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Xu JY, Li HQ, Chen JM, Chen FZ. Crystal structure and characterization of monascin from the extracts of Monascus purpureus-fermented rice. Acta Crystallogr C Struct Chem 2024; 80:425-433. [PMID: 39028308 DOI: 10.1107/s2053229624006788] [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: 05/15/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
We present a novel solid form of monascin, an azaphilonoid derivative extracted from Monascus purpureus-fermented rice. The crystal structure, C21H26O5, was characterized by single-crystal X-ray diffraction and belongs to the orthorhombic space group P212121. To gain insight into the electronic properties of the short contacts in the crystalline state of monascin, we utilized the Experimental Library of Multipolar Atom Model 2 (ELMAM2) database to transfer the electron density of monascin in its crystalline state. Hirshfeld surface analysis, fingerprint analysis, electronic properties and energetic characterization reveal that intermolecular C-H...O hydrogen bonds play a crucial role in the noncovalent bonding interactions by connecting molecules into two- and three-dimensional networks. The molecular electrostatic potential (MEP) map of the monascin molecule demonstrates that negatively charged regions located at four O atoms are favoured binding sites for more positively charged amino acid residues during molecular recognition. In addition, powder X-ray diffraction confirms that no transformation occurs during the crystallization of monascin.
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Affiliation(s)
- Jia Yin Xu
- Mongolian Pharmaceutical Preparation Center, International Mongolian Hospital of Inner Mongolia, Hohhot, Inner Mongolia 010065, People's Republic of China
| | - Han Qing Li
- State Clinical Trial Institution of New Drugs, International Mongolian Hospital of Inner Mongolia, Hohhot, Inner Mongolia 010065, People's Republic of China
| | - Jian Ming Chen
- Department of Natural Chemistry, Greenpure Biopharma Co. Ltd, Chengdu, Sichuan 614041, People's Republic of China
| | - Feng Zheng Chen
- School of New Energy Materials and Chemistry, Leshan Normal University, Leshan, Sichuan 614000, People's Republic of China
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2
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Li HQ, Xu JY, Wu SS, Jin L. Molecular Insights into Water-Chloride and Water-Water Interactions in the Supramolecular Architecture of Aconine Hydrochloride Dihydrate. ACS OMEGA 2024; 9:11925-11941. [PMID: 38496984 PMCID: PMC10938397 DOI: 10.1021/acsomega.3c09696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/23/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024]
Abstract
Despite the previous preparation of aconine hydrochloride monohydrate (AHM), accurate determination of the crystal's composition was hindered by severely disordered water molecules within the crystal. In this study, we successfully prepared a new dihydrate form of the aconine hydrochloride [C25H42NO9+Cl-·2(H2O), aconine hydrochloride dihydrate (AHD)] and accurately refined all water molecules within the AHD crystal. Our objective is to elucidate both water-chloride and water-water interactions in the AHD crystal. The crystal structure of AHD was determined at 136 K using X-ray diffraction and a multipolar atom model was constructed by transferring charge-density parameters to explore the topological features of key short contacts. By comparing the crystal structures of dihydrate and monohydrate forms, we have observed that both AHD and AHM exhibit identical aconine cations, except for variations in the number of water molecules present. In the AHD crystal, chloride anions and water molecules serve as pivotal connecting hubs to establish three-dimensional hydrogen bonding networks and one-dimensional hydrogen bonding chain; both water-chloride and water-water interactions assemble supramolecular architectures. The crystal packing of AHD exhibits a complete reversal in the stacking order compared to AHM, thereby emphasizing distinct disparities between them. Hirshfeld surface analysis reveals that H···Cl- and H···O contacts play a significant role in constructing the hydrogen bonding network and chain within these supramolecular architectures. Furthermore, topological analysis and electrostatic interaction energy confirm that both water-chloride and water-water interactions stabilize supramolecular architectures through electrostatic attraction facilitated by H···Cl- and H···O contacts. Importantly, these findings are strongly supported by the existing literature evidence. Consequently, navigating these water-chloride and water-water interactions is imperative for ensuring storage and safe processing of this pharmaceutical compound.
