, Sec. 2, Da Hsueh Rd, Shoufeng, Hualien 97401, Taiwan, R.O.C
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Katla J, Shaik A, Dahiwadkar R, Thiruvenkatam V, Kanvah S. One- and Two-Component Organogels Containing Cyanostilbene without any Auxiliary Substituents. Chempluschem 2020; 84:1789-1795. [PMID: 31943862 DOI: 10.1002/cplu.201900564] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 09/27/2019] [Indexed: 12/11/2022]
Abstract
Pyridyl acrylonitrile without traditional auxiliary groups form stable organogels in ethanol. The addition of a second non-gelating cyanostilbene component results in a more stable two-component gel. Single crystal X-ray data reveal the influence of C-H⋅ ⋅ ⋅N, C-H⋅ ⋅ ⋅π, and π-π interactions in the formation of organogels. The morphology of the xerogels was studied by using SEM, which showed the self-assembly of molecules to fibers and sheet-like structures, and phase differences upon the gel formation and the structural phase characterization was measured using powder XRD. Exposure of the organogels to acidic (TFA) vapors results in distinct color changes and loss of gelation properties, thus highlighting the potential of these gels in sensing. The results represent a rare example of two-component organogels using two different cyanostilbene units and show that functional two-component organogels can be formed by utilizing the synergistic effects of the individual components.
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Affiliation(s)
- Jagadish Katla
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj Gandhinagar, 382355, India
| | - Althaf Shaik
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj Gandhinagar, 382355, India
| | - Rahul Dahiwadkar
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj Gandhinagar, 382355, India
| | - Vijay Thiruvenkatam
- Department of Biological Engineering and Physics, Indian Institute of Technology Gandhinagar, Palaj Gandhinagar, 382355, India
| | - Sriram Kanvah
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj Gandhinagar, 382355, India
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Albino M, Lhoste J, Body M, Legein C, Hémon-Ribaud A, Maisonneuve V, Leblanc M. Topotactic desolvation and condensation reactions of 3D Zn 3TiF 7(H 2O) 2(taz) 3·S (S = 3H 2O or C 2H 5OH). Dalton Trans 2020; 49:17758-17771. [DOI: 10.1039/d0dt03391j] [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
Thermodiffraction, IR, DFT calculations, and 1H and 19F NMR characterizations of the desolvatation and reversible condensation reactions of Zn3TiF7(taz)3 family.
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Affiliation(s)
- M. Albino
- Institut des Molécules et des Matériaux du Mans (IMMM)
- UMR 6283 CNRS
- Le Mans Université
- 72085 Le Mans
- France
| | - J. Lhoste
- Institut des Molécules et des Matériaux du Mans (IMMM)
- UMR 6283 CNRS
- Le Mans Université
- 72085 Le Mans
- France
| | - M. Body
- Institut des Molécules et des Matériaux du Mans (IMMM)
- UMR 6283 CNRS
- Le Mans Université
- 72085 Le Mans
- France
| | - C. Legein
- Institut des Molécules et des Matériaux du Mans (IMMM)
- UMR 6283 CNRS
- Le Mans Université
- 72085 Le Mans
- France
| | - A. Hémon-Ribaud
- Institut des Molécules et des Matériaux du Mans (IMMM)
- UMR 6283 CNRS
- Le Mans Université
- 72085 Le Mans
- France
| | - V. Maisonneuve
- Institut des Molécules et des Matériaux du Mans (IMMM)
- UMR 6283 CNRS
- Le Mans Université
- 72085 Le Mans
- France
| | - M. Leblanc
- Institut des Molécules et des Matériaux du Mans (IMMM)
- UMR 6283 CNRS
- Le Mans Université
- 72085 Le Mans
- France
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49
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Liebschner D, Afonine PV, Urzhumtsev AG, Adams PD. Implementation of the riding hydrogen model in CCTBX to support the next generation of X-ray and neutron joint refinement in Phenix. Methods Enzymol 2020; 634:177-199. [PMID: 32093832 PMCID: PMC7574815 DOI: 10.1016/bs.mie.2020.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A fundamental prerequisite for implementing new procedures of atomic model refinement against neutron diffraction data is the efficient handling of hydrogen atoms. The riding hydrogen model, which constrains hydrogen atom parameters to those of the non-hydrogen atoms, is a plausible parameterization for refinements. This work describes the implementation of the riding hydrogen model in the Computational Crystallography Toolbox and in Phenix. Riding hydrogen atoms can be found in several different configurations that are characterized by specific geometries. For each configuration, the hydrogen atom parameterization and the expressions for the gradients of refinement target function with respect to non-hydrogen parameters are described.
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Affiliation(s)
- Dorothee Liebschner
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States.
| | - Pavel V Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States
| | - Alexandre G Urzhumtsev
- Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Faculté des Sciences et Technologies, Université de Lorraine, Nancy, France
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States; Department of Bioengineering, University of California Berkeley, Berkeley, CA, United States
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50
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Manna AK, Chowdhury S, Patra GK. Combined experimental and theoretical studies on a phenyl thiadiazole-based novel turn-on fluorescent colorimetric Schiff base chemosensor for the selective and sensitive detection of Al3+. NEW J CHEM 2020. [DOI: 10.1039/d0nj01954b] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A phenyl thiadiazole based receptor (L) has been presented for fluorescent colorimetric detection of Al3+ ion with very low detection limit in aqueous medium. The probe L can be applied for logic gate formation, recovery of contaminated water samples and smart-phone based analysis.
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Affiliation(s)
- Amit Kumar Manna
- Department of Chemistry
- Guru Ghasidas Vishwavidyalaya
- Bilaspur (CG)
- India
| | | | - Goutam K. Patra
- Department of Chemistry
- Guru Ghasidas Vishwavidyalaya
- Bilaspur (CG)
- India
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