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The Relevance of Experimental Charge Density Analysis in Unraveling Noncovalent Interactions in Molecular Crystals. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123690. [PMID: 35744821 PMCID: PMC9229234 DOI: 10.3390/molecules27123690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/22/2022] [Accepted: 05/29/2022] [Indexed: 11/17/2022]
Abstract
The work carried out by our research group over the last couple of decades in the context of quantitative crystal engineering involves the analysis of intermolecular interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding using experimental charge density methodology is reviewed. The focus is to extract electron density distribution in the intermolecular space and to obtain guidelines to evaluate the strength and directionality of such interactions towards the design of molecular crystals with desired properties. Following the early studies on halogen bonding interactions, several "sigma-hole" interaction types with similar electrostatic origins have been explored in recent times for their strength, origin, and structural consequences. These include interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding. Experimental X-ray charge density analysis has proved to be a powerful tool in unraveling the strength and electronic origin of such interactions, providing insights beyond the theoretical estimates from gas-phase molecular dimer calculations. In this mini-review, we outline some selected contributions from the X-ray charge density studies to the field of non-covalent interactions (NCIs) involving elements of the groups 14-17 of the periodic table. Quantitative insights into the nature of these interactions obtained from the experimental electron density distribution and subsequent topological analysis by the quantum theory of atoms in molecules (QTAIM) have been discussed. A few notable examples of weak interactions have been presented in terms of their experimental charge density features. These examples reveal not only the strength and beauty of X-ray charge density multipole modeling as an advanced structural chemistry tool but also its utility in providing experimental benchmarks for the theoretical studies of weak interactions in crystals.
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2
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Bailly C. The bacterial thiopeptide thiostrepton. An update of its mode of action, pharmacological properties and applications. Eur J Pharmacol 2022; 914:174661. [PMID: 34863996 DOI: 10.1016/j.ejphar.2021.174661] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/29/2021] [Indexed: 12/20/2022]
Abstract
The bacterial thiopeptide thiostrepton (TS) is used as a veterinary medicine to treat bacterial infections. TS is a protein translation inhibitor, essentially active against Gram-positive bacteria and some Gram-negative bacteria. In procaryotes, TS abrogates binding of GTPase elongation factors to the 70S ribosome, by altering the structure of rRNA-L11 protein complexes. TS exerts also antimalarial effects by disrupting protein synthesis in the apicoplast genome of Plasmodium falciparum. Interestingly, the drug targets both the infectious pathogen (bacteria or parasite) and host cell, by inducing endoplasmic reticulum stress-mediated autophagy which contributes to enhance the host cell defense. In addition, TS has been characterized as a potent chemical inhibitor of the oncogenic transcription factor FoxM1, frequently overexpressed in cancers or other diseases. The capacity of TS to crosslink FoxM1, and a few other proteins such as peroxiredoxin 3 (PRX3) and the 19S proteasome, contributes to the anticancer effects of the thiopeptide. The anticancer activities of TS evidenced using diverse tumor cell lines, in vivo models and drug combinations are reviewed here, together with the implicated targets and mechanisms. The difficulty to formulate TS is a drag on the pharmaceutical development of the natural product. However, the design of hemisynthetic analogues and the use of micellar drug delivery systems should facilitate a broader utilization of the compound in human and veterinary medicines. This review shed light on the many pharmacological properties of TS, with the objective to promote its use as a pharmacological tool and medicinal product.
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Affiliation(s)
- Christian Bailly
- OncoWitan, Scientific Consulting Office, Lille, Wasquehal, 59290, France.
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3
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Dittrich B, Chan S, Wiggin S, Stevens JS, Pidcock E. Fast energy minimization of the CCDC drug-subset structures by molecule-in-cluster computations allows independent structure validation and model completion. CrystEngComm 2020. [DOI: 10.1039/d0ce00488j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Optimizing structures with computations on clusters of molecules permits generation of structure-specific restraints for refinement and structure validation.
