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Pradhan BL, Lodhi L, Dey KK, Ghosh M. Analyzing atomic scale structural details and nuclear spin dynamics of four macrolide antibiotics: erythromycin, clarithromycin, azithromycin, and roxithromycin. RSC Adv 2024; 14:17733-17770. [PMID: 38832242 PMCID: PMC11145140 DOI: 10.1039/d4ra00718b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 05/26/2024] [Indexed: 06/05/2024] Open
Abstract
The current investigation centers on elucidating the intricate molecular architecture and dynamic behavior of four macrolide antibiotics, specifically erythromycin, clarithromycin, azithromycin, and roxithromycin, through the application of sophisticated solid-state nuclear magnetic resonance (SSNMR) methodologies. We have measured the principal components of chemical shift anisotropy (CSA) parameters, and the site-specific spin-lattice relaxation time at carbon nuclei sites. To extract the principal components of CSA parameters, we have employed 13C 2DPASS CP-MAS SSNMR experiments at two different values of magic angle spinning (MAS) frequencies, namely 2 kHz and 600 Hz. Additionally, the spatial correlation between 13C and 1H nuclei has been investigated using 1H-13C frequency switched Lee-Goldburg heteronuclear correlation (FSLGHETCOR) experiment at a MAS frequency of 24 kHz. Our findings demonstrate that the incorporation of diverse functional groups, such as the ketone group and oxime group with the lactone ring, exerts notable influences on the structure and dynamics of the macrolide antibiotic. In particular, we have observed a significant decrease in the spin-lattice relaxation time of carbon nuclei residing on the lactone ring, desosamine, and cladinose in roxithromycin, compared to erythromycin. Overall, our findings provide detailed insight into the relationship between the structure and dynamics of macrolide antibiotics, which is eventually correlated with their biological activity. This knowledge can be utilized to develop new and more effective drugs by providing a rational basis for drug discovery and design.
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Affiliation(s)
- Bijay Laxmi Pradhan
- Physics Section, Mahila Maha Vidyalaya, Banaras Hindu University Varanasi-221005 Uttar-Pradesh India
- Department of Physics, Institute of Science, Banaras Hindu University Varanasi-221005 Uttar-Pradesh India
| | - Lekhan Lodhi
- Department of Zoology, Dr Harisingh Gour Central University Sagar-470003 Madhya-Pradesh India
| | - Krishna Kishor Dey
- Department of Physics, Dr Harisingh Gour Central University Sagar-470003 Madhya-Pradesh India
| | - Manasi Ghosh
- Physics Section, Mahila Maha Vidyalaya, Banaras Hindu University Varanasi-221005 Uttar-Pradesh India
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2
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Pradhan B, Yadav JP, Lodhi L, Sen P, Dey KK, Ghosh M. Atomic-Scale Resolution Insights into Structural and Dynamic Differences between Ofloxacin and Levofloxacin. ACS OMEGA 2023; 8:24093-24105. [PMID: 37426250 PMCID: PMC10323956 DOI: 10.1021/acsomega.3c03406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023]
Abstract
This study employs advanced solid-state NMR techniques to investigate the atomic-level structure and dynamics of two enantiomers: ofloxacin and levofloxacin. The investigation focuses on critical attributes, such as the principal components of the chemical shift anisotropy (CSA) tensor, the spatial proximity of 1H and 13C nuclei, and site-specific 13C spin-lattice relaxation time, to reveal the local electronic environment surrounding specific nuclei. Levofloxacin, the levo-isomer of ofloxacin, exhibits higher antibiotic efficacy than its counterpart, and the dissimilarities in the CSA parameters indicate significant differences in the local electronic configuration and nuclear spin dynamics between the two enantiomers. Additionally, the study employs the 1H-13C frequency-switched Lee-Goldburg heteronuclear correlation (FSLGHETCOR) experiment to identify the presence of heteronuclear correlations between specific nuclei (C15 and H7 nuclei and C13 and H12 nuclei) in ofloxacin but not in levofloxacin. These observations offer insights into the link between bioavailability and nuclear spin dynamics, underscoring the significance of NMR crystallography approaches in advanced drug design.
