1
|
Bürgi HB. The Cambridge Structural Database and structural dynamics. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:021302. [PMID: 38504974 PMCID: PMC10950365 DOI: 10.1063/4.0000244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/13/2024] [Indexed: 03/21/2024]
Abstract
With the availability of the computer readable information in the Cambridge Structural Database (CSD), wide ranging, largely automated comparisons of fragment, molecular, and crystal structures have become possible. They show that the distributions of interatomic distances, angles, and torsion angles for a given structural fragment occurring in different environments are highly correlated among themselves and with other observables such as spectroscopic signals, reaction and activation energies. The correlations often extend continuously over large ranges of parameter values. They are reminiscent of bond breaking and forming reactions, polyhedral rearrangements, and conformational changes. They map-qualitatively-the regions of the structural parameter space in which molecular dynamics take place, namely, the low energy regions of the respective (free) energy surfaces. The extension and continuous nature of the correlations provides an organizing principle of large groups of structural data and suggests a reconsideration of traditional definitions and descriptions of bonds, "nonbonded" and "noncovalent" interactions in terms of Lewis acids interacting with Lewis bases. These aspects are illustrated with selected examples of historic importance and with some later developments. It seems that the amount of information in the CSD (and other structural databases) and the knowledge on the nature of, and the correlations within, this body of information should allow one-in the near future-to make credible interpolations and possibly predictions of structures and their properties with machine learning methods.
Collapse
Affiliation(s)
- Hans-Beat Bürgi
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Berne, Freiestr. 3, CH-3012 Bern, Switzerland
| |
Collapse
|
2
|
Savastano M. Ye Olde supramolecular chemistry, its modern rebranding and overarching trends in chemistry. Dalton Trans 2024; 53:1373-1392. [PMID: 38180341 DOI: 10.1039/d3dt03686c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
We can describe current contingency of supramolecular chemistry as "post-halogen bonding", with clear reference to the success of the σ-hole model and the halogen bond concepts. This phase is characterized by a strong push towards a new nomenclature for non-covalent interactions, a group-by-group one focusing on the electrophile. As such nomenclature increasingly meets IUPAC endorsement, its proposers report resistances to such ideas, especially in the inorganic and coordination chemistry communities. The whole issue has been generating considerable debate in the last decade. Herein we fully embrace such discussion in the hope of involving a larger share of the relevant communities. Alternative descriptions are here reevaluated, novel views reconnected with older ones, and it is ultimately questioned whether the introduction of such a nomenclature and its subtending ideas would be beneficial. The themes of appreciation of general trends in chemistry, of counterintuitive interactions, of positioning of novel nomenclature with respect to existing ones, and of the extension of group-by-group naming from main block to d-block elements - as key and currently unresolved issues - are discussed. Equivalent, alternative and arguably more comprehensive descriptions are tentatively given, in the hope to overcome controversies together in the pursuit of higher rewards: a comprehensive shared view of supramolecular forces and a common language to express it.
Collapse
Affiliation(s)
- Matteo Savastano
- Department of Human Sciences for the Promotion of Quality of Life, University San Raffaele Roma, via di Val Cannuta 247, 00166, Rome, Italy.
| |
Collapse
|
3
|
Bürgi HB. Crystal structures. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:283-289. [PMID: 35695099 DOI: 10.1107/s205252062200292x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/16/2022] [Indexed: 06/15/2023]
Abstract
A personal view is offered on various solved and open problems related to crystal structures: the present state of reconstructing the crystal electron density from X-ray diffraction data; characterization of atomic and molecular motion from a combination of atomic displacement parameters and quantum chemical calculations; Bragg diffraction and diffuse scattering: twins, but different; models of real (as opposed to ideal) crystal structures from diffuse scattering; exploiting unexplored neighbourhoods of crystallography to mathematics, physics and chemistry.
Collapse
Affiliation(s)
- Hans Beat Bürgi
- Department of Chemistry, Biochemistry and Pharmacy, University of Berne, Freiestrasse 12, Bern, CH-3012, Switzerland
| |
Collapse
|
4
|
Pal R, Jelsch C, Momma K, Grabowsky S. π-Hole bonding in a new co-crystal hydrate of gallic acid and pyrazine: static and dynamic charge density analysis. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2022; 78:231-246. [PMID: 35411861 PMCID: PMC9004022 DOI: 10.1107/s2052520622001457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
A new cocrystal hydrate of gallic acid with pyrazine (4GA, Py, 4H2O; GA4PyW4) was obtained and characterized by single crystal X-ray diffraction. In addition to structure determination, experimental charge density analysis was carried out in terms of Multipole Modelling (MP), X-ray wavefunction refinement (XWR) and maximum entropy method (MEM). As a part of XWR, the structural refinement via Hirshfeld atom refinement was carried out and resulted in O-H bond lengths close to values from neutron diffraction. A systematic comparison of molecular conformations and aromatic interactions in this new cocrystal hydrate was performed with other existing polymorphs of gallic acid. In GA4PyW4, the two symmetry-independent gallic acid molecules have a syn COOH orientation and form the common (COOH)2 dimeric synthon. The carboxyl C atom displays the characteristics of π-holes with electropositive regions above and below the molecular plane and engages in acceptor-donor interactions with oxygen atoms of acidic O-H groups and phenol groups of neighbouring gallic acid molecules. The signature of the π-hole was identified from experimental charge density analysis, both in static density maps in MP and XWR as well as dynamic density in MEM, but it cannot be pinned down to a specific atom-atom interaction. This study presents the first comparison between an XWR and a MEM experimental electron-density determination.
