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Noncovalent Bonds Through Sigma and Pi-Hole Located on the Same Molecule. Guiding Principles and Comparisons
molecules Review Noncovalent Bonds through Sigma and Pi-Hole Located on the Same Molecule. Guiding Principles and Comparisons Wiktor Zierkiewicz 1,* , Mariusz Michalczyk 1,* and Steve Scheiner 2 1 Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeze˙ Wyspia´nskiego27, 50-370 Wrocław, Poland 2 Department of Chemistry and Biochemistry, Utah State University Logan, Logan, UT 84322-0300, USA; [email protected] * Correspondence: [email protected] (W.Z.); [email protected] (M.M.) Abstract: Over the last years, scientific interest in noncovalent interactions based on the presence of electron-depleted regions called σ-holes or π-holes has markedly accelerated. Their high directionality and strength, comparable to hydrogen bonds, has been documented in many fields of modern chemistry. The current review gathers and digests recent results concerning these bonds, with a focus on those systems where both σ and π-holes are present on the same molecule. The underlying principles guiding the bonding in both sorts of interactions are discussed, and the trends that emerge from recent work offer a guide as to how one might design systems that allow multiple noncovalent bonds to occur simultaneously, or that prefer one bond type over another. Keywords: molecular electrostatic potential; halogen bond; pnicogen bond; tetrel bond; chalcogen bond; cooperativity Citation: Zierkiewicz, W.; Michalczyk, M.; Scheiner, S. Noncovalent Bonds through Sigma and Pi-Hole Located on the Same 1. Introduction Molecule. Guiding Principles and The concept of the σ-hole, introduced to a wide audience in 2005 at a conference in Comparisons. Molecules 2021, 26, Prague by Tim Clark [1], influenced a way of thinking about noncovalent interactions 1740. -
The Hydrogen Bond: a Hundred Years and Counting
J. Indian Inst. Sci. A Multidisciplinary Reviews Journal ISSN: 0970-4140 Coden-JIISAD © Indian Institute of Science 2019. The Hydrogen Bond: A Hundred Years and Counting Steve Scheiner* REVIEW REVIEW ARTICLE Abstract | Since its original inception, a great deal has been learned about the nature, properties, and applications of the H-bond. This review summarizes some of the unexpected paths that inquiry into this phenom- enon has taken researchers. The transfer of the bridging proton from one molecule to another can occur not only in the ground electronic state, but also in various excited states. Study of the latter process has devel- oped insights into the relationships between the nature of the state, the strength of the H-bond, and the height of the transfer barrier. The enormous broadening of the range of atoms that can act as both pro- ton donor and acceptor has led to the concept of the CH O HB, whose ··· properties are of immense importance in biomolecular structure and function. The idea that the central bridging proton can be replaced by any of various electronegative atoms has fostered the rapidly growing exploration of related noncovalent bonds that include halogen, chalco- gen, pnicogen, and tetrel bonds. Keywords: Halogen bond, Chalcogen bond, Pnicogen bond, Tetrel bond, Excited-state proton transfer, CH O H-bond ··· 1 Introduction charge on the proton. The latter can thus attract Over the course of its century of study following the partial negative charge of an approaching its earliest conceptual formulation1,2, the hydro- nucleophile D. Another important factor resides gen bond (HB) has surrendered many of the in the perturbation of the electronic structure mysteries of its source of stability and its myriad of the two species as they approach one another. -
Chemical Physics 524 (2019) 55–62