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Affiliation(s)
- Bijay
Laxmi Pradhan
- Department
of Physics, Institute of Science, Banaras
Hindu University, Varanasi 221005, Uttar-Pradesh, India
- Physics
Section, Mahila Maha Vidyalaya, Banaras
Hindu University, Varanasi 221005, Uttar-Pradesh, India
| | - Jai Prakash Yadav
- Physics
Section, Mahila Maha Vidyalaya, Banaras
Hindu University, Varanasi 221005, Uttar-Pradesh, India
| | - Lekhan Lodhi
- Department
of Zoology, Dr. Harisingh Gour Central University, Sagar 470003, Madhya-Pradesh, India
| | - Prince Sen
- Department
of Physics, Dr. Harisingh Gour Central University, Sagar 470003, Madhya-Pradesh, India
| | - Krishna Kishor Dey
- Department
of Physics, Dr. Harisingh Gour Central University, Sagar 470003, Madhya-Pradesh, India
| | - Manasi Ghosh
- Physics
Section, Mahila Maha Vidyalaya, Banaras
Hindu University, Varanasi 221005, Uttar-Pradesh, India
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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: 22] [Impact Index Per Article: 5.5] [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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Danelius E, Poongavanam V, Peintner S, Wieske LHE, Erdélyi M, Kihlberg J. Solution Conformations Explain the Chameleonic Behaviour of Macrocyclic Drugs. Chemistry 2020; 26:5231-5244. [DOI: 10.1002/chem.201905599] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Indexed: 02/02/2023]
Affiliation(s)
- Emma Danelius
- Department of Chemistry-BMCUppsala University 75123 Uppsala Sweden
| | | | - Stefan Peintner
- Department of Chemistry-BMCUppsala University 75123 Uppsala Sweden
| | | | - Máté Erdélyi
- Department of Chemistry-BMCUppsala University 75123 Uppsala Sweden
| | - Jan Kihlberg
- Department of Chemistry-BMCUppsala University 75123 Uppsala Sweden
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Zhang Y, Pan Z, Rong C, Shao Y, Wang Y, Yu K. Transformation of antibacterial agent roxithromycin in sodium hypochlorite disinfection process of different water matrices. Sep Purif Technol 2019. [DOI: 10.1016/j.seppur.2018.11.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Hübschle CB, Ruhmlieb C, Burkhardt A, van Smaalen S, Dittrich B. On avoiding negative electron density in Gram-Charlier refinements of anharmonic motion: the example of glutathione. Z KRIST-CRYST MATER 2018. [DOI: 10.1515/zkri-2018-2060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Abstract
The structure of glutathione, γ-l-Glutamyl-l-cysteinyl-glycine (C10H17N3O6S), was studied by multi-temperature single-crystal X-ray diffraction. Residual density maps from conventional independent atom model refinement gave indication of anharmonic motion in the molecule. This was further investigated by invariom refinement with anisotropic displacement parameters for all atoms, which described asphericity due to chemical bonding and lone pairs; afterwards only the residual-density signal of anharmonic motion remained. Treating anharmonicity with third-order Gram-Charlier displacement parameters led to regions with unphysical negative electron density. In contrast, a maximum entropy method (MEM) determination of the electron density successfully takes the features into account. Respective difference electron density plots (MEM minus prior and [Invariom+GC] minus invariom) agree well with each other. Challenges in treating and understanding the phenomenon are discussed. A procedure is proposed how unphysical negative electron density can be avoided. It is closely related to the free lunch algorithm.
