1
|
Shi R, Wang Z, Yu D, Wei C, Qin R, Mu T. An innovative deep eutectic solvent: chalcogen bonding as the primary driving force. Phys Chem Chem Phys 2024. [PMID: 39158020 DOI: 10.1039/d4cp01419g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Chalcogen bonding (ChB) interactions have drawn intensive attention in the last few decades as interesting alternatives to hydrogen bonding. The applications of ChB were mostly centered on the solid state and have rarely been explored in solution. In this work, a novel strategy for forming ChB-based deep eutectic solvents (DESs) was exploited. We set forth the formation, physicochemical properties, and interaction sites in detail. This work not only provides a new idea to design DES systems but also to exploit the potential application of ChB complexes.
Collapse
Affiliation(s)
- Ruifen Shi
- Zhejiang Institute of Mechanical and Electrical Engineering Corporation Limited, Hangzhou 310051, China
| | - Zeyu Wang
- School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, China.
| | - Dongkun Yu
- Department of Applied Physics, KTH Royal Institute of Technology, Hannes Alfvéns väg 12, 11419, Stockholm, Sweden
| | - Chenyang Wei
- School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, China.
| | - Rui Qin
- School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, China.
| | - Tiancheng Mu
- School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, China.
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| |
Collapse
|
2
|
Shen H, Head-Gordon M. Occupied-Virtual Orbitals for Chemical Valence with Applications to Charge Transfer in Energy Decomposition Analysis. J Phys Chem A 2024; 128:5202-5211. [PMID: 38900728 DOI: 10.1021/acs.jpca.4c02364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
In this article, we introduce the occupied-virtual orbitals for chemical valence (OVOCV). The OVOCVs can replace or complement the closely related idea of the natural orbitals for chemical valence (NOCV). The input is a difference density matrix connecting any initial single determinant to any final determinant, at a given molecular geometry, and a given one-particle basis. This arises in problems such as orbital rearrangement or charge transfer (CT) in energy decomposition analysis (EDA). The OVOCVs block-diagonalize the density difference operator into 2 × 2 blocks, which are spanned by one level that is filled in the initial state (the occupied OVOCV) and one that is empty (the virtual OVOCV). By contrast, the NOCVs fully diagonalize the density difference matrix and therefore are orbitals with mixed occupied-virtual character. Use of the OVOCVs makes it much easier to identify the donor and acceptor orbitals. We also introduce two different types of EDA methods with the OVOCVs and, most importantly, a charge decomposition analysis method that fixes the unreasonably large CT amount obtained directly from NOCV analysis. The square of the CT amount associated with each NOCV pair emerges as the appropriate value from the OVOCV analysis. When connecting the same initial and final states, this value is identical to the CT amount obtained from the independent absolutely localized molecular orbital (ALMO) complementary occupied-virtual orbital pair (COVP) analysis. The total, summed over all pairs, is also exactly the same as the independently suggested excitation number, as proved herein. Several examples are presented to compare NOCVs and OVOCVs: stretched H2+, a strong halogen bond between tetramethylthiourea and iodine, coordination of ethene in Zeise's salt, and binding in the Cp3La···C≡NCy complex.
Collapse
Affiliation(s)
- Hengyuan Shen
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| |
Collapse
|
3
|
Wang Y, Cao Z, He Q, Huang X, Liu J, Neumann H, Chen G, Beller M. Activation of perfluoroalkyl iodides by anions: extending the scope of halogen bond activation to C(sp 3)-H amidation, C(sp 2)-H iodination, and perfluoroalkylation reactions. Chem Sci 2023; 14:1732-1741. [PMID: 36819859 PMCID: PMC9930934 DOI: 10.1039/d2sc06145g] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/29/2022] [Indexed: 01/26/2023] Open
Abstract
A simple, efficient, and convenient activation of perfluoroalkyl iodides by tBuONa or KOH, without expensive photo- or transition metal catalysts, allows the promotion of versatile α-sp3 C-H amidation reactions of alkyl ethers and benzylic hydrocarbons, C-H iodination of heteroaryl compounds, and perfluoroalkylations of electron-rich π bonds. Mechanistic studies show that these novel protocols are based on the halogen bond interaction between perfluoroalkyl iodides and tBuONa or KOH, which promote homolysis of perfluoroalkyl iodides under mild conditions.
