1
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Irshad H, Azhar MA, Qvortrup K. Thiazole modified covalent triazine framework as carcinogenic metabolites adsorbent: A DFT insight. J Mol Graph Model 2025; 137:109009. [PMID: 40081004 DOI: 10.1016/j.jmgm.2025.109009] [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: 12/21/2024] [Revised: 03/05/2025] [Accepted: 03/08/2025] [Indexed: 03/15/2025]
Abstract
The potential of a novel thiazole-modified covalent triazine framework (S-CTF) as surface for the adsorption and sensing of the carcinogenic metabolites acrylamide (AM), 2-amino-3,8-dimethylimidazo-[4,5-f]quinoxaline (MEIQX), 2-amino-1-methyl-6-phenylimidazole[4,5-f]pyridine (PhlP) and 3-amino-1,4-dimethyl-5H-pyrido[4,3-b]indole (Trp-P-1) is explored. The selectivity, sensitivity, and adsorption properties of the S-CTF surface are investigated through noncovalent interaction (NCI), quantum theory of atoms in molecules (QTAIM) and symmetry adapted perturbation theory (SAPT0) analyses. All the analytes were found to be physiosorbed on the surface of the sensor with the following strength of interaction: MEIQX@S-CTF = PhlP@S-CTF > Trp-P-1@S-CTF > AM@S-CTF. Evaluation of the electronic properties was done by natural bond orbital (NBO), electron density difference (EDD), frontier molecular orbital (FMO) and density of states (DOS) analyses. Through SAPT0 analysis, MEIQX@S-CTF has shown to have the highest ESAPT0 energy data (-24.58 kcal/mol) whereas FMO analysis reveals that the S-CTF surface shows the highest sensing power for Trp-P-1 among all analytes.
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Affiliation(s)
- Hasher Irshad
- Department of Chemistry, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | | | - Katrine Qvortrup
- Department of Chemistry, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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2
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Mehmood A, Janesko BG. An orbital-overlap complement to σ-hole electrostatic potentials. Phys Chem Chem Phys 2025; 27:861-867. [PMID: 39661027 DOI: 10.1039/d4cp03851g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2024]
Abstract
A σ-hole is an electron-deficient region of positive electrostatic potential (ESP) opposite from a half-filled p orbital involved in forming a covalent bond. The σ-hole concept helps rationalize directional noncovalent interactions, known as σ-hole bonds, between covalently bonded group V-VII atoms and electron-pair donors. The magnitude and orientation of σ-holes are correlated with the strength and geometry of halogen bonds. However, ESP computed for isolated σ-holes are not always predictive of interaction energies. For example, the σ-holes of isolated CHFBr2 and isolated CH2FI have identical ESP on the molecule surface, but halogen bonds to these molecules generally have different strengths. Here we show that the compact/diffuse nature of the orbitals involved plays an important role. Our orbital overlap distance quantifies the compact/diffuse nature of the "test orbital" that best overlaps with a systems orbitals at each point. The overlap distance captures the response properties of σ-holes: diffuse σ-holes with large overlap distance are typically "softer" and more polarizable. This aids visualization and interpretation. A linear fit to overlap distance and ESP is predictive of the halogen bond strengths of CH3X and CF3X (X = Cl, Br and I). We suggest that the overlap distance will be a useful partner to ESP for characterizing σ-holes.
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Affiliation(s)
- Arshad Mehmood
- Division of Information Technology - Research Computing, Informatics & Innovation and Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, USA.
