1
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Nakajima Y, Ohmura T, Seino J. Using atomic clustering based on structural and electronic descriptors that consider surrounding environment to evaluate local properties of DFT functionals. J Comput Chem 2024; 45:1870-1879. [PMID: 38686778 DOI: 10.1002/jcc.27375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
We developed a method for evaluating the accuracies of the local properties of DFT functionals in detail using a clustering method based on machine learning and structural/electronic descriptors. We generated 36 clusters consistent with human intuition using 30,436 carbon atoms from the QM9 dataset. The results were used to evaluate 13C NMR chemical shifts calculated using 84 DFT functionals. Carbon atoms were grouped based on their similar environments, reducing errors within these groups. This enables more accurate assessment of the accuracy using a specific DFT functional. Therefore, the present atomic clustering provides more detailed insight into accuracy verification.
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Affiliation(s)
- Yuya Nakajima
- Waseda Research Institute for Science and Engineering, Tokyo, Japan
| | - Takuto Ohmura
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Junji Seino
- Waseda Research Institute for Science and Engineering, Tokyo, Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
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2
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Piña MDLN, Bauzá A. Diphenylene Iodonium as a Prominent Halogen Bond Donor: The Case of Human Monoamine Oxidase B. Chemphyschem 2024; 25:e202400161. [PMID: 38687202 DOI: 10.1002/cphc.202400161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/25/2024] [Accepted: 04/30/2024] [Indexed: 05/02/2024]
Abstract
Herein we have investigated the formation and interplay of several noncovalent interactions (NCIs) involved in the inhibition of human monoamine oxidase B (MAO B). Concretely, an inspection of the Protein Data Bank (PDB) revealed the formation of a halogen bond (HlgB) between a diphenylene iodonium (DPI) inhibitor and a water molecule present in the active site, in addition to a noncovalent network of interactions (e. g. lone pair-π, hydrogen bonding, OH-π, CH-π and π-stacking interactions) with surrounding protein residues. Several theoretical models were built to understand the strength and directionality features of the HlgB in addition to the interplay with other NCIs present in the active site of the enzyme. Besides, a computational study was carried out using DPI as HlgB donor and several electron rich molecules (CO, H2O, CH2O, HCN, pyridine, OCN-, SCN-, Cl- and Br-) as HlgB acceptors. The results were analyzed using several state-of-the-art computational tools. We expect that our results will be useful for those scientists working in the fields of rational drug design, chemical biology as well as supramolecular chemistry.
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Affiliation(s)
- María de Las Nieves Piña
- Department of Chemistry, Universitat de les Illes Balears, Ctra. de Valldemossa, km. 7.5, 07122, Palma de Mallorca, Islas Baleares, Spain
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Ctra. de Valldemossa, km. 7.5, 07122, Palma de Mallorca, Islas Baleares, Spain
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3
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Li H, Briccolani-Bandini L, Tirri B, Cardini G, Brémond E, Sancho-García JC, Adamo C. Evaluating Noncovalent Interactions in Halogenated Molecules with Double-Hybrid Functionals and a Dedicated Small Basis Set. J Phys Chem A 2024. [PMID: 39067011 DOI: 10.1021/acs.jpca.4c03007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
We present here an extension of our recently developed PBE-QIDH/DH-SVPD basis set to halogen atoms, with the aim of obtaining, for weakly interacting halogenated molecules, interaction energies close to those provided by a large basis set (def2-TZVPP) coupled to empirical dispersion potential. The core of our approach is the split-valence basis set, DH-SVPD, that has been developed for F, Cl, Br, and I atoms using a self-consistent formula, containing only energy terms computed for dimers and the corresponding monomers at the same level of theory. The basis set developed considering four systems, one for each halogen atoms, has been then tested on the X40, X4 × 10 benchmarks as well as on other two, less standard, data sets. Finally, a large system (380 atoms) has been also considered as a "crash" test. Our results show that the simple and nonempirical PBE-QIDH/DH-SVPD approach is able to provide accurate results for interaction energies of all the considered systems and can thus be considered as a cheaper alternative to DH functionals paired with empirical dispersion corrections and a large basis set of triple-ζ quality.
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Affiliation(s)
- Hanwei Li
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France
| | - Lorenzo Briccolani-Bandini
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Bernardino Tirri
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France
| | - Gianni Cardini
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Eric Brémond
- ITODYS, CNRS, Université de Paris, Paris F-75006, France
| | | | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences, F-75005 Paris, France
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4
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Rahali E, Noori Z, Arfaoui Y, Poater J. Chalcogen Noncovalent Interactions between Diazines and Sulfur Oxides in Supramolecular Circular Chains. Int J Mol Sci 2024; 25:7497. [PMID: 39000604 PMCID: PMC11242197 DOI: 10.3390/ijms25137497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 06/30/2024] [Accepted: 07/06/2024] [Indexed: 07/16/2024] Open
Abstract
The noncovalent chalcogen interaction between SO2/SO3 and diazines was studied through a dispersion-corrected DFT Kohn-Sham molecular orbital together with quantitative energy decomposition analyses. For this, supramolecular circular chains of up to 12 molecules were built with the aim of checking the capability of diazine molecules to detect SO2/SO3 compounds within the atmosphere. Trends in the interaction energies with the increasing number of molecules are mainly determined by the Pauli steric repulsion involved in these σ-hole/π-hole interactions. But more importantly, despite the assumed electrostatic nature of the involved interactions, the covalent component also plays a determinant role in its strength in the involved chalcogen bonds. Noticeably, π-hole interactions are supported by the charge transfer from diazines to SO2/SO3 molecules. Interaction energies in these supramolecular complexes are not only determined by the S···N bond lengths but attractive electrostatic and orbital interactions also determine the trends. These results should allow us to establish the fundamental characteristics of chalcogen bonding based on its strength and nature, which is of relevance for the capture of sulfur oxides.
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Affiliation(s)
- Emna Rahali
- Laboratory of Characterizations, Applications and Modeling of Materials (LR18ES08), Department of Chemistry, University of Tunis El Manar, Tunis 1068, Tunisia; (E.R.); (Y.A.)
- Department de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain;
| | - Zahra Noori
- Department de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain;
| | - Youssef Arfaoui
- Laboratory of Characterizations, Applications and Modeling of Materials (LR18ES08), Department of Chemistry, University of Tunis El Manar, Tunis 1068, Tunisia; (E.R.); (Y.A.)
| | - Jordi Poater
- Department de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain;
- ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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5
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Zhang Y, Wang W. Chalcogen-Bond-Assisted Formation of the N→C Dative Bonds in the Complexes between Chalcogenadiazoles/Chalcogenatriazoles and Fullerene C 60. Molecules 2024; 29:2685. [PMID: 38893559 PMCID: PMC11173879 DOI: 10.3390/molecules29112685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
The existence of the N→C dative bonds in the complexes between N-containing molecules and fullerenes have been verified both theoretically and experimentally. However, finding stable N→C dative bonds is still a highly challenging task. In this work, we investigated computationally the N→C dative bonds in the complexes formed by fullerene C60 with 1,2,5-chalcogenadiazoles, 2,1,3-benzochalcogenadiazoles, and 1,2,4,5-chalcogenatriazoles, respectively. It was found that the N→C dative bonds are formed along with the formation of the N-Ch···C (Ch = S, Se, Te) chalcogen bonds. In the gas phase, from S-containing complexes through Se-containing complexes to Te-containing complexes, the intrinsic interaction energies become more and more negative, which indicates that the N-Ch···C chalcogen bonds can facilitate the formation of the N→C dative bonds. The intrinsic interaction energies are compensated by the large deformation energy of fullerene C60. The total interaction energies of Te-containing complexes are negative, while both total interaction energies of the S-containing complexes and Se-containing complexes are positive. This means that the N→C dative bonds in the Te-containing complexes are more easily observed in experiments in comparison with those in the S-containing complexes and Se-containing complexes. This study provides a new theoretical perspective on the experimental observation of the N→C dative bonds in complexes involving fullerenes. Further, the formation of stable N→C dative bonds in the complexes involving fullerenes can significantly change the properties of fullerenes, which will greatly simulate and expand the application range of fullerenes.
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Affiliation(s)
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering, and Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934, China;
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6
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Pomogaeva AV, Lisovenko AS, Timoshkin AY. Structures and stability of I 2 and ICl complexes with pyridine: Ab initio and DFT study. J Comput Chem 2024; 45:903-914. [PMID: 38165152 DOI: 10.1002/jcc.27300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 01/03/2024]
Abstract
Theoretical investigation of thermodynamic stability and bonding features of possible isomers of the molecular and ionic complexes of pyridine with molecular iodine and iodine monochloride IX (X = I,Cl) is presented. M06-2X DFT functional is found to provide bond distances and dissociation energies which are close to those obtained at high-level ab initio CCSD(T)/aug-cc-pvtz//CCSD/aug-cc-pvtz benchmark computations for the most stable isomers, formed via donation of a lone pair of nitrogen atom of pyridine to the iodine atom. These isomers are by 23-33 kJ mol-1 (in case of I2) and by 39-56 kJ mol-1 (in case of ICl) more stable than other molecular complexes. T-shaped π-σ* bonded isomers turn out to be energetically comparable with van der Waals bound compounds. Among the ionic isomers, structures featuring [IPy2]+ cation with I3 - or ICl2 - counterions are more stable. Oligomerization favors ionic isomers starting from the tetrameric clusters of the composition (IX)4Py4.