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Affiliation(s)
- Christian B. Hübschle
- Laboratory of Crystallography , University of Bayreuth, BGI-Gebäude , 95440 Bayreuth , Germany
| | - Charlotte Ruhmlieb
- Institut für Physikalische Chemie der Universität Hamburg , Martin-Luther-King-Platz 6 , 20146 Hamburg , Germany
| | - Anja Burkhardt
- Deutsches Elektronensynchrotron DESY, Hamburg , Notkestrasse 85 , 22607 Hamburg , Germany
| | - Sander van Smaalen
- Laboratory of Crystallography , University of Bayreuth, BGI-Gebäude , 95440 Bayreuth , Germany
| | - Birger Dittrich
- Heinrich-Heine Universität Düsseldorf , Institut für Anorganische Chemie und Strukturchemie , Universitätsstraße 1 , 40225 Düsseldorf , Germany
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Gionda A, Macetti G, Loconte L, Rizzato S, Orlando AM, Gatti C, Lo Presti L. A variable-temperature X-ray diffraction and theoretical study of conformational polymorphism in a complex organic molecule (DTC). RSC Adv 2018; 8:38445-38454. [PMID: 35559076 PMCID: PMC9090575 DOI: 10.1039/c8ra08063a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/07/2018] [Indexed: 11/28/2022] Open
Abstract
Two conformational crystal polymorphs of 3-diethylamino-4-(4-methoxyphenyl)-1,1-dioxo-4H-1λ6,2-thiazete-4-carbonitrile (DTC) have been analyzed in the 100 K-room temperature range by single crystal X-ray diffraction and high quality DFT calculations. DTC has strongly polar as well as aliphatic substituents but no hydrogen bonding groups, and thus qualifies as a test molecule for the relative importance of electrostatic vs. dispersion–repulsion terms. The two polymorphs have the same P21/n space group and differ by a flipping of the –OCH3 group, the two conformations being almost equi-energetic and separated by a low barrier. The system is monotropic in the observed temperature range with nearly identical thermal expansion coefficients and energy–temperature slopes, one phase consistently predicted to be more stable in agreement with the relative ease of appearance. Energy decompositions show that the electrostatic term is dominant and stabilizes with decreasing temperature. Dispersion and repulsion show the expected behavior, the former becoming more stabilizing at lower temperature in contrast with increasing repulsion at higher density. Absolute values and trends are very similar in the two phases, explaining the small total energy difference. Geometrical analyses of intermolecular contacts using fingerprint plots, as well as the study of molecular dipole moments as a function of T in the framework of the Quantum Theory of Atoms in Molecules, reveal more details of phase stability. A small conformational change in the asymmetric unit has a significant effect on how non-covalent interactions determine (i) the crystal packing and (ii) the effect of T on the relative balance of electrostatics and dispersion–repulsions.![]()
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Affiliation(s)
- Andrea Gionda
- Università degli Studi di Milano
- Department of Chemistry
- Italy
| | - Giovanni Macetti
- Università degli Studi di Milano
- Department of Chemistry
- Italy
- Centre for Materials Crystallography
- Århus University
| | - Laura Loconte
- Università degli Studi di Milano
- Department of Chemistry
- Italy
| | - Silvia Rizzato
- Università degli Studi di Milano
- Department of Chemistry
- Italy
| | | | - Carlo Gatti
- Centre for Materials Crystallography
- Århus University
- Denmark
- Istituto di Scienze e Tecnologie Molecolari
- Italian CNR
| | - Leonardo Lo Presti
- Università degli Studi di Milano
- Department of Chemistry
- Italy
- Centre for Materials Crystallography
- Århus University
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Woińska M, Jayatilaka D, Dittrich B, Flaig R, Luger P, Woźniak K, Dominiak PM, Grabowsky S. Validation of X-ray Wavefunction Refinement. Chemphyschem 2017; 18:3334-3351. [PMID: 29168318 DOI: 10.1002/cphc.201700810] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/22/2017] [Indexed: 11/10/2022]
Abstract
In this work, the quality of the electron density in crystals reconstructed by the multipolar model (MM) and by X-ray wavefunction refinement (XWR) is tested on a set of high-resolution X-ray diffraction data sets of four amino acids and six tripeptides. It results in the first thorough validation of XWR. Agreement statistics, figures of merit, residual- and deformation-density maps, as well as atomic displacement parameters are used to measure the quality of the reconstruction relative to the measured structure factors. Topological analysis of the reconstructed density is carried out to obtain atomic and bond-topological properties, which are subsequently compared to the values derived from benchmarking periodic DFT geometry optimizations. XWR is simultaneously in better agreement than the MM with both benchmarking theory and the measured diffraction pattern. In particular, the obvious problems with the description of polar bonds in the MM are significantly reduced by using XWR. Similarly, modeling of electron density in the vicinity of hydrogen atoms with XWR is visibly improved.