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Affiliation(s)
| | | | - Seth Wiggin
- The Cambridge Crystallographic Data Center
- Cambridge
- UK
| | | | - Elna Pidcock
- The Cambridge Crystallographic Data Center
- Cambridge
- UK
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4
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Malaspina LA, Wieduwilt EK, Bergmann J, Kleemiss F, Meyer B, Ruiz-López MF, Pal R, Hupf E, Beckmann J, Piltz RO, Edwards AJ, Grabowsky S, Genoni A. Fast and Accurate Quantum Crystallography: From Small to Large, from Light to Heavy. J Phys Chem Lett 2019; 10:6973-6982. [PMID: 31633355 DOI: 10.1021/acs.jpclett.9b02646] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The coupling of the crystallographic refinement technique Hirshfeld atom refinement (HAR) with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) gives rise to the new quantum-crystallographic method HAR-ELMO. This method is significantly faster than HAR but as accurate and precise, especially concerning the free refinement of hydrogen atoms from X-ray diffraction data, so that the first fully quantum-crystallographic refinement of a protein is presented here. However, the promise of HAR-ELMO exceeds large molecules and protein crystallography. In fact, it also renders possible electron-density investigations of heavy elements in small molecules and facilitates the detection and isolation of systematic errors from physical effects.
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Affiliation(s)
- Lorraine A Malaspina
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Erna K Wieduwilt
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
| | - Justin Bergmann
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Florian Kleemiss
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
- Departement für Chemie und Biochemie , Universität Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Benjamin Meyer
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
| | - Manuel F Ruiz-López
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
| | - Rumpa Pal
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Emanuel Hupf
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Jens Beckmann
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Ross O Piltz
- Australian Nuclear Science and Technology Organisation , Australian Centre for Neutron Scattering , New Illawarra Road , Lucas Heights , NSW 2234 , Australia
| | - Alison J Edwards
- Australian Nuclear Science and Technology Organisation , Australian Centre for Neutron Scattering , New Illawarra Road , Lucas Heights , NSW 2234 , Australia
| | - Simon Grabowsky
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
- Departement für Chemie und Biochemie , Universität Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Alessandro Genoni
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
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5
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Korlyukov AA, Nelyubina YV. Quantum chemical methods in charge density studies from X-ray diffraction data. RUSSIAN CHEMICAL REVIEWS 2019. [DOI: 10.1070/rcr4866] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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6
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Meyer B, Genoni A. Libraries of Extremely Localized Molecular Orbitals. 3. Construction and Preliminary Assessment of the New Databanks. J Phys Chem A 2018; 122:8965-8981. [PMID: 30339393 DOI: 10.1021/acs.jpca.8b09056] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The fast and reliable determination of wave functions and electron densities of macromolecules has been one of the goals of theoretical chemistry for a long time, and in this context, several linear scaling techniques have been successfully devised over the years. Different approaches have been adopted to tackle this problem, and one of them exploits the fact that, according to the traditional chemical perception, molecules can be seen as constituted of recurring units (e.g., functional groups) with well-defined chemical features. This has led to the development of methods in which the global wave functions or electron densities of macromolecules are obtained by simply transferring density matrices or fuzzy electron densities associated with molecular fragments. In this context, we propose an alternative strategy that aims at quickly reconstructing wave functions and electron densities of proteins through the transfer of extremely localized molecular orbitals (ELMOs), which are orbitals strictly localized on small molecular units and, for this reason, easily transferable from molecule to molecule. To accomplish this task we have constructed original libraries of ELMOs that cover all the possible elementary fragments of the 20 natural amino acids in all their possible protonation states and forms. Our preliminary test calculations have shown that, compared to more traditional methods of quantum chemistry, the transfers from the novel ELMO databanks allow to obtain wave function and electron densities of large polypeptides and proteins at a significantly reduced computational cost. Furthermore, notwithstanding expected discrepancies, the obtained electron distributions and electrostatic potentials are in very good agreement with those obtained at Hartree-Fock and density functional theory (DFT) levels. Therefore, the results encourage to use the new libraries as alternatives to the popular pseudoatom-databases of crystallography in the refinement of crystallographic structures of macromolecules. In particular, in this context, we have already envisaged the coupling of the ELMO databanks with the promising Hirshfeld atom refinement technique to extend the applicability of the latter to very large systems.