Collapse
Affiliation(s)
- Yaxin Wang
- College of Pharmacy, Nanjing University of Chinese Medicine Nanjing 210023 China .,Leibniz-Institute for Catalysis Albert-Einstein-Str. 29a Rostock 18059 Germany
| | - Zehui Cao
- College of Pharmacy, Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Qin He
- College of Pharmacy, Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Xin Huang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Nankai UniversityTianjin 300071China
| | - Jiaxi Liu
- College of Pharmacy, Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Helfried Neumann
- Leibniz-Institute for Catalysis Albert-Einstein-Str. 29a Rostock 18059 Germany
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Nankai UniversityTianjin 300071China
| | - Matthias Beller
- Leibniz-Institute for Catalysis Albert-Einstein-Str. 29a Rostock 18059 Germany
| |
Collapse
|
4
|
Kenouche S, Bachir N, Martínez-Araya JI. Explaining the High Catalytic Activity in Bis(indenyl)methyl Zirconium Cation Using Combined EDA-NOCV/QTAIM Approach. Chemphyschem 2023; 24:e202200488. [PMID: 36161688 DOI: 10.1002/cphc.202200488] [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: 07/11/2022] [Revised: 09/24/2022] [Indexed: 01/20/2023]
Abstract
The main purpose of this study is to elucidate some discrepancies already observed in the catalytic activity values of some zirconocene methyl cations. The EDA-NOCV scheme was employed for a theoretical description of the interactions between an ethylene molecule and five catalysts of zirconocene methyl cation. The nature of the chemical interactions has been elucidated through the QTAIM topological analysis. The steric hindrance due to the ligands was evaluated qualitatively by means of an IRI-based analysis and quantitively through Fisher information. The findings prove that the indenyl ligand seems to favor the orbital interaction between the ethylene molecule and the metal centre of zirconocene methyl cation. Both electrostatic and orbital contributions play a crucial role in stabilising the studied complexes. Based on the NOCV deformation density contributions, the strongest orbital interaction is reached with the bis(indenyl)methyl zirconium cation, which is the only one exhibiting covalent interactions. Especially, the strong contribution of π-back donation (occurring from the occupied orbitals of the zirconium atom to the π* anti-bonding orbital of ethylene) may be a key to understand why this catalyst has a higher polymerisation yield than the other studied catalysts. This work suggests a perspective for predicting values of catalytic activity when theoretically designing novel catalysts of zirconocene type.
Collapse
Affiliation(s)
- Samir Kenouche
- Group of Modeling of Chemical Systems using Quantum Calculations, Applied Chemistry Laboratory (LCA)., University of M. Khider of Biskra, BP 145 RP, 07000, Biskra, Algeria
| | - Nassima Bachir
- Group of Modeling of Chemical Systems using Quantum Calculations, Applied Chemistry Laboratory (LCA)., University of M. Khider of Biskra, BP 145 RP, 07000, Biskra, Algeria
| | - Jorge I Martínez-Araya
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello (UNAB), Av. República 275, 8370146, Santiago, Chile
| |
Collapse
|
5
|
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] [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 (\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$${\Delta E}_{Int}$$\end{document}ΔEInt) of the complexes is accurately reproduced by the scaled interaction energy with the point charge (\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$${\Delta E}_{Int}^{PC}$$\end{document}ΔEIntPC).This is demonstrated by \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$${\Delta E}_{Int}=0.86{\Delta E}_{Int}^{PC}$$\end{document}ΔEInt=0.86ΔEIntPC 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. \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$${\Delta E}_{Int}^{PC}$$\end{document}ΔEIntPC can be divided rigorously into an electrostatic contribution (\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$${\Delta E}_{ES}^{PC}$$\end{document}ΔEESPC) and a polarization contribution (\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$${\Delta E}_{Pol}^{PC}$$\end{document}ΔEPolPC).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 \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$${\Delta E}_{Int}$$\end{document}ΔEInt at short distances in this complex to a large extent can be attributed to charge penetration.
Collapse
|
6
|
Ciancaleoni G, Rocchigiani L. Assessing the Orbital Contribution in the "Spodium Bond" by Natural Orbital for Chemical Valence-Charge Displacement Analysis. Inorg Chem 2021; 60:4683-4692. [PMID: 33760600 DOI: 10.1021/acs.inorgchem.0c03650] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The term "spodium bond" (SpB) has been recently proposed to describe the noncoordinative interaction that can be established between a polarized group 12 metal and a mild Lewis base (LB). Most of the systems showing short metal-donor distances compatible with SpB are characterized by the coexistence of multiple weak interactions, including hydrogen and halogen bonding, making the assessment of real importance of SpB difficult. Here, we show that the relative importance of each contribution can be probed by dissecting the orbital component of the interaction through the extended transition state-natural orbital for chemical valence-charge displacement analysis (ETS-NOCV-CD). The latter gives useful information about relative energies and electrons involved, for model systems ([(thiourea)2MX2]···LB; M = Zn, Cd, and Hg; X = Cl and I; and LB = CH2S, CH2O, CH3CN, and CO) and a variety of structures extracted from experimentally characterized adducts, allowing us to demonstrate the lack of a direct correlation between a favorable metal-base distance and the presence of an orbital contribution for the SpB.
