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Type II Halogen...Halogen Contacts Are Halogen Bonds
scientific commentaries Type II halogenÁÁÁhalogen contacts are halogen IUCrJ bonds ISSN 2052-2525 CHEMISTRYjCRYSTENG Pierangelo Metrangolo* and Giuseppe Resnati Laboratory of Nanostructured Fluorinated Materials of the Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, Milano, 20131, Italy Halogenated phenols (HPs) are naturally present in the marine environment (Gribble, 2010). They are also important man-made compounds owing to their chemical inertness and applications in many industrial processes. For instance, chlorinated phenols, e.g. 2,4,6-trichlorophenol and its isomers, have been routinely used as pesticides, bactericides Keywords: halogen bonds; halogenated phenols and fungicides, and a number of tribromophenols are commercially produced as flame retardants and wood preservatives. The carbon–halogen bond can be quite stable in the environment and HPs are recalcitrant molecules, widespread organic pollutants found in air, water, soil and sedi- ments (Shao et al., 2011). The HPs mentioned above have, in fact, been detected and quantified in blood from birds, fish and mammals, including humans. The retention of HPs by living organisms is related to their structural resemblance to the thyroid hormones 3,30,5,50-tetraiodo-l-thyroxin (thyroxine, T4) and 3,30,5-triiodo-l-thyronine (T3). In fact, para-andmeta-halophenols bind to some proteins such as transthyretin (TTR), thyroxin-binding globulin (TGB) and albumin (ALB), and the receptor affinity of o,o’-dihalophenols is remarkably high (Kitamura et al., 2008). To understand the recognition features of HPs at molecular level is thus of paramount importance as it may help to rationalize the adverse biological effects of HPs to which humans are commonly exposed. -
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. -
Naming Polyatomic Ions and Acids Oxyanions
Oxyanions Naming Polyatomic Ions and Oxyanions Acids Oxyanions- negative ions containing Oxyanions may contain the prefix oxygen. “hypo-”, less than, or “per-”, more than. These have the suffix “-ate” or “-ite” For example - “-ate” means it has more oxygen atoms ClO4 Perchlorate bonded, “-ite” has less - ClO3 Chlorate For example - ClO2 Chlorite 2- SO4 sulfate ClO- Hypochlorite 2- SO3 sulfite Acids Naming acids Naming Acids Certain compounds produce H+ ions in Does it contain oxygen? water, these are called acids. If it does not, it gets the prefix “hydro-” and If it does contain an oxyanion, then the suffix “-ic acid” replace the ending. You can recognize them because the neutral compound starts with “H”. HCl If the ending was “–ate”, add “-ic acid” Hydrochloric acid If the ending was “–ite”, add “-ous acid” For example HCl, H2SO4, and HNO3. HF Don’t confuse a polyatomic ion with a H2SO4 Sulfuric Acid Hydrofluoric acid neutral compound. H2SO3 Sulfurous Acid HCN HCO - is hydrogen carbonate, not an acid. 3 Hydrocyanic acid Examples Examples Nomenclature (naming) of Covalent compounds HNO3 HNO3 Nitric Acid HI HI Hydroiodic acid H3AsO4 H3AsO4 Arsenic Acid HClO2 HClO2 Chlorous Acid 1 Determining the type of bond Covalent bonding is very Covalent bonding is very First, determine if you have an ionic different from ionic naming compound or a covalent compound. similar to ionic naming A metal and a nonmetal will form an You always name the one that is least Ionic names ignored the subscript ionic bond. electronegative first (furthest from because there was only one possible Compounds with Polyatomic ions form fluorine) ratio of elements. -
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. -
And Inter-Protein Couplings of Backbone Motions Underlie
www.nature.com/scientificreports OPEN Intra- and inter-protein couplings of backbone motions underlie protein thiol-disulfde exchange cascade Received: 26 July 2018 Wenbo Zhang1,3, Xiaogang Niu2,3, Jienv Ding1,3,5, Yunfei Hu2,3,6 & Changwen Jin1,2,3,4 Accepted: 6 October 2018 The thioredoxin (Trx)-coupled arsenate reductase (ArsC) is a family of enzymes that catalyzes the Published: xx xx xxxx reduction of arsenate to arsenite in the arsenic detoxifcation pathway. The catalytic cycle involves a series of relayed intramolecular and intermolecular thiol-disulfde exchange reactions. Structures at diferent reaction stages have been determined, suggesting signifcant conformational fuctuations along the reaction pathway. Herein, we use two state-of-the-art NMR methods, the chemical exchange saturation transfer (CEST) and the CPMG-based relaxation dispersion (CPMG RD) experiments, to probe the conformational dynamics of B. subtilis ArsC in all reaction stages, namely the enzymatic active reduced state, the intra-molecular C10–C82 disulfde-bonded intermediate state, the inactive oxidized state, and the inter-molecular disulfde-bonded protein complex with Trx. Our results reveal highly rugged energy landscapes in the active reduced state, and suggest global collective motions in both the C10–C82 disulfde-bonded intermediate and the mixed-disulfde Trx-ArsC complex. Protein thiol-disulfde exchange reactions play fundamental roles in living systems, represented by the thiore- doxin (Trx) and glutaredoxin (Grx) systems that maintain the cytoplasmic reducing environment, the protein DsbA that catalyzes the formation of protein disulfde bonds in bacterial periplasm, as well as the protein disulfde isomerase (PDI) proteins that facilitate correct disulfde bonding1–5. -
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. -
Halogen Bonding Based Recognition Processes: a World Parallel To
