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Somtua T, Rakrai W, Tabtimsai C, Wanno B. Oxoanion complexation of nitroisophthalamide receptors: Insights from the DFT calculations. J Mol Graph Model 2024; 133:108870. [PMID: 39317003 DOI: 10.1016/j.jmgm.2024.108870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 09/17/2024] [Accepted: 09/18/2024] [Indexed: 09/26/2024]
Abstract
Amide derivative receptors have been designed to investigate the oxoanion complexation ability via hydrogen and halogen bond interactions. Structural, energetic and electronic properties of nitroisophthalamide receptors, i.e., di(benzyl)- (R1), di(hexafluoro)- (R2), di(chloro-,tetrafluoro)- (R3), di(hexachloro)-(R4), di(fluoro-,tetrachloro)-nitroisophthalamide (R5), and their complexes with C2H3O2-, C7H5O2-, NO3-, H2PO4-, and ClO4- oxoanions were computed and obtained using the density functional theory calculations at the B3LYP/6-31G(d,p) theoretical level in gas phase. According to the computed results, all of oxoanions can form the stable complexes with amide receptors R1-R5 via exothermic process in which receptor R1 is found to interact with oxoanions through hydrogen bonds whereas the receptors R2-R5 are found to interact with oxoanion through both of hydrogen and halogen bonds. It is clearly seen that acetate ion displays the strongest complexation interaction with all receptors compared to the other oxoanions. In addition, electronic properties of receptors R1-R5 in both gas and DMSO phases are modified after complexation with oxoanions. Therefore, the designed amide receptors may be potentially used for oxoanion sensing application.
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Affiliation(s)
- Thanawat Somtua
- Computational Chemistry Center for Nanotechnology, Department of Chemistry, Faculty of Science and Technology, Rajabhat Maha Sarakham University, Maha Sarakham, 44000, Thailand
| | - Wandee Rakrai
- Computational Chemistry Center for Nanotechnology, Department of Chemistry, Faculty of Science and Technology, Rajabhat Maha Sarakham University, Maha Sarakham, 44000, Thailand
| | - Chanukorn Tabtimsai
- Computational Chemistry Center for Nanotechnology, Department of Chemistry, Faculty of Science and Technology, Rajabhat Maha Sarakham University, Maha Sarakham, 44000, Thailand
| | - Banchob Wanno
- Supramolecular Chemistry Research Unit and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Department of Chemistry, Faculty of Science, Mahasarakham University, Maha Sarakham, 44150, Thailand.
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2
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Ramasami P, Murray JS. Anisotropies in electronic densities and electrostatic potentials of Halonium Ions: focus on Chlorine, Bromine and Iodine. J Mol Model 2024; 30:81. [PMID: 38393388 DOI: 10.1007/s00894-024-05869-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 02/05/2024] [Indexed: 02/25/2024]
Abstract
CONTEXT Why are the halonium cations so effective in forming strongly-bound complexes? We directed our research to address this question and we present electrostatic potential data for the valence-state halogen atoms X and halonium cations X+, where X = Cl, Br, I. The electron densities and electrostatic potentials of the halonium cations show considerably greater anisotropy than do the valence state halogens. The distances from the electrostatic potential surface maxima to the halogen nuclei are about 0.5 Å smaller than the distances from the electrostatic potential surface minima to the nuclei, giving the halonium cations each a more disk-like shape than the corresponding neutral valence state halogens. Their surface electrostatic potentials are totally consistent with the directionalities of halonium cations in complexes and the strengths of their interactions. To add perspective to this brief report, we have included calculations of the isotropic cation K+ and noble gas Kr. METHODS The calculations of the electrostatic potentials of the valence states of the halogen atoms Cl, Br and I and the halonium cations Cl+, Br+ and I+, as well as K+ and Kr, on 0.001 au contours of their electronic densities were carried out with Gaussian O9 and the Wave Function Analysis - Surface Analysis Suite (WFA-SAS) at the M06-2X/6-31 + G(d,p) and M06-2X/3-21G* levels.
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Affiliation(s)
- Ponnadurai Ramasami
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit, 80837, Mauritius
- Centre of Natural Product Research, Department of Chemical Sciences, University of Johannesburg, Doornfontein Campus, Johannesburg, 2028, South Africa
| | - Jane S Murray
- Department of Chemistry, University of New Orleans, New Orleans, LA, 70148, USA.
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3
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Wang A, Kennepohl P. Catalytic activation via π-backbonding in halogen bonds. Faraday Discuss 2023; 244:241-251. [PMID: 37186101 DOI: 10.1039/d2fd00140c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The role of halogen bonding (XB) in chemical catalysis has largely involved using XB donors as Lewis acid activators to modulate the reactivity of partner Lewis bases. We explore a more uncommon scenario, where a Lewis base modulates reactivity via a spectator halogen bond interaction. Our computational studies reveal that spectator halogen bonds may play an important role in modulating the rate of SN2 reactions. Most notably, π acceptors such as PF3 significantly decrease the barrier to substitution by decreasing electron density in the very electron rich transition state. Such π-backbonding represents an example of a heretofore unexplored situation in halogen bonding: the combination of both σ-donation and π-backdonation in this "non-covalent" interaction. The broader implications of this observation are discussed.
