1
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Sharifi N, Liu T, Clarke SM. A Novel Study on the Role of Pressure on Surface Adsorption from Solutions. J Phys Chem B 2023. [PMID: 37229794 DOI: 10.1021/acs.jpcb.3c01492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this work, we present experimental data on the behavior of model additives adsorbed at the solid/liquid interface as a function of pressure. We report that some additives adsorbed from non-aqueous solvents exhibit rather little variation with pressure, while others exhibit more significant changes. We also display the important pressure dependence of added water. This pressure dependence is relevant, indeed central to many commercially important situations where the adsorption of molecular species to the solid/liquid interface under high pressure is key, such as wind turbines, and this work should help in understanding how protective, anti-wear, or friction-reducing agents can persist (or not) under these extreme conditions. With a very significant gap in the fundamental understanding of the role of pressure on adsorption from solution phases, this important fundamental study provides a methodology to investigate the pressure dependence of these academically and commercially important systems. In the best case, one may even be able to predict which additives will lead to more adsorption under pressure and avoid those that may desorb.
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Affiliation(s)
- N Sharifi
- Institute for Energy and Environmental Flows and Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW, U.K
| | - Tristan Liu
- Institute for Energy and Environmental Flows and Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW, U.K
| | - S M Clarke
- Institute for Energy and Environmental Flows and Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW, U.K
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2
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Mo Y, Danovich D, Shaik S. The roles of charge transfer and polarization in non-covalent interactions: a perspective from ab initio valence bond methods. J Mol Model 2022; 28:274. [PMID: 36006511 DOI: 10.1007/s00894-022-05187-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 12/03/2021] [Indexed: 11/28/2022]
Abstract
Noncovalent interactions are ubiquitous and have been well recognized in chemistry, biology and material science. Yet, there are still recurring controversies over their natures, due to the wide range of noncovalent interaction terms. In this Essay, we employed the Valence Bond (VB) methods to address two types of interactions which recently have drawn intensive attention, i.e., the halogen bonding and the CH‧‧‧HC dihydrogen bonding. The VB methods have the advantage of interpreting molecular structures and properties in the term of electron-localized Lewis (resonance) states (structures), which thereby shed specific light on the alteration of the bonding patterns. Due to the electron localization nature of Lewis states, it is possible to define individually and measure both polarization and charge transfer effects which have different physical origins. We demonstrated that both the ab initio VB method and the block-localized wavefunction (BLW) method can provide consistent pictures for halogen bonding systems, where strong Lewis bases NH3, H2O and NMe3 partake as the halogen bond acceptors, and the halogen bond donors include dihalogen molecules and XNO2 (X = Cl, Br, I). Based on the structural, spectral, and energetic changes, we confirm the remarkable roles of charge transfer in these halogen bonding complexes. Although the weak C-H∙∙∙H-C interactions in alkane dimers and graphene sheets are thought to involve dispersion only, we show that this term embeds delicate yet important charge transfer, bond reorganization and polarization interactions.
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Affiliation(s)
- Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, NC, 27401, USA.
| | - David Danovich
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190407, Jerusalem, Israel
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190407, Jerusalem, Israel.
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3
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Davidson JA, Jenkins SJ, Gorrec F, Clarke SM. 2D constraint modifies packing behaviour: a halobenzene monolayer with X 3 halogen-bonding motif. Mol Phys 2021; 119:e1900940. [PMID: 34848893 PMCID: PMC7612049 DOI: 10.1080/00268976.2021.1900940] [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] [Indexed: 11/06/2022]
Abstract
Using a combination of X-ray diffraction and simulation techniques, we are able to identify a crystalline monolayer of 1,3,5-triiodotrifluorobenzene formed on graphite. The monolayer is found to exhibit an incommensurate hexagonal unit cell with a lattice parameter of 9.28(7) Å, exhibiting a trigonal arrangement of iodine atoms not found in the bulk structure. DFT simulations have been performed exhibiting close agreement with the experimental structure. Importantly these simulations can be used to compare the strength of the intermolecular interactions both with and without Van der Waals corrections. Thus it is possible to estimate that halogen bonding consists of approximately half the total interaction energy. This demonstrates that despite the presence of strong directional non-covalent bonding, dispersion interactions account for a very significant proportion of the total energy. ![]()
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4