Collapse
Affiliation(s)
- Gianluca Ciancaleoni
- Università degli Studi di Pisa, Dipartimento di Chimica e Chimica Industriale, via Giuseppe Moruzzi 13, 56124 Pisa, Italy
| | - Luca Rocchigiani
- School of Chemistry, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, U.K
| |
Collapse
|
7
|
Treto-Suárez MA, Tapia J, Hidalgo-Rosa Y, Páez-Hernández D, Molins E, Zarate X, Schott E. New Sensitive and Selective Chemical Sensors for Ni 2+ and Cu 2+ Ions: Insights into the Sensing Mechanism through DFT Methods. J Phys Chem A 2020; 124:6493-6503. [PMID: 32635732 DOI: 10.1021/acs.jpca.0c03834] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the synthesis and theoretical study of two new colorimetric chemosensors with special selectivity and sensitivity to Ni2+ and Cu2+ ions over other metal cations in the CH3CN/H2O solution. Compounds (E)-4-((2-nitrophenyl)diazenyl)-N,N-bis(pyridin-2-ylmethyl)aniline (A) and (E)-4-((3-nitrophenyl)diazenyl)-N,N-bis(pyridin-2-ylmethyl)aniline (B) exhibited a drastic color change from yellow to colorless, which allows the detection of the mentioned metal cations through different techniques. The interaction of sensors with these metal ions induced a new absorption band with a hypsochromic shift to the characteristic signal of the free sensors. A theoretical study via time-dependent density functional theory (TD-DFT) was performed. This method has enabled us to reproduce the hypsochromic shift in the maximum UV-vis absorption band and explain the selective sensing of the ions. For all of the systems studied, the absorption band is characterized by a π → π* transition centered in the ligand. Instead of Ni2+ and Cu2+ ions, the transition is set toward the σ* molecular orbital with a strong contribution of the 3dx2-y2 transition (π → 3dx2-y2). These absorptions imply a ligand-to-metal charge transfer (LMCT) mechanism that results in the hypsochromic shift in the absorption band of these systems.
Collapse
Affiliation(s)
- Manuel A Treto-Suárez
- Doctorado en Fisicoquímica Molecular, Universidad Andres Bello, Ave. República #275, 8320000, Santiago de Chile, Chile
| | - Jorge Tapia
- Universidad Bernardo OHiggins, Facultad de Salud, Departamento de Ciencias Quı́micas y Biológicas, General Gana 1702, Santiago, Chile.,Millennium Nuclei on Catalytic Processes towards Sustainable Chemistry (CSC), Santiago, Chile
| | - Yoan Hidalgo-Rosa
- Doctorado en Fisicoquímica Molecular, Universidad Andres Bello, Ave. República #275, 8320000, Santiago de Chile, Chile.,Millennium Nuclei on Catalytic Processes towards Sustainable Chemistry (CSC), Santiago, Chile
| | - Dayan Páez-Hernández
- Doctorado en Fisicoquímica Molecular, Universidad Andres Bello, Ave. República #275, 8320000, Santiago de Chile, Chile.,Center of Applied Nanosciences (CANS), Chile República #275, 8320000, Santiago de Chile, Chile
| | - Elies Molins
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Bellaterra, Spain
| | - Ximena Zarate
- Instituto de Ciencias Químicas Aplicadas, Theoretical and Computational Chemistry Center, Facultad de Ingeniería, Universidad Autónoma de Chile, Av. Pedro de Valdivia 425, 7500912, Santiago, Chile
| | - Eduardo Schott
- Departamento de Química Inorgánica, Facultad de Quı́mica y Farmacia, Centro de Energı́a UC, Centro de Investigación en Nanotecnologı́a y Materiales Avanzados CIEN-UC, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna, 4860, 7820244, Santiago, Chile.,Millennium Nuclei on Catalytic Processes towards Sustainable Chemistry (CSC), Santiago, Chile
| |
Collapse
|
8
|
Ciancaleoni G, Belpassi L. Disentanglement of orthogonal hydrogen and halogen bonds via natural orbital for chemical valence: A charge displacement analysis. J Comput Chem 2020; 41:1185-1193. [PMID: 32011001 DOI: 10.1002/jcc.26165] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/21/2020] [Accepted: 01/21/2020] [Indexed: 01/01/2023]
Abstract
As known, the electron density of covalently bound halogen atoms is anisotropically distributed, making them potentially able to establish many weak interactions, acting at the same time as halogen bond donors and hydrogen bond acceptors. Indeed, there are many examples in which the halogen and hydrogen bond coexist in the same structure and, if a correct bond analysis is required, their separation is mandatory. Here, the advantages and limitations of coupling the charge displacement analysis with natural orbital for chemical valence method (NOCV-CD) to separately analyze orthogonal weak interactions are shown, for both symmetric and asymmetric adducts. The methodology gives optimal results with intermolecular adducts but, in the presence of an organometallic complex, also intramolecular interactions can be correctly analyzed. Beyond the methodological aspects, it is shown that correctly separate and quantify the interactions can give interesting chemical insights about the systems.
