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Abstract
Halogen bonds are prevalent in many areas of chemistry, physics, and biology. We present a statistical model for the interaction energies of halogen-bonded systems at equilibrium based on high-accuracy ab initio benchmark calculations for a range of complexes. Remarkably, the resulting model requires only two fitted parameters, X and B—one for each molecule—and optionally the equilibrium separation, R e , between them, taking the simple form E = X B / R e n . For n = 4 , it gives negligible root-mean-squared deviations of 0.14 and 0.28 kcal mol - 1 over separate fitting and validation data sets of 60 and 74 systems, respectively. The simple model is shown to outperform some of the best density functionals for non-covalent interactions, once parameters are available, at essentially zero computational cost. Additionally, we demonstrate how it can be transferred to completely new, much larger complexes and still achieve accuracy within 0.5 kcal mol - 1 . Using a principal component analysis and symmetry-adapted perturbation theory, we further show how the model can be used to predict the physical nature of a halogen bond, providing an efficient way to gain insight into the behavior of halogen-bonded systems. This means that the model can be used to highlight cases where induction or dispersion significantly affect the underlying nature of the interaction.
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52
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Varadwaj A, Marques HM, Varadwaj PR. Is the Fluorine in Molecules Dispersive? Is Molecular Electrostatic Potential a Valid Property to Explore Fluorine-Centered Non-Covalent Interactions? Molecules 2019; 24:E379. [PMID: 30678158 PMCID: PMC6384640 DOI: 10.3390/molecules24030379] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 11/23/2022] Open
Abstract
Can two sites of positive electrostatic potential localized on the outer surfaces of two halogen atoms (and especially fluorine) in different molecular domains attract each other to form a non-covalent engagement? The answer, perhaps counterintuitive, is yes as shown here using the electronic structures and binding energies of the interactions for a series of 22 binary complexes formed between identical or different atomic domains in similar or related halogen-substituted molecules containing fluorine. These were obtained using various computational approaches, including density functional and ab initio first-principles theories with M06-2X, RHF, MP2 and CCSD(T). The physical chemistry of non-covalent bonding interactions in these complexes was explored using both Quantum Theory of Atoms in Molecules and Symmetry Adapted Perturbation Theories. The surface reactivity of the 17 monomers was examined using the Molecular Electrostatic Surface Potential approach. We have demonstrated inter alia that the dispersion term, the significance of which is not always appreciated, which emerges either from an energy decomposition analysis, or from a correlated calculation, plays a structure-determining role, although other contributions arising from electrostatic, exchange-repulsion and polarization effects are also important. The 0.0010 a.u. isodensity envelope, often used for mapping the electrostatic potential is found to provide incorrect information about the complete nature of the surface reactive sites on some of the isolated monomers, and can lead to a misinterpretation of the results obtained.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku 113-8656, Japan.
- National Institute of Advanced Industrial Science and Technology, 1 Chome-1-1 Umezono, Tsukuba, Ibaraki Prefecture, Ibaraki 305-8560, Japan.
| | - Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
| | - Pradeep R Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku 113-8656, Japan.
- National Institute of Advanced Industrial Science and Technology, 1 Chome-1-1 Umezono, Tsukuba, Ibaraki Prefecture, Ibaraki 305-8560, Japan.
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53
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Lange A, Heidrich J, Zimmermann MO, Exner TE, Boeckler FM. Scaffold Effects on Halogen Bonding Strength. J Chem Inf Model 2019; 59:885-894. [DOI: 10.1021/acs.jcim.8b00621] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Andreas Lange
- Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Johannes Heidrich
- Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Markus O. Zimmermann
- Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Thomas E. Exner
- Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
- Center for Bioinformatics Tuebingen (ZBIT), Eberhard Karls University Tuebingen, Sand 1, 72076 Tuebingen, Germany
| | - Frank M. Boeckler
- Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
- Center for Bioinformatics Tuebingen (ZBIT), Eberhard Karls University Tuebingen, Sand 1, 72076 Tuebingen, Germany
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54
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Lisac K, Topić F, Arhangelskis M, Cepić S, Julien PA, Nickels CW, Morris AJ, Friščić T, Cinčić D. Halogen-bonded cocrystallization with phosphorus, arsenic and antimony acceptors. Nat Commun 2019; 10:61. [PMID: 30610194 PMCID: PMC6320372 DOI: 10.1038/s41467-018-07957-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/06/2018] [Indexed: 11/21/2022] Open
Abstract
The formation of non-covalent directional interactions, such as hydrogen or halogen bonds, is a central concept of materials design, which hinges on using small compact atoms of the 2nd period, notably nitrogen and oxygen, as acceptors. Heavier atoms are much less prominent in that context, and mostly limited to sulfur. Here, we report the experimental observation and theoretical study of halogen bonds to phosphorus, arsenic and antimony in the solid state. Combining 1,3,5-trifluoro-2,4,6-triiodobenzene with triphenylphosphine, -arsine, and -stibine provides cocrystals based on I···P, I···As and I···Sb halogen bonds. The demonstration that increasingly metallic pnictogens form halogen bonds sufficiently strong to enable cocrystal formation is an advance in supramolecular chemistry which opens up opportunities in materials science, as shown by colossal thermal expansion of the cocrystal involving I···Sb halogen bonds. Halogen bonding can be exploited for the design of functional supramolecular materials, but heavier elements that are known to accept a halogen bond remain limited. Here, the authors demonstrate the formation of two-component cocrystals based on halogen bonds with phosphorus, arsenic and antimony.