Chemical Physics 524 (2019) 55–62 Contents lists available at ScienceDirect Chemical Physics journal homepage: www.elsevier.com/locate/chemphys Structures of clusters surrounding ions stabilized by hydrogen, halogen, T chalcogen, and pnicogen bonds ⁎ ⁎ Steve Scheinera, , Mariusz Michalczykb, Wiktor Zierkiewiczb, a Department of Chemistry and Biochemistry, Utah State University Logan, Utah 84322-0300, United States b Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland ARTICLE INFO ABSTRACT Keywords: Four H-binding HCl and HF molecules position themselves at the vertices of a tetrahedron when surrounding a Tetrahedral central Cl−. Halogen bonding BrF and ClF form a slightly distorted tetrahedron, a tendency that is amplified for QTAIM ClCN which forms a trigonal pyramid. Chalcogen bonding SF2, SeF2, SeFMe, and SeCSe occupy one hemisphere NBO of the central ion, leaving the other hemisphere empty. This pattern is repeated for pnicogen bonding PF3, SeF3 Cl− and AsCF. The clustering of solvent molecules on one side of the Cl− is attributed to weak attractive interactions Na+ between them, including chalcogen, pnicogen, halogen, and hydrogen bonds. Binding energies of four solvent molecules around a central Na+ are considerably reduced relative to chloride, and the geometries are different, with no empty hemisphere. The driving force maximizes the number of electronegative (F or O) atoms close to the Na+, and the presence of noncovalent bonds between solvent molecules. 1. Introduction particular, the S, Se, etc group can engage in chalcogen bonds (YBs) [19–25], and the same is true of the P, As family which forms pnicogen The hydrogen bond (HB) is arguably the most important and in- bonds (ZBs) [26–34]. -
Quantitative Analysis of Hydrogen and Chalcogen Bonds in Two Pyrimidine
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2020 Quantitative analysis of hydrogen and chalcogen bonds in two pyrimidine-5-carbonitrile derivatives, potential DHFR inhibitors: an integrated crystallographic and theoretical study Al-Wahaibi, Lamya H ; Chakraborty, Kushumita ; Al-Shaalan, Nora H ; Syed Majeed, Mohamed Yehya Annavi ; Blacque, Olivier ; Al-Mutairi, Aamal A ; El-Emam, Ali A ; Percino, M Judith ; Thamotharan, Subbiah Abstract: Two potential bioactive pyrimidine-5-carbonitrile derivatives have been synthesized and char- acterized by spectroscopic techniques (1H and 13C-NMR) and the three dimensional structures were elucidated by single crystal X-ray diffraction at low temperature (160 K). In both structures, the molec- ular conformation is locked by an intramolecular C–HC interaction involving the cyano and CH of the thiophene and phenyl rings. The intermolecular interactions were analyzed in a qualitative man- ner based on the Hirshfeld surface and 2D-fingerprint plots. The results suggest that the phenyl and thiophene moieties have an effect on the crystal packing. For instance, the chalcogen bonds areonly preferred in the thiophene derivative. However, both structures uses a common N–HO hydrogen bond motif. Moreover, the structures of 1 and 2 display 1D isostructurality and molecular chains stabilize by intermolecular N–HO and N–HN hydrogen bonds. The nature and extent of different non-covalent interactions were further characterized by the topological parameters derived from the quantum the- ory of atoms-in-molecules approach. This analysis indicates that apart from N–HO hydrogen bonds, other non-covalent interactions are closed-shell in nature. -
Frontiers in Halogen and Chalcogen-Bond Donor
DOI: 10.1002/cctc.201901215 Minireviews 1 2 3 Frontiers in Halogen and Chalcogen-Bond Donor 4 5 Organocatalysis 6 [a] [a] [a] 7 Julia Bamberger, Florian Ostler, and Olga García Mancheño* 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 ChemCatChem 2019, 11, 1–15 1 © 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim These are not the final page numbers! �� Wiley VCH Mittwoch, 21.08.2019 1999 / 145245 [S. 1/15] 1 Minireviews 1 Non-covalent molecular interactions on the basis of halogen Being particularly relevant in the binding of “soft” substrates, 2 and chalcogen bonding represent a promising, powerful the similar strength to hydrogen bonding interactions and its 3 catalytic activation mode. However, these “unusual” non- higher directionality allows for solution-phase applications with 4 covalent interactions are typically employed in the solid state halogen and chalcogen bonding as the key interaction. In this 5 and scarcely exploited in catalysis. In recent years, an increased mini-review, the special features, state-of-the-art and key 6 interest in halogen and chalcogen bonding have been awaken, examples of these so-called σ-hole interactions in the field of 7 as they provide profound characteristics that make them an organocatalysis are presented. 