Collapse
Affiliation(s)
- Gianluca Ciancaleoni
- Dipartimento di Chimica e Chimica Industriale, Università degli Studi di Pisa, Pisa, Italy
| | - Leonardo Belpassi
- Istituto di Scienze e Tecnologie Chimiche "G. Natta"-CNR (CNR-SCITEC), c/o Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| |
Collapse
|
9
|
Margiotta E, van der Lubbe SCC, de Azevedo Santos L, Paragi G, Moro S, Bickelhaupt FM, Fonseca Guerra C. Halogen Bonds in Ligand-Protein Systems: Molecular Orbital Theory for Drug Design. J Chem Inf Model 2020; 60:1317-1328. [PMID: 32003997 PMCID: PMC7093837 DOI: 10.1021/acs.jcim.9b00946] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
Halogen bonds are highly important
in medicinal chemistry as halogenation
of drugs, generally, improves both selectivity and efficacy toward
protein active sites. However, accurate modeling of halogen bond interactions
remains a challenge, since a thorough theoretical investigation of
the bonding mechanism, focusing on the realistic complexity of drug–receptor
systems, is lacking. Our systematic quantum-chemical study on ligand/peptide-like
systems reveals that halogen bonding is driven by the same bonding
interactions as hydrogen bonding. Besides the electrostatic and the
dispersion interactions, our bonding analyses, based on quantitative
Kohn–Sham molecular orbital theory together with energy decomposition
analysis, reveal that donor–acceptor interactions and steric
repulsion between the occupied orbitals of the halogenated ligand
and the protein need to be considered more carefully within the drug
design process.
Collapse
Affiliation(s)
- Enrico Margiotta
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova, via Marzolo 5, 35131 Padova, Italy
| | - Stephanie C C van der Lubbe
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Lucas de Azevedo Santos
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Department of Chemistry, Federal University of Lavras, CEP 37200-000 Lavras, Minas Gerais, Brazil
| | - Gabor Paragi
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,MTA-SZTE Biomimetic Systems Research Group, Dom ter 8, 6720 Szeged, Hungary.,Institute of Physics, University of Pecs, Ifjusag utja 6, 7624 Pecs, Hungary
| | - Stefano Moro
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova, via Marzolo 5, 35131 Padova, Italy
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Institute of Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| |
Collapse
|
10
|
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.
Collapse
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;
| |
Collapse
|
11
|
|
12
|
Chen L, Liu S, Xu Z, Yang X. Electrically Tunable Electron Transfer and Binding Interaction between Hydrated Ions and Graphene Oxide. J Phys Chem Lett 2019; 10:5735-5741. [PMID: 31508964 DOI: 10.1021/acs.jpclett.9b02074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Density functional theory simulations were carried out to study the binding interaction between hydrated Na+/Cl- and graphene oxide (GO) under electric fields. External electric fields can modify the binding interactions of the hydrated ions with GO. The field-dependent binding energy is mainly controlled by the orbital interaction driven by the field-dependent electron transfer, in which miscellaneous electron-transfer routes in the interfaces between hydrated ions and GO surface were disclosed. The electric field is able to influence the electron-transfer degree for each route, thereby creating various electron acceptor-donor coupling interactions. Furthermore, we preliminarily explored the effect of the electric field on the interlayer structure of bilayer GO with NaCl and water confined inside. Electric fields can enlarge the interlayer spacing through tuning of the hydrated ion-GO interactions. Our simulations present a new understanding of hydrated ion-GO interactions in the presence of an electric field, which is expected to be valuable in the electrical modulation of GO nanomaterials.
Collapse
|
13
|
Brinck T, Borrfors AN. Electrostatics and polarization determine the strength of the halogen bond: a red card for charge transfer. J Mol Model 2019; 25:125. [DOI: 10.1007/s00894-019-4014-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/29/2019] [Indexed: 10/27/2022]
|
14
|
Brinck T, Stenlid JH. The Molecular Surface Property Approach: A Guide to Chemical Interactions in Chemistry, Medicine, and Material Science. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201800149] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Tore Brinck
- Applied Physical ChemistryDepartment of ChemistryCBHKTH Royal Institute of Technology SE‐100 44 Stockholm Sweden
| | - Joakim H. Stenlid
- Department of PhysicsAlbaNova University CenterStockholm University SE‐106 91 Stockholm Sweden
| |
Collapse
|
15
|
Kurczab R, Śliwa P, Rataj K, Kafel R, Bojarski AJ. Salt Bridge in Ligand-Protein Complexes-Systematic Theoretical and Statistical Investigations. J Chem Inf Model 2018; 58:2224-2238. [PMID: 30351056 DOI: 10.1021/acs.jcim.8b00266] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Although the salt bridge is the strongest among all known noncovalent molecular interactions, no comprehensive studies have been conducted to date to examine its role and significance in drug design. Thus, a systematic study of the salt bridge in biological systems is reported herein, with a broad analysis of publicly available data from Protein Data Bank, DrugBank, ChEMBL, and GPCRdb. The results revealed the distance and angular preferences as well as privileged molecular motifs of salt bridges in ligand-receptor complexes, which could be used to design the strongest interactions. Moreover, using quantum chemical calculations at the MP2 level, the energetic, directionality, and spatial variabilities of salt bridges were investigated using simple model systems mimicking salt bridges in a biological environment. Additionally, natural orbitals for chemical valence (NOCV) combined with the extended-transition-state (ETS) bond-energy decomposition method (ETS-NOCV) were analyzed and indicated a strong covalent contribution to the salt bridge interaction. The present results could be useful for implementation in rational drug design protocols.