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Affiliation(s)
- Anna V Pomogaeva
- Institute of Chemistry, Saint Petersburg State University, St. Petersburg, Russia
| | - Anna S Lisovenko
- Institute of Chemistry, Saint Petersburg State University, St. Petersburg, Russia
| | - Alexey Y Timoshkin
- Institute of Chemistry, Saint Petersburg State University, St. Petersburg, Russia
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7
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Martins Filho PEC, Haiduke RLA. A Charge-Charge Flux-Dipole Flux Analysis of Simple Molecular Systems with Halogen Bonds. J Phys Chem A 2024; 128:2058-2071. [PMID: 38457530 DOI: 10.1021/acs.jpca.3c08229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
The presence of halogen bonds (R-X···B; R = substituent group, X = halogen, and B = Lewis base) provides quite amazing molecular systems for electronic structure investigations, presenting unique characteristics of fundamental relevance to supramolecular chemistry among other areas. Here, we use a double-hybrid approach from Density Functional Theory and triple-ζ basis sets augmented with diffuse functions (B2PLYP/def2-TZVPD) to deal with a large group of simple molecular systems containing halogen bonds (XBs), focusing on geometrical structures, binding energies, harmonic vibrational frequencies, and fundamental infrared intensities. Next, the electron densities and their variations on vibrations are carefully studied with the Quantum Theory of Atoms in Molecules (QTAIM) formalism and the charge-charge flux-dipole flux (CCFDF) model. We notice that the R-X stretching mode usually shows vibrational frequency decrements and infrared intensifications during the XB formation. Such features were also observed in hydrogen bonds, although the explanation for the band strengthening is different. Surprisingly, the most important contribution to these intensity increments due to complexation is now the interaction term between the charge flux and dipole flux (CF × DF). Thus, the use of atomic dipoles is mandatory to fully understand this phenomenon. In fact, the huge charge flux contributions to changes in dipole moment derivatives of R-X stretchings on halogen bonding are no longer accompanied by opposite variations of similar magnitudes in polarizations described by atomic dipole fluxes, which provided nearly unaltered values during the XB formation. Thus, the electronic charge flux direction change that takes place in complexes (from B to R) now reinforces dipole moment derivative terms from such atomic polarizations (mainly from the X atom). This intermolecular charge flux seems to be responsible for the unusual features noticed in the R-X stretching mode with the CCDDF/QTAIM model.
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Affiliation(s)
| | - Roberto Luiz Andrade Haiduke
- Departamento de Química e Física Molecular, Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos, SP 13560-970, Brazil
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8
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Qin C, Zhang RH, Li Z, Zhao HM, Li YW, Feng NX, Li H, Cai QY, Hu X, Gao Y, Xiang L, Mo CH, Xing B. Insights into the enzymatic degradation of DNA expedited by typical perfluoroalkyl acids. ECO-ENVIRONMENT & HEALTH (ONLINE) 2023; 2:278-286. [PMID: 38435362 PMCID: PMC10902504 DOI: 10.1016/j.eehl.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/27/2023] [Accepted: 09/05/2023] [Indexed: 03/05/2024]
Abstract
Perfluoroalkyl acids (PFAAs) are considered forever chemicals, gaining increasing attention for their hazardous impacts. However, the ecological effects of PFAAs remain unclear. Environmental DNA (eDNA), as the environmental gene pool, is often collected for evaluating the ecotoxicological effects of pollutants. In this study, we found that all PFAAs investigated, including perfluorohexanoic acid, perfluorooctanoic acid, perfluorononanoic acid, and perfluorooctane sulfonate, even at low concentrations (0.02 and 0.05 mg/L), expedited the enzymatic degradation of DNA in a nonlinear dose-effect relationship, with DNA degradation fragment sizes being lower than 1,000 bp and 200 bp after 15 and 30 min of degradation, respectively. This phenomenon was attributed to the binding interaction between PFAAs and AT bases in DNA via groove binding. van der Waals force (especially dispersion force) and hydrogen bonding are the main binding forces. DNA binding with PFAAs led to decreased base stacking and right-handed helicity, resulting in loose DNA structure exposing more digestion sites for degrading enzymes, and accelerating the enzymatic degradation of DNA. The global ecological risk evaluation results indicated that PFAA contamination could cause medium and high molecular ecological risk in 497 samples from 11 contamination-hot countries (such as the USA, Canada, and China). The findings of this study show new insights into the influence of PFAAs on the environmental fates of biomacromolecules and reveal the hidden molecular ecological effects of PFAAs in the environment.
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Affiliation(s)
- Chao Qin
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Run-Hao Zhang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zekai Li
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Nai-Xian Feng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, United States
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9
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Jayasree EG, Sukumar C. Strained thiacyclophanes: Reducing properties and gauge of transannular interactions. J Mol Graph Model 2023; 125:108607. [PMID: 37634277 DOI: 10.1016/j.jmgm.2023.108607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 08/07/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023]
Abstract
The current study involves the investigation of reducing properties of disulfide bonded heteraphanes. The calculated adiabatic electron affinity (AEA) values of heteraphanes are found comparable to that of cystine molecule and are capable of undergoing reversible redox reactions. In aqueous phase, these show high propensity to get reduced. The reaction energies calculated using isodesmic equations reflect the strain associated with the studied thiacyclophane models. Increase in the number of disulfide bonds results in less strain and more stabilization. Through-space transannular interactions in the selected heteraphanes have a decisive influence on the structure stabilization associated with the systems. The results reported in the current study are expected to play a vital role while designing redox driven drug carriers by incorporating these systems in biomolecules.
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Affiliation(s)
| | - Chinthu Sukumar
- Department of Chemistry, University of Kerala, Kerala, 695581, India
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10
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Aragoni MC, Podda E, Chaudhary S, Bhasin AKK, Bhasin KK, Coles SJ, Orton JB, Isaia F, Lippolis V, Pintus A, Slawin AMZ, Woollins JD, Arca M. An Experimental and Theoretical Insight into I 2 /Br 2 Oxidation of Bis(pyridin-2-yl)Diselane and Ditellane. Chem Asian J 2023; 18:e202300836. [PMID: 37843415 DOI: 10.1002/asia.202300836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 10/17/2023]
Abstract
The reactivity between bis(pyridin-2-yl)diselane o Py2 Se2 and ditellane o Py2 Te2 (L1 and L2, respectively; o Py=pyridyn-2-yl) and I2 /Br2 is discussed. Single-crystal structure analysis revealed that the reaction of L1 with I2 yielded [(HL1+ )(I- )⋅5/2I2 ]∞ (1) in which monoprotonated cations HL1+ template a self-assembled infinite pseudo-cubic polyiodide 3D-network, while the reaction with Br2 yielded the dibromide Ho PySeII Br2 (2). The oxidation of L2 with I2 and Br2 yielded the compounds Ho PyTeII I2 (3) and Ho PyTeIV Br4 (6), respectively, whose structures were elucidated by X-ray diffraction analysis. FT-Raman spectroscopy measurements are consistent with a 3c-4e description of all the X-Ch-X three-body systems (Ch=Se, Te; X=Br, I) in compounds 2, 3, Ho PyTeII Br2 (5), and 6. The structural and spectroscopic observations are supported by extensive theoretical calculations carried out at the DFT level that were employed to study the electronic structure of the investigated compounds, the thermodynamic aspects of their formation, and the role of noncovalent σ-hole halogen and chalcogen bonds in the X⋅⋅⋅X, X⋅⋅⋅Ch and Ch⋅⋅⋅Ch interactions evidenced structurally.
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Affiliation(s)
- M Carla Aragoni
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042, Monserrato (Cagliari), Italy
| | - Enrico Podda
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042, Monserrato (Cagliari), Italy
- Centro Servizi di Ateneo per la Ricerca (CeSAR), Università degli Studi di Cagliari, S.S. 554 bivio Sestu, 09042, Monserrato (Cagliari), Italy
| | - Savita Chaudhary
- Department of Chemistry, Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Aman K K Bhasin
- Department of Chemistry, Amity University, Sector 82 A, Mohali, Punjab-140306, India
| | - Kuldip K Bhasin
- Department of Chemistry, Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Simon J Coles
- UK National Crystallography Service, School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - James B Orton
- UK National Crystallography Service, School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Francesco Isaia
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042, Monserrato (Cagliari), Italy
| | - Vito Lippolis
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042, Monserrato (Cagliari), Italy
| | - Anna Pintus
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042, Monserrato (Cagliari), Italy
| | - Alexandra M Z Slawin
- EaStCHEM School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, UK
| | - J Derek Woollins
- EaStCHEM School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, UK
- Department of Chemistry, Khalifa University, Abu Dhabi, 127788, United Arab Emirates
| | - Massimiliano Arca
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042, Monserrato (Cagliari), Italy
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11
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Piña MDLN, Bauzá A. On the Importance of Halogen and Chalcogen Bonds in the Solid State of Nucleic Acids: A Combined Crystallographic and Theoretical Perspective. Int J Mol Sci 2023; 24:13035. [PMID: 37685843 PMCID: PMC10488009 DOI: 10.3390/ijms241713035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/16/2023] [Accepted: 08/20/2023] [Indexed: 09/10/2023] Open
Abstract
In this work, intra- and intermolecular halogen and chalcogen bonds (HlgBs and ChBs, respectively) present in the solid state of nucleic acids (NAs) have been studied at the RI-MP2/def2-TZVP level of theory. To achieve this, a Protein Data Bank (PDB) survey was carried out, revealing a series of structures in which Br/I or S/Se/Te atoms belonging to nucleobases or pentose rings were involved in noncovalent interactions (NCIs) with electron-rich species. The energetics and directionality of these NCIs were rationalized through a computational study, which included the use of Molecular Electrostatic Potential (MEP) surfaces, the Quantum Theory of Atoms in Molecules (QTAIM), and Non Covalent Interaction plot (NCIplot) and Natural Bonding Orbital (NBO) techniques.