8 appealing alternative to the well-explored hydrogen bonding. 9 10 1. Introduction including crystal engineering,[8] supramolecular[9] and medicinal 11 chemistry.[8a,10] Besides the correlation to the electrostatic 12 To achieve an effective catalytic transformation, the structural potential, also charge transfer and dispersion is believed to give 13 design of selective catalyst structures requires the correct rise to σ-hole interactions.[11] Associated with σ* orbitals, the σ- 14 manipulation of the energetic and stereochemical features of hole deepens with heavier atoms (going from the top to the 15 intermolecular forces. -
Theoretical Study on the Noncovalent Interactions Involving Triplet Diphenylcarbene
Theoretical Study on the Noncovalent Interactions Involving Triplet Diphenylcarbene Chunhong Zhao Hebei Normal University Huihua College Hui Lin Hebei Normal University Aiting Shan Hebei Normal University Shaofu Guo Hebei Normal University Huihua College Xiaoyan Li Hebei Normal University Xueying Zhang ( [email protected] ) Hebei Normal University https://orcid.org/0000-0003-1598-8501 Research Article Keywords: triplet diphenylcarbene, noncovalent interaction, electron density shift, electron spin density Posted Date: May 19th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-445417/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at Journal of Molecular Modeling on July 9th, 2021. See the published version at https://doi.org/10.1007/s00894-021-04838-6. Page 1/21 Abstract The properties of some types of noncovalent interactions formed by triplet diphenylcarbene (DPC3) have been investigated by means of density functional theory (DFT) calculations and quantum theory of 3 atoms in molecules (QTAIM) studies. The DPC ···LA (LA = AlF3, SiF4, PF5, SF2, ClF) complexes have been analyzed from their equilibrium geometries, binding energies, charge transfer and properties of electron 3 density. The triel bond in the DPC ···AlF3 complex exhibits a partially covalent nature, with the binding energy − 65.7kJ/mol. The tetrel bond, pnicogen bond, chalcogen bond and halogen bond in the DPC3···LA (LA = SiF4, PF5, SF2, ClF) complexes show the character of a weak closed-shell noncovalent interaction. Polarization plays an important role in the formation of the studied complexes. -
Differential Binding of Tetrel-Bonding Bipodal Receptors to Monatomic and Polyatomic Anions
molecules Article Differential Binding of Tetrel-Bonding Bipodal Receptors to Monatomic and Polyatomic Anions Steve Scheiner Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA; [email protected]; Tel.: +435-797-7419 Received: 26 December 2018; Accepted: 5 January 2019; Published: 9 January 2019 Abstract: Previous work has demonstrated that a bidentate receptor containing a pair of Sn atoms can engage in very strong interactions with halide ions via tetrel bonds. The question that is addressed here concerns the possibility that a receptor of this type might be designed that would preferentially bind a polyatomic over a monatomic anion since the former might better span the distance between − − − − the two Sn atoms. The binding of Cl was thus compared to that of HCOO , HSO4 , and H2PO4 with a wide variety of bidentate receptors. A pair of SnFH2 groups, as strong tetrel-binding agents, were first added to a phenyl ring in ortho, meta, and para arrangements. These same groups were also added in 1,3 and 1,4 positions of an aliphatic cyclohexyl ring. The tetrel-bonding groups were placed at the termini of (-C≡C-)n (n = 1,2) extending arms so as to further separate the two Sn atoms. Finally, the Sn atoms were incorporated directly into an eight-membered ring, rather than as − − − − appendages. The ordering of the binding energetics follows the HCO2 > Cl > H2PO4 > HSO4 general pattern, with some variations in selected systems. The tetrel bonding is strong enough that in most cases, it engenders internal deformations within the receptors that allow them to engage in bidentate bonding, even for the monatomic chloride, which mutes any effects of a long Sn···Sn distance within the receptor. -