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Affiliation(s)
- Magdalena Woińska
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Dylan Jayatilaka
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Birger Dittrich
- Heinrich-Heine-Universität Düsseldorf, Anorganische Chemie und Strukturchemie, Gebäude 26.42.01.21, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Ralf Flaig
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxon, OX11 0DE, UK
| | - Peter Luger
- Freie Universität Berlin, Institut für Chemie und Biochemie, Fabeckstraße 36a, 14195, Berlin, Germany
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Simon Grabowsky
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2-Biologie/Chemie, Universität Bremen, Leobener Straße NW2, 28359, Bremen, Germany
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Dittrich B, Schürmann C, Hübschle CB. Invariom modeling of disordered structures: case studies on a dipeptide, an amino acid, and cefaclor, a cephalosporin antibiotic. Z KRIST-CRYST MATER 2016. [DOI: 10.1515/zkri-2016-1955] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Routines to facilitate the treatment of disorder in invariom modeling have been implemented in the open-source program MolecoolQt, a visualization program for charge-density work, and InvariomTool, a pre-processor program. Two published structures of an amino acid and a dipeptide and the new structure of cefaclor, a cephalosporin antibiotic, provide examples with increasing amounts of disorder, which can now be successfully modeled with invarioms. Like for ordered structures, these non-spherical scattering factors predicted by density functional theory significantly improve the structural model (figures of merit and standard deviations) also in these cases. Furthermore, they allow rapid calculation and comparison of the electrostatic potential and the molecular dipole moment for the different conformers present in the crystal structures.
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Affiliation(s)
- Birger Dittrich
- Heinrich-Heine Universität Düsseldorf, Anorganische Chemie und Strukturchemie, Material- und Strukturforschung, Universitätsstraße, 1, D-40225 Düsseldorf, Germany , Tel.: +49-211-8113147
| | - Christian Schürmann
- Institut für Anorganische Chemie der Universität Göttingen, Tammannstr., 4, D-37077 Göttingen, Germany
| | - Christian B. Hübschle
- University of Bayreuth, Lehrstuhl für Kristallographie, Universitätsstraße 30, D-95440 Bayreuth, Germany
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Wandtke CM, Lübben J, Dittrich B. Molecular Electrostatic Potentials from Invariom Point Charges. Chemphyschem 2016; 17:2238-46. [DOI: 10.1002/cphc.201600213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Claudia M. Wandtke
- Institut für Anorganische Chemie; Georg-August-Universität; Tammannstr. 4 37077 Göttingen Germany
| | - Jens Lübben
- Anorganische Chemie und Strukturchemie; Heinrich-Heine Universität Düsseldorf; Universitätsstraße 1, Gebäude 26.42.01.21 40225 Düsseldorf Germany
- Institut für Anorganische Chemie; Georg-August-Universität; Tammannstr. 4 37077 Göttingen Germany
| | - Birger Dittrich
- Anorganische Chemie und Strukturchemie; Heinrich-Heine Universität Düsseldorf; Universitätsstraße 1, Gebäude 26.42.01.21 40225 Düsseldorf Germany
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11
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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: 172] [Impact Index Per Article: 21.5] [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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12
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Ericson DL, Yin X, Scalia A, Samara YN, Stearns R, Vlahos H, Ellson R, Sweet RM, Soares AS. Acoustic Methods to Monitor Protein Crystallization and to Detect Protein Crystals in Suspensions of Agarose and Lipidic Cubic Phase. ACTA ACUST UNITED AC 2016; 21:107-14. [DOI: 10.1177/2211068215616365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Indexed: 11/16/2022]
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13
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Nelyubina YV, Ananyev IV, Novikov VV, Lyssenko KA. Invariom approach to electron density studies of open-shell compounds: the case of an organic nitroxide radical. RSC Adv 2016. [DOI: 10.1039/c6ra21365k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The study reports the successful modeling of electron density with invarioms for an open-shell compound, an organic nitroxide radical.
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Affiliation(s)
- Yu. V. Nelyubina
- A.N.Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
| | - I. V. Ananyev
- A.N.Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
| | - V. V. Novikov
- A.N.Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
| | - K. A. Lyssenko
- A.N.Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
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14
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Methodical aspects of experimental studies for the relationship of static and dynamic features of crystal structure: application of various atomic scattering factors to study the vibrational characteristics of molecular crystals. Russ Chem Bull 2015. [DOI: 10.1007/s11172-014-0726-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Nelyubina YV, Lyssenko KA. Probing Ionic Crystals by the Invariom Approach: An Electron Density Study of Guanidinium Chloride and Carbonate. Chemistry 2015; 21:9733-41. [PMID: 26015224 DOI: 10.1002/chem.201500296] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/21/2015] [Indexed: 11/09/2022]
Abstract
A comparative study of two guanidinium salts, chloride and carbonate, is carried out to test the performance of the invariom approach for ionic crystals. Although treating them as formed by isolated ions with no charge transfer between them, the invariom approach provides features of interionic contacts that are amazingly similar to those obtained from conventional charge density analysis of high-resolution X-ray diffraction data, thus emerging as an easy way towards reliable description of chemical bonding peculiarities in ionic crystals.