Collapse
Affiliation(s)
- Rumpa Pal
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
- Institute of Inorganic Chemistry and Crystallography, Department 2 – Biology/Chemistry, University of Bremen, Leobener Str. 3, 28359 Bremen, Germany
| | | | - Koichi Momma
- National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, Japan
| | - Simon Grabowsky
- Institute of Inorganic Chemistry and Crystallography, Department 2 – Biology/Chemistry, University of Bremen, Leobener Str. 3, 28359 Bremen, Germany
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| |
Collapse
|
5
|
Savastano M, Bazzicalupi C, Bianchi A. Novel cyclen-polyiodide complexes: a reappraisal of I-I covalent and secondary bond limits. Dalton Trans 2022; 51:10728-10739. [PMID: 35293413 DOI: 10.1039/d2dt00185c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Supramolecular stabilization of polyiodides and iodine-dense phases is of high interest: this study explores the possibilities offered in this sense by diprotonated cyclen, affording two novel crystal structures. One of them contains at least one peculiar I⋯I interatomic distance (3.305(1) Å), falling well below the region commonly described by secondary bonding (3.4-3.7 Å) and essentially equal to the accepted limit for covalent bonding (3.30 Å): in other words, according to threshold distance values, we are relatively free to regard this interaction either as a bond or as contact. Lest the flip of a coin decides if we should or should not draw a bond in a polyiodide, statistical insights based on CSD surveys were used to put in perspective literature material and work out a meaningful assignment (as I82-). In doing so, we address how currently accepted threshold distance values came to be in the first place, their significance, soundness, and shortcomings in describing I82- and its formal fragments (I2, I3-, I5-). Discussion of the chemical meaning of the line representing bonding in I-I fragments in similar fringe cases, relating CSD data herein presented with the previous literature, is provided. Available information coincides quite well in supporting the necessity of a revision of broadly accepted threshold distance values.
Collapse
Affiliation(s)
- Matteo Savastano
- Department of Chemistry "Ugo Schiff", Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
| | - Carla Bazzicalupi
- Department of Chemistry "Ugo Schiff", Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
| | - Antonio Bianchi
- Department of Chemistry "Ugo Schiff", Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
| |
Collapse
|
6
|
Classification of So-Called Non-Covalent Interactions Based on VSEPR Model. Molecules 2021; 26:molecules26164939. [PMID: 34443526 PMCID: PMC8399763 DOI: 10.3390/molecules26164939] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 11/20/2022] Open
Abstract
The variety of interactions have been analyzed in numerous studies. They are often compared with the hydrogen bond that is crucial in numerous chemical and biological processes. One can mention such interactions as the halogen bond, pnicogen bond, and others that may be classified as σ-hole bonds. However, not only σ-holes may act as Lewis acid centers. Numerous species are characterized by the occurrence of π-holes, which also may play a role of the electron acceptor. The situation is complicated since numerous interactions, such as the pnicogen bond or the chalcogen bond, for example, may be classified as a σ-hole bond or π-hole bond; it ultimately depends on the configuration at the Lewis acid centre. The disadvantage of classifications of interactions is also connected with their names, derived from the names of groups such as halogen and tetrel bonds or from single elements such as hydrogen and carbon bonds. The chaos is aggravated by the properties of elements. For example, a hydrogen atom can act as the Lewis acid or as the Lewis base site if it is positively or negatively charged, respectively. Hence names of the corresponding interactions occur in literature, namely hydrogen bonds and hydride bonds. There are other numerous disadvantages connected with classifications and names of interactions; these are discussed in this study. Several studies show that the majority of interactions are ruled by the same mechanisms related to the electron charge shifts, and that the occurrence of numerous interactions leads to specific changes in geometries of interacting species. These changes follow the rules of the valence-shell electron-pair repulsion model (VSEPR). That is why the simple classification of interactions based on VSEPR is proposed here. This classification is still open since numerous processes and interactions not discussed in this study may be included within it.
Collapse
|
7
|
Bankura A, Saha J, Maity R, Das I. Non‐Bonding 1,4‐Sulphur‐Oxygen Interaction Governs the Reactivity of α‐Ketothioesters in Triphenylphosphine‐Catalyzed Cyclization with Acetylenedicarboxylates. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202001376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Abhijit Bankura
- Organic and Medicinal Chemistry Division CSIR-Indian Institute of Chemical Biology 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700 032 India
| | - Jayanta Saha
- Organic and Medicinal Chemistry Division CSIR-Indian Institute of Chemical Biology 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700 032 India
| | - Rajib Maity
- Organic and Medicinal Chemistry Division CSIR-Indian Institute of Chemical Biology 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700 032 India
| | - Indrajit Das
- Organic and Medicinal Chemistry Division CSIR-Indian Institute of Chemical Biology 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700 032 India
| |
Collapse
|
8
|
Mooibroek TJ. DFT and IsoStar Analyses to Assess the Utility of σ- and π-Hole Interactions for Crystal Engineering. Chemphyschem 2021; 22:141-153. [PMID: 33241585 PMCID: PMC7898519 DOI: 10.1002/cphc.202000927] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 11/25/2020] [Indexed: 11/25/2022]
Abstract
The interpretation of 36 charge neutral 'contact pairs' from the IsoStar database was supported by DFT calculations of model molecules 1-12, and bimolecular adducts thereof. The 'central groups' are σ-hole donors (H2 O and aromatic C-I), π-hole donors (R-C(O)Me, R-NO2 and R-C6 F5 ) and for comparison R-C6 H5 (R=any group or atom). The 'contact groups' are hydrogen bond donors X-H (X=N, O, S, or R2 C, or R3 C) and lone-pair containing fragments (R3 C-F, R-C≡N and R2 C=O). Nearly all the IsoStar distributions follow expectations based on the electrostatic potential of the 'central-' and 'contact group'. Interaction energies (ΔEBSSE ) are dominated by electrostatics (particularly between two polarized molecules) or dispersion (especially in case of large contact area). Orbital interactions never dominate, but could be significant (∼30 %) and of the n/π→σ*/π* kind. The largest degree of directionality in the IsoStar plots was typically observed for adducts more stable than ΔEBSSE ≈-4 kcal⋅mol-1 , which can be seen as a benchmark-value for the utility of an interaction in crystal engineering. This benchmark could be met with all the σ- and π-hole donors studied.