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Inscoe B, Rathnayake H, Mo Y. Role of Charge Transfer in Halogen Bonding. J Phys Chem A 2021; 125:2944-2953. [PMID: 33797922 DOI: 10.1021/acs.jpca.1c01412] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Halogen bonding has received intensive attention recently for its applications in the construction of supramolecular assemblies and crystal engineering and its implications and potentials in chemical and biological processes and rational drug design. Peculiarly, in intermolecular interactions, halogen atoms are known as electron-donating groups carrying partial negative charges in molecules due to its high electronegativity, but they can counterintuitively act as Lewis acids and bind with Lewis bases in the form of a halogen bond. The unsettling issue regarding the nature of the halogen bonding is whether the electrostatics or charge transfer interaction dominates. The recently proposed σ-hole concept nicely reinforces the role of electrostatic attraction. Also, good correlations between the halogen bonding strength and the interaction energy from the simple point-charge model have been found. This leads to the claim that there is no need to invoke the charge transfer concept in the halogen bond. But there is alternative evidence supporting the importance of charge transfer interaction. Here, we visited a series of prominent halogen bonded complexes of the types Y3C-X···Z (X = Br, I; Y = F, Cl, Br; Z = F-, Cl-, Br-, I-, NMe3) with the block-localized wave function (BLW) method at the M06-2X-D3/6-311+G(d,p) (def2-SVP for iodine) level of theory. As the simplest variant of ab initio valence bond (VB) theory, the BLW method is unique in the strict localization of electrons within interacting moieties, allowing for quantitative evaluation of the charge transfer effect on geometries, spectral properties, and energetics in halogen bonding complexes. By comparing the halogen bonding complexes with and without the charge transfer interaction, we proved that the charge transfer interaction significantly shortens the X···Z bonding distance and stretches the C-X bonds. But the shortening of the halogen bonding results in the less favorable steric effect, which is composed of Pauli repulsion, electrostatics, and electron correlation. There are approximate linear correlations between the charge transfer effect and binding energy and between bonding distance and binding energy. These correlations may lead to the illusion that the charge transfer interaction is unimportant or irrelevant, but further analyses showed that the inclusion of charge transfer is critical for the proper description of the halogen bonding, as considering only electrostatics and polarization leads to only about 45-60% of the binding strengths and much elongated bonding distances.
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Affiliation(s)
- Brandon Inscoe
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
| | - Hemali Rathnayake
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
| | - Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
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5
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Davidson JA, Sacchi M, Gorrec F, Clarke SM, Jenkins SJ. Halogen Bonding in Bicomponent Monolayers: Self-Assembly of a Homologous Series of Iodinated Perfluoroalkanes with Bipyridine. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:627-635. [PMID: 33404242 PMCID: PMC8397337 DOI: 10.1021/acs.langmuir.0c02126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 12/18/2020] [Indexed: 06/12/2023]
Abstract
A homologous series of halogen bonding monolayers based on terminally iodinated perfluoroalkanes and 4,4'-bipyridine have been observed on a graphitic surface and noninvasively probed using powder X-ray diffraction. An excellent agreement is observed between the X-ray structures and density functional theory calculations with dispersion force corrections. Theoretical analysis of the binding energies of the structures indicate that these halogen bonds are strong (25 kJ mol-1), indicating that the layers are highly stable. The monolayer structures are found to be distinct from any plane of the corresponding bulk structures, with limited evidence of partitioning of hydrocarbon and perfluoro tectons. The interchain interactions are found to be slightly stronger than those in related aromatic systems, with important implications for 2D crystal engineering.
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Affiliation(s)
| | - Marco Sacchi
- Department
of Chemistry, University of Surrey, Guildford, United Kingdom
| | - Fabrice Gorrec
- MRC
Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Stuart M. Clarke
- Department
of Chemistry, University of Cambridge, Cambridge, United Kingdom
- BP
Institute, University of Cambridge, Cambridge, United Kingdom
| | - Stephen J. Jenkins
- Department
of Chemistry, University of Cambridge, Cambridge, United Kingdom
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6
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Lawrence J, Sosso GC, Đorđević L, Pinfold H, Bonifazi D, Costantini G. Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding. Nat Commun 2020; 11:2103. [PMID: 32355173 PMCID: PMC7192931 DOI: 10.1038/s41467-020-15898-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/24/2020] [Indexed: 12/02/2022] Open
Abstract
Scanning tunnelling microscopy (STM) is commonly used to identify on-surface molecular self-assembled structures. However, its limited ability to reveal only the overall shape of molecules and their relative positions is not always enough to fully solve a supramolecular structure. Here, we analyse the assembly of a brominated polycyclic aromatic molecule on Au(111) and demonstrate that standard STM measurements cannot conclusively establish the nature of the intermolecular interactions. By performing high-resolution STM with a CO-functionalised tip, we clearly identify the location of rings and halogen atoms, determining that halogen bonding governs the assemblies. This is supported by density functional theory calculations that predict a stronger interaction energy for halogen rather than hydrogen bonding and by an electron density topology analysis that identifies characteristic features of halogen bonding. A similar approach should be able to solve many complex 2D supramolecular structures, and we predict its increasing use in molecular nanoscience at surfaces.