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Affiliation(s)
- Andrew Wang
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada
| | - Pierre Kennepohl
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada.
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Brinck T, Sahoo SK. Anomalous π-backbonding in complexes between B(SiR 3) 3 and N 2: catalytic activation and breaking of scaling relations. Phys Chem Chem Phys 2023; 25:21006-21019. [PMID: 37519222 DOI: 10.1039/d3cp00248a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Chemical transformations of molecular nitrogen (N2), including the nitrogen reduction reaction (NRR), are difficult to catalyze because of the weak Lewis basicity of N2. In this study, it is shown that Lewis acids of the types B(SiR3)3 and B(GeR3)3 bind N2 and CO with anomalously short and strong B-N or B-C bonds. B(SiH3)3·N2 has a B-N bond length of 1.48 Å and a complexation enthalpy of -15.9 kcal mol-1 at the M06-2X/jun-cc-pVTZ level. The selective binding enhancement of N2 and CO is due to π-backbonding from Lewis acid to Lewis base, as demonstrated by orbital analysis and density difference plots. The π-backbonding is found to be a consequence of constructive orbital interactions between the diffuse and highly polarizable B-Si and B-Ge bond regions and the π and π* orbitals of N2. This interaction is strengthened by electron donating substituents on Si or Ge. The π-backbonding interaction is predicted to activate N2 for chemical transformation and reduction, as it decreases the electron density and increases the length of the N-N bond. The binding of N2 and CO by the B(SiR3)3 and B(GeR3)3 types of Lewis acids also has a strong σ-bonding contribution. The relatively high σ-bond strength is connected to the highly positive surface electrostatic potential [VS(r)] above the B atom in the tetragonal binding conformation, but the σ-bonding also has a significant coordinate covalent (dative) contribution. Electron withdrawing substituents increase the potential and the σ-bond strength, but favor the binding of regular Lewis acids, such as NH3 and F-, more strongly than binding of N2 and CO. Molecules of the types B(SiR3)3 and B(GeR3)3 are chemically labile and difficult to synthesize. Heterogenous catalysts with the wanted B(Si-)3 or B(Ge-)3 bonding motif may be prepared by boron doping of nanostructured silicon or germanium compounds. B-doped and hydrogenated silicene is found to have promising properties as catalyst for the electrochemical NRR.
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Affiliation(s)
- Tore Brinck
- Department of Chemistry, CBH, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden.
| | - Suman Kalyan Sahoo
- Department of Chemistry, CBH, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden.
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5
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Clark T. How deeply should we analyze non-covalent interactions? J Mol Model 2023; 29:66. [PMID: 36757533 PMCID: PMC9911493 DOI: 10.1007/s00894-023-05460-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/18/2023] [Indexed: 02/10/2023]
Abstract
CONTEXT Just how much effort and detail should we invest in analyzing interactions of the order of 5 kcal mol-1? This comment attempts to provide a conciliatory overview of what is often a contentious field and to pose some questions that I hope will eventually lead at least to some consensus. METHODS This is an opinion article without calculations or data.
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Affiliation(s)
- Timothy Clark
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstrasse 25, 91052, Erlangen, Germany.
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Omondi RO, Fadaka AO, Fatokun AA, Jaganyi D, Ojwach SO. Synthesis, substitution kinetics, DNA/BSA binding and cytotoxicity of tridentate N^E^N (E = NH, O, S) pyrazolyl palladium(II) complexes. J Biol Inorg Chem 2022; 27:653-664. [PMID: 36197522 DOI: 10.1007/s00775-022-01959-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022]
Abstract
The pincer complexes, [Pd(L1)Cl]BF4 (PdL1), [Pd(L2)Cl]BF4 (PdL2), [Pd(L3)Cl]BF4 (PdL3), [Pd(L4)Cl]BF4 (PdL4) were prepared by reacting the corresponding ligands, 2,6-bis[(1H-pyrazol-1-yl)methyl]pyridine (L1), bis[2-(1H-pyrazol-1-yl)ethyl]amine (L2), bis[2-(1H-pyrazol-1-yl)ethyl]ether (L3), and bis[2-(1H-prazol-1-yl)ethyl]sulphide (L4) with [PdCl2(NCMe)]2 in the presence NaBF4. The solid-state structures of complexes PdL1-PdL4 confirmed a tridentate coordination mode, with one chloro ligand completing the coordination sphere to afford square-planar complexes. Chemical behaviour of the complexes in solution confirms their stability in both aqueous and DMSO stock media. The electrochemical properties of the compounds showed irreversible two-electron reduction process. Kinetic reactivity of Pd complexes with the biological nucleophiles viz, thiourea (Tu), L-methionine (L-Met) and guanosine 5'-diphosphate disodium salt (5'-GMP) followed the order: PdL2 < PdL3 < PdL4, and PdL2 < PdL1. The kinetic reactivity is subject to the electronic effects of the spectator ligand(s), and the trend was supported by the DFT computed results. The palladium complexes PdL1-PdL4 bind to calf thymus (CT-DNA) via intercalation mode. In addition, the bovine serum albumin (BSA) showed good binding affinity to the complexes. The mode of quenching mechanism of the intrinsic fluorescence of CT-DNA and BSA by the complexes was found to be static. The order of interactions of the complexes with DNA and BSA was in tandem with the rate of substitution kinetics. The complexes, however, displayed relatively low cytotoxicity (IC50 > 100 µM) when tested against the human cervical adenocarcinoma (HeLa) cell line and the transformed human lung fibroblast cell line (MRC-5 SV2).