Hazardous Substances (Chemicals) Transfer Notice 2006
16551655 OF THURSDAY, 22 JUNE 2006 WELLINGTON: WEDNESDAY, 28 JUNE 2006 — ISSUE NO. 72 ENVIRONMENTAL RISK MANAGEMENT AUTHORITY HAZARDOUS SUBSTANCES (CHEMICALS) TRANSFER NOTICE 2006 PURSUANT TO THE HAZARDOUS SUBSTANCES AND NEW ORGANISMS ACT 1996 1656 NEW ZEALAND GAZETTE, No. 72 28 JUNE 2006 Hazardous Substances and New Organisms Act 1996 Hazardous Substances (Chemicals) Transfer Notice 2006 Pursuant to section 160A of the Hazardous Substances and New Organisms Act 1996 (in this notice referred to as the Act), the Environmental Risk Management Authority gives the following notice. Contents 1 Title 2 Commencement 3 Interpretation 4 Deemed assessment and approval 5 Deemed hazard classification 6 Application of controls and changes to controls 7 Other obligations and restrictions 8 Exposure limits Schedule 1 List of substances to be transferred Schedule 2 Changes to controls Schedule 3 New controls Schedule 4 Transitional controls ______________________________ 1 Title This notice is the Hazardous Substances (Chemicals) Transfer Notice 2006. 2 Commencement This notice comes into force on 1 July 2006. 3 Interpretation In this notice, unless the context otherwise requires,— (a) words and phrases have the meanings given to them in the Act and in regulations made under the Act; and (b) the following words and phrases have the following meanings: 28 JUNE 2006 NEW ZEALAND GAZETTE, No. 72 1657 manufacture has the meaning given to it in the Act, and for the avoidance of doubt includes formulation of other hazardous substances pesticide includes but -
Cyclometalation of Phosphinines Via C-H Activation : Towards Functional Coordination Compounds
Cyclometalation of phosphinines via C-H activation : towards functional coordination compounds Citation for published version (APA): Broeckx, L. E. E. (2013). Cyclometalation of phosphinines via C-H activation : towards functional coordination compounds. Technische Universiteit Eindhoven. https://doi.org/10.6100/IR760622 DOI: 10.6100/IR760622 Document status and date: Published: 04/12/2013 Document Version: Publisher’s PDF, also known as Version of Record (includes final page, issue and volume numbers) Please check the document version of this publication: • A submitted manuscript is the version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers. Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal. -
Molecular Recognition by Chalcogen Bond
Molecular Recognition by Chalcogen Bond: Selective Chargetransfer Crystal Formation of Dimethylnaphthalene with Selenadiazolotetracyanonaphthoquinodimethane Yusuke Ishigaki, Kota Asai, Henri-Pierre Jacquot de Rouville, Takuya Shimajiri, Valérie Heitz, Hiroshi Fujii-Shinomiya, Takanori Suzuki To cite this version: Yusuke Ishigaki, Kota Asai, Henri-Pierre Jacquot de Rouville, Takuya Shimajiri, Valérie Heitz, et al.. Molecular Recognition by Chalcogen Bond: Selective Chargetransfer Crystal Formation of Dimethyl- naphthalene with Selenadiazolotetracyanonaphthoquinodimethane. European Journal of Organic Chemistry, Wiley-VCH Verlag, In press, 10.1002/ejoc.202001554. hal-03114533 HAL Id: hal-03114533 https://hal.archives-ouvertes.fr/hal-03114533 Submitted on 19 Jan 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Molecular Recognition by Chalcogen Bond: Selective Charge- transfer Crystal Formation of Dimethylnaphthalene with Selenadiazolotetracyanonaphthoquinodimethane Yusuke Ishigaki,[a] Kota Asai,[a] Henri-Pierre Jacquot de Rouville,[b] Takuya Shimajiri,[a] Valérie Heitz,[b] Hiroshi Fujii-Shinomiya,[c,d] and Takanori Suzuki*[a] In memory of François Diederich and Tsutomu Miyashi Abstract: The title nonplanar electron acceptor (1) fused with a selenadiazole ring selectively forms a crystalline charge-transfer complex (CT crystal) with 2,6-dimethylnaphthalene (2,6-DMN). On the other hand, the sulfur analogue (2) has less recognition ability and forms CT crystals with both 2,6- and 2,7-DMN. -