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Affiliation(s)
- Han-Qing Li
- State
Clinical Trial Institution of New Drugs, International Mongolian Hospital of Inner Mongolia, Hohhot, Inner Mongolia 010065, People’s Republic
of China
- Mongolian
Medicine Laboratory, International Mongolian
Hospital of Inner Mongolia, Hohhot, Inner Mongolia 010065, People’s Republic of China
| | - Jia-Yin Xu
- Mongolian
Pharmaceutical Preparation Center, International
Mongolian Hospital of Inner Mongolia, Hohhot, Inner Mongolia 010065, People’s Republic
of China
| | - Shan-Shan Wu
- State
Clinical Trial Institution of New Drugs, International Mongolian Hospital of Inner Mongolia, Hohhot, Inner Mongolia 010065, People’s Republic
of China
| | - Liang Jin
- State
Clinical Trial Institution of New Drugs, International Mongolian Hospital of Inner Mongolia, Hohhot, Inner Mongolia 010065, People’s Republic
of China
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Chen K, Ray D, Ziebel ME, Gaggioli CA, Gagliardi L, Marinescu SC. Cu[Ni(2,3-pyrazinedithiolate) 2] Metal-Organic Framework for Electrocatalytic Hydrogen Evolution. ACS APPLIED MATERIALS & INTERFACES 2021; 13:34419-34427. [PMID: 34275268 DOI: 10.1021/acsami.1c08998] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The application of metal-organic frameworks (MOFs) as electrocatalysts for small molecule activation has been an emerging topic of research. Previous studies have suggested that two-dimensional (2D) dithiolene-based MOFs are among the most active for the hydrogen evolution reaction (HER). Here, a three-dimensional (3D) dithiolene-based MOF, Cu[Ni(2,3-pyrazinedithiolate)2] (1), is evaluated as an electrocatalyst for the HER. In pH 1.3 aqueous electrolyte solution, 1 exhibits a catalytic onset at -0.43 V vs the reversible hydrogen electrode (RHE), an overpotential (η10 mA/cm2) of 0.53 V to reach a current density of 10 mA/cm2, and a Tafel slope of 69.0 mV/dec. Interestingly, under controlled potential electrolysis, 1 undergoes an activation process that results in a more active catalyst with a 200 mV reduction in the catalytic onset and η10 mA/cm2. It is proposed that the activation process is a result of the cleavage of Cu-N bonds in the presence of protons and electrons. This hypothesis is supported by various experimental studies and density functional theory calculations.
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Affiliation(s)
- Keying Chen
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Debmalya Ray
- Department of Chemistry, Chemical Theory Center and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Michael E Ziebel
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Carlo A Gaggioli
- Department of Chemistry, Chemical Theory Center and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Laura Gagliardi
- Department of Chemistry, Pritzker School of Molecular Engineering, James Franck Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Smaranda C Marinescu
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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Jha KK, Gruza B, Chodkiewicz ML, Jelsch C, Dominiak PM. Refinements on electron diffraction data of β-glycine in MoPro: a quest for an improved structure model. J Appl Crystallogr 2021. [DOI: 10.1107/s160057672100580x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The advancement in 3D electron diffraction (3D ED) techniques that lead to a revolution in molecular structure determination using nano-sized crystals is now achieving atomic resolution. The structures can be obtained from 3D ED data with tools similar to those used for X-ray structure determination. In this context, the MoPro software, originally designed for structure and charge density refinements using X-ray diffraction data, has been adapted. Structure refinement on 3D ED data was achieved via implementation of electron scattering factors available in the literature and by application of the Mott–Bethe equation to X-ray scattering factors computed from the multipolar atom model. The multipolar model was parametrized using the transferable pseudoatom databanks ELMAM2 and UBDB. Applying the independent atom model (IAM), i.e. spherical neutral atom refinement, to 3D ED data on β-glycine in MoPro resulted in structure and refinement statistics comparable to those obtained from other well known software. Use of the transferred aspherical atom model (TAAM) led to improvement of the refinement statistics and a better fit of the model to the 3D ED data as compared with the spherical atom refinement. The anisotropic displacement parameters of non-H atoms appear underestimated by typically 0.003 Å2 for the non-H atoms in IAM refinement compared with TAAM. Thus, MoPro is shown to be an effective tool for crystal structure refinement on 3D ED data and allows use of a spherical or a multipolar atom model. Electron density databases can be readily transferred with no further modification needed when the Mott–Bethe equation is applied.