Collapse
Affiliation(s)
- Rafał Kurczab
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smetna 12 , 31-343 Cracow , Poland
| | - Paweł Śliwa
- Faculty of Chemical Engineering and Technology , Cracow University of Technology , Warszawska 24 , 31-155 Cracow , Poland
| | - Krzysztof Rataj
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smetna 12 , 31-343 Cracow , Poland
| | - Rafał Kafel
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smetna 12 , 31-343 Cracow , Poland
| | - Andrzej J Bojarski
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smetna 12 , 31-343 Cracow , Poland
| |
Collapse
|
16
|
Oliveira V, Kraka E, Cremer D. The intrinsic strength of the halogen bond: electrostatic and covalent contributions described by coupled cluster theory. Phys Chem Chem Phys 2018; 18:33031-33046. [PMID: 27886325 DOI: 10.1039/c6cp06613e] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
36 halogen-bonded complexes YXARm (X: F, Cl, Br; Y: donor group; ARm acceptor group) have been investigated at the CCSD(T)/aug-cc-pVTZ level of theory. Binding energies, geometries, NBO charges, charge transfer, dipole moments, electrostatic potential, electron and energy density distributions, difference density distributions, vibrational frequencies, local stretching and bending force constants, and relative bond strength orders n have been calculated and used to order the halogen bonds according to their intrinsic strength. Halogen bonding is found to arise from electrostatic and strong covalent contributions. It can be strengthened by H-bonding or lone pair delocalization. The covalent character of a halogen bond increases in the way 3c-4e (three-center-four-electron) bonding becomes possible. One can characterize halogen bonds by their percentage of 3c-4e bonding. FCl-phosphine complexes can form relatively strong halogen bonds provided electronegative substituents increase the covalent contributions in form of 3c-4e halogen bonding. Binding energies between 1 and 45 kcal mol-1 are calculated, which reflects the large variety in halogen bonding.
Collapse
Affiliation(s)
- Vytor Oliveira
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas 75275-0314, USA.
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas 75275-0314, USA.
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas 75275-0314, USA.
| |
Collapse
|
17
|
Menacer R, May A, Belkhiri L, Mousser A. Electronic structure and bonding of the dinuclear metal M 2(CO) 10 decacarbonyls: applications of natural orbitals for chemical valence. J Mol Model 2017; 23:358. [PMID: 29185066 DOI: 10.1007/s00894-017-3523-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/06/2017] [Indexed: 10/18/2022]
Abstract
The nature of the chemical metal-metal bond in M2(CO)10 (M = Mn, Re, Tc) dinuclear decacarbonyls complexes was investigated for the first time using the natural orbital chemical valence (NOCV) approach combined with the extended transition state (ETS) for energy decomposition analysis (EDA). The optimized geometries carried out at different levels of theory BP86, BLYP, BLYPD and BP86D, showed that the latter method, i.e., BP86D, led to the best agreement with X-ray experimental measurements. The BP86D/TZP results revealed that the computed covalent contribution to the metal-metal bond are 60.5%, 54.1% and 52.0% for Mn-Mn, Re-Re and Tc-Tc, respectively. The computed total interaction energies resulting from attractive terms (ΔE orb and ΔE eles), correspond well to experimental predictions, based on bond lengths and energy interaction analysis for the studied complexes.
Collapse
Affiliation(s)
- Rafik Menacer
- Laboratoire de Physicochimie Analytique et Cristallochimie des Matériaux Organométalliques et Biomoléculaires LPACMOB, Département de Chimie, Université Frères Mentouri, 25017, Constantine, Algeria.,Centre de Recherche Scientifique et Technique en Analyses Physico-Chimiques CRAPC, BP 384, Zone Industrielle, Bou-ismail, Tipaza, RP 42004, Algeria
| | - Abdelghani May
- Département de Chimie, Université Frères Mentouri, Route de Ain El Bey, 25017, Constantine, Algeria
| | - Lotfi Belkhiri
- URCHEMS, Département de Chimie, Université Frères Mentouri, Route de Ain El Bey, 25017, Constantine, Algeria.