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Affiliation(s)
- Reinner O Omondi
- School of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
- Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | - Adewale O Fadaka
- Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town, 7535, South Africa
- Department of Anesthesia, Division of Pain Management, Cincinnati Children's Hospital, Medical Center, Burnet 3322, Avenue, Cincinnati, OH, 45229, USA
| | - Amos A Fatokun
- Centre for Natural Products Discovery (CNPD), School of Pharmacy and Biomolecular Sciences, Faculty of Science, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Deogratius Jaganyi
- School of Pure and Applied Sciences, Mount Kenya University, P.O. Box 342-01000, Thika, Kenya
- Department of Chemistry, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Stephen O Ojwach
- School of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa.
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Enhancing Effects of the Cyano Group on the C-X∙∙∙N Hydrogen or Halogen Bond in Complexes of X-Cyanomethanes with Trimethyl Amine: CH3−n(CN)nX∙∙∙NMe3, (n = 0–3; X = H, Cl, Br, I). Int J Mol Sci 2022; 23:ijms231911289. [PMID: 36232589 PMCID: PMC9570363 DOI: 10.3390/ijms231911289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/28/2022] Open
Abstract
In this paper, density functional theory and wave function theory calculations are carried out to investigate the strength and nature of the intermolecular C-X∙∙∙N bond interaction as a function of the number of cyano groups, CN, in the X-bond donor while maintaining the X-bond acceptor as fixed. Specifically, complexes of X-cyanomethanes with trimethyl amine CH3−n(CN)nX∙∙∙NMe3 (n = 0–3; X = H, Cl, Br, I) are used as model systems. Geometrical parameters and vibrational C-X-stretching frequencies as well as interaction energies are used as relevant indicators to gauge hydrogen or halogen bond strength in the complexes. Additional characteristics of interactions that link these complexes, i.e., hydrogen or halogen bonds, are calculated with the use of the following theoretical tools: the atoms in molecules (AIM) approach, the natural bond orbital (NBO) method, and energy decomposition analysis (EDA). The results show that, for the specified X-center, the strength of C-X∙∙∙N interaction increases significantly and in a non-additive fashion with the number of CN groups. Moreover, the nature (noncovalent or partly covalent) of the interactions is revealed via the AIM approach.
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8
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Brinck T, Borrfors AN. The Importance of Electrostatics and Polarization for Noncovalent Interactions: Ionic Hydrogen Bonds vs Ionic Halogen Bonds. J Mol Model 2022; 28:275. [PMID: 36006525 PMCID: PMC9411100 DOI: 10.1007/s00894-022-05189-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/19/2022] [Indexed: 11/05/2022]
Abstract
A series of 26 hydrogen-bonded complexes between Br- and halogen, oxygen and sulfur hydrogen-bond (HB) donors is investigated at the M06-2X/6-311 + G(2df,2p) level of theory. Analysis using a model in which Br- is replaced by a point charge shows that the interaction energy ([Formula: see text]) of the complexes is accurately reproduced by the scaled interaction energy with the point charge ([Formula: see text]).This is demonstrated by [Formula: see text] with a correlation coefficient, R2 =0.999. The only outlier is (Br-H-Br)-, which generally is classified as a strong charge-transfer complex with covalent character rather than a HB complex. [Formula: see text] can be divided rigorously into an electrostatic contribution ([Formula: see text]) and a polarization contribution ([Formula: see text]).Within the set of HB complexes investigated, the former varies between -7.2 and -32.7 kcal mol-1, whereas the latter varies between -1.6 and -11.5 kcal mol-1. Compared to our previous study of halogen-bonded (XB) complexes between Br- and C-Br XB donors, the electrostatic contribution is generally stronger and the polarization contribution is generally weaker in the HB complexes. However, for both types of bonding, the variation in interaction strength can be reproduced accurately without invoking a charge-transfer term. For the Br-···HF complex, the importance of charge penetration on the variation of the interaction energy with intermolecular distance is investigated. It is shown that the repulsive character of [Formula: see text] at short distances in this complex to a large extent can be attributed to charge penetration.
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Affiliation(s)
- Tore Brinck
- Applied Physical Chemistry, Department of Chemistry, CBH, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden.