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Affiliation(s)
- Benjamin Meyer
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019 , 1 Boulevard Arago , F-57078 Metz , France
| | - Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019 , 1 Boulevard Arago , F-57078 Metz , France
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7
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Di Costanzo L, Dutta S, Burley SK. Amino acid modifications for conformationally constraining naturally occurring and engineered peptide backbones: Insights from the Protein Data Bank. Biopolymers 2018; 109:e23230. [PMID: 30368772 DOI: 10.1002/bip.23230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 01/08/2023]
Abstract
Extensive efforts invested in understanding the rules of protein folding are now being applied, with good effect, in de novo design of proteins/peptides. For proteins containing standard α-amino acids alone, knowledge derived from experimentally determined three-dimensional (3D) structures of proteins and biologically active peptides are available from the Protein Data Bank (PDB), and the Cambridge Structural Database (CSD). These help predict and design protein structures, with reasonable confidence. However, our knowledge of 3D structures of biomolecules containing backbone modified amino acids is still evolving. A major challenge in de novo protein/peptide design concerns the engineering of conformationally constrained molecules with specific structural elements and chemical groups appropriately positioned for biological activity. This review explores four classes of amino acid modifications that constrain protein/peptide backbone structure. Systematic analysis of peptidic molecule structures (eg, bioactive peptides, inhibitors, antibiotics, and designed molecules), containing these backbone-modified amino acids, found in the PDB and CSD are discussed. The review aims to provide structure-function insights that will guide future design of proteins/peptides.
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Affiliation(s)
- Luigi Di Costanzo
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, U.S.A
| | - Shuchismita Dutta
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, U.S.A.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, U.S.A
| | - Stephen K Burley
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, U.S.A.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, U.S.A.,RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, U.S.A.,Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, U.S.A
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8
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Chodkiewicz ML, Migacz S, Rudnicki W, Makal A, Kalinowski JA, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Adams PD, Dominiak PM. DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs. J Appl Crystallogr 2018; 51:193-199. [PMID: 29507550 PMCID: PMC5822993 DOI: 10.1107/s1600576717015825] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/30/2017] [Indexed: 11/10/2022] Open
Abstract
It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB, 'densities in structural chemistry and molecular biology', has been developed. It addresses the challenge of providing for high performance on modern computing architectures. With parallelization options for both multi-core processors and graphics processing units (using CUDA), the library features calculation of X-ray scattering factors and their derivatives with respect to structural parameters, gives access to intermediate steps of the scattering factor calculations (thus allowing for experimentation with modifications of the underlying electron density model), and provides tools for basic structural crystallographic operations. Permissively (MIT) licensed, DiSCaMB is an open-source C++ library that can be embedded in both academic and commercial tools for X-ray structure refinement.
