1
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Scheiner S. Properties and Stabilities of Cyclic and Open Chains of Halogen Bonds. J Phys Chem A 2022; 126:6443-6455. [PMID: 36084144 DOI: 10.1021/acs.jpca.2c04967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Open and cyclic chains from two to eight units of ICl and IF are constructed and examined by density functional theory (DFT) calculations. These chains contain either I···I or I···X halogen bonds (XBs) where X refers to Cl or F. The closed rings are more stable than the open chains due to the presence of an additional XB and enhanced cooperativity. This pattern is true even for most trimers where there is sizable geometric distortion in the rings. I···F rings are generally more stable than the corresponding I···I cycles as the I···F bond is stronger than I···I even in the simple dimer. However, I···I rings are comparable in energy to I···Cl. It is possible to construct I···I rings of at least as large as eight units, which are held together exclusively by XBs. On the other hand, the maximum possible size of I···X rings is 6. Red shifts are observed in the I-X stretching frequency bands, which magnify as the chain, both cyclic and open, grows longer. The NMR chemical shielding of the I atoms increases for I···I chains but diminishes when I···Cl bonds are present.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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2
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Vermeeren P, Wolters LP, Paragi G, Fonseca Guerra C. Cooperative Self-Assembly in Linear Chains Based on Halogen Bonds. Chempluschem 2021; 86:812-819. [PMID: 33905182 PMCID: PMC8252609 DOI: 10.1002/cplu.202100093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/30/2021] [Indexed: 12/03/2022]
Abstract
Cooperative properties of halogen bonds were investigated with computational experiments based on dispersion-corrected relativistic density functional theory. The bonding mechanism in linear chains of cyanogen halide (X-CN), halocyanoacetylene (X-CC-CN), and 4-halobenzonitrile (X-C6 H4 -CN) were examined for X = H, Cl, Br, and I. Our energy decomposition and Kohn-Sham molecular-orbital analyses revealed the bonding mechanism of the studied systems. Cyanogen halide and halocyanoacetylene chains possess an extra stabilizing effect with increasing chain size, whereas the 4-halobenzonitrile chains do not. This cooperativity can be traced back to charge separation within the σ-electronic system by charge-transfer between the lone-pair orbital of the nitrogen (σHOMO ) on one unit and the acceptor orbital of the C-X (σ*LUMO ) on the adjacent unit. As such, the HOMO-LUMO gap in the σ-system decreases, and the cooperativity increases with chain length revealing the similarity in the bonding mechanisms of hydrogen and halogen bonds.
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Affiliation(s)
- Pascal Vermeeren
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Lando P. Wolters
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Gábor Paragi
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- MTA-SZTE Biomimetic Systems Research GroupEötvös Loránd Research Network (ELKH)Dóm tér 86720SzegedHungary
- Institute of PhysicsUniversity of PécsIfjúság útja 67624PécsHungary
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Leiden Institute of Chemistry, Gorlaeus LaboratoriesLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
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3
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Dominikowska J, Rybarczyk-Pirek AJ, Fonseca Guerra C. Lack of Cooperativity in the Triangular X 3 Halogen-Bonded Synthon? CRYSTAL GROWTH & DESIGN 2021; 21:597-607. [PMID: 33442333 PMCID: PMC7792510 DOI: 10.1021/acs.cgd.0c01410] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/06/2020] [Indexed: 05/26/2023]
Abstract
We have investigated 44 crystal structures, found in the Cambridge Structural Database, containing the X3 synthon (where X = Cl, Br, I) in order to verify whether three type II halogen-halogen contacts forming the synthon exhibit cooperativity. A hypothesis that this triangular halogen-bonded motif is stabilized by cooperative effects is postulated on the basis of structural data. However, theoretical investigations of simplified model systems in which the X3 motif is present demonstrate that weak synergy occurs only in the case of the I3 motif. In the present paper we computationally investigate crystal structures in which the X3 synthon is present, including halomesitylene structures, that are usually described as being additionally stabilized by a synergic interaction. Our computations find no cooperativity for halomesitylene trimers containing the X3 motif. Only in the case of two other structures containing the I3 synthon a very weak or weak synergy, i.e. the cooperative effect being stronger than -0.40 kcal mol-1, is found. The crystal structure of iodoform has the most pronounced cooperativity of all investigated systems, amounting to about 10% of the total interaction energy.