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Affiliation(s)
- James Lawrence
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Gabriele C Sosso
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
- Centre for Scientific Computing, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
| | - Luka Đorđević
- School of Chemistry, Cardiff University, Park Place Main Building, Cardiff, CF10 3AT, UK
| | - Harry Pinfold
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Davide Bonifazi
- School of Chemistry, Cardiff University, Park Place Main Building, Cardiff, CF10 3AT, UK.
| | - Giovanni Costantini
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
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7
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Davidson JA, Jenkins SJ, Gorrec F, Clarke SM. C-H … N hydrogen bonding in an overlayer of s-triazine physisorbed on a graphite surface. Mol Phys 2019; 118:e1706777. [PMID: 32848279 PMCID: PMC7115976 DOI: 10.1080/00268976.2019.1706777] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 12/10/2019] [Indexed: 11/24/2022]
Abstract
The structure of a crystalline monolayer of 1,3,5-triazine has been characterised using X-ray diffraction. The monolayer is found to exhibit a hexagonal unit cell with a lattice parameter of 6.161(5) Å, indicating the formation of C-H … N hydrogen bonds. DFT simulations have been performed exhibiting close agreement with the experimental structure. By comparing the strength of the intermolecular interactions both with and in the absence of Van der Waals corrections, it is possible to estimate an interaction strength for the weak C-H … N hydrogen bonds.
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8
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Affiliation(s)
- Marco Saccone
- Institut für Organische Chemie, Universität Duisburg-Essen, Universitätsstraße 7, 45141 Essen, Germany
- Dipartimento di Ingegneria, Università degli Studi di Palermo, Viale delle Scienze 6, 90128 Palermo, Italy
| | - Luca Catalano
- New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
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9
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Structural and Reactivity Analyses of Nitrofurantoin–4-dimethylaminopyridine Salt Using Spectroscopic and Density Functional Theory Calculations. CRYSTALS 2019. [DOI: 10.3390/cryst9080413] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Pharmaceutical salt, nitrofurantoin–4-dimethylaminopyridine (NF-DMAP), along with its native components NF and DMAP are scrutinized by FT-IR and FT-Raman spectroscopy along with density functional theory so that an insight into the H-bond patterns in the respective crystalline lattices can be gained. Two different functionals, B3LYP and wB97X-D, have been used to compare the theoretical results. The FT-IR spectra obtained for NF-DMAP and NF clearly validate the presence of C33–H34⋅⋅⋅O4 and N23–H24⋅⋅⋅N9 hydrogen bonds by shifting in the stretching vibration of –NH and –CH group of DMAP+ towards the lower wavenumber side. To explore the significance of hydrogen bonding, quantum theory of atoms in molecules (QTAIM) has been employed, and the findings suggest that the N23–H24⋅⋅⋅N9 bond is a strong intermolecular hydrogen bond. The decrement in the HOMO-LUMO gap, which is calculated from NF → NF-DMAP, reveals that the active pharmaceutical ingredient is chemically less reactive compared to the salt. The electrophilicity index (ω) profiles for NF and DMAP confirms that NF is acting as electron acceptor while DMAP acts as electron donor. The reactive sites of the salt are plotted by molecular electrostatic potential (MEP) surface and calculated using local reactivity descriptors.
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10
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Mukherjee A, Sanz-Matias A, Velpula G, Waghray D, Ivasenko O, Bilbao N, Harvey JN, Mali KS, De Feyter S. Halogenated building blocks for 2D crystal engineering on solid surfaces: lessons from hydrogen bonding. Chem Sci 2019; 10:3881-3891. [PMID: 31015930 PMCID: PMC6461103 DOI: 10.1039/c8sc04499f] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/22/2019] [Indexed: 12/14/2022] Open
Abstract
Halogen bonding has emerged as a promising tool in two-dimensional (2D) crystal engineering. Since halogen bonds are similar to hydrogen bonds in a number of aspects, the existing knowledge of hydrogen bonded systems can be applied to halogenated systems. Here we evaluate the applicability of a retrosynthetic approach based on topological similarity between hydrogen and halogen bonds to obtain predictable halogen bonded networks. The self-assembly of 1,3-dibromo-5-alkoxybenzene derivatives was studied in analogy with well-explored alkoxy isophthalic acids using a combination of experimental and theoretical tools. Scanning tunneling microscopy (STM) characterization of the networks formed at the liquid-graphite interface revealed that while the retrosynthetic approach works at the level of small clusters of molecules within the 2D network, the overall structure of the network deviates from the anticipated structure. The monolayers consist of fractured rows of halogen-bonded modules instead of the expected continuous lamellar structure. Each module consists of a discrete number of halogen-bonded molecules. The interactions responsible for the stabilization of halogen bonded dimers are delineated through detailed density functional theory (DFT) calculations coupled with natural bonding orbitals (NBO) and perturbation analysis. A modified force field that includes an extra charged site to imitate the σ hole on the halogen atom was developed and applied to extract total potential energies of the anticipated and observed networks. Plausible reasons for the deviation from the anticipated structure are discussed. Finally, a modified molecular design that allows successful application of the hydrogen bond-halogen bond analogy was tested experimentally.