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Affiliation(s)
- Katarina Lisac
- Faculty of Science, Department of Chemistry, University of Zagreb, Horvatovac 102a, HR-10000, Zagreb, Croatia
| | - Filip Topić
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, H3A 0B8, Canada
| | - Mihails Arhangelskis
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, H3A 0B8, Canada
| | - Sara Cepić
- Faculty of Science, Department of Chemistry, University of Zagreb, Horvatovac 102a, HR-10000, Zagreb, Croatia
| | - Patrick A Julien
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, H3A 0B8, Canada
| | - Christopher W Nickels
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, H3A 0B8, Canada
| | - Andrew J Morris
- School of Metallurgy and Materials, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Tomislav Friščić
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, H3A 0B8, Canada.
| | - Dominik Cinčić
- Faculty of Science, Department of Chemistry, University of Zagreb, Horvatovac 102a, HR-10000, Zagreb, Croatia.
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55
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Wolf ME, Zhang B, Turney JM, Schaefer HF. A comparison between hydrogen and halogen bonding: the hypohalous acid–water dimers, HOX⋯H2O (X = F, Cl, Br). Phys Chem Chem Phys 2019; 21:6160-6170. [DOI: 10.1039/c9cp00422j] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hypohalous acids (HOX) are a class of molecules that play a key role in the atmospheric seasonal depletion of ozone and have the ability to form both hydrogen and halogen bonds.
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Affiliation(s)
- Mark E. Wolf
- Center for Computational Quantum Chemistry
- University of Georgia
- Athens
- USA
| | - Boyi Zhang
- Center for Computational Quantum Chemistry
- University of Georgia
- Athens
- USA
| | - Justin M. Turney
- Center for Computational Quantum Chemistry
- University of Georgia
- Athens
- USA
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry
- University of Georgia
- Athens
- USA
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56
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Xu L, Kumar A, Wong BM. Linear polarizabilities and second hyperpolarizabilities of streptocyanines: Results from broken‐Symmetry DFT and new CCSD(T) benchmarks. J Comput Chem 2018; 39:2350-2359. [DOI: 10.1002/jcc.25519] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 05/06/2018] [Accepted: 06/14/2018] [Indexed: 01/29/2023]
Affiliation(s)
- Lihua Xu
- Department of Chemical & Environmental Engineering, Materials Science & Engineering Program and Department of Physics & Astronomy University of California‐Riverside Riverside California 92521
| | - Anshuman Kumar
- Department of Chemical & Environmental Engineering, Materials Science & Engineering Program and Department of Physics & Astronomy University of California‐Riverside Riverside California 92521
| | - Bryan M. Wong
- Department of Chemical & Environmental Engineering, Materials Science & Engineering Program and Department of Physics & Astronomy University of California‐Riverside Riverside California 92521
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57
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Varadwaj A, Varadwaj PR, Marques HM, Yamashita K. A DFT assessment of some physical properties of iodine-centered halogen bonding and other non-covalent interactions in some experimentally reported crystal geometries. Phys Chem Chem Phys 2018; 20:15316-15329. [PMID: 29796486 DOI: 10.1039/c8cp01085d] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A set of six binary complexes that feature iodine-centered halogen bonding, extracted from structures deposited in the Cambridge Structure Database, has been examined computationally using density functional theory calculations with the M06-2X global hybrid, and dispersion corrected B3LYP-D3 and B97-D3, to determine their equilibrium geometries, binding energies and electronic properties. The results show that gas phase calculations are very informative in evaluating what occurs in the solid state, even though these calculations ignore the importance of lattice packing and counter ion effects. The calculated binding energies for the non-covalent interactions responsible for these complexes lie between -4.15 and -7.48 kcal mol-1 (M06-2X), which enables us to characterize them as weak-to-moderate in strength. The basis set superposition error energies are calculated to vary between 0.60 and 2.42 kcal mol-1 for all the complexes examined, even though an all-electron QZP basis set used in the analysis was of quadrupole-ζ (plus polarization) quality. Dispersion is found to have a profound effect on the binding energy of some of these complexes, and was estimated to be as large as 5.0 kcal mol-1. For one complex, the crystal geometry could not be precisely reproduced using a gas phase calculation. While both halogen- and hydrogen-bonding interactions were found competitive, they cooperate with each other to determine the stable configuration of the binary complex. The molecular electrostatic surface potential, quantum theory of atoms in molecules, and reduced density gradient non-covalent Interaction models were utilized to arrive at a fundamental understanding of the various inter- and intra-molecular molecular interactions involved, as well as some other previously-overlooked non-covalent interactions that emerge in the modelling.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, 113-8656, Japan.