Acc. Chem. Res. 2005, 38, 386-395 to acquaint the nonexperts. This overview will show how Halogen Bonding Based XB is a strong, specific, and directional interaction that Recognition Processes: A World gives rise to well-defined supramolecular synthons. Then ² we will focus on interactions involving halocarbons and Parallel to Hydrogen Bonding on the supramolecular architectures that they produce. Some heuristic principles will spring from this, enabling ,³ PIERANGELO METRANGOLO,* us to develop an XB based crystal engineering, which may ³ § HANNES NEUKIRCH, TULLIO PILATI, AND complement the possibilities offered by HB. Applications ,³ GIUSEPPE RESNATI* and prospects will conclude the paper. Department of Chemistry, Materials, and Chemical The first unequivocal report on the ability of halogen Engineering ªGiulio Nattaº, 7 via Mancinelli, I-20131 Milan, and Campus of Como, 7 via Castelnuovo, I-22100 Como, atoms to form well-defined adducts with electron donor Polytechnic of Milan, Italy, and C.N.R.-Institute of Molecular species dates back to 1863 when Guthrie described the 3 Sciences, 9 via Golgi, I-20133 Milan, Italy formation of the NH3‚‚‚I2 complex. In 1896, Remsen and Received October 28, 2004 Norris proved the general tendency of amines to form adducts with bromine and chlorine.4 Sixty years later, the crystallographic studies of Hassel were a landmark in the ABSTRACT Halogen bonding is the noncovalent interaction between halogen understanding of the XB characteristics. In his Nobel atoms (Lewis acids) and neutral or anionic Lewis bases. The main lecture, Hassel stressed the similarities between interac- features of the interaction are given, and the close similarity with tions where halogen and hydrogen atoms work as electron the hydrogen bonding will become apparent. -
Evidence Against Stabilization of the Transition State Oxyanion by a Pka-Perturbed RNA Base in the Peptidyl Transferase Center
Evidence against stabilization of the transition state oxyanion by a pKa-perturbed RNA base in the peptidyl transferase center K. Mark Parnell*, Amy C. Seila†, and Scott A. Strobel*‡§ Departments of *Molecular Biophysics and Biochemistry, †Genetics, and ‡Chemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520-8114 Edited by Harry F. Noller, University of California, Santa Cruz, CA, and approved July 16, 2002 (received for review April 8, 2002) The crystal structure of the ribosomal 50S subunit from Haloarcula activity, suggesting that 23S and 5S rRNA may constitute the marismortui in complex with the transition state analog CCdA- bulk of the peptidyl transferase center (8). phosphate-puromycin (CCdApPmn) led to a mechanistic proposal The most unambiguous evidence that the active site of the wherein the universally conversed A2451 in the ribosomal active ribosome is comprised of RNA came from the 2.4-Å crystal site acts as an ‘‘oxyanion hole’’ to promote the peptidyl transferase structure of the Haloarcula marismortui 50S ribosomal subunit reaction [Nissen, P., Hansen, J., Ban, N., Moore, P.B., and Steitz, T.A. reported by Ban et al. (9) and Nissen et al. (10). The structure of the (2000) Science 289, 920–929]. In the model, close proximity (3 Å) 50S subunit complexed with the transition-state analog CCdA- between the A2451 N3 and the nonbridging phosphoramidate phosphate-puromycin (CCdApPmn) was vital to this structural oxygen of CCdApPmn suggested that the carbonyl oxyanion identification. CCdApPmn includes the minimal components of formed during the tetrahedral transition state is stabilized by both peptidyl transferase substrates (11). CCdA binds the P site, and hydrogen bonding to the protonated A2451 N3, the pKa of which puromycin binds the A site (Fig. -
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. -
The Halogen Bond in the Design of Functional Supramolecular Materials
The Halogen Bond in the Design of Functional Supramolecular Materials: Recent Advances † ‡ ARRI PRIIMAGI,*, GABRIELLA CAVALLO, ‡ ‡ PIERANGELO METRANGOLO,*, ,§ AND GIUSEPPE RESNATI*, † Department of Applied Physics, Aalto University, P.O. Box 13500, FI-00076 ‡ Aalto, Finland, NFMLab-DCMIC “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, IT-20131 Milano, Italy, and §VTT-Technical Research Centre of Finland, Tietotie 2, Espoo, FI-02044 VTT, Finland RECEIVED ON APRIL 9, 2013 CONSPECTUS alogen bonding is an emerging noncovalent interaction for constructing supramolecular assemblies. Though similar to the H more familiar hydrogen bonding, four primary differences between these two interactions make halogen bonding a unique tool for molecular recognition and the design of functional materials. First, halogen bonds tend to be much more directional than (single) hydrogen bonds. Second, the interaction strength scales with the polarizability of the bond-donor atom, a feature that researchers can tune through single-atom mutation. In addition, halogen bonds are hydrophobic whereas hydrogen bonds are hydrophilic. Lastly, the size of the bond-donor atom (halogen) is significantly larger than hydrogen. As a result, halogen bonding provides supramolecular chemists with design tools that cannot be easily met with other types of noncovalent interactions and opens up unprecedented possibilities in the design of smart functional materials. This Account highlights the recent advances in the design of halogen-bond-based functional materials. Each of the unique features of halogen bonding, directionality, tunable interaction strength, hydrophobicity, and large donor atom size, makes a difference. Taking advantage of the hydrophobicity, researchers have designed small-size ion transporters. The large halogen atom size provided a platform for constructing all-organic light-emitting crystals that efficiently generate triplet electrons and have a high phosphorescence quantum yield.