George Andrew Olah Across Conventional Lines
GENERAL ARTICLE George Andrew Olah Across Conventional Lines Ripudaman Malhotra, Thomas Mathew and G K Surya Prakash Hungarian born American chemist, George Andrew Olah was aprolific researcher. The central theme of his career was the 12 pursuit of structure and mechanisms in chemistry, particu- larly focused on electron-deficient intermediates. He leaves behind a large body of work comprising almost 1500 papers and twenty books for the scientific community. Some selected works have been published in three aptly entitled volumes, 3 Across Conventional Lines. There is no way to capture the many contributions of Olah in a short essay. For this appreciation, we have chosen to high- 1 light some of those contributions that to our mind represent Ripudaman Malhotra, a student of Prof. Olah, is a asignificant advance to the state of knowledge. retired chemist who spent his entire career at SRI International working mostly Organofluorine Chemistry on energy-related issues. He co-authored the book on Early on in his career, while still in Hungary, Olah began studying global energy – A Cubic Mile organofluorine compounds. Olah’s interest in fluorinated com- of Oil. pounds was piqued by the theoretical ramifications of a strong 2 Thomas Mathew, a senior C-F bond. Thus, whereas chloromethanol immediately decom- scientist at the Loker Hydrocarbon Research poses into formaldehyde and HCl, he reasoned that the stronger Institute, has been a close C-F bond might render fluoromethanol stable. He succeeded in associate of Prof. Olah over preparing fluoromethanol by the reduction of ethyl flouorofor- two decades. 3 mate with lithium aluminum hydride [1]. -
Catalysis with Chalcogen Bonds: Neutral Benzodiselenazole Scaffolds with High-Precision Cite This: Chem
Chemical Science View Article Online EDGE ARTICLE View Journal | View Issue Catalysis with chalcogen bonds: neutral benzodiselenazole scaffolds with high-precision Cite this: Chem. Sci.,2017,8,8164 selenium donors of variable strength† Sebastian Benz, Jiri Mareda, Celine´ Besnard, Naomi Sakai and Stefan Matile * The benzodiselenazoles (BDS) introduced in this report fulfill, for the first time, all the prerequisites for non- covalent high-precision chalcogen-bonding catalysis in the focal point of conformationally immobilized s holes on strong selenium donors in a neutral scaffold. Rational bite-angle adjustment to the long Se–C bonds was the key for BDS design. For the unprecedented BDS motif, synthesis of 12 analogs from Received 4th September 2017 o-xylene, crystal structure, s hole variation strategies, optoelectronic properties, theoretical and Accepted 6th October 2017 experimental anion binding as well as catalytic activity are reported. Chloride binding increases with the DOI: 10.1039/c7sc03866f depth of the s holes down to KD ¼ 11 mM in THF. Catalytic activities follow the same trend and rsc.li/chemical-science culminate in rate enhancements for transfer hydrogenation of quinolines beyond 100 000. Creative Commons Attribution 3.0 Unported Licence. The integration of new interactions into functional systems is attractive to stabilize anionic transition states with high preci- an objective of highest, most fundamental importance.1–7 It sion in the focal point of the two cofacial s holes (Fig. 1),8 expands our ability to create function and promises access to but they are limited to weak sulfur donors. Bis(2- new properties. In organocatalysis, a renewed interest in the selanylbenzimidazolium)s, used in stoichiometric amounts, integration of conventional interactions such as dispersion provide access to more powerful selenium donors but suffer forces,3 ion pairing4 or cation–p interactions5 accounts for from lack of precision due to conformational exibility and much recent progress in the eld.