| | - André Nyberg Borrfors
- Applied Physical Chemistry, Department of Chemistry, CBH, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden
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9
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Mo Y, Danovich D, Shaik S. The roles of charge transfer and polarization in non-covalent interactions: a perspective from ab initio valence bond methods. J Mol Model 2022; 28:274. [PMID: 36006511 DOI: 10.1007/s00894-022-05187-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 12/03/2021] [Indexed: 11/28/2022]
Abstract
Noncovalent interactions are ubiquitous and have been well recognized in chemistry, biology and material science. Yet, there are still recurring controversies over their natures, due to the wide range of noncovalent interaction terms. In this Essay, we employed the Valence Bond (VB) methods to address two types of interactions which recently have drawn intensive attention, i.e., the halogen bonding and the CH‧‧‧HC dihydrogen bonding. The VB methods have the advantage of interpreting molecular structures and properties in the term of electron-localized Lewis (resonance) states (structures), which thereby shed specific light on the alteration of the bonding patterns. Due to the electron localization nature of Lewis states, it is possible to define individually and measure both polarization and charge transfer effects which have different physical origins. We demonstrated that both the ab initio VB method and the block-localized wavefunction (BLW) method can provide consistent pictures for halogen bonding systems, where strong Lewis bases NH3, H2O and NMe3 partake as the halogen bond acceptors, and the halogen bond donors include dihalogen molecules and XNO2 (X = Cl, Br, I). Based on the structural, spectral, and energetic changes, we confirm the remarkable roles of charge transfer in these halogen bonding complexes. Although the weak C-H∙∙∙H-C interactions in alkane dimers and graphene sheets are thought to involve dispersion only, we show that this term embeds delicate yet important charge transfer, bond reorganization and polarization interactions.
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Affiliation(s)
- Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, NC, 27401, USA.
| | - David Danovich
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190407, Jerusalem, Israel
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190407, Jerusalem, Israel.
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10
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Ciancaleoni G, Marchetti F, Santi C, Merlino O, Zacchini S. Assessing the effects of covalent, dative and halogen bonds on the electronic structure of selenoamides. NEW J CHEM 2022. [DOI: 10.1039/d2nj01421a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The C–NMe2 bond rotation of a selenoamide is proposed as an experimental probe to compare different chemical interactions.
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Affiliation(s)
- Gianluca Ciancaleoni
- Dipartimento di Chimica e Chimica Industriale, Università degli studi di Pisa, via Giuseppe Moruzzi 13, 56124, Italy
| | - Fabio Marchetti
- Dipartimento di Chimica e Chimica Industriale, Università degli studi di Pisa, via Giuseppe Moruzzi 13, 56124, Italy
| | - Claudio Santi
- Dipartimento di Scienze Farmaceutiche, Università degli studi di Perugia, via del Liceo, 06132, Perugia, Italy
| | - Orsola Merlino
- Dipartimento di Scienze Farmaceutiche, Università degli studi di Perugia, via del Liceo, 06132, Perugia, Italy
| | - Stefano Zacchini
- Dipartimento di Chimica Fisica ed Inorganica, Università di Bologna, viale Risorgimento 4, 40136 Bologna, Italy
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Holthoff JM, Weiss R, Rosokha SV, Huber SM. "Anti-electrostatic" Halogen Bonding between Ions of Like Charge. Chemistry 2021; 27:16530-16542. [PMID: 34409662 PMCID: PMC9293363 DOI: 10.1002/chem.202102549] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Indexed: 12/15/2022]
Abstract
Halogen bonding occurs between molecules featuring Lewis acidic halogen substituents and Lewis bases. It is often rationalized as a predominantly electrostatic interaction and thus interactions between ions of like charge (e. g., of anionic halogen bond donors with halides) seem counter-intuitive. Herein, we provide an overview on such complexes. First, theoretical studies are described and their findings are compared. Next, experimental evidences are presented in the form of crystal structure database analyses, recent examples of strong "anti-electrostatic" halogen bonding in crystals, and the observation of such interactions also in solution. We then compare these complexes to select examples of "counter-intuitive" adducts formed by other interactions, like hydrogen bonding. Finally, we comment on key differences between charge-transfer and electrostatic polarization.
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Affiliation(s)
- Jana M. Holthoff
- Fakultät für Chemie und BiochemieRuhr-Universität BochumUniversitätsstraße 15044801BochumGermany
| | - Robert Weiss
- Institut für Organische ChemieFriedrich-Alexander-Universität Erlangen-NürnbergHenkestraße 4291054ErlangenGermany
| | | | - Stefan M. Huber
- Fakultät für Chemie und BiochemieRuhr-Universität BochumUniversitätsstraße 15044801BochumGermany
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12
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Tarannam N, Shukla R, Kozuch S. Yet another perspective on hole interactions. Phys Chem Chem Phys 2021; 23:19948-19963. [PMID: 34514473 DOI: 10.1039/d1cp03533a] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hole interactions are known by different names depending on the key atom of the bond (halogen bond, chalcogen bond, hydrogen bond, etc.), and the geometry of the interaction (σ if in line, π if perpendicular to the Lewis acid plane). However, its origin starts with the creation of a Lewis acid by an underlying covalent bond, which forms an electrostatic depletion and a virtual antibonding orbital, which can create non-covalent interactions with Lewis bases. In this (maybe subjective) perspective, we will claim that hole interactions must be defined via the molecular orbital origin of the molecule. Under this premise we can better explore the richness of such bonding patterns. For that, we will study old, recent and new systems, trying to pinpoint some misinterpretations that are often associated with them. We will use as exemplars the triel bonds, a couple of metal complexes, a discussion on convergent σ-holes, and many cases of anti-electrostatic hole interactions.