| | - Benjamin G Janesko
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, USA
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3
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Ibrahim MAA, Abd Elhafez HSM, Shehata MNI, Moussa NAM, Sayed SRM, Soliman MES, Ahmed MN, El-Rahman MK, Shoeib T. Unconventional Radical and Radical-Hole Site-Based Interactions in Halogen-Bearing Dimers and Trimers: A Comparative Study. ACS OMEGA 2024; 9:38743-38752. [PMID: 39310195 PMCID: PMC11411553 DOI: 10.1021/acsomega.4c04620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/21/2024] [Accepted: 07/31/2024] [Indexed: 09/25/2024]
Abstract
Radical (R•) and R•-hole site-based interactions are comparatively studied, for the first time, using ab initio methods. In this regard, R•-bearing molecules •XO3 (where X = Cl, Br, and I) were subjected to direct interaction with NH3 within dimeric and trimeric forms in the form of NH3···•XO3/•XO3···NH3 and NH3···•XO3···NH3 complexes, respectively. As confirmed by electrostatic potential analysis, the studied R•-bearing molecules •XO3 had the outstanding potentiality to interact as Lewis acid centers via two positive sites dubbed as R• and R•-hole sites. Such an observation proposed the potentiality of the considered •XO3 molecules to engage in unconventional R• and well-established R•-hole site-based interactions with Lewis bases. This was confirmed by negative interaction (E int) energies, ranging from -4.93 to -19.89 kcal/mol, with higher favorability for R• site-based interactions over the R•-hole site-based ones. MP2 energetic features furnished higher preferability for the R• site-based interactions than the R•-hole site-based ones in the case of chlorine- and bromine-bearing complexes, and the reverse was true for the iodine-bearing complexes. Moreover, elevated E int values were recorded for the NH3···•XO3···NH3 trimers over the NH3···•XO3 and •XO3···NH3 dimers, outlining the higher preference of the •XO3 molecules to engage in R• and R•-hole site-based interactions in the trimeric form over the dimeric one. These results might be considered a requisite linchpin for numerous forthcoming supramolecular chemistry and crystal engineering studies.
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Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
- School
of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Heba S. M. Abd Elhafez
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Mohammed N. I. Shehata
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Nayra A. M. Moussa
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
- Basic
and Clinical Medical Science Department, Faculty of Dentistry, Deraya University, New Minya 61768, Egypt
| | - Shaban R. M. Sayed
- Department
of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mahmoud E. S. Soliman
- Molecular
Bio-Computation and Drug Design Research Laboratory, School of Health
Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Muhammad Naeem Ahmed
- Department
of Chemistry, The University of Azad Jammu
and Kashmir, Muzaffarabad 13100, Pakistan
| | - Mohamed Khaled
Abd El-Rahman
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Tamer Shoeib
- Department
of Chemistry, The American University in
Cairo, New Cairo 11835, Egypt
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4
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Fu K, Huang J, Luo F, Fang Z, Yu D, Zhang X, Wang D, Xing M, Luo J. Understanding the Selective Removal of Perfluoroalkyl and Polyfluoroalkyl Substances via Fluorine-Fluorine Interactions: A Critical Review. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 39264176 DOI: 10.1021/acs.est.4c06519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
As regulatory standards for per- and polyfluoroalkyl substances (PFAS) become increasingly stringent, innovative water treatment technologies are urgently demanded for effective PFAS removal. Reported sorbents often exhibit limited affinity for PFAS and are frequently hindered by competitive background substances. Recently, fluorinated sorbents (abbreviated as fluorosorbents) have emerged as a potent solution by leveraging fluorine-fluorine (F···F) interactions to enhance selectivity and efficiency in PFAS removal. This review delves into the designs and applications of fluorosorbents, emphasizing how F···F interactions improve PFAS binding affinity. Specifically, the existence of F···F interactions results in removal efficiencies orders of magnitude higher than other counterpart sorbents, particularly under competitive conditions. Furthermore, we provide a detailed analysis of the fundamental principles underlying F···F interactions and elucidate their synergistic effects with other sorption forces, which contribute to the enhanced efficacy and selectivity. Subsequently, we examine various fluorosorbents and their synthesis and fluorination techniques, underscore the importance of accurately characterizing F···F interactions through advanced analytical methods, and emphasize the significance of this interaction in developing selective sorbents. Finally, we discuss challenges and opportunities associated with employing advanced techniques to guide the design of selective sorbents and advocate for further research in the development of sustainable and cost-effective treatment technologies leveraging F···F interactions.