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Affiliation(s)
- Justyna Dominikowska
- Theoretical
and Structural Chemistry Group, Department of Physical Chemistry,
Faculty of Chemistry, University of Lodz, Pomorska 163/165, 90-236 Łódź, Poland
- Department
of Theoretical Chemistry and Amsterdam Centre for Multiscale Modelling, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Agnieszka J. Rybarczyk-Pirek
- Theoretical
and Structural Chemistry Group, Department of Physical Chemistry,
Faculty of Chemistry, University of Lodz, Pomorska 163/165, 90-236 Łódź, Poland
| | - Célia Fonseca Guerra
- Department
of Theoretical Chemistry and Amsterdam Centre for Multiscale Modelling, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
- Leiden
Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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4
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Zhang Z, Lu T, Ding L, Wang G, Wang Z, Zheng B, Liu Y, Ding XL. Cooperativity effects between regium-bonding and pnicogen-bonding interactions in ternary MF···PH3O···MF (M = Cu, Ag, Au): an ab initio study. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1784478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Zan Zhang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecular, Ministry of Education, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
- Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
| | - Tian Lu
- Beijing Kein Research Center for Natural Sciences, Beijing, People’s Republic of China
| | - Luyang Ding
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecular, Ministry of Education, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
- Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
| | - Guanyu Wang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecular, Ministry of Education, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
- Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
| | - Zhaoxu Wang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecular, Ministry of Education, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
- Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
| | - Baishu Zheng
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecular, Ministry of Education, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
- Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
| | - Yuan Liu
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecular, Ministry of Education, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
- Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, People’s Republic of China
| | - Xun Lei Ding
- Institute of Clusters and Low Dimensional Nanomaterials, School of Mathematics and Physics, North China Electric Power University, Beijing, People’s Republic of China
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5
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Dominikowska J. Halogen-bonded haloamine trimers - modelling the X 3 synthon. Phys Chem Chem Phys 2020; 22:21938-21946. [PMID: 32974627 DOI: 10.1039/d0cp03352a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Halogen-halogen bonded haloamine trimers serve as model systems for the X3 synthon present in numerous crystal structures and in two-dimensional self-assembled nanoarchitectures. Halogen bonds forming the synthon are often considered to display cooperativity. Synergy effects were previously found for halogen-halogen bonded bromoamine and iodoamine tetramers. In the present study comparison between haloamine cyclic trimers and tetramers is made. The cooperativity occurring in bromoamine and iodoamine clusters is significantly weaker in the case of the trimers. The present study demonstrates that the bromoamine and iodoamine trimers display weaker cooperativity due to a smaller number of synergy components in comparison to the corresponding tetramers of stronger cooperativity. Moreover, the halogen-halogen interactions in bromoamine and iodoamine dimers with the geometries of the corresponding trimers and tetramers are examined using energy decomposition analysis methods (supermolecular, canonical EDA and SAPT) and the Kohn-Sham molecular orbital model. The results of the analysis indicate that although the interaction energy values for the dimers of the different spatial arrangement are very close to each other, their origin is substantially different. For pairs with the geometry of the trimers orbital interactions and electrostatic attraction are both weaker than for the corresponding dimers with the geometry of the tetramers. This is especially important because both donor-acceptor interactions and electrostatic attraction were previously proven to be responsible for cooperative effects occurring in the bromoamine and iodoamine tetramers.