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Affiliation(s)
- Naziha Tarannam
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| | - Rahul Shukla
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| | - Sebastian Kozuch
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
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13
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Abstract
It follows from the Schrödinger equation that the forces operating within molecules and molecular complexes are Coulombic, which necessarily entails both electrostatics and polarization. A common and important class of molecular complexes is due to π-holes. These are molecular regions of low electronic density that are perpendicular to planar portions of the molecular frameworks. π-Holes often have positive electrostatic potentials associated with them, which result in mutually polarizing attractive forces with negative sites such as lone pairs, π electrons or anions. In many molecules, π-holes correspond to a flattening of the electronic density surface but in benzene derivatives and in polyazines the π-holes are craters above and below the rings. The interaction energies of π-hole complexes can be expressed quite well in terms of regression relationships that account for both the electrostatics and the polarization. There is a marked gradation in the interaction energies, from quite weak (about -2 kcal mol-1) to relatively strong (about -40 kcal mol-1). Gradations are also evident in the ratios of the intermolecular separations to the sums of the respective van der Waals radii and in the gradual transition of the π-hole atoms from trigonal to quasi-tetrahedral configurations. These trends are consistent with the concept that chemical interactions form a continuum, from very weak to very strong.
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Affiliation(s)
- Peter Politzer
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA.
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14
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Murray JS, Politzer P. Can Counter-Intuitive Halogen Bonding Be Coulombic? Chemphyschem 2021; 22:1201-1207. [PMID: 33844430 DOI: 10.1002/cphc.202100202] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/05/2021] [Indexed: 01/14/2023]
Abstract
We use the term "counter-intuitive" to describe an intermolecular interaction in which the electrostatic potentials of the interacting regions of the ground-state molecules have the same sign, both positive or both negative. In the present work, we consider counter-intuitive halogen bonding with nitrogen bases, in which both the halogen σ-hole and the nitrogen lone pair have negative potentials on their molecular surfaces. We show that these interactions can be treated as Coulombic despite the apparent repulsion between the ground-state molecules, provided that both electrostatics and polarization are explicitly taken into account. We demonstrate first that the energies of 20 counter-intuitive interactions with four nitrogen bases can be expressed very well in terms of just two molecular properties: the electrostatic potential of the halogen σ-hole and the average polarizability of the nitrogen base. Then we show that the same two properties can also represent the energies of an expanded data base that includes the 20 counter-intuitive plus an additional 20 weak and moderately-strong intuitive halogen bonding interactions (in which the σ-hole potentials are now positive).
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Affiliation(s)
- Jane S Murray
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA
| | - Peter Politzer
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA
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15
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Inscoe B, Rathnayake H, Mo Y. Role of Charge Transfer in Halogen Bonding. J Phys Chem A 2021; 125:2944-2953. [PMID: 33797922 DOI: 10.1021/acs.jpca.1c01412] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Halogen bonding has received intensive attention recently for its applications in the construction of supramolecular assemblies and crystal engineering and its implications and potentials in chemical and biological processes and rational drug design. Peculiarly, in intermolecular interactions, halogen atoms are known as electron-donating groups carrying partial negative charges in molecules due to its high electronegativity, but they can counterintuitively act as Lewis acids and bind with Lewis bases in the form of a halogen bond. The unsettling issue regarding the nature of the halogen bonding is whether the electrostatics or charge transfer interaction dominates. The recently proposed σ-hole concept nicely reinforces the role of electrostatic attraction. Also, good correlations between the halogen bonding strength and the interaction energy from the simple point-charge model have been found. This leads to the claim that there is no need to invoke the charge transfer concept in the halogen bond. But there is alternative evidence supporting the importance of charge transfer interaction. Here, we visited a series of prominent halogen bonded complexes of the types Y3C-X···Z (X = Br, I; Y = F, Cl, Br; Z = F-, Cl-, Br-, I-, NMe3) with the block-localized wave function (BLW) method at the M06-2X-D3/6-311+G(d,p) (def2-SVP for iodine) level of theory. As the simplest variant of ab initio valence bond (VB) theory, the BLW method is unique in the strict localization of electrons within interacting moieties, allowing for quantitative evaluation of the charge transfer effect on geometries, spectral properties, and energetics in halogen bonding complexes. By comparing the halogen bonding complexes with and without the charge transfer interaction, we proved that the charge transfer interaction significantly shortens the X···Z bonding distance and stretches the C-X bonds. But the shortening of the halogen bonding results in the less favorable steric effect, which is composed of Pauli repulsion, electrostatics, and electron correlation. There are approximate linear correlations between the charge transfer effect and binding energy and between bonding distance and binding energy. These correlations may lead to the illusion that the charge transfer interaction is unimportant or irrelevant, but further analyses showed that the inclusion of charge transfer is critical for the proper description of the halogen bonding, as considering only electrostatics and polarization leads to only about 45-60% of the binding strengths and much elongated bonding distances.
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Affiliation(s)
- Brandon Inscoe
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
| | - Hemali Rathnayake
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
| | - Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
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16
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Li Y, Kong QR, Guo Y, Tang Z. Thermal hysteresis induced by external pressure in a 3D Hofmann-type SCO-MOF. Dalton Trans 2021; 50:1384-1389. [DOI: 10.1039/d0dt03796f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Two 3D Hofmann-type compounds [FeII(dbdpe)MII(CN)4]·4H2O have been synthesized. The application of pressure on compound 1 shifted the transition temperature from 185 K to 298 K and led to a hysteresis loop of 13–25 K.