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Affiliation(s)
- Kaixing Fu
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Jinjing Huang
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Fang Luo
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Zhuoya Fang
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Deyou Yu
- Engineering Research Center for Eco-Dyeing and Finishing of Textiles (Ministry of Education), Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China
| | - Xiaolin Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, P. R. China
| | - Dawei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, P. R. China
| | - Mingyang Xing
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Jinming Luo
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
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5
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Varadwaj PR. Halogen Bond via an Electrophilic π-Hole on Halogen in Molecules: Does It Exist? Int J Mol Sci 2024; 25:4587. [PMID: 38731806 PMCID: PMC11083155 DOI: 10.3390/ijms25094587] [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: 02/29/2024] [Revised: 03/31/2024] [Accepted: 04/07/2024] [Indexed: 05/13/2024] Open
Abstract
This study reveals a new non-covalent interaction called a π-hole halogen bond, which is directional and potentially non-linear compared to its sister analog (σ-hole halogen bond). A π-hole is shown here to be observed on the surface of halogen in halogenated molecules, which can be tempered to display the aptness to form a π-hole halogen bond with a series of electron density-rich sites (Lewis bases) hosted individually by 32 other partner molecules. The [MP2/aug-cc-pVTZ] level characteristics of the π-hole halogen bonds in 33 binary complexes obtained from the charge density approaches (quantum theory of intramolecular atoms, molecular electrostatic surface potential, independent gradient model (IGM-δginter)), intermolecular geometries and energies, and second-order hyperconjugative charge transfer analyses are discussed, which are similar to other non-covalent interactions. That a π-hole can be observed on halogen in halogenated molecules is substantiated by experimentally reported crystals documented in the Cambridge Crystal Structure Database. The importance of the π-hole halogen bond in the design and growth of chemical systems in synthetic chemistry, crystallography, and crystal engineering is yet to be fully explicated.
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Affiliation(s)
- Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan;
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
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6
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Asif M, Kosar N, Sajid H, Qureshi S, Gilani MA, Ayub K, Arshad M, Imran M, Hamid MHS, Bayach I, Sheikh NS, Mahmood T. Exploring the Sensing Potential of g-C 3N 4 versus Li/g-C 3N 4 Nanoflakes toward Hazardous Organic Volatiles: A DFT Simulation Study. ACS OMEGA 2024; 9:3541-3553. [PMID: 38284053 PMCID: PMC10810007 DOI: 10.1021/acsomega.3c07350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/19/2023] [Accepted: 12/27/2023] [Indexed: 01/30/2024]
Abstract
Ab initio calculations were performed to determine the sensing behavior of g-C3N4 and Li metal-doped g-C3N4 (Li/g-C3N4) quantum dots toward toxic compounds acetamide (AA), benzamide (BA), and their thio-analogues, namely, thioacetamide (TAA) and thiobenzamide (TAA). For optimization and interaction energies, the ωB97XD/6-31G(d,p) level of theory was used. Interaction energies (Eint) illustrate the high thermodynamic stabilities of the designed complexes due to the presence of the noncovalent interactions. The presence of electrostatic forces in some complexes is also observed. The observed trend of Eint in g-C3N4 complexes was BA > TAA > AA > TBA, while in Li/g-C3N4, the trend was BA > AA > TBA > TAA. The electronic properties were studied by frontier molecular orbital (FMO) and natural bond orbital analyses. According to FMO, lithium metal doping greatly enhanced the conductivity of the complexes by generating new HOMOs near the Fermi level. A significant amount of charge transfer was also observed in complexes, reflecting the increase in charge conductivity. NCI and QTAIM analyses evidenced the presence of significant noncovalent dispersion and electrostatic forces in Li/g-C3N4 and respective complexes. Charge decomposition analysis gave an idea of the transfer of charge density between quantum dots and analytes. Finally, TD-DFT explained the optical behavior of the reported complexes. The findings of this study suggested that both bare g-C3N4 and Li/g-C3N4 can effectively be used as atmospheric sensors having excellent adsorbing properties toward toxic analytes.