Collapse
Affiliation(s)
- Tiddo Jonathan Mooibroek
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van Amsterdam, Science Park 9041098 XHAmsterdamThe Netherlands
| |
Collapse
|
9
|
Grabowski SJ. Hydrogen Bond and Other Lewis Acid-Lewis Base Interactions as Preliminary Stages of Chemical Reactions. Molecules 2020; 25:E4668. [PMID: 33066201 PMCID: PMC7587390 DOI: 10.3390/molecules25204668] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/09/2020] [Accepted: 10/10/2020] [Indexed: 01/21/2023] Open
Abstract
Various Lewis acid-Lewis base interactions are discussed as initiating chemical reactions and processes. For example, the hydrogen bond is often a preliminary stage of the proton transfer process or the tetrel and pnicogen bonds lead sometimes to the SN2 reactions. There are numerous characteristics of interactions being first stages of reactions; one can observe a meaningful electron charge transfer from the Lewis base unit to the Lewis acid; such interactions possess at least partly covalent character, one can mention other features. The results of different methods and approaches that are applied in numerous studies to describe the character of interactions are presented here. These are, for example, the results of the Quantum Theory of Atoms in Molecules, of the decomposition of the energy of interaction or of the structure-correlation method.
Collapse
Affiliation(s)
- Sławomir J. Grabowski
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU & Donostia International Physics Center (DIPC) PK 1072, 20080 Donostia, Euskadi, Spain; ; Tel.: +34-943-018-187
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| |
Collapse
|
10
|
Roeleveld JJ, Lekanne Deprez SJ, Verhoofstad A, Frontera A, van der Vlugt JI, Mooibroek TJ. Engineering Crystals Using sp 3 -C Centred Tetrel Bonding Interactions. Chemistry 2020; 26:10126-10132. [PMID: 32557861 PMCID: PMC7496358 DOI: 10.1002/chem.202002613] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/16/2020] [Indexed: 11/06/2022]
Abstract
1,1,2,2-Tetracyanocyclopropane derivatives 1 and 2 were designed and synthesized to probe the utility of sp3 -C centred tetrel bonding interactions in crystal engineering. The crystal packing of 1 and 2 and their 1,4-dioxane cocrystals is dominated by sp3 -C(CN)2 ⋅⋅⋅O interactions, has significant C⋅⋅⋅O van der Waals overlap (≤0.266 Å) and DFT calculations indicate interaction energies of up to -11.0 kcal mol-1 . A cocrystal of 2 with 1,4-thioxane reveals that the cyclopropane synthon prefers interacting with O over S. Computational analyses revealed that the electropositive C2 (CN)4 pocket in 1 and 2 can be seen as a strongly directional 'tetrel-bond donor', similar to halogen bond or hydrogen bond donors. This disclosure is expected to have implications for the utility of such 'tetrel bond donors' in molecular disciplines such as crystal engineering, supramolecular chemistry, molecular recognition and medicinal chemistry.
Collapse
Affiliation(s)
- Julius J. Roeleveld
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
| | - Siebe J. Lekanne Deprez
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
| | - Abraham Verhoofstad
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
| | - Antonio Frontera
- Department of ChemistryUniversitat de les Illes BalearsCrta de Valldemossa km 7.507122Palmade Mallorca (BalearesSpain
| | - Jarl Ivar van der Vlugt
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
- Institute of ChemistryCarl von Ossietzky University OldenburgCarl-von-Ossietzky-Straße 9–1126219OldenburgGermany
| | - Tiddo Jonathan Mooibroek
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
| |
Collapse
|
11
|
Heywood VL, Alford TPJ, Roeleveld JJ, Lekanne Deprez SJ, Verhoofstad A, van der Vlugt JI, Domingos SR, Schnell M, Davis AP, Mooibroek TJ. Observations of tetrel bonding between sp 3-carbon and THF. Chem Sci 2020; 11:5289-5293. [PMID: 34122986 PMCID: PMC8159407 DOI: 10.1039/d0sc01559h] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/05/2020] [Indexed: 12/15/2022] Open
Abstract
We report the direct observation of tetrel bonding interactions between sp3-carbons of the supramolecular synthon 3,3-dimethyl-tetracyanocyclopropane (1) and tetrahydrofuran in the gas and crystalline phase. The intermolecular contact is established via σ-holes and is driven mainly by electrostatic forces. The complex manifests distinct binding geometries when captured in the crystalline phase and in the gas phase. We elucidate these binding trends using complementary gas phase quantum chemical calculations and find a total binding energy of -11.2 kcal mol-1 for the adduct. Our observations pave the way for novel strategies to engineer sp3-C centred non-covalent bonding schemes for supramolecular chemistry.