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Affiliation(s)
- Yue Li
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005
- People's Republic of China
| | - Qing-Rong Kong
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005
- People's Republic of China
| | - Ying Guo
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005
- People's Republic of China
| | - Zheng Tang
- Key Laboratory of Cluster Science of Ministry of Education
- School of Chemistry and Chemical Engineering
- Liangxiang Campus
- Beijing Institute of Technology
- Beijing 102488
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17
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Zhao Q. Mutual influence of tetrel and halogen bonds between XCN (X=Cl, Br) and 4-TF3-pyridine (T=C, Si, Ge). J Mol Model 2020; 26:329. [DOI: 10.1007/s00894-020-04596-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 10/28/2020] [Indexed: 12/01/2022]
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18
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Halogen bonds and other noncovalent interactions in the crystal structures of trans-1,2-diiodo alkenes: an ab initio and QTAIM study. J Mol Model 2020; 26:331. [PMID: 33150494 DOI: 10.1007/s00894-020-04591-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 10/27/2020] [Indexed: 10/23/2022]
Abstract
A series of interatomic interactions interpretable as halogen bonds involving I…I, I…O, and I…C(π), as well as the noncovalent interactions I…H and O…O, were observed in the crystal structures of trans-1,2-diiodoolefins dimers according to ab initio calculations and the quantum theory of "atoms in molecules" (QTAIM) method. The interplay between each type of halogen bond and other noncovalent interactions was studied systematically in terms of bond length, electrostatic potential, and interaction energy, which are calculated via ab initio methods at the B3LYP-D3/6-311++G(d,p) and B3LYP-D3/def2-TZVP levels of theory. Characteristics and nature of the halogen bonds and other noncovalent interactions, including the topological properties of the electron density, the charge transfer, and their strengthening or weakening, were analyzed by means of both QTAIM and "natural bond order" (NBO). These computational methods provide additional insight into observed intermolecular interactions and are utilized to explain the differences seen in the crystal structures. Graphical abstract The contour map presents the regions of electronic concentration and depletion along each bond in one dimer. The blue points denote the BCPs. The blue lines denote positive Laplacian of electron density, which indicate the ionic interactions, van der Waals or intermolecular interactions, and the red lines denote negative Laplacian of electron density which indicate the covalent bonds.
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Santos GFN, Carvalho LC, Oliveira DAS, Rego DG, Bueno MA, Oliveira BG. The definitive challenge of forming uncommon pseudo‐π···H–F and C···H–F hydrogen bonds on cyclic and cubic nonpolar hydrocarbons. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Leila Cardoso Carvalho
- Centro das Ciências Exatas e das Tecnologias Universidade Federal do Oeste da Bahia Barreiras Brazil
| | | | - Danilo Guimarães Rego
- Centro das Ciências Exatas e das Tecnologias Universidade Federal do Oeste da Bahia Barreiras Brazil
| | - Mauro Alves Bueno
- Centro das Ciências Exatas e das Tecnologias Universidade Federal do Oeste da Bahia Barreiras Brazil
| | - Boaz Galdino Oliveira
- Centro das Ciências Exatas e das Tecnologias Universidade Federal do Oeste da Bahia Barreiras Brazil
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20
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Santos MS, Cybularczyk‐Cecotka M, König B, Giedyk M. Minisci C−H Alkylation of Heteroarenes Enabled by Dual Photoredox/Bromide Catalysis in Micellar Solutions**. Chemistry 2020; 26:15323-15329. [DOI: 10.1002/chem.202002320] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/23/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Marilia S. Santos
- Institute of Organic Chemistry Faculty of Chemistry and Pharmacy University of Regensburg Universitätsstraße 31 93053 Regensburg Germany
| | | | - Burkhard König
- Institute of Organic Chemistry Faculty of Chemistry and Pharmacy University of Regensburg Universitätsstraße 31 93053 Regensburg Germany
| | - Maciej Giedyk
- Institute of Organic Chemistry Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
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21
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Du J, Wang C, Yin S, Wang W, Mo Y. Resonance-assisted/impaired anion-π interaction: towards the design of novel anion receptors. RSC Adv 2020; 10:36181-36191. [PMID: 35517107 PMCID: PMC9056982 DOI: 10.1039/d0ra07877h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/23/2020] [Indexed: 01/23/2023] Open
Abstract
Substituents alter the electron density distribution in benzene in various ways, depending on their electron withdrawing and donating capabilities, as summarized by the empirical Hammett equation. The change of the π electron density distribution subsequently impacts the interaction of substituted benzenes or other cyclic conjugated rings with anions. Currently the design and synthesis of conjugated cyclic receptors capable of binding anions is an active field due to their applications in the sensing and removal of environmental contaminants and molecular recognition. By using the block-localized wavefunction (BLW) method, which is a variant of ab initio valence bond (VB) theory and can derive the reference resonance-free state self-consistently, we quantified the resonance-assisted (RA) or resonance-impaired (RI) phenomena in anion–π interactions from both structural and energetic perspectives. The frozen interaction, in which the electrostatic attraction is involved, has been shown to be the governing factor for