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Affiliation(s)
- Yulia V Nelyubina
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 119991, Vavilova Str., 28, Moscow (Russia).
| | - Konstantin A Lyssenko
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 119991, Vavilova Str., 28, Moscow (Russia)
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16
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Nelyubina YV, Korlyukov AA, Lyssenko KA. Invariom approach as a new tool in electron density studies of ionic liquids: a model case of 1-butyl-2,3-dimethylimidazolium chloride BDMIM[Cl]. RSC Adv 2015. [DOI: 10.1039/c5ra13752g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this comparative study of an ionic liquid (IL), BDMIM[Cl], the invariom approximation emerges as a useful tool in search for ‘structure–property’ relations in ILs, as entangling complex interplay of interionic interactions that operate in them.
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Affiliation(s)
- Yu. V. Nelyubina
- A.N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
| | - A. A. Korlyukov
- A.N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
- Pirogov Russian National Research Medical University
| | - K. A. Lyssenko
- A.N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russia
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17
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Dittrich B, Wandtke CM, Meents A, Pröpper K, Mondal KC, Samuel PP, Amin Sk N, Singh AP, Roesky HW, Sidhu N. Aspherical-atom modeling of coordination compounds by single-crystal X-ray diffraction allows the correct metal atom to be identified. Chemphyschem 2014; 16:412-9. [PMID: 25393218 DOI: 10.1002/cphc.201402600] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 09/13/2014] [Indexed: 11/10/2022]
Abstract
Single-crystal X-ray diffraction (XRD) is often considered the gold standard in analytical chemistry, as it allows element identification as well as determination of atom connectivity and the solid-state structure of completely unknown samples. Element assignment is based on the number of electrons of an atom, so that a distinction of neighboring heavier elements in the periodic table by XRD is often difficult. A computationally efficient procedure for aspherical-atom least-squares refinement of conventional diffraction data of organometallic compounds is proposed. The iterative procedure is conceptually similar to Hirshfeld-atom refinement (Acta Crystallogr. Sect. A- 2008, 64, 383-393; IUCrJ. 2014, 1,61-79), but it relies on tabulated invariom scattering factors (Acta Crystallogr. Sect. B- 2013, 69, 91-104) and the Hansen/Coppens multipole model; disordered structures can be handled as well. Five linear-coordinate 3d metal complexes, for which the wrong element is found if standard independent-atom model scattering factors are relied upon, are studied, and it is shown that only aspherical-atom scattering factors allow a reliable assignment. The influence of anomalous dispersion in identifying the correct element is investigated and discussed.
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Affiliation(s)
- Birger Dittrich
- Institut für Anorganische und Angewandte Chemie, Universität Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg (Germany); Institut für Anorganische Chemie, Georg-August-Universität, Tammannstrasse 4, 37077 Göttingen (Germany).
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18
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Dittrich B, Matta CF. Contributions of charge-density research to medicinal chemistry. IUCRJ 2014; 1:457-69. [PMID: 25485126 PMCID: PMC4224464 DOI: 10.1107/s2052252514018867] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 08/20/2014] [Indexed: 06/04/2023]
Abstract
This article reviews efforts in accurate experimental charge-density studies with relevance to medicinal chemistry. Initially, classical charge-density studies that measure electron density distribution via least-squares refinement of aspherical-atom population parameters are summarized. Next, interaction density is discussed as an idealized situation resembling drug-receptor interactions. Scattering-factor databases play an increasing role in charge-density research, and they can be applied both to small-molecule and macromolecular structures in refinement and analysis; software development facilitates their use. Therefore combining both of these complementary branches of X-ray crystallography is recommended, and examples are given where such a combination already proved useful. On the side of the experiment, new pixel detectors are allowing rapid measurements, thereby enabling both high-throughput small-molecule studies and macromolecular structure determination to higher resolutions. Currently, the most ambitious studies compute intermolecular interaction energies of drug-receptor complexes, and it is recommended that future studies benefit from recent method developments. Selected new developments in theoretical charge-density studies are discussed with emphasis on its symbiotic relation to crystallography.