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Affiliation(s)
| | - Antonio Bauzá
- Departament de Química, Universitat de les Illes Balears, Ctra. de Valldemossa Km 7.5, 07122 Palma de Mallorca, Baleares, Spain;
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12
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Tyagi R, Zen A, Voora VK. Quantifying the Impact of Halogenation on Intermolecular Interactions and Binding Modes of Aromatic Molecules. J Phys Chem A 2023. [PMID: 37406194 DOI: 10.1021/acs.jpca.3c02291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Halogenation of aromatic molecules is frequently used to modulate intermolecular interactions with ramifications for optoelectronic and mechanical properties. In this work, we accurately quantify and understand the nature of intermolecular interactions in perhalogenated benzene (PHB) clusters. Using benchmark binding energies from the fixed-node diffusion Monte Carlo (FN-DMC) method, we show that generalized Kohn-Sham semicanonical projected random phase approximation (GKS-spRPA) plus approximate exchange kernel (AKX) provides reliable interaction energies with mean absolute error (MAE) of 0.23 kcal/mol. Using the GKS-spRPA+AXK method, we quantify the interaction energies of several binding modes of PHB clusters ((C6X6)n; X = F, Cl, Br, I; n = 2, 3). For a given binding mode, the interaction energies increase 3-4 times from X = F to X = I; the X-X binding modes have energies in the range of 2-4 kcal/mol, while the π-π binding mode has interaction energies in the range of 4-12 kcal/mol. SAPT-DFT-based energy decomposition analysis is then used to show that the equilibrium geometries are dictated primarily by the dispersion and exchange interactions. Finally, we test the accuracy of several dispersion-corrected density functional approximations and show that only the r2SCAN-D4 method has a low MAE and correct long-range behavior, which makes it suitable for large-scale simulations and for developing structure-function relationships of halogenated aromatic systems.
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Affiliation(s)
- Ritaj Tyagi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Andrea Zen
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte S. Angelo, I-80126 Napoli, Italy
| | - Vamsee K Voora
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
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13
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Morera-Boado C, Bernal-Uruchurtu MI. Interaction energy of Cl 2 and Br 2 with H 2 O: Exchange, dispersion and density the crucial ingredients. J Comput Chem 2023; 44:1073-1087. [PMID: 36578228 DOI: 10.1002/jcc.27066] [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: 03/23/2022] [Revised: 11/10/2022] [Accepted: 12/18/2022] [Indexed: 12/30/2022]
Abstract
Modern Density Functional Theory models are now suitable for many molecular and condensed phase studies. The study of noncovalent interactions, a well-known drawback, is no longer an insurmountable obstacle through design and empirical corrections. However, using empirical corrections as in the DFT-D methods might not be an all-in-one solution. This work uses a simple system, X2 -H2 O with X = Cl or Br, with two different interactions, halogen-bonded (XB) and hydrogen-halogen (HX), to investigate the capability of current density functional approximations (DFA) in predicting interaction energies with eight different exchange-correlation functionals. SAPT(DFT) provides, for all the studied cases, better predictions than the widely used supermolecular approach. In addition, the components of the interaction energy suggest where some of the shortcomings originate in each DFA. The analysis of the functionals used confirms that PBE0 and ω-B97X-D have a physically correct behavior. Using SAPT(DFT) and PBE0, and ω-B97X-D, we obtained the interaction energy of Cl2 and Br2 inside different clathrate cages and satisfactorily compared with wavefunction results; hence, the lower and upper limits of this value are defined: Cl2 @512 , -5.3 ± 0.3 kcal/mol; Cl2 @512 62 , -5.5 ± 0.1 kcal/mol; Br2 @512 62 , -7.6 ± 1.0 kcal/mol; Br2 @512 63 , -10.6 ± 1.0 kcal/mol; Br2 @512 64 , -10.9 ± 0.8 kcal/mol.
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Affiliation(s)
- Cercis Morera-Boado
- CONACYT - Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico.,Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
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14
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A Comprehensive Ab Initio Study of Halogenated A···U and G···C Base Pair Geometries and Energies. Int J Mol Sci 2023; 24:ijms24065530. [PMID: 36982603 PMCID: PMC10056977 DOI: 10.3390/ijms24065530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/09/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023] Open
Abstract
Unraveling the binding preferences involved in the formation of a supramolecular complex is key to properly understand molecular recognition and aggregation phenomena, which are of pivotal importance to biology. The halogenation of nucleic acids has been routinely carried out for decades to assist in their X-ray diffraction analysis. The incorporation of a halogen atom on a DNA/RNA base not only affected its electronic distribution, but also expanded the noncovalent interactions toolbox beyond the classical hydrogen bond (HB) by incorporating the halogen bond (HalB). In this regard, an inspection of the Protein Data Bank (PDB) revealed 187 structures involving halogenated nucleic acids (either unbound or bound to a protein) where at least 1 base pair (BP) exhibited halogenation. Herein, we were interested in disclosing the strength and binding preferences of halogenated A···U and G···C BPs, which are predominant in halogenated nucleic acids. To achieve that, computations at the RI-MP2/def2-TZVP level of theory together with state of the art theoretical modeling tools (including the computation of molecular electrostatic potential (MEP) surfaces, the quantum theory of “Atoms in Molecules” (QTAIM) and the non-covalent interactions plot (NCIplot) analyses) allowed for the characterization of the HB and HalB complexes studied herein.
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15
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Perkins MA, Tschumper GS. Characterization of competing halogen-bonding and hydrogen-bonding motifs in the acetonitrile/hydrogen iodide dimer. Chem Phys 2023. [DOI: 10.1016/j.chemphys.2023.111843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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16
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Zhang C, Verma P, Wang J, Liu Y, He X, Wang Y, Truhlar DG, Liu Z. Performance of Screened-Exchange Functionals for Band Gaps and Lattice Constants of Crystals. J Chem Theory Comput 2023; 19:311-323. [PMID: 36520598 DOI: 10.1021/acs.jctc.2c00822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Kohn-Sham density functional theory is the most widely used method for electronic structure calculations of solid-state systems. The screened-exchange functionals developed following the influential work of Scuseria and co-workers in 2003-2006 have significantly improved the accuracy of the predictions of solid-state properties. This work assesses six screened-exchange density functionals for the prediction of 60 band gaps (database BG60) and 68 lattice constants (database LC68). The band gaps are calculated with both consistently calculated lattice constants and experimental lattice constants. Results for the nonlocal screened-exchange functionals are compared with those for six widely used or recently developed local functionals. The results show that all the screened-exchange functionals have smaller mean absolute errors (MAEs) than any of the local functionals. All the functionals except HLE17 overestimate (on average) the lattice constants, and M06-SX gives the best performance among the compared functionals, with a MAE of 0.051 Å. All the functionals underestimate (on average) the band gaps, and M06-SX outperforms all other functionals, with a MAE of 0.47 eV. M06-SX also has the lowest root-mean-squared error for both LC68 and BG60. For the subdatabases of BG60, M06-SX shows better performance for ionic crystals and systems with large band gaps, while HSE12s gives better results for semiconductors and systems with small band gaps. Overall, M06-SX shows the best performance for solid-state systems, followed by N12-SX and HSE12s. The best-performing local functionals are M06-L, revM06-L, and HLE17 for band gaps and M06-L and revM06-L for lattice constants. We found that M06-SX, revM06-L, and N12-SX not only are well optimized for a broad array of chemical properties but also have very good performance for the databases in this paper, making them well-suited for applications involving heterogeneous chemistry.