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Affiliation(s)
- Justyna Dominikowska
- University of Lodz, Faculty of Chemistry, Department of Physical Chemistry, Theoretical and Structural Chemistry Group, Pomorska 163/165, 90-236 Łódź, Poland.
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6
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Santos LDA, Prandi IG, Ramalho TC. Could Quantum Mechanical Properties Be Reflected on Classical Molecular Dynamics? The Case of Halogenated Organic Compounds of Biological Interest. Front Chem 2019; 7:848. [PMID: 31921771 PMCID: PMC6923750 DOI: 10.3389/fchem.2019.00848] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 11/21/2019] [Indexed: 12/15/2022] Open
Abstract
Essential to understanding life, the biomolecular phenomena have been an important subject in science, therefore a necessary path to be covered to make progress in human knowledge. To fully comprehend these processes, the non-covalent interactions are the key. In this review, we discuss how specific protein-ligand interactions can be efficiently described by low computational cost methods, such as Molecular Mechanics (MM). We have taken as example the case of the halogen bonds (XB). Albeit generally weaker than the hydrogen bonds (HB), the XBs play a key role to drug design, enhancing the affinity and selectivity toward the biological target. Along with the attraction between two electronegative atoms in XBs explained by the σ-hole model, important orbital interactions, as well as relief of Pauli repulsion take place. Nonetheless, such electronic effects can be only well-described by accurate quantum chemical methods that have strong limitations dealing with supramolecular systems due to their high computational cost. To go beyond the poor description of XBs by MM methods, reparametrizing the force-fields equations can be a way to keep the balance between accuracy and computational cost. Thus, we have shown the steps to be considered when parametrizing force-fields to achieve reliable results of complex non-covalent interactions at MM level for In Silico drug design methods.
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Affiliation(s)
| | - Ingrid G. Prandi
- Department of Chemistry, Federal University of Lavras, Lavras, Brazil
| | - Teodorico C. Ramalho
- Department of Chemistry, Federal University of Lavras, Lavras, Brazil
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czechia
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7
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Wzgarda-Raj K, Rybarczyk-Pirek AJ, Wojtulewski S, Palusiak M. N-Oxide–N-oxide interactions and Cl...Cl halogen bonds in pentachloropyridine N-oxide: the many-body approach to interactions in the crystal state. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2018; 74:113-119. [DOI: 10.1107/s2053229617017922] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 12/15/2017] [Indexed: 11/10/2022]
Abstract
Pentachloropyridine N-oxide, C5Cl5NO, crystallizes in the monoclinic space group P21/c. In the crystal structure, molecules are linked by C—Cl...Cl halogen bonds into infinite ribbons extending along the crystallographic [100] direction. These molecular aggregates are further stabilized by very short intermolecular N-oxide–N-oxide interactions into herringbone motifs. Computations based on quantum chemistry methods allowed for a more detailed description of the N-oxide–N-oxide interactions and Cl...Cl halogen bonds. For this purpose, Hirshfeld surface analysis and the many-body approach to interaction energy were applied.
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Petelski AN, Peruchena NM, Pamies SC, Sosa GL. Insights into the self-assembly steps of cyanuric acid toward rosette motifs: a DFT study. J Mol Model 2017; 23:263. [PMID: 28808800 DOI: 10.1007/s00894-017-3428-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/19/2017] [Indexed: 11/28/2022]
Abstract
The nature of non-covalent interactions in self-assembling systems is a topic that has aroused great attention in literature. In this field, the 1,3,5-triazinane-2,4,6-trione or cyanuric acid (CA) is one of the most widely used molecules to formulate self-assembled materials or monolayers. In the present work, a variety of molecular aggregates of CA are examined using three different DFT functionals (B3LYP, B3LYP-D3, and ω-B97XD) in the framework of the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. Herein, a step by step aggregation path is proposed and the origin of cooperative effects is also examined. It is shown that a greater cooperativity is not always associated with a greater binding energy, and the greatest cooperative effect occurs with highly directional hydrogen bonds. The intramolecular charge transfers play a key role in this effect. Graphical abstract The noncovalent interactions in cyanuric acid supramolecules were analyzed. The calculations provide insights into the self-assembly steps from dimers to rosette-like motif. The complexes with collinear hydrogen bonds show positive cooperativity, while in the arrangement with double hydrogen bonds the cooperative effect is essentially zero.