Collapse
Affiliation(s)
- Victoria L Heywood
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Thomas P J Alford
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Julius J Roeleveld
- van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Siebe J Lekanne Deprez
- van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Abraham Verhoofstad
- van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Jarl Ivar van der Vlugt
- van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
- Institute of Chemistry, Carl von Ossietzky University Oldenburg Carl-von-Ossietzky-Straße 9-11 D-12629 Oldenburg Germany
| | - Sérgio R Domingos
- Deutsches Elektronen-Synchrotron (DESY) Notkestraße 85 22607 Hamburg Germany
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron (DESY) Notkestraße 85 22607 Hamburg Germany
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel Max-Eyth-Str. 1 24118 Kiel Germany
| | - Anthony P Davis
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tiddo J Mooibroek
- van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| |
Collapse
|
12
|
Fabijańska M, Orzechowska M, Rybarczyk-Pirek AJ, Dominikowska J, Bieńkowska A, Małecki M, Ochocki J. Simple Trans-Platinum Complex Bearing 3-Aminoflavone Ligand Could Be a Useful Drug: Structure-Activity Relationship of Platinum Complex in Comparison with Cisplatin. Int J Mol Sci 2020; 21:ijms21062116. [PMID: 32204470 PMCID: PMC7139614 DOI: 10.3390/ijms21062116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/11/2020] [Accepted: 03/17/2020] [Indexed: 01/05/2023] Open
Abstract
Following previous studies devoted to trans–Pt(3-af)2Cl2, in this paper, the molecular structure and intermolecular interactions of the title complex are compared with other cisplatin analogues of which the crystal structures are presented in the Cambridge Structural Database (CSD). Molecular Hirshfeld surface analysis and computational methods were used to examine a possible relationship between the structure and anticancer activity of trans–Pt(3-af)2Cl2. The purpose of the article was also to investigate the effect of hyperthermia on the anticancer activity of cisplatin, cytostatics used in the treatment of patients with ovarian cancer and a new analogue of cisplatin-trans–Pt(3-af)2Cl2. The study was conducted on two cell lines of ovarian cancer sensitive to Caov-3 cytostatics and the OVCAR-3 resistant cisplatin line. The study used the MTT (3-(4,5-dimethylthiazol-2,5-diphenyltetrazolium bromide) cell viability assay, LDH (lactate dehydrogenase), and the quantitative evaluation method for measuring gene expression, i.e., qPCR with TagMan probes. Reduced survivability of OVCAR-3 and Caov-3 cells exposed to cytostatics at elevated temperatures (37 °C, 40 °C, 43 °C) was observed. Hyperthermia may increase the sensitivity of cells to platinum-based antineoplastic drugs and paclitaxel, which may be associated with the reduction of gene expression related to apoptotic processes.
Collapse
Affiliation(s)
- Małgorzata Fabijańska
- Department of Bioinorganic Chemistry, Medical University of Lodz, 1 Muszynskiego St., 90-151 Łódź, Poland
- Correspondence: (M.F.); (J.O.); Tel.: +48-(42)-6779220 (J.O.)
| | - Magdalena Orzechowska
- Department of Applied Pharmacy, Medical University of Warsaw, 1 Banacha St., 02–097 Warsaw, Poland; (M.O.); (A.B.); (M.M.)
| | - Agnieszka J. Rybarczyk-Pirek
- Theoretical and Structural Chemistry Group, Department of Physical Chemistry, Faculty of Chemistry, University of Łódź, Pomorska 163/165, 90-236 Łódź, Poland; (A.J.R.-P.); (J.D.)
| | - Justyna Dominikowska
- Theoretical and Structural Chemistry Group, Department of Physical Chemistry, Faculty of Chemistry, University of Łódź, Pomorska 163/165, 90-236 Łódź, Poland; (A.J.R.-P.); (J.D.)
| | - Alicja Bieńkowska
- Department of Applied Pharmacy, Medical University of Warsaw, 1 Banacha St., 02–097 Warsaw, Poland; (M.O.); (A.B.); (M.M.)
| | - Maciej Małecki
- Department of Applied Pharmacy, Medical University of Warsaw, 1 Banacha St., 02–097 Warsaw, Poland; (M.O.); (A.B.); (M.M.)
| | - Justyn Ochocki
- Department of Bioinorganic Chemistry, Medical University of Lodz, 1 Muszynskiego St., 90-151 Łódź, Poland
- Correspondence: (M.F.); (J.O.); Tel.: +48-(42)-6779220 (J.O.)
| |
Collapse
|
13
|
Szlachcic P, Uchacz T, Gryl M, Danel A, Wojtasik K, Kolek P, Jarosz B, Stadnicka KM. Combined XRD and DFT studies towards understanding the impact of intramolecular H-bonding on the reductive cyclization process in pyrazole derivatives. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
14
|
Bauzá A, Frontera A, Mooibroek TJ. π-Hole Interactions Involving Nitro Aromatic Ligands in Protein Structures. Chemistry 2019; 25:13436-13443. [PMID: 31453653 PMCID: PMC6856858 DOI: 10.1002/chem.201903404] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Indexed: 01/03/2023]
Abstract
Studying noncanonical intermolecular interactions between a ligand and a protein constitutes an emerging research field. Identifying synthetically accessible molecular fragments that can engage in intermolecular interactions is a key objective in this area. Here, it is shown that so-called "π-hole interactions" are present between the nitro moiety in nitro aromatic ligands and lone pairs within protein structures (water and protein carbonyls and sulfurs). Ample structural evidence was found in a PDB analysis and computations reveal interaction energies of about -5 kcal mol-1 for ligand-protein π-hole interactions. Several examples are highlighted for which a π-hole interaction is implicated in the superior binding affinity or inhibition of a nitro aromatic ligand versus a similar non-nitro analogue. The discovery that π-hole interactions with nitro aromatics are significant within protein structures parallels the finding that halogen bonds are biologically relevant. This has implications for the interpretation of ligand-protein complexation phenomena, for example, involving the more than 50 approved drugs that contain a nitro aromatic moiety.
Collapse
Affiliation(s)
- Antonio Bauzá
- Department of ChemistryUniversitat de les Illes BalearsCrta. de Valldemossa km 7.507122Palma (Baleares)Spain
| | - Antonio Frontera
- Department of ChemistryUniversitat de les Illes BalearsCrta. de Valldemossa km 7.507122Palma (Baleares)Spain
| | - Tiddo Jonathan Mooibroek
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
| |
Collapse
|
15
|
Intermolecular Non-Covalent Carbon-Bonding Interactions with Methyl Groups: A CSD, PDB and DFT Study. Molecules 2019; 24:molecules24183370. [PMID: 31527496 PMCID: PMC6767229 DOI: 10.3390/molecules24183370] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/05/2019] [Accepted: 09/12/2019] [Indexed: 01/15/2023] Open
Abstract
A systematic evaluation of the CSD and the PDB in conjunction with DFT calculations reveal that non-covalent Carbon-bonding interactions with X-CH3 can be weakly directional in the solid state (P ≤ 1.5) when X = N or O. This is comparable to very weak CH hydrogen bonding interactions and is in line with the weak interaction energies calculated (≤ -1.5 kcal·mol-1) of typical charge neutral adducts such as [Me3N-CH3···OH2] (2a). The interaction energy is enhanced to ≤-5 kcal·mol-1 when X is more electron withdrawing such as in [O2N-CH3··O=Cdme] (20b) and to ≤18 kcal·mol-1 in cationic species like [Me3O+-CH3···OH2]+ (8a).