| | - Abdelhamid Mousser
- Laboratoire de Physicochimie Analytique et Cristallochimie des Matériaux Organométalliques et Biomoléculaires LPACMOB, Département de Chimie, Université Frères Mentouri, 25017, Constantine, Algeria
| |
Collapse
|
18
|
Arokiyanathan AL, Lakshmipathi S. Molecular properties of metal difluorides and their interactions with CO 2 and H 2O molecules: a DFT investigation. J Mol Model 2017; 23:345. [PMID: 29150809 DOI: 10.1007/s00894-017-3511-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/24/2017] [Indexed: 12/01/2022]
Abstract
A computational study of metal difluorides (MF2; M = Ca to Zn) and their interactions with carbon dioxide and water molecules was performed. The structural parameter values obtained and the results of AIM analysis and energy decomposition analysis indicated that the Ca-F bond is weaker and less ionic than the bonds in the transition metal difluorides. A deformation density plot revealed the stablizing influence of the Jahn-Teller effect in nonlinear MF2 molecules (e.g., where M= Sc, Ti, Cr). An anaysis of the metal K-edge peaks of the difluorides showed that shifts in the edge energy were due to the combined effects of the ionicity, effective nuclear charge, and the spin state of the metal. The interactions of CO2 with ScF2 (Scc3 geometry) and TiF2 (Tic2 geometry) caused CO2 to shift from its usual linear geometry to a bent geometry (η2(C=O) binding mode), while it retained its linear geometry (η1(O) binding mode) when it interacted with the other metal difluorides. Energy decomposition analysis showed that, among the various geometries considered, the Scc3 and Tic2 geometries possessed the highest interaction energies and orbital interaction energies. Heavier transition metal difluorides showed stronger affinities for H2O, whereas the lighter transition metal (Sc and Ti) difluorides preferred CO2. Overall, the results of this study suggest that fluorides of lighter transition metals with partially filled d orbitals (e.g., Sc and Ti) could be used for CO2 capture under moist conditions. Graphical abstract Interaction of metal difluorides with carbon dioxide and water.
Collapse
|
19
|
Priya AM, Lakshmipathi S. Atmospheric fate of diketones and OH radical–kinetics, reaction force, ETS-NOCV analysis. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1290840] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
20
|
|
21
|
Oliveira V, Kraka E, Cremer D. Quantitative Assessment of Halogen Bonding Utilizing Vibrational Spectroscopy. Inorg Chem 2016; 56:488-502. [PMID: 27966937 DOI: 10.1021/acs.inorgchem.6b02358] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A total of 202 halogen-bonded complexes have been studied using a dual-level approach: ωB97XD/aug-cc-pVTZ was used to determine geometries, natural bond order charges, charge transfer, dipole moments, electron and energy density distributions, vibrational frequencies, local stretching force constants, and relative bond strength orders n. The accuracy of these calculations was checked for a subset of complexes at the CCSD(T)/aug-cc-pVTZ level of theory. Apart from this, all binding energies were verified at the CCSD(T) level. A total of 10 different electronic effects have been identified that contribute to halogen bonding and explain the variation in its intrinsic strength. Strong halogen bonds are found for systems with three-center-four-electron (3c-4e) bonding such as chlorine donors in interaction with substituted phosphines. If halogen bonding is supported by hydrogen bonding, genuine 3c-4e bonding can be realized. Perfluorinated diiodobenzenes form relatively strong halogen bonds with alkylamines as they gain stability due to increased electrostatic interactions.
Collapse
Affiliation(s)
- Vytor Oliveira
- Computational and Theoretical Chemistry Group, Department of Chemistry, Southern Methodist University (SMU) , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group, Department of Chemistry, Southern Methodist University (SMU) , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group, Department of Chemistry, Southern Methodist University (SMU) , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| |
Collapse
|
22
|
Brinck T, Carlqvist P, Stenlid JH. Local Electron Attachment Energy and Its Use for Predicting Nucleophilic Reactions and Halogen Bonding. J Phys Chem A 2016; 120:10023-10032. [DOI: 10.1021/acs.jpca.6b10142] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Tore Brinck
- Applied Physical Chemistry,
School of Chemical Science and Engineering, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Peter Carlqvist
- Applied Physical Chemistry,
School of Chemical Science and Engineering, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Joakim H. Stenlid
- Applied Physical Chemistry,
School of Chemical Science and Engineering, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| |
Collapse
|
23
|
Cukrowski I, Sagan F, Mitoraj MP. On the Stability of Cis- and Trans-2-Butene Isomers. An Insight Based on the FAMSEC, IQA, and ETS-NOCV Schemes. J Comput Chem 2016; 37:2783-2798. [PMID: 27730662 DOI: 10.1002/jcc.24504] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/08/2016] [Accepted: 09/10/2016] [Indexed: 01/19/2023]
Abstract