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Affiliation(s)
- Cheng Zhang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410006, China
| | - Pragya Verma
- Department of Chemistry, Chemical Theory Center and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Jiaxu Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410006, China
| | - Yiwei Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200062, China
| | - Ying Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410006, China
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Zhonghua Liu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410006, China
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17
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Aragoni MC, Cherchi MF, Lippolis V, Pintus A, Podda E, Slawin AMZ, Woollins JD, Arca M. Self-Assembly of Supramolecular Architectures Driven by σ-Hole Interactions: A Halogen-Bonded 2D Network Based on a Diiminedibromido Gold(III) Complex and Tribromide Building Blocks. Molecules 2022; 27:molecules27196289. [PMID: 36234826 PMCID: PMC9571214 DOI: 10.3390/molecules27196289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
The reaction of the complex [Au(phen)Br2](PF6) (phen = 1,10-phenanthroline) with molecular dibromine afforded {[Au(phen)Br2](Br3)}∞ (1). Single crystal diffraction analysis showed that the [Au(phen)Br2]+ complex cations were bridged by asymmetric tribromide anions to form infinite zig-zag chains featuring the motif ···Au–Br···Br–Br–Br···Au–Br···Br–Br–Br···. The complex cation played an unprecedented halogen bonding (XB) donor role engaging type-I and type-II XB noncovalent interactions of comparable strength with symmetry related [Br3]− anions. A network of hydrogen bonds connects parallel chains in an infinite 2D network, contributing to the layered supramolecular architecture. DFT calculations allowed clarification of the nature of the XB interactions, showing the interplay between orbital mixing, analyzed at the NBO level, and electrostatic contribution, explored based on the molecular potential energy (MEP) maps of the interacting synthons.
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Affiliation(s)
- M. Carla Aragoni
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042 Monserrato, Italy
| | - M. Francesca Cherchi
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042 Monserrato, Italy
| | - Vito Lippolis
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042 Monserrato, Italy
| | - Anna Pintus
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042 Monserrato, Italy
| | - Enrico Podda
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042 Monserrato, Italy
- Centro Servizi di Ateneo per la Ricerca (CeSAR), Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042 Monserrato, Italy
| | - Alexandra M. Z. Slawin
- EaStCHEM School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, UK
| | - J. Derek Woollins
- EaStCHEM School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, UK
- Department of Chemistry, Khalifa University, Abu Dhabi 127788, United Arab Emirates
| | - Massimiliano Arca
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 bivio per Sestu, 09042 Monserrato, Italy
- Correspondence:
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18
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Novikov AS, Bolotin DS. Halonium, chalconium, and pnictonium salts as noncovalent organocatalysts: a computational study on relative catalytic activity. Org Biomol Chem 2022; 20:7632-7639. [PMID: 36111866 DOI: 10.1039/d2ob01415g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This theoretical study sheds light on the relative catalytic activity of pnictonium, chalconium, and halonium salts in reactions involving elimination of chloride and electrophilic activation of a carbonyl group. DFT calculations indicate that for cationic aromatic onium salts, values of the electrostatic potential on heteroatom σ-holes gradually increase from pnictogen- to halogen-containing species. The higher values of the potential on the halogen atoms of halonium salts result in the overall higher catalytic activity of these species, but in the case of pnictonium and chalconium cations, weak interactions from the side groups provide an additional stabilization effect on the reaction transition states. Based upon quantum-chemical calculations, the catalytic activity of phosphonium(V) and arsenonium(V) salts is expected to be too low to obtain effective noncovalent organocatalytic compounds, whereas stibonium(V), telluronium(IV) and iodonium(III) salts exhibit higher potential in application as noncovalent organocatalysts.
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Affiliation(s)
- Alexander S Novikov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg, 199034, Russian Federation. .,Infochemistry Scientific Center, ITMO University, Kronverksky Pr. 49, Bldg. A, Saint Petersburg, 197101, Russian Federation
| | - Dmitrii S Bolotin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, Saint Petersburg, 199034, Russian Federation.
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19
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Effects of non-local exchange functionals in the density functional theories for the description of molecular vibrations. J CHEM SCI 2022. [DOI: 10.1007/s12039-022-02061-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Perkins MA, Tschumper GS. Characterization of Competing Halogen- and Hydrogen-Bonding Motifs in Simple Mixed Dimers of HCN and HX (X = F, Cl, Br, and I). J Phys Chem A 2022; 126:3688-3695. [PMID: 35652358 DOI: 10.1021/acs.jpca.2c02041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work performs the first systematic comparison of hydrogen- and halogen-bonded configurations of the HCN/HX mixed dimer, where X = F, Cl, Br, and I. Eleven different minima have been characterized for these four heterogeneous dimers near the CCSD(T) complete basis set (CBS) limit. For each complex, two different hydrogen-bonded minima were identified: the global minimum where HX acts as the hydrogen bond donor and a local minimum where HX acts as the hydrogen bond acceptor. A halogen-bonded local minimum was also identified for all but the fluorine mixed dimer. To the best of our knowledge, three of the minima are identified here for the first time. The hydrogen- and halogen-bonded local minima of each complex become more energetically competitive with the global minimum as the atomic radius of the halogen atom increases. CCSD(T) relative energies of the hydrogen-bonded local minima computed near the CBS limit decrease from 4.5 kcal mol-1 for HCN/HF to 2.9, 2.4, and 1.2 kcal mol-1 for X = Cl, Br, and I, respectively. Corresponding relative energies for the halogen-bonded local minima range from 4.0 kcal mol-1 for X = Cl to 2.7 kcal mol-1 for X = Br and to as little as 0.5 kcal mol-1 X = I. Harmonic vibrational frequency shifts reported here suggest that it may be feasible to differentiate between the various minima for X = Cl, Br, and I via spectroscopic analysis, as was the case for the HCN/HF dimer.
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Affiliation(s)
- Morgan A Perkins
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Gregory S Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
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21
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Harry SA, Vemulapalli S, Dudding T, Lectka T. Rational Computational Design of Systems Exhibiting Strong Halogen Bonding Involving Fluorine in Bicyclic Diamine Derivatives. J Org Chem 2022; 87:8413-8419. [PMID: 35658438 DOI: 10.1021/acs.joc.2c00497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Perhaps the most controversial and rare aspect of the halogen bonding interaction is the potential of fluorine in compounds to serve as a halogen bond donor. In this note, we provide clear and convincing examples of hypothetical molecules in which fluorine is strongly halogen bonding in a metastable state. Of particular note is a polycyclic system inspired by Selectfluor, which has been controversially proposed to engage in halogen bonding.
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Affiliation(s)
- Stefan Andrew Harry
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Srini Vemulapalli
- Department of Chemistry, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Travis Dudding
- Department of Chemistry, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Thomas Lectka
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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22
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Synthesis, crystal, and Hirschfeld surface, DFT and molecular docking studies of 6-(3‑chloro-4-fluorophenyl)-4-ethoxy-2-(4-methoxyphenyl)quinazoline derivative. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Preparation and Characterization of TCPP-CaMMT Nanocompound and Its Composite with Polypropylene. NANOMATERIALS 2022; 12:nano12091428. [PMID: 35564137 PMCID: PMC9101571 DOI: 10.3390/nano12091428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/15/2022] [Accepted: 04/20/2022] [Indexed: 11/17/2022]
Abstract
Based on the molecular dynamics method, the tris-(1-chloropropan-2yl) phosphate (TCPP)/montmorillonite (MMT) molecular model was established to study the binding energy and microstructure changes in TCPP and MMT. The theoretical simulation results showed that TCPP can enter the MMT layer and increase the layer spacing. From this, an organic intercalated Ca-montmorillonite TCPP-CaMMT was prepared by a very simple direct mixing method using flame retardant TCPP as a modifier. Polypropylene (PP) composites were prepared by TCPP, CaMMT, and TCPP-CaMMT. The microstructures of TCPP-CaMMT nanocompounds and PP composites were studied by X-ray diffraction (XRD), scanning electron microscope (SEM), and transmission electron microscope (TEM). The results showed that TCPP-CaMMT nanocompounds could be exfoliated into nanosheets in PP. The flame retardancy and mechanical properties of PP/TCPP-CaMMT samples were studied by limited oxygen index (LOI) measurements and tensile tests. The PP/TCPP-CaMMT composites showed better LOI, tensile strength, and elongation at break than the machine-mixed PP/TCPP + CaMMT.
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24
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Sikorska C, Gaston N. Molecular crystals vs. superatomic lattice: a case study with superalkali-superhalogen compounds. Phys Chem Chem Phys 2022; 24:8763-8774. [PMID: 35352731 DOI: 10.1039/d1cp05761h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Using a first-principles approach, we study the assembly of atomically-precise cluster solids with atomic precision. The aims are to create binary assemblies of clusters through charge transfer between neutral molecular clusters, and employing intercluster electrostatic attraction as a driving force for co-assembly. We combined pairs of complementary clusters in which one cluster is electron-donating (superalkali) and the other is electron-accepting (superhalogen). From the analysis of the binding energy between superatomic counterparts, charge transfer, and the relative size of the clusters, we analyze the resulting structures as either molecular crystals or superatomic lattices. We demonstrate that the substitution of a single atom can result in minor changes to the crystal structure of the binary solids or entirely new packing structures. The [N4Mg6Li]+[AlCl4]-, [N4Mg6Na]+[AlCl4]-, [N4Mg6K]+[AlCl4]-, [N4Mg6Li]+[AlF4]-, [N4Mg6Na]+[AlF4]-, and [N4Mg6K]+[AlF4]- compounds all form the same close-packed superatomic lattice structure through halogen bonding, with subtle differences in the orientation of the superatoms. These salts may also form molecular crystals where clusters are held to one another by electrostatic interactions. Our results emphasize how the structure of superatomic solids can be tuned upon single atom substitution.