Collapse
|
16
|
Marshall WG, Jones RH, Knight KS, Pulham CR, Smith RI. Investigation of the changes in hydrogen bonding accompanying the structural reorganization at 103 K in ammonium iodate. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019; 75:152-159. [PMID: 32830739 DOI: 10.1107/s2052520619000325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 01/07/2019] [Indexed: 06/11/2023]
Abstract
Neutron powder diffraction has been used to observe the changes in hydrogen bonding that occur as a function of temperature in ND4IO3 and, thus, determine the structural features that occur during the low-temperature (103 K) phase transition. It is shown that in the deuterated material the change is not a phase change per se but rather a structural reorganization in which the hydrogen bonding becomes firmly locked in at the phase transition temperature, and stays in this configuration upon further cooling to 4.2 K. In addition, both the differences and changes in the axial thermal expansion coefficients in the region 100-290 K can be explained by the changes involving both the hydrogen bonding and the secondary I...O halogen bonds.
Collapse
Affiliation(s)
- W G Marshall
- ISIS Facility, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - R H Jones
- School of Chemical and Physical Sciences, Keele University, Keele ST5 5BG, UK
| | - K S Knight
- ISIS Facility, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - C R Pulham
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - R I Smith
- ISIS Facility, STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| |
Collapse
|
17
|
Dmitrienko AO, Ananyev IV. Clustering of nonvalently bonded NO2…O2N fragments at C(sp3) atoms. Russ Chem Bull 2019. [DOI: 10.1007/s11172-019-2408-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
18
|
Hosseini-Hashemi Z, Mirzaei M, Jafari A, Hosseinpour P, Yousefi M, Frontera A, Lari Dashtbayaz M, Shamsipur M, Ardalani M. Effects of N-oxidation on the molecular and crystal structures and properties of isocinchomeronic acid, its metal complexes and their supramolecular architectures: experimental, CSD survey, solution and theoretical approaches. RSC Adv 2019; 9:25382-25404. [PMID: 35530069 PMCID: PMC9070054 DOI: 10.1039/c9ra05143k] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 08/01/2019] [Indexed: 12/17/2022] Open
Abstract
A series of new coordination complexes bearing H2pydco, an O-donor ligand, were synthesized and compared to corresponding complexes with H2pydc. The molecular and supramolecular structures were investigated using crystallography, solution phase and high level DFT studies.
Collapse
Affiliation(s)
| | - Masoud Mirzaei
- Department of Chemistry
- Faculty of Science
- Ferdowsi University of Mashhad
- Mashhad
- Iran
| | - Ameneh Jafari
- Department of Chemistry
- Faculty of Science
- Ferdowsi University of Mashhad
- Mashhad
- Iran
| | - Peyman Hosseinpour
- Department of Chemistry
- Faculty of Science
- Ferdowsi University of Mashhad
- Mashhad
- Iran
| | - Mohammad Yousefi
- Department of Chemistry
- Yadegar-e-Imam Khomeini (RAH) Shahr-e-Rey Branch
- Islamic Azad University
- Tehran
- Iran
| | - Antonio Frontera
- Department of Chemistry
- Universitat de les Illes Balears
- 07122 Palma de Mallorca (Baleares)
- Spain
| | - Mahmoud Lari Dashtbayaz
- Department of Economics and Administrative Sciences
- Ferdowsi University of Mashhad
- Mashhad
- Iran
| | | | - Mehdi Ardalani
- Department of Analytical Chemistry
- Razi University
- Kermanshah
- Iran
| |
Collapse
|
19
|
Doppert MT, van Overeem H, Mooibroek TJ. Intermolecular π-hole/n→π* interactions with carbon monoxide ligands in crystal structures. Chem Commun (Camb) 2018; 54:12049-12052. [PMID: 30294741 DOI: 10.1039/c8cc07557c] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A thorough analysis of the Cambridge Structure Database reveals that intermolecular π-hole/n→π* interactions with carbon monoxide ligands are abundant in the solid state and somewhat directional, particularly with fac-like M(CO)3 fragments (P < 4.0). High level DFT calculations suggest interacting energies up to about -10 kcal mol-1 for adducts of charge neutral complexes.
Collapse
Affiliation(s)
- Michael Timothy Doppert
- van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | | | | |
Collapse
|
20
|
Ruigrok van der Werve A, van Dijk YR, Mooibroek TJ. π-Hole/n→π* interactions with acetonitrile in crystal structures. Chem Commun (Camb) 2018; 54:10742-10745. [PMID: 30191212 DOI: 10.1039/c8cc06797j] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A thorough analysis of the Cambridge Structure Database shows that π-hole/n→π* interactions with acetonitrile are abundant in the solid state, particularly when acetonitrile is coordinated to a metal. The interaction is weakly directional (P ≤ 1.5) and high level computations suggest a complexation energy of about -5 kcal mol-1.
Collapse
Affiliation(s)
- Ad Ruigrok van der Werve
- van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | | | | |
Collapse
|
21
|
Marshall WG, Jones RH, Knight KS, Clews J, Darton RJ, Miller W, Coles SJ, Pitak MB. Structural organization in the trimethylamine iodine monochloride complex. CrystEngComm 2017. [DOI: 10.1039/c7ce00869d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The combination of a strong N⋯I–Cl halogen bond and a weak C–H⋯Cl hydrogen bond lead to the formation of dimeric species in the solid.