In the present account, the real space fragment attributed molecular system energy change (FAMSEC) approach, interacting quantum atoms energy decomposition scheme as well as molecular orbitals based the extended transition state scheme coupled with natural orbitals for chemical valence (ETS-NOCV) have been, for the first time, successfully used to delineate factors of importance for stability of the 2-butene conformers (cis-eq, cis-TS, trans-eq, trans-TS). Our results demonstrate that atoms of the controversial H-H contact in cis-eq (i) are involved in attractive interaction dominated by the exchange-correlation term, (ii) are weekly stabilized, (iii) show trends in several descriptors found in other typical H-bonds, and (iv) are part of most stabilized CH-HC fragment (loc-FAMSEC = -3.6 kcal/mol) with most favourably changed intrafragment interactions on trans-eq→cis-eq. Moreover, lower stability of cis-eq vs. trans-eq is linked with the entire HCCH (ethylenic) fragment which destabilized cis-eq (mol-FAMSEC, +3.9 kcal/mol) the most. Although the H-H contact can be linked with smaller, relative to trans-, rotational energy barrier in cis-2-butene, we have proven that to rationalize this phenomenon one must account for changes in interactions between various fragments that constitute the entire molecule. Importantly, we discovered a number of comparable trends in fundamental properties of equivalent molecular fragments on a methyl group rotation; for example, interaction between BP-free H-atoms in trans-eq (involving CH bonds of the methyl and ethylenic units) and BP-linked H-atoms in cis-eq. Clearly, rotational energy barrier cannot be entirely (i) rationalized by the properties of or (ii) attributed to the H-H contact in cis-eq. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Ignacy Cukrowski
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
| | - Filip Sagan
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Cracow, 30-060, Poland
| | - Mariusz Paweł Mitoraj
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Cracow, 30-060, Poland
| |
Collapse
|
24
|
Chen Z, Wang G, Xu Z, Wang J, Yu Y, Cai T, Shao Q, Shi J, Zhu W. How Do Distance and Solvent Affect Halogen Bonding Involving Negatively Charged Donors? J Phys Chem B 2016; 120:8784-93. [DOI: 10.1021/acs.jpcb.6b05027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhaoqiang Chen
- 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, No.19A Yuquan Road, Beijing 100049, China
| | - Guimin Wang
- 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, No.19A Yuquan Road, 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
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Jinan Wang
- 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, No.19A Yuquan Road, Beijing 100049, China
| | - Yuqi Yu
- 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, No.19A Yuquan Road, Beijing 100049, China
| | - Tingting Cai
- 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, No.19A Yuquan Road, Beijing 100049, China
| | - Qiang Shao
- 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, No.19A Yuquan Road, Beijing 100049, China
| | - Jiye Shi
- UCB Biopharma SPRL, Chemin
du Foriest, Braine-l’Alleud B-1420, Belgium
| | - 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, No.19A Yuquan Road, Beijing 100049, China
| |
Collapse
|
25
|
Ardizzoia GA, Bea M, Brenna S, Therrien B. A Quantitative Description of the σ-Donor and π-Acceptor Properties of Substituted Phenanthrolines. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201600647] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- G. Attilio Ardizzoia
- Department of Science and High Technology; University of Insubria; Via Valleggio, 9 22100 Como Italy
| | - Michela Bea
- Department of Science and High Technology; University of Insubria; Via Valleggio, 9 22100 Como Italy
| | - Stefano Brenna
- Department of Science and High Technology; University of Insubria; Via Valleggio, 9 22100 Como Italy
| | - Bruno Therrien
- Institute of Chemistry; University of Neuchâtel; Avenue de Bellevaux 51 2000 Neuchâtel Switzerland
| |
Collapse
|
26
|
Non-Covalent Interactions in Hydrogen Storage Materials LiN(CH3)2BH3 and KN(CH3)2BH3. CRYSTALS 2016. [DOI: 10.3390/cryst6030028] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
27
|
Kroutil O, Předota M, Chval Z. Pt···H Nonclassical Interaction in Water-Dissolved Pt(II) Complexes: Coaction of Electronic Effects with Solvent-Assisted Stabilization. Inorg Chem 2016; 55:3252-64. [DOI: 10.1021/acs.inorgchem.5b02261] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Ondřej Kroutil
- Institute of Laboratory Diagnostics and Public Health,
Faculty of Health and Social Studies, University of South Bohemia, J.
Boreckého 27, 37011 České Budějovice, Czech Republic
- Institute of Physics and Biophysics, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
| | - Milan Předota
- Institute of Physics and Biophysics, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
| | - Zdeněk Chval
- Institute of Laboratory Diagnostics and Public Health,
Faculty of Health and Social Studies, University of South Bohemia, J.
Boreckého 27, 37011 České Budějovice, Czech Republic
| |
Collapse
|
28
|
Abstract
The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.
Collapse
Affiliation(s)
- Gabriella Cavallo
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
| | - Pierangelo Metrangolo
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
- VTT-Technical
Research Centre of Finland, Biologinkuja 7, 02150 Espoo, Finland
| | - Roberto Milani
- VTT-Technical
Research Centre of Finland, Biologinkuja 7, 02150 Espoo, Finland
| | - Tullio Pilati
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
| | - Arri Priimagi
- Department
of Chemistry and Bioengineering, Tampere
University of Technology, Korkeakoulunkatu 8, FI-33101 Tampere, Finland
| | - Giuseppe Resnati
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
| | - Giancarlo Terraneo
- Laboratory
of Nanostructured Fluorinated Materials (NFMLab), Department of Chemistry,
Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Via L. Mancinelli 7, I-20131 Milano, Italy
| |
Collapse
|
29
|
Koskinen L, Hirva P, Kalenius E, Jääskeläinen S, Rissanen K, Haukka M. Halogen bonds with coordinative nature: halogen bonding in a S–I+–S iodonium complex. CrystEngComm 2015. [DOI: 10.1039/c4ce01735h] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A thorough characterization of unusually strong I+–S halogen bonds indicates that halogen bonding is not merely an electrostatic contact but also has a strong coordinative nature, thus expanding the scope of halogen bonding.