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Affiliation(s)
- Celina Sikorska
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Department of Physics, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Nicola Gaston
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Department of Physics, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
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25
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Sikorska C, Gaston N. Bimetallic superalkali substitution in the CsPbBr 3 perovskite: Pseudocubic phases and tunable bandgap. J Chem Phys 2021; 155:174307. [PMID: 34742223 DOI: 10.1063/5.0067708] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Perovskites attract attention as efficient light absorbers for solar cells due to their high-power conversion efficiency (up to 24%). The high photoelectric conversion efficiency is greatly affected by a suitable band structure. Cation substitution can be an effective approach to tune the electronic band structure of lead halide perovskites. In this work, superalkali cations were introduced to replace the Cs+ cation in the CsPbBr3 material. The bimetallic superalkalis (LiMg, NaMg, LiCa, and NaCa) were inserted since they are structurally simple systems and have a strong tendency to lose one electron to achieve a closed-shell cation. The cation substitution in the lead halide perovskite leads to changes in the shape of both valence and conduction bands compared to CsPbBr3. Introducing superalkali cations produces extra electronic states close to the Fermi level, which arise from the formation of alkali earth metal states at the top of the valence band. Our first-principles computations reveal that bimetallic superalkali substitution decreases the bandgap of the perovskite. The bandgaps of MgLi-PbBr3 (1.35 eV) and MgNa-PbBr3 (1.06 eV) are lower than the bandgap of CsPbBr3 (2.48 eV) and within the optimal bandgap (i.e., 1.1-1.4 eV) for single-junction solar cells. Thus, the MgLi-PbBr3 and MgNa-PbBr3 inorganic perovskites are promising candidates for high-efficiency solar cells.
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Affiliation(s)
- Celina Sikorska
- The MacDiarmid Institute of Advanced Materials and Nanotechnology, A New Zealand Centre of Research Excellence, Wellington, New Zealand
| | - Nicola Gaston
- The MacDiarmid Institute of Advanced Materials and Nanotechnology, A New Zealand Centre of Research Excellence, Wellington, New Zealand
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26
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Aza-BODIPY molecular assembly at the liquid-solid interface driven by Br⋯F BF interactions. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.02.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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27
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Mersal GA, Yahia I, El-Sheshtawy HS. Lone pair Halogen (X2)…π Interactions Stabilizes Molecular Halogens (X2=I2, Br2, Cl2, and F2) on Reduced Graphene Oxide surface: Structural, Solvent Effect and optical properties. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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28
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Cooperation/Competition between Halogen Bonds and Hydrogen Bonds in Complexes of 2,6-Diaminopyridines and X-CY3 (X = Cl, Br; Y = H, F). Symmetry (Basel) 2021. [DOI: 10.3390/sym13050766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The DFT calculations have been performed on a series of two-element complexes formed by substituted 2,6-diaminopyridine (R−PDA) and pyridine (R−Pyr) with X−CY3 molecules (where X = Cl, Br and Y = H, F). The primary aim of this study was to examine the intermolecular hydrogen and halogen bonds in the condition of their mutual coexistence. Symmetry/antisymmetry of the interrelation between three individual interactions is addressed. It appears that halogen bonds play the main role in the stabilization of the structures of the selected systems. However, the occurrence of one or two hydrogen bonds was associated with the favourable geometry of the complexes. Moreover, the impact of different substituent groups attached in the para position to the aromatic ring of the 2,6-diaminopyridine and pyridine on the character of the intermolecular hydrogen and halogen bonds was examined. The results indicate that the presence of electron-donating substituents strengthens the bonds. In turn, the presence of electron-withdrawing substituents reduces the strength of halogen bonds. Additionally, when hydrogen and halogen bonds lose their leading role in the complex formation, the nonspecific electrostatic interactions between dipole moments take their place. Analysis was based on geometric, energetic, and topological parameters of the studied systems.
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29
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Karbalaei Khani S, Geissler B, Engelage E, Nuernberger P, Hättig C. Tracing absorption and emission characteristics of halogen-bonded ion pairs involving halogenated imidazolium species. Phys Chem Chem Phys 2021; 23:7480-7494. [PMID: 33876108 DOI: 10.1039/d1cp00009h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We investigate how the absorption and fluorescence of halogenated imidazolium compounds in acetonitrile solution is influenced by the presence of counterions and the ability to act as halogen-bond donors. Experimental measurements and quantum chemical calculations with correlated wavefunction methods are applied to study three monodentate halogen-bond complexes of iodo-imidazolium, iodo-benzimidazolium and bromo-benzimidazolium cations with triflate counterions, and a bidentate complex of bis(iodo-benzimidazolium) dications with chloride as counterion. The three monodentate complexes with triflate counterions relax after photoexcitation to minima on the S1 potential energy surface where the C-I bond and the IO halogen bond are partially broken. For the bidentate complex with the smaller chloride counterion the halogen-bond interaction stays intact in the S1 minimum that is reached by relaxation from the Franck-Condon point. In a complementing experimental approach, stationary absorption and emission as well as transient fluorescence spectra are recorded for iodo- and bromo-benzimidazolium in acetonitrile. Variation of the counterion, substitution of the iodine by bromine, hydrogen, or methyl, and the comparison to theory allows the identification of spectroscopic signatures and photoinduced dynamics associated with ion-pairing.
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30
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Frosch J, Koneczny M, Bannenberg T, Tamm M. Halogen Complexes of Anionic N-Heterocyclic Carbenes. Chemistry 2021; 27:4349-4363. [PMID: 33094865 PMCID: PMC7986712 DOI: 10.1002/chem.202004418] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Indexed: 12/12/2022]
Abstract
The lithium complexes [(WCA-NHC)Li(toluene)] of anionic N-heterocyclic carbenes with a weakly coordinating anionic borate moiety (WCA-NHC) reacted with iodine, bromine, or CCl4 to afford the zwitterionic 2-halogenoimidazolium borates (WCA-NHC)X (X=I, Br, Cl; WCA=B(C6 F5 )3 , B{3,5-C6 H3 (CF3 )2 }3 ; NHC=IDipp=1,3-bis(2,6-diisopropylphenyl)imidazolin-2-ylidene, or NHC=IMes=1,3-bis(2,4,6-trimethylphenyl)imidazolin-2-ylidene). The iodine derivative (WCA-IDipp)I (WCA=B(C6 F5 )3 ) formed several complexes of the type (WCA-IDipp)I⋅L (L=C6 H5 Cl, C6 H5 Me, CH3 CN, THF, ONMe3 ), revealing its ability to act as an efficient halogen bond donor, which was also exploited for the preparation of hypervalent bis(carbene)iodine(I) complexes of the type [(WCA-IDipp)I(NHC)] and [PPh4 ][(WCA-IDipp)I(WCA-NHC)] (NHC=IDipp, IMes). The corresponding bromine complex [PPh4 ][(WCA-IDipp)2 Br] was isolated as a rare example of a hypervalent (10-Br-2) system. DFT calculations reveal that London dispersion contributes significantly to the stability of the bis(carbene)halogen(I) complexes, and the bonding was further analyzed by quantum theory of atoms in molecules (QTAIM) analysis.
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Affiliation(s)
- Jenni Frosch
- Institut für Anorganische und Analytische ChemieTechnische Universität BraunschweigHagenring 3038106BraunschweigGermany
| | - Marvin Koneczny
- Institut für Anorganische und Analytische ChemieTechnische Universität BraunschweigHagenring 3038106BraunschweigGermany
| | - Thomas Bannenberg
- Institut für Anorganische und Analytische ChemieTechnische Universität BraunschweigHagenring 3038106BraunschweigGermany
| | - Matthias Tamm
- Institut für Anorganische und Analytische ChemieTechnische Universität BraunschweigHagenring 3038106BraunschweigGermany
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Rocha M, Echeverría GA, Piro OE, Jios JL, Ulic SE, Gil DM. Role of fluorine-fluorine and weak intermolecular interactions in the supramolecular network of a new trifluoromethyl-1,5-benzodiazepine: Crystal structure, Hirshfeld surface analysis and theoretical study. J Fluor Chem 2021. [DOI: 10.1016/j.jfluchem.2020.109697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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32
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Alipour M, Fallahzadeh P. On the role of steric and exchange–correlation effects in halogenated complexes. NEW J CHEM 2021. [DOI: 10.1039/d1nj02581c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Density functional theory formalisms of energy partitioning schemes are utilized to find out what energetic components govern interactions in halogenated complexes.