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Affiliation(s)
- Andre N Petelski
- Grupo de Investigación en Química Teórica y Experimental (QuiTEx), Departamento de Ingeniería Química, Facultad Regional Resistencia, Universidad Tecnológica Nacional, French 414 (H3500CHJ), Resistencia, Chaco, Argentina.,Instituto de Química Básica y Aplicada del Nordeste Argentino (IQUIBA-NEA), UNNE-CONICET, Avenida Libertad 5460 (3400), Corrientes, Argentina
| | - Nélida M Peruchena
- Instituto de Química Básica y Aplicada del Nordeste Argentino (IQUIBA-NEA), UNNE-CONICET, Avenida Libertad 5460 (3400), Corrientes, Argentina. .,Laboratorio de Estructura Molecular y Propiedades (LEMYP), Área de Química Física, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avenida Libertad 5460 (3400), Corrientes, Argentina.
| | - Silvana C Pamies
- Grupo de Investigación en Química Teórica y Experimental (QuiTEx), Departamento de Ingeniería Química, Facultad Regional Resistencia, Universidad Tecnológica Nacional, French 414 (H3500CHJ), Resistencia, Chaco, Argentina
| | - Gladis L Sosa
- Grupo de Investigación en Química Teórica y Experimental (QuiTEx), Departamento de Ingeniería Química, Facultad Regional Resistencia, Universidad Tecnológica Nacional, French 414 (H3500CHJ), Resistencia, Chaco, Argentina. .,Instituto de Química Básica y Aplicada del Nordeste Argentino (IQUIBA-NEA), UNNE-CONICET, Avenida Libertad 5460 (3400), Corrientes, Argentina.
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9
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Esrafili MD, Mousavian P. Unusual cooperativity effects between halogen bond and donor-acceptor interactions: The role of orbital interaction. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.04.052] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Esrafili MD, Sadr-Mousavi A. Chalcogen bonds tuned by an N–H···π or C–H···π interaction: investigation of substituent, cooperativity and solvent effects. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1318227] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
| | - Asma Sadr-Mousavi
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
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11
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Bora PL, Novák M, Novotný J, Foroutan-Nejad C, Marek R. Supramolecular Covalence in Bifurcated Chalcogen Bonding. Chemistry 2017; 23:7315-7323. [DOI: 10.1002/chem.201700179] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Pankaj Lochan Bora
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
- Department of Chemistry; Faculty of Science; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Martin Novák
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
- National Center for Biomolecular Research; Faculty of Science; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Jan Novotný
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Cina Foroutan-Nejad
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Radek Marek
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
- Department of Chemistry; Faculty of Science; Masaryk University; Kamenice 5 62500 Brno Czech Republic
- National Center for Biomolecular Research; Faculty of Science; Masaryk University; Kamenice 5 62500 Brno Czech Republic
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12
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Nepal B, Scheiner S. NX⋯Y halogen bonds. Comparison with NH⋯Y H-bonds and CX⋯Y halogen bonds. Phys Chem Chem Phys 2016; 18:18015-23. [DOI: 10.1039/c6cp03771b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Quantum calculations examine how the NH⋯Y H-bond compares to the equivalent NX⋯Y halogen bond, as well as to comparable CH/CX donors.
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Affiliation(s)
- Binod Nepal
- Department of Chemistry and Biochemistry
- Utah State University
- Logan
- USA
| | - Steve Scheiner
- Department of Chemistry and Biochemistry
- Utah State University
- Logan
- USA
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