Collapse
Affiliation(s)
- L. Koskinen
- Department of Chemistry
- University of Eastern Finland
- FI-80101 Joensuu, Finland
| | - P. Hirva
- Department of Chemistry
- University of Eastern Finland
- FI-80101 Joensuu, Finland
| | - E. Kalenius
- Department of Chemistry
- Nanoscience Center
- University of Jyväskylä
- FI-40014 Jyväskylä, Finland
| | - S. Jääskeläinen
- Department of Chemistry
- University of Eastern Finland
- FI-80101 Joensuu, Finland
| | - K. Rissanen
- Department of Chemistry
- Nanoscience Center
- University of Jyväskylä
- FI-40014 Jyväskylä, Finland
| | - M. Haukka
- Department of Chemistry
- University of Jyväskylä
- FI-40014 Jyväskylä, Finland
| |
Collapse
|
30
|
Koskinen L, Hirva P, Hasu A, Jääskeläinen S, Koivistoinen J, Pettersson M, Haukka M. Modification of the supramolecular structure of [(thione)IY] (Y = Cl, Br) systems by cooperation of strong halogen bonds and hydrogen bonds. CrystEngComm 2015. [DOI: 10.1039/c4ce02449d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Strong halogen bonds and hydrogen bonds cooperated to control the supramolecular structures of [(thione)IY] (Y = Cl, Br) compounds.
Collapse
Affiliation(s)
- L. Koskinen
- Department of Chemistry
- University of Eastern Finland
- FI-80101 Joensuu, Finland
| | - P. Hirva
- Department of Chemistry
- University of Eastern Finland
- FI-80101 Joensuu, Finland
| | - A. Hasu
- Department of Chemistry
- University of Eastern Finland
- FI-80101 Joensuu, Finland
| | - S. Jääskeläinen
- Department of Chemistry
- University of Eastern Finland
- FI-80101 Joensuu, Finland
| | - J. Koivistoinen
- Department of Chemistry
- Nanoscience Center
- University of Jyväskylä
- FI-40014 Jyväskylä, Finland
| | - M. Pettersson
- Department of Chemistry
- Nanoscience Center
- University of Jyväskylä
- FI-40014 Jyväskylä, Finland
| | - M. Haukka
- Department of Chemistry
- University of Jyväskylä
- FI-40014 Jyväskylä, Finland
| |
Collapse
|
31
|
Syzgantseva OA, Tognetti V, Joubert L. On the Physical Nature of Halogen Bonds: A QTAIM Study. J Phys Chem A 2013; 117:8969-80. [DOI: 10.1021/jp4059774] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Olga A. Syzgantseva
- Normandy Université, COBRA UMR 6014 and FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére, 76821
Mont Saint Aignan, Cedex, France
| | - Vincent Tognetti
- Normandy Université, COBRA UMR 6014 and FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére, 76821
Mont Saint Aignan, Cedex, France
| | - Laurent Joubert
- Normandy Université, COBRA UMR 6014 and FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére, 76821
Mont Saint Aignan, Cedex, France
| |
Collapse
|
32
|
Dyduch K, Mitoraj MP, Michalak A. ETS-NOCV description of σ-hole bonding. J Mol Model 2012; 19:2747-58. [PMID: 23053006 PMCID: PMC3693432 DOI: 10.1007/s00894-012-1591-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 08/30/2012] [Indexed: 11/27/2022]
Abstract
The ETS-NOCV analysis was applied to describe the σ-hole in a systematic way in a series of halogen compounds, CF3-X (X = I, Br, Cl, F), CH3I, and C(CH3)nH3-n-I (n = 1,2,3), as well as for the example germanium-based systems. GeXH3, X = F, Cl, H. Further, the ETS-NOCV analysis was used to characterize bonding with ammonia for these systems. The results show that the dominating contribution to the deformation density, Δρ 1 , exhibits the negative-value area with a minimum, corresponding to σ-hole. The "size" (spatial extension of negative value) and "depth" (minium value) of the σ-hole varies for different X in CF3-X, and is influenced by the carbon substituents (fluorine atoms, hydrogen atoms, methyl groups). The size and depth of σ-hole decreases in the order: I, Br, Cl, F in CF3-X. In CH3-I and C(CH3)nH3-n-I, compared to CF3-I, introduction of hydrogen atoms and their subsequent replacements by methyl groups lead to the systematic decrease in the σ-hole size and depth. The ETS-NOCV σ-hole picture is consistent with the existence the positive MEP area at the extension of σ-hole generating bond. Finally, the NOCV deformation density contours as well as by the ETS orbital-interaction energy indicate that the σ-hole-based bond with ammonia contains a degree of covalent contribution. In all analyzed systems, it was found that the electrostatic energy is approximately two times larger than the orbital-interaction term, confirming the indisputable role of the electrostatic stabilization in halogen bonding and σ-hole bonding.
Collapse
Affiliation(s)
- Karol Dyduch
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Krakow, Poland
| | - Mariusz P. Mitoraj
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Krakow, Poland
| | - Artur Michalak
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, 30-060 Krakow, Poland
| |
Collapse
|