the RA or RI interactions with anions. Energy analyses based on the empirical point charge (EPC) model indicated that the anion–π interactions can be simplified as the attraction between a negative point charge (anion) and a group of local dipoles, affected by the enriched or diminished π-cloud due to the resonance between the substituents and the conjugated ring. Hence, two strategies for the design of novel anion receptors can be envisioned. One is the enhancement of the magnitudes and/or numbers of local dipoles (polarized σ bonds), and the other is the reduction of π electron density in conjugated rings. For cases with the RI characteristics, “curved” aromatic molecules are preferred to be anion receptors. Indeed, extremely strong binding was found in complexes formed with fluorinated corannulene (F-CDD) and fluorinated [5]cycloparaphenylene (F-[5]CPP). Inspired by the RA phenomenon, complexes of p-, o- and m-benzoquinones with halides were revisited. Substituents alter the electron density distribution in benzene in various ways, depending on their electron withdrawing and donating capabilities, as summarized by the empirical Hammett equation.![]()
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Affiliation(s)
- Juan Du
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Changwei Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Shiwei Yin
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Wenliang Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University Xi'an 710119 China
| | - Yirong Mo
- Department of Nanoscience Joint School of Nanoscience & Nanoengineering, University of North Carolina at Greensboro Greensboro NC 27401 USA
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22
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Zhu Z, Xu Z, Zhu W. Interaction Nature and Computational Methods for Halogen Bonding: A Perspective. J Chem Inf Model 2020; 60:2683-2696. [DOI: 10.1021/acs.jcim.0c00032] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zhengdan Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China
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Abstract
In this review, we provide a consistent description of noncovalent interactions, covering most groups of the Periodic Table. Different types of bonds are discussed using their trivial names. Moreover, the new name “Spodium bonds” is proposed for group 12 since noncovalent interactions involving this group of elements as electron acceptors have not yet been named. Excluding hydrogen bonds, the following noncovalent interactions will be discussed: alkali, alkaline earth, regium, spodium, triel, tetrel, pnictogen, chalcogen, halogen, and aerogen, which almost covers the Periodic Table entirely. Other interactions, such as orthogonal interactions and π-π stacking, will also be considered. Research and applications of σ-hole and π-hole interactions involving the p-block element is growing exponentially. The important applications include supramolecular chemistry, crystal engineering, catalysis, enzymatic chemistry molecular machines, membrane ion transport, etc. Despite the fact that this review is not intended to be comprehensive, a number of representative works for each type of interaction is provided. The possibility of modeling the dissociation energies of the complexes using different models (HSAB, ECW, Alkorta-Legon) was analyzed. Finally, the extension of Cahn-Ingold-Prelog priority rules to noncovalent is proposed.
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24
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Abstract
The CH3Cl molecule has been used in several studies as an example purportedly to demonstrate that while Cl is weakly negative, a positive potential can be induced on its axial surface by the electric field of a reasonably strong Lewis base (such as O=CH2). The induced positive potential then has the ability to attract the negative site of the Lewis base, thus explaining the importance of polarization leading to the formation of the H3C–Cl···O=CH2 complex. By examining the nature of the chlorine’s surface in CH3Cl using the molecular electrostatic surface potential (MESP) approach, with MP2/aug-cc-pVTZ, we show that this view is not correct. The results of our calculations demonstrate that the local potential associated with the axial surface of the Cl atom is inherently positive. Therefore, it should be able to inherently act as a halogen bond donor. This is shown to be the case by examining several halogen-bonded complexes of CH3Cl with a series of negative sites. In addition, it is also shown that the lateral portions of Cl in CH3Cl features a belt of negative electrostatic potential that can participate in forming halogen-, chalcogen-, and hydrogen-bonded interactions. The results of the theoretical models used, viz. the quantum theory of atoms in molecules; the reduced density gradient noncovalent index; the natural bond orbital analysis; and the symmetry adapted perturbation theory show that Cl-centered intermolecular bonding interactions revealed in a series of 18 binary complexes do not involve a polarization-induced potential on the Cl atom.
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25
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Abstract
We demonstrate that a wide range of σ- and π-hole interaction energies can be related to (a) the electrostatic potentials and electric fields of the σ- and π-hole molecules at the approximate positions of the negative sites and (b) the electrostatic potentials and polarizabilities of the latter. This is consistent with the Coulombic nature of these interactions, which should be understood to include both electrostatics and polarization. The energies associated with polarization were estimated and were shown to overall be greater for the stronger interactions; no new factors need be introduced to account for these. All of the interactions can be treated in the same manner.