Collapse
Affiliation(s)
| | - Richard H. Jones
- Birchall Centre for Inorganic Materials
- School of Chemical and Physical Sciences
- Keele University
- Keele
- ST5 5BG UK
| | - Kevin S. Knight
- ISIS Facility
- STFC Rutherford Appleton Lab
- Harwell Oxford
- Oxon
- UK
| | - John Clews
- Birchall Centre for Inorganic Materials
- School of Chemical and Physical Sciences
- Keele University
- Keele
- ST5 5BG UK
| | - Richard J. Darton
- Birchall Centre for Inorganic Materials
- School of Chemical and Physical Sciences
- Keele University
- Keele
- ST5 5BG UK
| | - William Miller
- Birchall Centre for Inorganic Materials
- School of Chemical and Physical Sciences
- Keele University
- Keele
- ST5 5BG UK
| | - Simon J. Coles
- UK National Crystallography Service, Chemistry
- Faculty of Natural and Environmental Sciences
- University of Southampton
- Southampton SO17 1BJ
- UK
| | - Mateusz B. Pitak
- UK National Crystallography Service, Chemistry
- Faculty of Natural and Environmental Sciences
- University of Southampton
- Southampton SO17 1BJ
- UK
| |
Collapse
|
22
|
Mooibroek TJ. Coordinated nitrate anions can be directional π-hole donors in the solid state: a CSD study. CrystEngComm 2017. [DOI: 10.1039/c7ce01266g] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Within the CSD sp2O-atoms cluster closer to the π-hole of NO3−when nitrate is coordinated to a metal.
Collapse
Affiliation(s)
- Tiddo J. Mooibroek
- van ‘t Hoff Institute for Molecular Sciences
- Universiteit van Amsterdam
- 1098 XH Amsterdam
- The Netherlands
| |
Collapse
|
23
|
Ciancaleoni G, Arca M, Caramori GF, Frenking G, Schneider FSS, Lippolis V. Bonding Analysis in Homo‐ and Hetero‐Trihalide Species: A Charge Displacement Study. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201600471] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Gianluca Ciancaleoni
- Departamento de Química Universidade Federal de Santa Catarina 88040‐900 Florianópolis SC Brazil
| | - Massimiliano Arca
- Università degli Studi di Cagliari Dipartimento di Scienze Chimiche e Geologiche S.S. 554 Bivio per Sestu 09042 Monserrato (CA) Italy
| | - Giovanni F. Caramori
- Departamento de Química Universidade Federal de Santa Catarina 88040‐900 Florianópolis SC Brazil
| | - Gernot Frenking
- Fachbereich Chemie Philipps‐Universität Marburg Hans‐Meerwein‐Strasse 35032 Marburg Germany
| | - Felipe S. S. Schneider
- Departamento de Química Universidade Federal de Santa Catarina 88040‐900 Florianópolis SC Brazil
| | - Vito Lippolis
- Università degli Studi di Cagliari Dipartimento di Scienze Chimiche e Geologiche S.S. 554 Bivio per Sestu 09042 Monserrato (CA) Italy
| |
Collapse
|
24
|
[FHF]−—The Strongest Hydrogen Bond under the Influence of External Interactions. CRYSTALS 2015. [DOI: 10.3390/cryst6010003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
25
|
Krygowski TM, Szatylowicz H, Stasyuk OA, Dominikowska J, Palusiak M. Aromaticity from the viewpoint of molecular geometry: application to planar systems. Chem Rev 2014; 114:6383-422. [PMID: 24779633 DOI: 10.1021/cr400252h] [Citation(s) in RCA: 366] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Tadeusz M Krygowski
- Department of Chemistry, Warsaw University , Pasteura 1, 02-093 Warsaw, Poland
| | | | | | | | | |
Collapse
|
26
|
Abstract
Saraines have been isolated by the group of Cimino from the marine sponge Reniera sarai collected in the Bay of Naples. These alkaloids can be classified into two categories, depending on the type of their structure. Saraines 1-3 and isosaraines 1-3 are characterized by a trans-2-oxoquinolizidine moiety bound directly to a tetrahydropyridine ring, both nuclei being also linked by two alkyl chains of different lengths. On the other hand, saraines A-C and misenine present a diazatricyclic central core, showing an unusual interaction between an aldehyde and a tertiary amine and giving them a zwitterionic character, and flanked with two chains forming macrocycles. In a first part of the chapter, the isolation, spectral data, and structure elucidation of saraines are presented. Biological properties and biogenetic proposals concerning these compounds are then described. The most important part is devoted to synthetic approaches and total synthesis of saraine A.