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Affiliation(s)
- Birger Dittrich
- Institut für Anorganische und Angewandte Chemie, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Chérif F. Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia B3M 2J6, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4J3M, Canada
- Department of Chemistry, Saint Mary’s University, Halifax, Nova Scotia B3H 3C3, Canada
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19
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Nelyubina YV, Korlyukov AA, Lyssenko KA. Probing Weak Intermolecular Interactions by Using the Invariom Approach: A Comparative Study ofs-Tetrazine. Chemistry 2014; 20:6978-84. [DOI: 10.1002/chem.201304551] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 03/12/2014] [Indexed: 11/10/2022]
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20
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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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21
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Sovago I, Gutmann M, Hill JG, Senn HM, Thomas LH, Wilson CC, Farrugia LJ. Experimental Electron Density and Neutron Diffraction Studies on the Polymorphs of Sulfathiazole. CRYSTAL GROWTH & DESIGN 2014; 14:1227-1239. [PMID: 24672285 PMCID: PMC3963452 DOI: 10.1021/cg401757z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/13/2014] [Indexed: 05/31/2023]
Abstract
High resolution X-ray diffraction data on forms I-IV of sulfathiazole and neutron diffraction data on forms II-IV have been collected at 100 K and analyzed using the Atoms in Molecules topological approach. The molecular thermal motion as judged by the anisotropic displacement parameters (adp's) is very similar in all four forms. The adp of the thiazole sulfur atom had the greatest amplitude perpendicular to the five-membered ring, and analysis of the temperature dependence of the adps indicates that this is due to genuine thermal motion rather than a concealed disorder. A minor disorder (∼1-2%) is evident for forms I and II, but a statistical analysis reveals no deleterious effect on the derived multipole populations. The topological analysis reveals an intramolecular S-O···S interaction, which is consistently present in all experimental topologies. Analysis of the gas-phase conformation of the molecule indicates two low-energy theoretical conformers, one of which possesses the same intramolecular S-O···S interaction observed in the experimental studies and the other an S-O···H-N intermolecular interaction. These two interactions appear responsible for "locking" the molecular conformation. The lattice energies of the various polymorphs computed from the experimental multipole populations are highly dependent on the exact refinement model. They are similar in magnitude to theoretically derived lattice energies, but the relatively high estimated errors mean that this method is insufficiently accurate to allow a definitive stability order for the sulfathiazole polymorphs at 0 K to be determined.
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Affiliation(s)
- Ioana Sovago
- WESTChem
School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K.
| | - Matthias
J. Gutmann
- ISIS
Facility, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Chilton,
Didcot, Oxfordshire OX11 0QX, U.K.
| | - J. Grant Hill
- WESTChem
School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K.
| | - Hans Martin Senn
- WESTChem
School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K.
| | - Lynne H. Thomas
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K.
| | - Chick C. Wilson
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K.
| | - Louis J. Farrugia
- WESTChem
School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K.
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22
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Kirby IL, Brightwell M, Pitak MB, Wilson C, Coles SJ, Gale PA. Systematic experimental charge density analysis of anion receptor complexes. Phys Chem Chem Phys 2014; 16:10943-58. [DOI: 10.1039/c3cp54858a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first systematic electronic resolution study of a series of urea-based anion receptor complexes is presented and shows the binding strength to be greater for more basic anion–receptor pairs in the solid state.
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Affiliation(s)
| | | | | | - Claire Wilson
- Diamond Light Source
- Diamond House
- Harwell Science and Innovation Campus
- Didcot, UK
| | | | - Philip A. Gale
- Chemistry
- University of Southampton
- Southampton, UK
- Department of Chemistry
- Faculty of Science
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23
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Evaluation of the role of “dilution” in ionic crystal formation by analysis of electron density distribution for two solvatomorphs of 4-amino-3,5-dinitropyrazole ammonium salt. Russ Chem Bull 2013. [DOI: 10.1007/s11172-013-0247-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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24
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Dittrich B, Hübschle CB, Pröpper K, Dietrich F, Stolper T, Holstein J. The generalized invariom database (GID). ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2013. [DOI: 10.1107/s0108768113002280] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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25
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Luger P, Weber M, Hübschle C, Tacke R. Electron densities of bexarotene and disila-bexarotene from invariom application: a comparative study. Org Biomol Chem 2013; 11:2348-54. [DOI: 10.1039/c3ob27346f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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26
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Grey JL, Thompson DH. Challenges and opportunities for new protein crystallization strategies in structure-based drug design. Expert Opin Drug Discov 2012; 5:1039-45. [PMID: 21116481 DOI: 10.1517/17460441.2010.515583] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Structure-based drug design (SBDD) has emerged as a valuable pharmaceutical lead discovery tool, showing potential for accelerating the discovery process,while reducing developmental costs and boosting potencies of the drug that is ultimately selected. SBDD is an iterative, rational, lead compound sculpting process that involves both the synthesis of new derivatives and the evaluation of their binding to the target structure either through computational docking or elucidation of the target structure as a complex with the lead compound. This method heavily relies on the production of high resolution(< 2 Å) 3D structures of the drug target, obtained through X-ray crystallographic analysis, in the presence or absence of the drug candidate.The lack of generalized methods for high quality crystal production is still a major bottleneck in the process of macromolecular crystallization. This review provides a brief introduction to SBDD and describes several macromolecular crystallization strategies, with an emphasis on advances and challenges facing researchers in the field today. Recent trends in the development of more universal macromolecular crystallization techniques, particularly nucleation-based techniques that are applicable to both soluble and integral membrane proteins, are also discussed.