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Affiliation(s)
- Arijit Mukherjee
- Division of Molecular Imaging and Photonics , Department of Chemistry , KU Leuven , Celestijnenlaan, 200F , B-3001 Leuven , Belgium . ;
| | - Ana Sanz-Matias
- Quantum Chemistry and Physical Chemistry , Department of Chemistry , KU Leuven , BE-3001 Leuven , Belgium .
| | - Gangamallaiah Velpula
- Division of Molecular Imaging and Photonics , Department of Chemistry , KU Leuven , Celestijnenlaan, 200F , B-3001 Leuven , Belgium . ;
| | - Deepali Waghray
- Division of Molecular Imaging and Photonics , Department of Chemistry , KU Leuven , Celestijnenlaan, 200F , B-3001 Leuven , Belgium . ;
| | - Oleksandr Ivasenko
- Division of Molecular Imaging and Photonics , Department of Chemistry , KU Leuven , Celestijnenlaan, 200F , B-3001 Leuven , Belgium . ;
| | - Nerea Bilbao
- Division of Molecular Imaging and Photonics , Department of Chemistry , KU Leuven , Celestijnenlaan, 200F , B-3001 Leuven , Belgium . ;
| | - Jeremy N Harvey
- Quantum Chemistry and Physical Chemistry , Department of Chemistry , KU Leuven , BE-3001 Leuven , Belgium .
| | - Kunal S Mali
- Division of Molecular Imaging and Photonics , Department of Chemistry , KU Leuven , Celestijnenlaan, 200F , B-3001 Leuven , Belgium . ;
| | - Steven De Feyter
- Division of Molecular Imaging and Photonics , Department of Chemistry , KU Leuven , Celestijnenlaan, 200F , B-3001 Leuven , Belgium . ;
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11
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Shukla A, Khan E, Srivastava K, Sinha K, Tandon P, Vangala VR. Study of molecular interactions and chemical reactivity of the nitrofurantoin–3-aminobenzoic acid cocrystal using quantum chemical and spectroscopic (IR, Raman, 13C SS-NMR) approaches. CrystEngComm 2017. [DOI: 10.1039/c7ce00864c] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Inquiries of structural reactivity, molecular interactions and vibrational characterization of drugs are essential in understanding their behaviour.
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Affiliation(s)
- Anuradha Shukla
- Department of Physics
- University of Lucknow
- Lucknow 226007
- India
| | - Eram Khan
- Department of Physics
- University of Lucknow
- Lucknow 226007
- India
| | | | - Kirti Sinha
- Department of Physics
- University of Lucknow
- Lucknow 226007
- India
| | - Poonam Tandon
- Department of Physics
- University of Lucknow
- Lucknow 226007
- India
| | - Venu R. Vangala
- Centre for Pharmaceutical Engineering Science
- School of Pharmacy and Medical Sciences
- University of Bradford
- Bradford BD7 1DP
- UK
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12
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Abstract
In this study, we use density functional theory (DFT) to investigate the surface co-adsorption of glycine with water on Cu{110}. Our results show that, under UHV conditions and for a wide range of temperatures, a pure glycine monolayer is more stable than either mixed gly-water phases or pure water (ice) monolayers, but for a high water pressure half-dissociated water layers can appear on the surface at low and medium temperatures.
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Affiliation(s)
- Marco Sacchi
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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13
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Brewer AY, Sacchi M, Parker JE, Truscott CL, Jenkins SJ, Clarke SM. Supramolecular self-assembled network formation containing N⋯Br halogen bonds in physisorbed overlayers. Phys Chem Chem Phys 2014; 16:19608-17. [DOI: 10.1039/c4cp03379e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The formation of a halogen bonded self-assembled co-crystal physisorbed monolayer containing N⋯Br interactions is reported for the first time.
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Affiliation(s)
- Adam Y. Brewer
- BP Institute and Department of Chemistry
- University of Cambridge
- Cambridge, UK
| | - Marco Sacchi
- University of Cambridge
- Department of Chemistry
- Cambridge, UK
| | - Julia E. Parker
- Diamond Light Source
- Harwell Science and Innovation Campus
- Didcot, UK
| | - Chris L. Truscott
- BP Institute and Department of Chemistry
- University of Cambridge
- Cambridge, UK
| | | | - Stuart M. Clarke
- BP Institute and Department of Chemistry
- University of Cambridge
- Cambridge, UK
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