Collapse
|
27
|
Eisenstein O, Dunitz JD. Potential Energy Surface of BH4−and Molecular Deformations Induced by an External Cation. Isr J Chem 2013. [DOI: 10.1002/ijch.198000035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
28
|
|
29
|
Diederich F. 125 Years of Chemistry in the Mirror of “Angewandte”. Angew Chem Int Ed Engl 2013; 52:2714-42. [DOI: 10.1002/anie.201300056] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Indexed: 01/09/2023]
|
30
|
|
31
|
Moberg C. Stereomutation in Trigonal-Bipyramidal Systems: A Unified Picture. Angew Chem Int Ed Engl 2011; 50:10290-2. [DOI: 10.1002/anie.201103375] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Indexed: 11/09/2022]
|
32
|
Moberg C. Konfigurationsänderung in trigonal-bipyramidalen Systemen: eine einheitliche Beschreibung. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103375] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
33
|
Mata I, Molins E, Alkorta I, Espinosa E. Tuning the Interaction Energy of Hydrogen Bonds: The Effect of the Substituent. J Phys Chem A 2011; 115:12561-71. [DOI: 10.1021/jp202917z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ignasi Mata
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Bellaterra, Spain
| | - Elies Molins
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Bellaterra, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
| | - Enrique Espinosa
- Laboratorie de Cristallographie, Résonance Magnétique et Modélisations, CRM2, UMR CNRS 7036, Institut Jean Barriol, Nancy-Université, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
| |
Collapse
|
34
|
Affiliation(s)
- Sławomir Janusz Grabowski
- Kimika Fakultatea, Euskal Herriko Unibertsitatea and Donostia International Physics Center (DIPC) P.K. 1072, 20080 Donostia, Euskadi, Spain
- IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain
| |
Collapse
|
35
|
Ohwada T. Orbital phase environments and stereoselectivities. Top Curr Chem (Cham) 2011; 289:129-81. [PMID: 21279574 DOI: 10.1007/128_2008_38] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Facial selections are reviewed to propose a new theory, orbital phase environment, for stereoselectivities of organic reactions. The orbital phase environment is a generalized idea of the secondary orbital interaction between the non-reacting centers and the unsymmetrization of the orbitals at the reacting centers arising from in-phase and out-of-phase overlapping with those at the neighboring non-reacting sites. In this context, the nucleophilic addition preferentially occurs on the face of the carbonyl functionality opposite to the better electron-donating orbital at the β position. In a similar manner to the carbonyl cases, the preferred reaction faces of olefins in electrophilic addition reactions are opposite to the better electron-donating orbitals at the β positions. The orbital phase environments in Diels-Alder reactions are also reviewed.
Collapse
Affiliation(s)
- Tomohiko Ohwada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113, Japan,
| |
Collapse
|
36
|
Bankiewicz B, Wojtulewski S, Grabowski SJ. Intramolecular Double Proton Transfer from 2-Hydroxy-2-iminoacetic Acid to 2-Amino-2-oxoacetic Acid. J Org Chem 2010; 75:1419-26. [DOI: 10.1021/jo9022414] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Barbara Bankiewicz
- Institute of Chemistry, University of Białystok, ul. Hurtowa 1, 15-399 Białystok, Poland
| | - Sławomir Wojtulewski
- Institute of Chemistry, University of Białystok, ul. Hurtowa 1, 15-399 Białystok, Poland
| | - Sławomir J. Grabowski
- Ikerbasque Research Professor, Kimika Fakultatea, Euskal Herriko Unibertsitatea and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
| |
Collapse
|
37
|
Szatyłowicz H, Krygowski TM. Long distance structural consequences of H-bonding: the case of complexes ofpara-substituted phenol derivatives. J PHYS ORG CHEM 2009. [DOI: 10.1002/poc.1511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
38
|
García-Fernández A, Díez J, Gamasa MP, Lastra E. Facile Modification of 1,3,5-Triaza-7-phosphatricyclo[3.3.1.13,7]decane Phosphanes Coordinated to Ruthenium(II). Inorg Chem 2009; 48:2471-81. [DOI: 10.1021/ic801710y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Almudena García-Fernández
- Departamento de Química Orgánica e Inorgánica, Instituto de Química Organometálica “Enrique Moles” (Unidad Asociada al C.S.I.C.), Universidad de Oviedo, 33006 Oviedo, Principado de Asturias, Spain
| | - Josefina Díez
- Departamento de Química Orgánica e Inorgánica, Instituto de Química Organometálica “Enrique Moles” (Unidad Asociada al C.S.I.C.), Universidad de Oviedo, 33006 Oviedo, Principado de Asturias, Spain
| | - M. Pilar Gamasa
- Departamento de Química Orgánica e Inorgánica, Instituto de Química Organometálica “Enrique Moles” (Unidad Asociada al C.S.I.C.), Universidad de Oviedo, 33006 Oviedo, Principado de Asturias, Spain
| | - Elena Lastra
- Departamento de Química Orgánica e Inorgánica, Instituto de Química Organometálica “Enrique Moles” (Unidad Asociada al C.S.I.C.), Universidad de Oviedo, 33006 Oviedo, Principado de Asturias, Spain
| |
Collapse
|
39
|
Krygowski TM, Zachara-Horeglad JE, Palusiak M, Pelloni S, Lazzeretti P. Relation between pi-electron localization/delocalization and H-bond strength in derivatives of omicron-hydroxy-schiff bases. J Org Chem 2008; 73:2138-45. [PMID: 18303912 DOI: 10.1021/jo7023174] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Detailed investigations of electronic effects taking place within the molecular system of o-hydroxy Schiff bases have been performed. The analysis of geometry, local and global aromaticity, selected AIM-based parameters, and finally, pi-electron currents induced in the systems under consideration have been performed on the basis of quantum chemical calculations at the B3LYP/6-311+G** level of theory. The relation between localization/delocalization of pi-electrons within the whole system has been described. It has been shown that the character of the bond which is common to the phenylic ring and the quasi-ring formed as a result of H-bond formation has a crucial impact on the strength of H-bonding. The strongest H-bonds can be observed for the systems in which the sequence of formally single and double bonds within the H-bridged quasi-ring enable a pi-electronic coupling. These observations indicate that pi-electron effects play a fundamental role in the stabilization of the hydrogen bridge within omicron-hydroxy Schiff bases. Analysis of pi-ring currents induced by a magnetic field perpendicular to the molecular plane of selected analyzed systems confirms these conclusions.