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Affiliation(s)
- Michał L. Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ulica Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Szymon Migacz
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
| | - Witold Rudnicki
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
- Institute of Informatics, University of Białystok, Białystok, Poland
| | - Anna Makal
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ulica Żwirki i Wigury 101, Warszawa, 02-089, Poland
| | - Jarosław A. Kalinowski
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Ralf W. Grosse-Kunstleve
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ulica Żwirki i Wigury 101, Warszawa, 02-089, Poland
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9
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Shi MW, Stewart SG, Sobolev AN, Dittrich B, Schirmeister T, Luger P, Hesse M, Chen Y, Spackman PR, Spackman MA, Grabowsky S. Approaching an experimental electron density model of the biologically active
trans
‐epoxysuccinyl amide group—Substituent effects vs. crystal packing. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ming W. Shi
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Scott G. Stewart
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Alexandre N. Sobolev
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Birger Dittrich
- Anorganische Chemie und Strukturchemie Heinrich‐Heine‐Universität Düsseldorf Düsseldorf Germany
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie Johannes‐Gutenberg‐Universität Mainz Mainz Germany
| | - Peter Luger
- Institut für Chemie und Biochemie, Anorganische Chemie Freie Universität Berlin Berlin Germany
| | - Malte Hesse
- Fachbereich 2—Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie Universität Bremen Bremen Germany
| | - Yu‐Sheng Chen
- ChemMatCARS The University of Chicago Argonne IL USA
| | - Peter R. Spackman
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Mark A. Spackman
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Simon Grabowsky
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
- Fachbereich 2—Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie Universität Bremen Bremen Germany
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10
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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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11
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Luger P, Dittrich B, Tacke R. Invariom based electron density studies on the C/Si analogues haloperidol/sila-haloperidol and venlafaxine/sila-venlafaxine. Org Biomol Chem 2015. [DOI: 10.1039/c5ob00728c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Hirshfeld surfaces of haloperidol hydropicrate (left) and sila-haloperidol hydrochloride (right) show comparable sites of ED concentrations due to comparable intermolecular environments.
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Affiliation(s)
- Peter Luger
- Institut für Chemie und Biochemie – Anorganische Chemie
- Freie Universität Berlin
- D-14195 Berlin
- Germany
| | - Birger Dittrich
- Institut für Angewandte und Anorganische Chemie
- Universität Hamburg
- D-20146 Hamburg
- Germany
| | - Reinhold Tacke
- Institut für Anorganische Chemie
- Universität Würzburg
- D-97074 Würzburg
- Germany
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12
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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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13
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Lübben J, Volkmann C, Grabowsky S, Edwards A, Morgenroth W, Fabbiani FPA, Sheldrick GM, Dittrich B. On the temperature dependence of H-U(iso) in the riding hydrogen model. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2014; 70:309-16. [PMID: 25970187 PMCID: PMC4075069 DOI: 10.1107/s2053273314010626] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/09/2014] [Indexed: 11/10/2022]
Abstract
The temperature dependence of hydrogen Uiso and parent Ueq in the riding hydrogen model is investigated by neutron diffraction, aspherical-atom refinements and QM/MM and MO/MO cluster calculations. Fixed values of 1.2 or 1.5 appear to be underestimated, especially at temperatures below 100 K. The temperature dependence of H-Uiso in N-acetyl-l-4-hydroxyproline monohydrate is investigated. Imposing a constant temperature-independent multiplier of 1.2 or 1.5 for the riding hydrogen model is found to be inaccurate, and severely underestimates H-Uiso below 100 K. Neutron diffraction data at temperatures of 9, 150, 200 and 250 K provide benchmark results for this study. X-ray diffraction data to high resolution, collected at temperatures of 9, 30, 50, 75, 100, 150, 200 and 250 K (synchrotron and home source), reproduce neutron results only when evaluated by aspherical-atom refinement models, since these take into account bonding and lone-pair electron density; both invariom and Hirshfeld-atom refinement models enable a more precise determination of the magnitude of H-atom displacements than independent-atom model refinements. Experimental efforts are complemented by computing displacement parameters following the TLS+ONIOM approach. A satisfactory agreement between all approaches is found.
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Affiliation(s)
- Jens Lübben
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Christian Volkmann
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Simon Grabowsky
- School of Chemistry and Biochemistry, Stirling Highway 35, WA-6009 Crawley, Australia
| | - Alison Edwards
- Bragg Institute, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Wolfgang Morgenroth
- Institut für Geowissenschaften, Abteilung Kristallographie, Goethe-Universität, Altenhöferallee 1, 60438 Frankfurt am Main, Germany
| | - Francesca P A Fabbiani
- GZG, Abteilung Kristallographie, Georg-August Universität, Goldschmidtstrasse 1, 37077 Göttingen, Germany
| | - George M Sheldrick
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Birger Dittrich
- Institut für Anorganische und Angewandte Chemie, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
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