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Affiliation(s)
- Jessica Lynn Grey
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA
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27
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Bąk JM, Czyżnikowska Z, Dominiak PM. Is it possible to derive quantitative information on polarization of electron density from the multipolar model? Acta Crystallogr A 2012; 68:705-14. [PMID: 23075613 DOI: 10.1107/s010876731203317x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 07/23/2012] [Indexed: 11/10/2022] Open
Abstract
The accuracy of electrostatic properties estimated from the Hansen-Coppens multipolar model was verified. Tests were carried out to determine whether the multipolar model is accurate enough to study changes of electrostatic properties under the influence of a crystal field. Perturbed and unperturbed electron densities of individual molecules of amino acids and dipeptides were obtained from cluster and perturbation theory calculations. This enabled the changes in electrostatic properties values caused by polarization of the electron density to be characterized. Multipolar models were then fitted to the subsequent theoretical electron densities. The study revealed that electrostatic properties obtained from the multipolar models are significantly different from those obtained directly from the theoretical densities. The electrostatic properties of isolated molecules are reproduced better by multipolar models than the electrostatic properties of molecules in a crystal. Changes of electrostatic properties caused by perturbation of electron density due to the crystal environment are barely described by the multipolar model. As a consequence, the electrostatic properties obtained from multipolar models fitted to the perturbed theoretical densities derived either from cluster or periodic calculations do not differ much from those estimated from multipolar models fitted to densities of isolated molecules. The main reason for this seems to be related to an inadequate description of electron-density polarization in the vicinity of the nuclei by the multipolar model.
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28
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Holstein JJ, Hübschle CB, Dittrich B. Electrostatic properties of nine fluoroquinoloneantibiotics derived directly from their crystal structure refinements. CrystEngComm 2012. [DOI: 10.1039/c1ce05966a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Hübschle CB, Sheldrick GM, Dittrich B. ShelXle: a Qt graphical user interface for SHELXL. J Appl Crystallogr 2011. [PMID: 22477785 DOI: 10.1107/s0021889811043202.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
ShelXle is a graphical user interface for SHELXL [Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (F(o)) and difference density (F(o)-F(c)) maps. Special features of ShelXle include intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions. ShelXle is completely compatible with all features of SHELXL and is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.
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Affiliation(s)
- Christian B Hübschle
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Göttingen, Germany
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30
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Hübschle CB, Sheldrick GM, Dittrich B. ShelXle: a Qt graphical user interface for SHELXL. J Appl Crystallogr 2011; 44:1281-1284. [PMID: 22477785 PMCID: PMC3246833 DOI: 10.1107/s0021889811043202] [Citation(s) in RCA: 2315] [Impact Index Per Article: 178.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 10/18/2011] [Indexed: 11/22/2022] Open
Abstract
ShelXle is a user-friendly graphical user interface for SHELXL. It combines an editor with syntax highlighting for SHELXL-associated files with an interactive graphical display for visualization of a three-dimensional structure. ShelXle is a graphical user interface for SHELXL [Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo–Fc) maps. Special features of ShelXle include intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions. ShelXle is completely compatible with all features of SHELXL and is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.