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Affiliation(s)
- Mojtaba Alipour
- Department of Chemistry, School of Science, Shiraz University, Shiraz 71946-84795, Iran
| | - Parisa Fallahzadeh
- Department of Chemistry, School of Science, Shiraz University, Shiraz 71946-84795, Iran
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33
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Kitzmiller NL, Wolf ME, Turney JM, Schaefer HF. The HOX⋯SO 2 (X=F, Cl, Br, I) Binary Complexes: Implications for Atmospheric Chemistry. Chemphyschem 2020; 22:112-126. [PMID: 33090675 DOI: 10.1002/cphc.202000746] [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: 08/31/2020] [Revised: 10/16/2020] [Indexed: 11/07/2022]
Abstract
Sulfur dioxide and hypohalous acids (HOX, X=F, Cl, Br, I) are ubiquitous molecules in the atmosphere that are central to important processes like seasonal ozone depletion, acid rain, and cloud nucleation. We present the first theoretical examination of the HOX⋯SO2 binary complexes and the associated trends due to halogen substitution. Reliable geometries were optimized at the CCSD(T)/aug-cc-pV(T+d)Z level of theory for HOF and HOCl complexes. The HOBr and HOI complexes were optimized at the CCSD(T)/aug-cc-pV(D+d)Z level of theory with the exception of the Br and I atoms which were modeled with an aug-cc-pwCVDZ-PP pseudopotential. 27 HOX⋯SO2 complexes were characterized and the focal point method was employed to produce CCSDT(Q)/CBS interaction energies. Natural Bond Orbital analysis and Symmetry Adapted Perturbation Theory were used to classify the nature of each principle interaction. The interaction energies of all HOX⋯SO2 complexes in this study ranged from 1.35 to 3.81 kcal mol-1 . The single-interaction hydrogen bonded complexes spanned a range of 2.62 to 3.07 kcal mol-1 , while the single-interaction halogen bonded complexes were far more sensitive to halogen substitution ranging from 1.35 to 3.06 kcal mol-1 , indicating that the two types of interactions are extremely competitive for heavier halogens. Our results provide insight into the interactions between HOX and SO2 which may guide further research of related systems.
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Affiliation(s)
- Nathaniel L Kitzmiller
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia, 30602
| | - Mark E Wolf
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia, 30602
| | - Justin M Turney
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia, 30602
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia, 30602
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34
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Torres AE, Fomine S. Halogen-Doping Effect on the Delithiation and Charge Transfer of (Li 2S) 10 Cluster. J Phys Chem A 2020; 124:8949-8958. [PMID: 32927945 DOI: 10.1021/acs.jpca.0c05767] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Previous studies have suggested beneficial effects in lithium-sulfur batteries containing iodide in a sulfur-based cathode or as an electrolyte additive. These effects include preventing electrolyte degradation and improving the cycle stability of Li-S cells. However, little is known regarding the underlying reasons of such performance improvements. In this work, we present a theoretical study of the halogen-doping effect on the delithiation (charge) process on a (Li2S)10 model structure representing a potential final discharge product. It is revealed that the electron polaron is the dominant charge carrier during the charge process, and iodine is a facilitating agent for lithium detachment from the lithium sulfide cluster. However, the graphene support was found as potentially slowing down the ionic transport during the delithiation process due to charge transfer exerted by the support to the doped cluster that may retain the positive ions in the particle.
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Affiliation(s)
- Ana E Torres
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Circuito Exterior S/N, C. U., 04510 Mexico City, Mexico
| | - Serguei Fomine
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, CU, Coyoacán, 04510 Mexico City Mexico
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35
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Sutradhar D, Bhattarai S, Parveen S, Chandra AK. Comparison between Chlorine-Shared and π-Halogen Bonds Involving Substituted Phosphabenzene and ClF Molecules. ACS OMEGA 2020; 5:24095-24105. [PMID: 32984731 PMCID: PMC7513335 DOI: 10.1021/acsomega.0c03567] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Ab initio MP2/aug-cc-pVTZ calculations have been carried out in order to study the nature of P···Cl halogen bonding interaction between a phosphorus atom in an aromatic ring in para-substituted phosphabenzene (PPBZ) and ClF molecule. The interaction of PPBZ with ClF results in two different types of complexes: (i) complex formation through the chlorine-shared halogen bond (T1-X-PPBZ·ClF) and (ii) complex formation via halogen-π interaction (T2-X-PPBZ·ClF). T1-X-PPBZ·ClF complexes are found to be more stable than the T2-X-PPBZ·ClF complexes. This work also presents a general criterion to distinguish a chlorine-shared halogen bond from a traditional halogen bond and sheds light on the formation of the chlorine-shared halogen bond. The binding energy of T1-X-PPBZ·ClF complexes correlates well with the negative electrostatic potential of the P atom and PA value of the substituted PPBZ. The properties of both T1-X-PPBZ·ClF and T2-X-PPBZ·ClF complexes are analyzed using atom-in-molecule, natural bond orbital, and symmetry-adapted perturbation theory calculations. The variation of the Cl-F bond distances and the redshifts of the ν(ClF) vibration resulting from the interaction with PPBZs are discussed.
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Affiliation(s)
- Dipankar Sutradhar
- Solid
State and Structural Chemistry Unit, Indian
Institute of Science, Bangalore, Karnataka 560012, India
| | - Sumitra Bhattarai
- Department
of Chemistry, North-Eastern Hill University, Shillong 793022, India
| | - Salma Parveen
- Department
of Chemistry, North-Eastern Hill University, Shillong 793022, India
| | - Asit K. Chandra
- Department
of Chemistry, North-Eastern Hill University, Shillong 793022, India
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36
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Alipour M, Kargar K. Anionic behavior and single-molecule crystal in fullerene confinements: A contribution from DFT energy decomposition and cooperativity analyses. J Comput Chem 2020; 41:1912-1920. [PMID: 32506442 DOI: 10.1002/jcc.26362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/20/2020] [Accepted: 05/22/2020] [Indexed: 11/09/2022]
Abstract
The recently proposed systems of various anions (A) confined inside C60 , A- @ C60 , which in turn behave as large and stable anions, (A @ C60 )- , can find potential applications in various fields. On the other hand, it has earlier been shown that from the dihalogens (X2 ) encapsulated C60 , X2 @ C60 , only F2 @ C60 can be introduced as a system in which the cage acts as a cation C60 + and interacts with an endohedral anion, F2 - , forming the F2 - @ C60 + as a single-molecule crystal compound. In this work, two density functional theory energy decomposition analysis (EDA) schemes, where in one of them the noninteracting kinetic, electrostatic, and exchange-correlation energies come into play while another scheme, called as EDA-SBL, includes the steric, electrostatic, and quantum effects as essential ingredients (S. Liu, J. Chem. Phys. 2007, 126, 244103), are utilized to find out what energetic components govern the unique characteristics of the (A @ C60 )- and X2 @ C60 confinements. It is shown that the noninteracting kinetic energy and steric energies have important contributions to the total interaction energies for the considered systems. However, there are other confinements for which the electrostatic and exchange-correlation contributions play also imperative roles. Furthermore, we find reasonable correlations between interaction energies and their components as well as the energetic components themselves, leading to an alternative EDA scheme including the noninteracting kinetic, steric, and electrostatic energies for investigations on other endohedral fullerenes. Extending our analyses to large size confinements, Cl- @ Cn with n up to 90 as illustrative examples, the quantitative cooperativity concept is also explored, where the positive and negative cooperativity profiles unveil a specific size of the anionic confinements to form the most stable large anion.
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Affiliation(s)
- Mojtaba Alipour
- Department of Chemistry, College of Sciences, Shiraz University, Shiraz, Iran
| | - Kimia Kargar
- Department of Chemistry, College of Sciences, Shiraz University, Shiraz, Iran
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Arhangelskis M, Topić F, Hindle P, Tran R, Morris AJ, Cinčić D, Friščić T. Mechanochemical reactions of cocrystals: comparing theory with experiment in the making and breaking of halogen bonds in the solid state. Chem Commun (Camb) 2020; 56:8293-8296. [PMID: 32573566 DOI: 10.1039/d0cc02935a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Mechanochemical re-investigation of the halogen-bonded cocrystallisation of 1,4-diazabicyclo[2.2.2]-octane and 1,2-diiodotetrafluorobenzene revealed an unexpectedly complex system with three distinct cocrystal compositions, one of which also exhibits temperature-dependent polymorphism. This provided an opportunity to experimentally test the ability of dispersion-corrected periodic density functional theory (DFT) to not only explain the formation, but also predict the interconversion between halogen-bonded cocrystals of different stoichiometries.
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Affiliation(s)
- Mihails Arhangelskis
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal H3A0B8, Canada.
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Bandyopadhyay P, Seikh MM. Components of the interaction energy of the odd-electron halogen bond: an ab initio study. Phys Chem Chem Phys 2020; 22:15389-15400. [PMID: 32598430 DOI: 10.1039/d0cp02619k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the realm of non-covalent interactions (NCI), the odd-electron halogen bond offers a fertile ground to explore the nature of such weak interactions. Here, an ab initio study of odd-electron halogen bonding (XB) is reported. The interactions of five radicals with several freons and interhalogens are studied using the Møller-Plesset (MP2) method. The regioselectivity, interaction energy and the components of the interaction energy of odd-electron XB were tuned by judicial selection of donor-acceptor pairs as revealed by scrutinizing the conceptual DFT parameters, NCI plot and LED-DLPNO-CCSD(T) analysis. The contribution from dispersion interaction is rather high for all XB bonded complexes and it increases when the interacting atom of the XB donor is highly polarizable. Additionally, the polarisation and intermolecular charge-transfer also contribute significantly when both the donor and acceptor atoms are soft species, resulting in a soft-soft interaction. We believe that our finding will not only shed new light on non-covalent interaction of odd-electron XB but will also be able to capture the pnictogen, chalcogen and tetrel bonding interactions. The ability of conceptual DFT parameters to predict the interaction energy and its components shown in this study will be helpful for tuning of substrates for desired products, modelling bio/macromolecules and crystal engineering.