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58
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Zhang Y, Wang JG, Sun X, Liu Q, Wang W, Wang YB. Supramolecular Interactions of Fullerene C 60
with 1,3,5-Trifluoro-2,4,6-triiodobenzene: A Combined Theoretical and Experimental Study. Chempluschem 2018; 83:470-477. [DOI: 10.1002/cplu.201800174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/01/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Yu Zhang
- College of Chemistry and Chemical Engineering; and Henan Key Laboratory of Function-Oriented Porous Materials; Luoyang Normal University; Luoyang 471934 P. R. China
| | - Jian-Ge Wang
- College of Chemistry and Chemical Engineering; and Henan Key Laboratory of Function-Oriented Porous Materials; Luoyang Normal University; Luoyang 471934 P. R. China
| | - Xiaotian Sun
- College of Chemistry and Chemical Engineering; and Henan Key Laboratory of Function-Oriented Porous Materials; Luoyang Normal University; Luoyang 471934 P. R. China
| | - Qiaohong Liu
- College of Chemistry and Chemical Engineering; and Henan Key Laboratory of Function-Oriented Porous Materials; Luoyang Normal University; Luoyang 471934 P. R. China
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering; and Henan Key Laboratory of Function-Oriented Porous Materials; Luoyang Normal University; Luoyang 471934 P. R. China
| | - Yi-Bo Wang
- Department of Chemistry; Key Laboratory of Guizhou High Performance Computational Chemistry; Guizhou University; Guiyang 550025 P. R. China
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59
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Varadwaj A, Varadwaj PR, Marques HM, Yamashita K. Revealing Factors Influencing the Fluorine-Centered Non-Covalent Interactions in Some Fluorine-Substituted Molecular Complexes: Insights from First-Principles Studies. Chemphyschem 2018; 19:1486-1499. [PMID: 29569853 DOI: 10.1002/cphc.201800023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Indexed: 01/13/2023]
Abstract
We examine the equilibrium structure and properties of six fully or partially fluorinated hydrocarbons and several of their binary complexes using computational methods. In the monomers, the electrostatic surface of the fluorine is predicted to be either entirely negative or weakly positive. However, its lateral sites are always negative. This enables the fluorine to display an anisotropic distribution of charge density on its electrostatic surface. While this is the electrostatic surface scenario of the fluorine atom, its negative sites in some of these monomers are shown to have the potential to engage in attractive engagements with the negative site(s) on the same atom in another molecule of the same type, or a molecule of a different type, to form bimolecular complexes. This is revealed by analyzing the results of current state-of-the-art computational approaches such as DFT, together with those obtained from the quantum theory of atoms in molecules, molecular electrostatic surface potential and symmetry adapted perturbation theories. We demonstrate that the intermolecular interaction energy arising in part from the universal London dispersion, which has been underappreciated for decades, is an essential factor in explaining the attraction between the negative sites, although energy arising from polarization strengthens the extent of the intermolecular interactions in these complexes.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku, Japan 113-8656, and CREST-JST, 7 Gobancho, Chiyoda-ku, Tokyo, Japan 102-0076
| | - Pradeep R Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku, Japan 113-8656, and CREST-JST, 7 Gobancho, Chiyoda-ku, Tokyo, Japan 102-0076
| | - Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku, Japan 113-8656, and CREST-JST, 7 Gobancho, Chiyoda-ku, Tokyo, Japan 102-0076
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