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Affiliation(s)
- Christian B Hübschle
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Göttingen, Germany
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31
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Soares AS, Engel MA, Stearns R, Datwani S, Olechno J, Ellson R, Skinner JM, Allaire M, Orville AM. Acoustically mounted microcrystals yield high-resolution X-ray structures. Biochemistry 2011; 50:4399-401. [PMID: 21542590 PMCID: PMC3144476 DOI: 10.1021/bi200549x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate a general strategy for determining structures from showers of microcrystals. It uses acoustic droplet ejection to transfer 2.5 nL droplets from the surface of microcrystal slurries, through the air, onto mounting micromesh pins. Individual microcrystals are located by raster-scanning a several-micrometer X-ray beam across the cryocooled micromeshes. X-ray diffraction data sets merged from several micrometer-sized crystals are used to determine 1.8 Ǻ resolution crystal structures.
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Affiliation(s)
- Alexei S. Soares
- Biology Department, Brookhaven National Laboratory, Upton NY 11973-5000
| | - Matthew A. Engel
- National Synchrotron Light Source, Brookhaven National Laboratory, Upton NY 11973-5000
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794-2580
| | - Richard Stearns
- Labcyte Inc. 1190 Borregas Avenue, Sunnyvale, California 94089
| | - Sammy Datwani
- Labcyte Inc. 1190 Borregas Avenue, Sunnyvale, California 94089
| | - Joe Olechno
- Labcyte Inc. 1190 Borregas Avenue, Sunnyvale, California 94089
| | - Richard Ellson
- Labcyte Inc. 1190 Borregas Avenue, Sunnyvale, California 94089
| | - John M. Skinner
- Biology Department, Brookhaven National Laboratory, Upton NY 11973-5000
| | - Marc Allaire
- National Synchrotron Light Source, Brookhaven National Laboratory, Upton NY 11973-5000
| | - Allen M. Orville
- Biology Department, Brookhaven National Laboratory, Upton NY 11973-5000
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32
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Weber M, Grabowsky S, Hazra A, Naskar S, Banerjee S, Mondal NB, Luger P. Electron Density of Two Bioactive Oligocyclic Indole and Oxindole Derivatives Obtained from Low-Order X-Ray Data and Invariom Application. Chem Asian J 2011; 6:1390-7. [DOI: 10.1002/asia.201000650] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Indexed: 11/06/2022]
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33
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Bąk JM, Domagała S, Hübschle C, Jelsch C, Dittrich B, Dominiak PM. Verification of structural and electrostatic properties obtained by the use of different pseudoatom databases. Acta Crystallogr A 2011; 67:141-53. [PMID: 21325717 DOI: 10.1107/s0108767310049731] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 11/28/2010] [Indexed: 11/11/2022] Open
Abstract
The existing pseudoatom databases (ELMAM, Invariom, UBDB and ELMAM2) enable structure refinement to be performed with the use of aspherical scattering factors computed from the transferable aspherical atom model (TAAM) as an alternative to independent atom model refinement. In addition, electrostatic properties can be estimated with the help of the databases. The quality of the structural and electrostatic properties obtained from the individual databases was tested. On the basis of a 100 K high-resolution single-crystal X-ray diffraction experiment on L-His-L-Ala dihydrate and 23 K high-resolution data for L-Ala [Destro & Marsh (1988). J. Phys. Chem. 92, 966-973], the structural properties, electron-density distributions and molecular electrostatic potentials obtained from different TAAMs were compared to each other and to reference models. Experimental multipolar models and theoretical models refined against theoretical structure factors computed from periodic density functional theory (DFT) calculations were compared to the TAAMs in order to determine which model best describes the crystal-field effect. Unperturbed wavefunctions based on the MP2 and DFT calculations and properties obtained directly from these were used as a reference to judge how properly the databases reproduce the properties of isolated molecules. For Gly-L-His dihydrate, D,L-His and the above-mentioned two crystal structures, deviations of the molecular dipole moments and Coulombic intermolecular interaction energies from the reference values were examined. Root-mean-square deviations (RMSDs) and correlation coefficients were used as a quantitative measure of the quality of the analysed properties. TAAM refinements reproduce X-H bond lengths optimized in theoretical periodic calculations. Structural properties obtained from different database models are similar to each other. The anisotropic displacement parameters from TAAMs are similar to the results of experimental multipolar refinement; differences are about 0.5 and 2.5% for high-resolution and low-resolution data, respectively. Differences in dipole-moment magnitudes calculated from database models are about 5%, and directions differ by up to 30°. The values of electrostatic interaction energies estimated from the individual TAAMs differ greatly from each other and from the reference values. RMSDs are about 9-15 and 22-33 kJ mol(-1) for UBDB and the other database models, respectively.
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Affiliation(s)
- Joanna Maria Bąk
- Department of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
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