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Jha KK, Gruza B, Kumar P, Chodkiewicz ML, Dominiak PM. TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:296-306. [PMID: 32831250 DOI: 10.1107/s2052520620002917] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X-H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X-H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (dmin ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.
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Affiliation(s)
- Kunal Kumar Jha
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Barbara Gruza
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Prashant Kumar
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Michal Leszek Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warszawa, 02-089, Poland
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Faroque MU, Yousuf S, Zafar S, Choudhary MI, Ahmed M. Transferred multipolar atom model for 10β,17β-dihydroxy-17α-methylestr-4-en-3-one dihydrate obtained from the biotransformation of methyloestrenolone. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2016; 72:398-404. [PMID: 27146568 DOI: 10.1107/s2053229616005441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 03/31/2016] [Indexed: 11/10/2022]
Abstract
Biotransformation is the structural modification of compounds using enzymes as the catalysts and it plays a key role in the synthesis of pharmaceutically important compounds. 10β,17β-Dihydroxy-17α-methylestr-4-en-3-one dihydrate, C19H28O3·2H2O, was obtained from the fungal biotransformation of methyloestrenolone. The structure was refined using the classical independent atom model (IAM) and a transferred multipolar atom model using the ELMAM2 database. The results from the two refinements have been compared. The ELMAM2 refinement has been found to be superior in terms of the refinement statistics. It has been shown that certain electron-density-derived properties can be calculated on the basis of the transferred parameters for crystals which diffract to ordinary resolution.
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Affiliation(s)
- Muhammad Umer Faroque
- Department of Chemistry, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Sammer Yousuf
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Salman Zafar
- Institute of Chemical Sciences, University of Peshawar, Peshawar 25120, Pakistan
| | - M Iqbal Choudhary
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Maqsood Ahmed
- Department of Chemistry, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
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Woińska M, Grabowsky S, Dominiak PM, Woźniak K, Jayatilaka D. Hydrogen atoms can be located accurately and precisely by x-ray crystallography. SCIENCE ADVANCES 2016; 2:e1600192. [PMID: 27386545 PMCID: PMC4928899 DOI: 10.1126/sciadv.1600192] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/28/2016] [Indexed: 05/14/2023]
Abstract
Precise and accurate structural information on hydrogen atoms is crucial to the study of energies of interactions important for crystal engineering, materials science, medicine, and pharmacy, and to the estimation of physical and chemical properties in solids. However, hydrogen atoms only scatter x-radiation weakly, so x-rays have not been used routinely to locate them accurately. Textbooks and teaching classes still emphasize that hydrogen atoms cannot be located with x-rays close to heavy elements; instead, neutron diffraction is needed. We show that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A-H) that are in agreement with results from neutron diffraction mostly within a single standard deviation. The precision of the determination is also comparable between x-ray and neutron diffraction results. This has been achieved at resolutions as low as 0.8 Å using Hirshfeld atom refinement (HAR). We have applied HAR to 81 crystal structures of organic molecules and compared the A-H bond lengths with those from neutron measurements for A-H bonds sorted into bonds of the same class. We further show in a selection of inorganic compounds that hydrogen atoms can be located in bridging positions and close to heavy transition metals accurately and precisely. We anticipate that, in the future, conventional x-radiation sources at in-house diffractometers can be used routinely for locating hydrogen atoms in small molecules accurately instead of large-scale facilities such as spallation sources or nuclear reactors.