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39
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Piña MDLN, Frontera A, Bauzá A. Quantifying Intramolecular Halogen Bonds in Nucleic Acids: A Combined Protein Data Bank and Theoretical Study. ACS Chem Biol 2020; 15:1942-1948. [PMID: 32469201 DOI: 10.1021/acschembio.0c00292] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In this study, we report experimental (Protein Data Bank (PDB) search) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of the nature, stability, and directionality properties of intramolecular halogen bonding interactions (HaBs) between 5-bromo/5-iodoracil bases and backbone phosphate groups in nucleic acids (NAs). A PDB survey revealed relevant examples where intramolecular HaBs are undertaken and serve as a structural source of stability in RNA and DNA molecules. In order to develop suitable energy predictors, we started this investigation by calculating the interaction energy values and both the potential V(r) and kinetic G(r) energy densities (using Bader's "atoms in molecules" theory) of several halogen bond complexes involving 5-bromo/5-iodoracil molecules and biologically relevant electron donors. Once the energy predictors based on V(r)/G(r) energy densities were developed, we analyzed the HaBs observed in the biological examples retrieved from the PDB search in order to estimate the strength of the interaction. As far as our knowledge extends, intramolecular halogen bonds in NAs have not been previously quantified in the literature using this methodology and may be of great importance in understanding their structural properties as well as in the construction of molecular materials with DNA and other biological macromolecules.
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Affiliation(s)
- María de las Nieves Piña
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, Palma, Baleares 07122, Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, Palma, Baleares 07122, Spain
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, Palma, Baleares 07122, Spain
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Abstract
Identifying new binding forces between electron donor and acceptor entities is key to properly understanding molecular recognition and aggregation phenomena, which are of inmense importance to biology. For decades, the halogenation of DNA/RNA bases has been routinely carried out to solve solid state structures of nucleic acids (NA). However, the effects of this modification might be deeper than just a simple atom substitution since halogens are also known to undergo noncovalent binding (halogen bonding). Herein we show that halogenated NAs with either Br or I atoms are able to establish halogen bonds with properly disposed protein residues. An inspection of the Protein Data Bank (PDB) reveals several examples involving 5-iodo/5-bromouracil, 8-bromoadenine, and 5-iodocytosine bases that are consistent with the halogen bond geometry features. Computations reveal the favorable and moderately strong nature of this interaction, thus confirming the ability of halogenated bases to actively participate in protein-NA binding.
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Affiliation(s)
- Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma, Baleares, Spain
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41
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Zhu Z, Xu Z, Zhu W. Interaction Nature and Computational Methods for Halogen Bonding: A Perspective. J Chem Inf Model 2020; 60:2683-2696. [DOI: 10.1021/acs.jcim.0c00032] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zhengdan Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China
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42
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Hulushe ST, Manyeruke MH, Louzada M, Rigin S, Hosten EC, Watkins GM. Exploring intermolecular contacts in multi-substituted benzaldehyde derivatives: X-ray, Hirshfeld surface and lattice energy analyses. RSC Adv 2020; 10:16861-16874. [PMID: 35496923 PMCID: PMC9053169 DOI: 10.1039/c9ra10752e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/01/2020] [Indexed: 11/21/2022] Open
Abstract
Crystal structures of six benzaldehyde derivatives (1-6) have been determined and their supramolecular networks were established by an X-ray crystallographic study. The study has shown that the compounds are linked by various intermolecular interactions such as weak C-H⋯O hydrogen bonding, and C-H⋯π, π-π and halogen bonding interactions which consolidate and strengthen the formation of these molecular assemblies. The carbonyl group generates diverse synthons in 1-6via intermolecular C-H⋯O hydrogen bonds. An interplay of C-H⋯O hydrogen bonds, and C-H⋯π and π-π stacking interactions facilitates the formation of multi-dimensional supramolecular networks. Crystal packings in 4 and 5 are further generated by type I halogen⋯halogen bonding interactions. The differences in crystal packing are represented by variation of substitution positions in the compounds. Structure 3 is isomorphous with 4 but there are subtle differences in their crystal packing. The nature of intermolecular contacts in the structures has been studied through the Hirshfeld surfaces and two-dimensional fingerprint plots which serve as a comparison in constructing different supramolecular networks. The intermolecular interaction energies are quantified utilizing theorectical calculations for the title compounds and various analogous structures retrieved from the Cambridge Structural Database (CSD). Also intermolecular interactions for the molecular pairs are exctrated from respective crystal structures. Essentially, there are some invariant and variable intermolecular contacts realized between different groups in all six structures. The ab initio DFT total lattice energy (E Tot) calculations showed a direct correlation with thermal strengths of the title compounds.
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Affiliation(s)
- Siya T Hulushe
- Department of Chemistry, Rhodes University P.O. Box 94 Grahamstown 6139 South Africa
| | - Meloddy H Manyeruke
- Department of Chemistry, Rhodes University P.O. Box 94 Grahamstown 6139 South Africa
| | - Marcel Louzada
- Department of Chemistry, Rhodes University P.O. Box 94 Grahamstown 6139 South Africa
| | - Sergei Rigin
- Department of Chemistry, New Mexico Highlands University Las Vegas New Mexico 87701 USA
| | - Eric C Hosten
- Department of Chemistry, Nelson Mandela University P.O. Box 77000 Port Elizabeth 6031 South Africa
| | - Gareth M Watkins
- Department of Chemistry, Rhodes University P.O. Box 94 Grahamstown 6139 South Africa
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Application of Halogen Bonding to Organocatalysis: A Theoretical Perspective. Molecules 2020; 25:molecules25051045. [PMID: 32110944 PMCID: PMC7179134 DOI: 10.3390/molecules25051045] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 11/18/2022] Open
Abstract
The strong, specific, and directional halogen bond (XB) is an ideal supramolecular synthon in crystal engineering, as well as rational catalyst and drug design. These attributes attracted strong growing interest in halogen bonding in the past decade and led to a wide range of applications in materials, biological, and catalysis applications. Recently, various research groups exploited the XB mode of activation in designing halogen-based Lewis acids in effecting organic transformation, and there is continual growth in this promising area. In addition to the rapid advancements in methodology development, computational investigations are well suited for mechanistic understanding, rational XB catalyst design, and the study of intermediates that are unstable when observed experimentally. In this review, we highlight recent computational studies of XB organocatalytic reactions, which provide valuable insights into the XB mode of activation, competing reaction pathways, effects of solvent and counterions, and design of novel XB catalysts.
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MacKeown H, Adusei Gyamfi J, Schoutteten KVKM, Dumoulin D, Verdickt L, Ouddane B, Criquet J. Formation and removal of disinfection by-products in a full scale drinking water treatment plant. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 704:135280. [PMID: 31896211 DOI: 10.1016/j.scitotenv.2019.135280] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/27/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
In this case study, high sensitivity simple methods for the analysis of trihalomethanes (THM4), iodinated-trihalomethanes (I-THMs), haloacetic acids (HAAs), bromide, iodide and iodate have been developed. A one-step procedure for the analysis of haloacetic acids by head-space GC-MS provides good reproducibility and low limits of quantification (≤50 ng L-1). These methods were applied to characterize the formation of disinfection by-products (DBPs) in a full scale drinking water treatment plant. In this treatment plant, the incorporation of bromine into THMs increases throughout the water treatment line, due to the formation of bromine reactive species favored by the decrease of competition between dissolved organic carbon (DOC) and bromide towards chlorine. A linear correlation has been observed between the bromine incorporation factor and the Br-/DOC mass ratio. The conversion of iodine to iodate by chlorination occurs in this water due to the relatively high bromide concentration. Moreover, a higher formation of iodate compared to iodide levels in the raw water is observed indicating a degradation of organic iodinated compounds. The formation of I-THMs was constant in terms of quantity and speciation between campaigns despite fluctuating concentrations of DOC and total iodine in the raw water. A preferential removal of DBPs formed by the intermediate chlorination in the order I-DBPs > Br-DBPs > Cl-DBPs occurs during the subsequent activated carbon filtration. The removal rates range from 25 to 36% for the regulated THM4, from 82 to 93% for the ∑I-THMs and 95% for haloacetic acids. The assessment of the relative toxicity shows that despite a much lower concentration of HAAs (<10% of the total mass of measured DBPs) compared to THMs, these compounds are responsible for 75% of the relative cytotoxicity of the treated water. Bromoacetic acid on its own accounts for more than 60% of the overall toxicity of the 17 compounds included in this study.