Collapse
Affiliation(s)
- Tadeusz M Krygowski
- Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
| | | | | | | | | |
Collapse
|
40
|
Parigoridi IE, Corban GJ, Hadjikakou SK, Hadjiliadis N, Kourkoumelis N, Kostakis G, Psycharis V, Raptopoulou CP, Kubicki M. Structural motifs of diiodine complexes with amides and thioamides. Dalton Trans 2008:5159-65. [DOI: 10.1039/b805825c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
41
|
Minkin VI, Nivorozhkin LE, Korobov MS. Stereodynamics and degenerate ligand exchange in solutions of tetracoordinate chelate complexes of nontransition metals. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1994v063n04abeh000085] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
42
|
Walbaum C, Pantenburg I, Meyer G. Komplexe einwertiger Dibenzo-18-Krone-6-Kationen mit Triiodid als Anionen. Z Anorg Allg Chem 2007. [DOI: 10.1002/zaac.200700080] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
43
|
Grabowski SJ, Sokalski WA, Leszczynski J. Wide spectrum of H⋯H interactions: van der Waals contacts, dihydrogen bonds and covalency. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.06.042] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
44
|
|
45
|
Green BS, Arad-Yellin R, Cohen MD. Stereochemistry and Organic Solid-State Reactions. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/9780470147252.ch3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
|
46
|
Krygowski TM, Zachara-Horeglad JE. Geometry-based analysis of azulene and azulene-like systems with H- or Li-bonding. J PHYS ORG CHEM 2007. [DOI: 10.1002/poc.1213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
47
|
Leroux Y, El Manouni D, Labaudiniere L, Burgada R, Safsaf A, Neuman A, Gillier H. ETUDE STRUCTURALE DU(N,N-DIMETHYLAMINOCARBONYL-l-METHOXYCARBONYL-2-ETHENYL(Z))-2-OXO-2-TETRAMETHYL- 4,4,5,5-DIOXAPHOSPHOLANE-1,3,2. PHENOMENE DE PREFIGURATION A L'ETAT SOLIDE D'UN INTERMEDIAIRE REACTIONNEL PENTACOORDINE. PHOSPHORUS SULFUR 2006. [DOI: 10.1080/10426509008038000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Y. Leroux
- a Laboratoire de Chimie Structurale Biomoléculaire , Université Paris-Nord , 74, rue Marcel Cachin, 93012 , Bobigny , Cedex , France
| | - D. El Manouni
- a Laboratoire de Chimie Structurale Biomoléculaire , Université Paris-Nord , 74, rue Marcel Cachin, 93012 , Bobigny , Cedex , France
| | - L. Labaudiniere
- b Laboratoire de Chimie des Organoeéléments, UA 473 CNRS , Université Pierre et Marie Curie , 75230 , Paris , Cedex 05 , France
| | - R. Burgada
- b Laboratoire de Chimie des Organoeéléments, UA 473 CNRS , Université Pierre et Marie Curie , 75230 , Paris , Cedex 05 , France
| | - A. Safsaf
- a Laboratoire de Chimie Structurale Biomoléculaire , Université Paris-Nord , 74, rue Marcel Cachin, 93012 , Bobigny , Cedex , France
| | - A. Neuman
- a Laboratoire de Chimie Structurale Biomoléculaire , Université Paris-Nord , 74, rue Marcel Cachin, 93012 , Bobigny , Cedex , France
| | - H. Gillier
- a Laboratoire de Chimie Structurale Biomoléculaire , Université Paris-Nord , 74, rue Marcel Cachin, 93012 , Bobigny , Cedex , France
| |
Collapse
|
48
|
Antoniadis CD, Hadjikakou SK, Hadjiliadis N, Papakyriakou A, Baril M, Butler IS. Synthesis and Structures of Se Analogues of the Antithyroid Drug 6-n-Propyl-2-thiouracil and Its Alkyl Derivatives: Formation of Dimeric Se–Se Compounds and Deselenation Reactions of Charge-Transfer Adducts of Diiodine. Chemistry 2006; 12:6888-97. [PMID: 16773663 DOI: 10.1002/chem.200501455] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Four selenium analogues of the antithyroid drug 6-n-propyl-2-thiouracil (PTU), of formulae RSeU, (R = methyl (Me) (1), ethyl (Et) (2), n-propyl (nPr) (3), and isopropyl (iPr) 4), have been synthesized. Reaction of 1-4 with diiodine in a 1:1 molar ratio in dichloromethane results in the formation of [(RSeU)I(2)] (R = methyl (5), ethyl (6), n-propyl (7) and isopropyl (8)). All compounds have been characterized by elemental analysis, FT-Raman, FT-IR, UV/Vis, (1)H-, (13)C-, (77)Se-1D and -2D NMR spectroscopy, and ESI-MS spectrometric techniques. Recrystallization of 4 from dichloromethane afforded (4CH(2)Cl(2)). Crystals of [(nPrSeU)I(2)] (7), a charge-transfer complex, were obtained from chloroform solutions, while crystallization of 6 and 7 from acetone afforded the diselenides [N-(6-Et-4-pyrimidone)(6-EtSeU)(2)] (92 H(2)O) and [N-(6-nPr-4-pyrimidone)(6-nPrSeU)(2)] (10) as oxidation products. Recrystallization of 7 from methanol/acetonitrile solutions led to deselenation with the formation of 6-n-propyl-2-uracil (nPrU) (11). [(nPrSeU)I(2)] (7) was found to be a charge-transfer complex with a Se--I bond. These results are discussed in relation to the mechanism of action of antithyroid drugs.
Collapse
Affiliation(s)
- Constantinos D Antoniadis
- Section of Inorganic and Analytical Chemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
| | | | | | | | | | | |
Collapse
|
49
|
Fresen JL, Fresen JW. Estimating the parameter in the Pauling equation. J Appl Stat 2006. [DOI: 10.1080/02664768600000003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
50
|
Rademacher P, Wiesmann RF. Transanulare Wechselwirkungen in difunktionellen mittleren Ringen, 4. Spektroskopische und theoretische Untersuchungen an bicyclischen Boraalkenen. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/cber.19941270309] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Paul Rademacher
- Institut für Organische Chemie, Universität GH Essen, Universitätsstraße 5–7, D‐45117 Essen
| | - Reinhard F. Wiesmann
- Institut für Organische Chemie, Universität GH Essen, Universitätsstraße 5–7, D‐45117 Essen
| |
Collapse
|