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26
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Politzer P, Murray JS. Electrostatics and Polarization in σ‐ and π‐Hole Noncovalent Interactions: An Overview. Chemphyschem 2020; 21:579-588. [DOI: 10.1002/cphc.201900968] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/11/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Peter Politzer
- Department of ChemistryUniversity of New Orleans New Orleans, LA 70148 USA
| | - Jane S. Murray
- Department of ChemistryUniversity of New Orleans New Orleans, LA 70148 USA
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27
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Ciancaleoni G, Nunzi F, Belpassi L. Charge Displacement Analysis-A Tool to Theoretically Characterize the Charge Transfer Contribution of Halogen Bonds. Molecules 2020; 25:molecules25020300. [PMID: 31940866 PMCID: PMC7024339 DOI: 10.3390/molecules25020300] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 11/17/2022] Open
Abstract
Theoretical bonding analysis is of prime importance for the deep understanding of the various chemical interactions, covalent or not. Among the various methods that have been developed in the last decades, the analysis of the Charge Displacement function (CD) demonstrated to be useful to reveal the charge transfer effects in many contexts, from weak hydrogen bonds, to the characterization of σ hole interactions, as halogen, chalcogen and pnictogen bonding or even in the decomposition of the metal-ligand bond. Quite often, the CD analysis has also been coupled with experimental techniques, in order to give a complete description of the system under study. In this review, we focus on the use of CD analysis on halogen bonded systems, describing the most relevant literature examples about gas phase and condensed phase systems. Chemical insights will be drawn about the nature of halogen bond, its cooperativity and its influence on metal-ligand bond components.
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Affiliation(s)
- Gianluca Ciancaleoni
- Dipartimento di Chimica e Chimica Industriale, Università degli Studi di Pisa, via Giuseppe Moruzzi 13, 56124 Pisa, Italy
- Correspondence: ; Tel.: +39-050-221-9351
| | - Francesca Nunzi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, via Elce di Sotto 8, I-06123 Perugia, Italy;
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” del CNR (SCITEC-CNR), via Elce di Sotto 8, I-06123 Perugia, Italy;
| | - Leonardo Belpassi
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” del CNR (SCITEC-CNR), via Elce di Sotto 8, I-06123 Perugia, Italy;
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28
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Theoretical study on the M-H···π interactions between metal hydrides and inorganic benzene B3X3H3(X = O, S, Se). Struct Chem 2019. [DOI: 10.1007/s11224-019-01474-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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29
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30
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Puttreddy R, Rautiainen JM, Mäkelä T, Rissanen K. Strong N−X⋅⋅⋅O−N Halogen Bonds: A Comprehensive Study on N‐Halosaccharin Pyridine
N
‐Oxide Complexes. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909759] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rakesh Puttreddy
- University of JyvaskylaDepartment of Chemistry P.O. BOX 35 40014 Jyväskylä Finland
| | - J. Mikko Rautiainen
- University of JyvaskylaDepartment of Chemistry P.O. BOX 35 40014 Jyväskylä Finland
| | - Toni Mäkelä
- University of JyvaskylaDepartment of Chemistry P.O. BOX 35 40014 Jyväskylä Finland
| | - Kari Rissanen
- University of JyvaskylaDepartment of Chemistry P.O. BOX 35 40014 Jyväskylä Finland
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31
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Puttreddy R, Rautiainen JM, Mäkelä T, Rissanen K. Strong N−X⋅⋅⋅O−N Halogen Bonds: A Comprehensive Study on N‐Halosaccharin Pyridine
N
‐Oxide Complexes. Angew Chem Int Ed Engl 2019; 58:18610-18618. [DOI: 10.1002/anie.201909759] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/27/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Rakesh Puttreddy
- University of JyvaskylaDepartment of Chemistry P.O. BOX 35 40014 Jyväskylä Finland
| | - J. Mikko Rautiainen
- University of JyvaskylaDepartment of Chemistry P.O. BOX 35 40014 Jyväskylä Finland
| | - Toni Mäkelä
- University of JyvaskylaDepartment of Chemistry P.O. BOX 35 40014 Jyväskylä Finland
| | - Kari Rissanen
- University of JyvaskylaDepartment of Chemistry P.O. BOX 35 40014 Jyväskylä Finland
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Politzer P, Murray JS, Clark T. Explicit Inclusion of Polarizing Electric Fields in σ- and π-Hole Interactions. J Phys Chem A 2019; 123:10123-10130. [DOI: 10.1021/acs.jpca.9b08750] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Peter Politzer
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Jane S. Murray
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, United States
| | - Timothy Clark
- Computer-Chemie-Centrum, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstr. 25, 91052 Erlangen, Germany
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33
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An Overview of Strengths and Directionalities of Noncovalent Interactions: σ-Holes and π-Holes. CRYSTALS 2019. [DOI: 10.3390/cryst9030165] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Quantum mechanics, through the Hellmann–Feynman theorem and the Schrödinger equation, show that noncovalent interactions are classically Coulombic in nature, which includes polarization as well as electrostatics. In the great majority of these interactions, the positive electrostatic potentials result from regions of low electronic density. These regions are of two types, designated as σ-holes and π-holes. They differ in directionality; in general, σ-holes are along the extensions of covalent bonds to atoms (or occasionally between such extensions), while π-holes are perpendicular to planar portions of molecules. The magnitudes and locations of the most positive electrostatic potentials associated with σ-holes and π-holes are often approximate guides to the strengths and directions of interactions with negative sites but should be used cautiously for this purpose since polarization is not being taken into account. Since these maximum positive potentials may not be in the immediate proximities of atoms, interatomic close contacts are not always reliable indicators of noncovalent interactions. This is demonstrated for some heterocyclic rings and cyclic polyketones. We briefly mention some problems associated with using Periodic Table Groups to label interactions resulting from σ-holes and π-holes; for example, the labels do not distinguish between these two possibilities with differing directionalities.
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