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Affiliation(s)
- Magdalena Woińska
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Simon Grabowsky
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2–Biologie/Chemie, Universität Bremen, Leobener Str. NW2, 28359 Bremen, Germany
| | - Paulina M. Dominiak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Dylan Jayatilaka
- School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Perth, Western Australia 6009, Australia
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Macchi P, Gillet JM, Taulelle F, Campo J, Claiser N, Lecomte C. Modelling the experimental electron density: only the synergy of various approaches can tackle the new challenges. IUCRJ 2015; 2:441-51. [PMID: 26175903 PMCID: PMC4491316 DOI: 10.1107/s2052252515007538] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/16/2015] [Indexed: 06/01/2023]
Abstract
Electron density is a fundamental quantity that enables understanding of the chemical bonding in a molecule or in a solid and the chemical/physical property of a material. Because electrons have a charge and a spin, two kinds of electron densities are available. Moreover, because electron distribution can be described in momentum or in position space, charge and spin density have two definitions and they can be observed through Bragg (for the position space) or Compton (for the momentum space) diffraction experiments, using X-rays (charge density) or polarized neutrons (spin density). In recent years, we have witnessed many advances in this field, stimulated by the increased power of experimental techniques. However, an accurate modelling is still necessary to determine the desired functions from the acquired data. The improved accuracy of measurements and the possibility to combine information from different experimental techniques require even more flexibility of the models. In this short review, we analyse some of the most important topics that have emerged in the recent literature, especially the most thought-provoking at the recent IUCr general meeting in Montreal.
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Affiliation(s)
- Piero Macchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Jean-Michel Gillet
- Laboratoire Structures Propriétés et Modélisation des Solides, UMR 8580, Université Paris Saclay CentraleSupélec, CNRS, Grande Voie des Vignes, 92295 Chatenay-Malabry, France
| | - Francis Taulelle
- Institut Lavoisier de Versailles, Université de Versailles Saint Quentin en Yvelines, 45 Avenue des Etats-Unis, Versailles, 78035, France
| | - Javier Campo
- Materials Science Institute of Aragón, CSIC-University of Zaragoza, Zaragoza, 50009, Spain
| | - Nicolas Claiser
- Cristallographie, Résonance Magnetique et Modélisations, CRM2, UMR 7036, Institut Jean Barriol, Université de Lorraine, Vandoeuvre-les-Nancy, BP239, F54506, France
| | - Claude Lecomte
- Cristallographie, Résonance Magnetique et Modélisations, CRM2, UMR 7036, Institut Jean Barriol, Université de Lorraine, Vandoeuvre-les-Nancy, BP239, F54506, France
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Henn J, Meindl K. About systematic errors in charge-density studies. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2014; 70:248-56. [PMID: 24815974 DOI: 10.1107/s2053273314000898] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 01/14/2014] [Indexed: 11/10/2022]
Abstract
The formerly introduced theoretical R values [Henn & Schönleber (2013). Acta Cryst. A69, 549-558] are used to develop a relative indicator of systematic errors in model refinements, R(meta), and applied to published charge-density data. The counter of R(meta) gives an absolute measure of systematic errors in percentage points. The residuals (Io - Ic)/σ(Io) of published data are examined. It is found that most published models correspond to residual distributions that are not consistent with the assumption of a Gaussian distribution. The consistency with a Gaussian distribution, however, is important, as the model parameter estimates and their standard uncertainties from a least-squares procedure are valid only under this assumption. The effect of correlations introduced by the structure model is briefly discussed with the help of artificial data and discarded as a source of serious correlations in the examined example. Intensity and significance cutoffs applied in the refinement procedure are found to be mechanisms preventing residual distributions from becoming Gaussian. Model refinements against artificial data yield zero or close-to-zero values for R(meta) when the data are not truncated and small negative values in the case of application of a moderate cutoff Io > 0. It is well known from the literature that the application of cutoff values leads to model bias [Hirshfeld & Rabinovich (1973). Acta Cryst. A29, 510-513].
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Affiliation(s)
| | - Kathrin Meindl
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona Science Park, Baldiri Reixach 15, 08028 Barcelona, Spain
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