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Roy S. The Transfer Free Energetics of L-Cysteine in Aqueous Sodium Chloride Solutions. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s0036024422130155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Solvation Thermodynamics of Amino Acids with Hydrophobic and Hydrophilic Side Chains in Aqueous Mixtures of Protic Ethylene Glycol. J SOLUTION CHEM 2020. [DOI: 10.1007/s10953-020-00996-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Saha S, Ghosh S, Ghosh S, Roy T, Dolui BK. Mode of hydrophilic and hydrophobic interactions of DL-Tyrosine, DL-Leucine, DL-Isoleucine and DL-Threonine in aqueous binary mixture of dipolar aprotic acetonitrile. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.136644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Topology of electron density and electrostatic potential of HIV reverse transcriptase inhibitor zidovudine from high resolution X-ray diffraction and charge density analysis. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.11.098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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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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Roy S, Guin PS, Mahali K, Dolui BK. Solvation thermodynamics of L-cystine, L-tyrosine, and L-leucine in aqueous-electrolyte media. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2017. [DOI: 10.1134/s0036024417120263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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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Roy S, Dolui BK. The chemical stability of L-isoleucine, L-threonine, and L-serine in aqueous solutions of KCl at 298.15 K. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2016. [DOI: 10.1134/s0036024416060224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Affiliation(s)
- Marta Marín-Luna
- Instituto de Química Médica (CSIC), C/Juan de la Cierva, 3, 28006-Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC), C/Juan de la Cierva, 3, 28006-Madrid, Spain
| | - José Elguero
- Instituto de Química Médica (CSIC), C/Juan de la Cierva, 3, 28006-Madrid, Spain
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Hossain A, Roy S, Ghosh S, Mondal S, Dolui BK. Solubility of dl-serine and dl-phenylalanine in aqueous mixtures of dimethyl sulfoxide and solvation thermodynamics. RSC Adv 2015. [DOI: 10.1039/c5ra12403d] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Solvation thermodynamic data of dl-serine and dl-phenylalanine in aqueous mixtures of dimethylsulfoxide at 298.15 K were determined from solubility measurement.
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Affiliation(s)
| | - Sanjay Roy
- Department of Chemistry
- Shibpur Dinobundhoo Institution (college)
- Howrah-711102
- India
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Capelli SC, Bürgi HB, Dittrich B, Grabowsky S, Jayatilaka D. Hirshfeld atom refinement. IUCRJ 2014; 1:361-79. [PMID: 25295177 PMCID: PMC4174878 DOI: 10.1107/s2052252514014845] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 06/24/2014] [Indexed: 05/20/2023]
Abstract
Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree-Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints - even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å(2) as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements - an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.
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Affiliation(s)
- Silvia C. Capelli
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milan, Italy
| | - Hans-Beat Bürgi
- Department of Chemistry and Biochemistry, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Department of Chemistry, Universität Zürich, Winterthurstrasse 190, 8057 Zürich, Switzerland
| | - 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 Göttingen, Tammannstr. 4, 37077 Göttingen, Germany
| | - Simon Grabowsky
- School of Chemistry and Biochemistry, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
| | - Dylan Jayatilaka
- School of Chemistry and Biochemistry, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
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Grabowsky S, Jayatilaka D, Fink RF, Schirmeister T, Engels B. Can Experimental Electron-Density Studies be Used as a Tool to Predict Biologically Relevant Properties of Low-Molecular Weight Enzyme Ligands? Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201200518] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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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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