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Affiliation(s)
- Henry MacKeown
- Univ. Lille CNRS, UMR 8516 - LASIR, Equipe Physico-Chimie de l'Environnement, Lille F-59000, France
| | - Junias Adusei Gyamfi
- Univ. Lille CNRS, UMR 8516 - LASIR, Equipe Physico-Chimie de l'Environnement, Lille F-59000, France; Delft University of Technology, Faculty of Civil Engineering and Geosciences, Department of Water Management, PO Box 5048, GA Delft 2600, The Netherlands
| | - Klaas Vital Kaat Marnix Schoutteten
- Ghent University, Faculty of Bioscience Engineering, Department of Green Chemistry and Technology, Coupure Links 653, Gent 9000, Belgium; De Watergroep, Vooruitgangstraat 189, Brussels 1030, Belgium
| | - David Dumoulin
- Univ. Lille CNRS, UMR 8516 - LASIR, Equipe Physico-Chimie de l'Environnement, Lille F-59000, France
| | | | - Baghdad Ouddane
- Univ. Lille CNRS, UMR 8516 - LASIR, Equipe Physico-Chimie de l'Environnement, Lille F-59000, France
| | - Justine Criquet
- Univ. Lille CNRS, UMR 8516 - LASIR, Equipe Physico-Chimie de l'Environnement, Lille F-59000, France.
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Theoretical Description of R-X⋯NH 3 Halogen Bond Complexes: Effect of the R Group on the Complex Stability and Sigma-Hole Electron Depletion. Molecules 2020; 25:molecules25030530. [PMID: 31991810 PMCID: PMC7037998 DOI: 10.3390/molecules25030530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/14/2020] [Accepted: 01/17/2020] [Indexed: 11/16/2022] Open
Abstract
In the present work, a number of R–X⋯NH3 (X = Cl, Br, and I) halogen bonded systems were theoretical studied by means of DFT calculations performed at the ωB97XD/6-31+G(d,p) level of theory in order to get insights on the effect of the electron-donating or electron-withdrawing character of the different R substituent groups (R = halogen, methyl, partially fluorinated methyl, perfluoro-methyl, ethyl, vinyl, and acetyl) on the stability of the halogen bond. The results indicate that the relative stability of the halogen bond follows the Cl < Br < I trend considering the same R substituent whereas the more electron-withdrawing character of the R substituent the more stable the halogen bond. Refinement of the latter results, performed at the MP2/6-31+G(d,p) level showed that the DFT and the MP2 binding energies correlate remarkably well, suggesting that the Grimme’s type dispersion-corrected functional produces reasonable structural and energetic features of halogen bond systems. DFT results were also observed to agree with more refined calculations performed at the CCSD(T) level. In a further stage, a more thorough analysis of the R–Br⋯NH3 complexes was performed by means of a novel electron localization/delocalization tool, defined in terms of an Information Theory, IT, based quantity obtained from the conditional pair density. For the latter, our in-house developed C++/CUDA program, called KLD (acronym of Kullback–Leibler divergence), was employed. KLD results mapped onto the one-electron density plotted at a 0.04 a.u. isovalue, showed that (i) as expected, the localized electron depletion of the Br sigma-hole is largely affected by the electron-withdrawing character of the R substituent group and (ii) the R–X bond is significantly polarized due to the presence of the NH3 molecule in the complexes. The afore-mentioned constitutes a clear indication of the dominant character of electrostatics on the stabilization of halogen bonds in agreement with a number of studies reported in the main literature. Finally, the cooperative effects on the [Br—CN]n system (n = 1–8) was evaluated at the MP2/6-31+G(d,p) level, where it was observed that an increase of about ~14.2% on the complex stability is obtained when going from n = 2 to n = 8. The latter results were corroborated by the analysis of the changes on the Fermi-hole localization pattern on the halogen bond zones, which suggests an also important contribution of the electron correlation in the stabilization of these systems.
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Sarr S, Graton J, Montavon G, Pilmé J, Galland N. On the Interplay between Charge-Shift Bonding and Halogen Bonding. Chemphyschem 2020; 21:240-250. [PMID: 31793159 DOI: 10.1002/cphc.201901023] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/29/2019] [Indexed: 01/11/2023]
Abstract
The nature of halogen-bond interactions has been analysed from the perspective of the astatine element, which is potentially the strongest halogen-bond donor. Relativistic quantum calculations on complexes formed between halide anions and a series of Y3 C-X (Y=F to X, X=I, At) halogen-bond donors disclosed unexpected trends, e. g., At3 C-At revealing a weaker donating ability than I3 C-I despite a stronger polarizability. All the observed peculiarities have their origin in a specific component of C-Y bonds: the charge-shift bonding. Descriptors of the Quantum Chemical Topology show that the halogen-bond strength can be quantitatively anticipated from the magnitude of charge-shift bonding operating in Y3 C-X. The charge-shift mechanism weakens the ability of the halogen atom X to engage in halogen bonds. This outcome provides rationales for outlier halogen-bond complexes, which are at variance with the consensus that the halogen-bond strength scales with the polarizability of the halogen atom.
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Affiliation(s)
- Serigne Sarr
- CEISAM, UMR CNRS 6230, Université de Nantes, 44000, Nantes, France
| | - Jérôme Graton
- CEISAM, UMR CNRS 6230, Université de Nantes, 44000, Nantes, France
| | - Gilles Montavon
- SUBATECH, UMR CNRS 6457 IMT Atlantique, 44307, Nantes, France
| | - Julien Pilmé
- Laboratoire de Chimie Théorique, UMR CNRS 7616, Sorbonne Université, 75005, Paris, France
| | - Nicolas Galland
- CEISAM, UMR CNRS 6230, Université de Nantes, 44000, Nantes, France
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Yang Q, Wu M, Zeng XC. Constructing Stable and Potentially High-Performance Hybrid Organic-Inorganic Perovskites with "Unstable" Cations. RESEARCH (WASHINGTON, D.C.) 2020; 2020:1986576. [PMID: 32566929 PMCID: PMC7288242 DOI: 10.34133/2020/1986576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 05/17/2020] [Indexed: 11/29/2022]
Abstract
A new family of functional hybrid organic-inorganic perovskites (HOIPs) is theoretically designed based on the following chemical insights: when a proton is adhered to molecules like water or ethanol, the newly formed larger-sized cations (e.g., H5O2 +, C2H5OH2 +, and CH3SH+) entail low electron affinities mimicking superalkalis; they are conjugated acids of weak bases that cannot survive in solution, while their chemistry behavior in the HOIP frameworks, however, may be markedly different due to greatly enhanced cohesive energies of the proton, which facilitate the formation of new HOIPs. First-principles computations show that the putative formation reactions for these newly designed HOIPs typically release much more energy compared with the prevailing HOIP MAPbI3, suggesting the likelihood of facile solution-based fabrications, while the suppression of reverse formation suggests that the humidity stability may be markedly enhanced. During their formations, halide acids are unlikely to react with ethanol or methanethiol without the presence of metal halides, a condition further favoring their stability. The proposed structure of (H5O2)PbI3 may also clarify the origin of the long-speculated existence of HPbI3. Importantly, density functional theory computations suggest that many of these HOIPs possess not only direct bandgaps with values within the optimal range for solar light absorbing but also more desirable optical absorption spectra than that of MAPbI3, where their ferroelectric polarizations also benefit photovoltaics. The stability and photovoltaic efficiency may be even further improved for the newly designed two-dimensional (2D) HOIPs and 2D/3D hybrid HOIP structures.
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Affiliation(s)
- Qing Yang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Menghao Wu
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
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Piña MDLN, Bauzá A, Frontera A. Halogen⋯halogen interactions in decahalo-closo-carboranes: CSD analysis and theoretical study. Phys Chem Chem Phys 2020; 22:6122-6130. [DOI: 10.1039/d0cp00114g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We theoretically (PBE0-D3/def2TZVP) and experimentally (CSD analysis) demonstrate the importance of “like–like” halogen interactions for the stability of several decahalo-closo-carborane dimers.
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Affiliation(s)
- Maria de las Nieves Piña
- Department of Chemistry Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
| | - Antonio Bauzá
- Department of Chemistry Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
| | - Antonio Frontera
- Department of Chemistry Universitat de les Illes Balears
- Crta. de Valldemossa km 7.5
- 07122 Palma (Baleares)
- Spain
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Li F, Zhang G, Xia S, Yu L. Host-guest interactions accompanying the cationic nitrogen heterocyclic guests encapsulation within pillar[5]arene: A theoretical research. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.07.109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Hua AM, Bidwell SL, Baker SI, Hratchian HP, Baxter RD. Experimental and Theoretical Evidence for Nitrogen–Fluorine Halogen Bonding in Silver-Initiated Radical Fluorinations. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00623] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alyssa M. Hua
- Department of Chemistry and Chemical Biology, University of California, 5200 N. Lake Road, Merced, California 95343, United States
| | - Samantha L. Bidwell
- Department of Chemistry and Chemical Biology, University of California, 5200 N. Lake Road, Merced, California 95343, United States
| | - Sarah I. Baker
- Department of Chemistry and Chemical Biology, University of California, 5200 N. Lake Road, Merced, California 95343, United States
| | - Hrant P. Hratchian
- Department of Chemistry and Chemical Biology, University of California, 5200 N. Lake Road, Merced, California 95343, United States
| | - Ryan D. Baxter
- Department of Chemistry and Chemical Biology, University of California, 5200 N. Lake Road, Merced, California 95343, United States
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