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Affiliation(s)
- Misbah Asif
- Department
of Chemistry, COMSATS University Islamabad,
Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Naveen Kosar
- Department
of Chemistry, University of Management and
Technology (UMT), C-11, Johar Town, Lahore 54782, Pakistan
| | - Hasnain Sajid
- School
of Science and Technology, Nottingham Trent
University, Clifton Lane, Nottingham NG11 8NS, U.K.
| | - Sana Qureshi
- Department
of Chemistry, COMSATS University Islamabad,
Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Mazhar Amjad Gilani
- Department
of Chemistry, COMSATS University Islamabad,
Lahore Campus, Lahore 54000, Pakistan
| | - Khurshid Ayub
- Department
of Chemistry, COMSATS University Islamabad,
Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Muhammad Arshad
- Institute
of Chemistry, The Islamia University of
Bahawalpur, Baghdad-ul-Jadeed Campus, Bahawalpur 63100, Pakistan
| | - Muhammad Imran
- Department
of Chemistry, Faculty of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Malai Haniti S.
A. Hamid
- Chemical
Sciences, Faculty of Science, Universiti
Brunei Darussalam, Jalan Tungku
Link, Gadong BE1410, Brunei Darussalam
| | - Imene Bayach
- Department
of Chemistry, College of Science, King Faisal
University, Al-Ahsa 31982, Saudi Arabia
| | - Nadeem S. Sheikh
- Chemical
Sciences, Faculty of Science, Universiti
Brunei Darussalam, Jalan Tungku
Link, Gadong BE1410, Brunei Darussalam
| | - Tariq Mahmood
- Department
of Chemistry, COMSATS University Islamabad,
Abbottabad Campus, Abbottabad 22060, Pakistan
- Department
of Chemistry, College of Science, University
of Bahrain, P.O. Box 32038, Sakhir 1054, Bahrain
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7
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Guidez EB. Quasi-atomic orbital analysis of halogen bonding interactions. J Chem Phys 2023; 159:194307. [PMID: 37987522 DOI: 10.1063/5.0174171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
A quasi-atomic orbital analysis of the halogen bonded NH3⋯XF complexes (X = F, Cl, Br, and I) is performed to gain insight into the electronic properties associated with these σ-hole interactions. It is shown that significant sharing of electrons between the nitrogen lone pair of the ammonia molecule and the XF molecule occurs, resulting in a weakening of the X-F bond. In addition, the N-X bond shows increasing covalent character as the size of the halogen atom X increases. While the Mulliken outer complex NH3⋯XF appears to be overall the main species, the strength of the covalent interaction of the N-X bond becomes increasingly similar to that of the N-X bond in the [NH3X]+ cation as the size of X increases.
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Affiliation(s)
- Emilie B Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, USA
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8
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Montgomery CA, Murphy GK. Exploring the role of halogen bonding in iodonium ylides: insights into unexpected reactivity and reaction control. Beilstein J Org Chem 2023; 19:1171-1190. [PMID: 37592937 PMCID: PMC10428621 DOI: 10.3762/bjoc.19.86] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/18/2023] [Indexed: 08/19/2023] Open
Abstract
Halogen bonding is commonly found with iodine-containing molecules, and it arises when Lewis bases interact with iodine's σ-holes. Halogen bonding and σ-holes have been encountered in numerous monovalent and hypervalent iodine-containing compounds, and in 2022 σ-holes were computationally confirmed and quantified in the iodonium ylide subset of hypervalent iodine compounds. In light of this new discovery, this article provides an overview of the reactions of iodonium ylides in which halogen bonding has been invoked. Herein, we summarize key discoveries and mechanistic proposals from the early iodonium ylide literature that invoked halogen bonding-type mechanisms, as well as recent reports of reactions between iodonium ylides and Lewis basic nucleophiles in which halogen bonding has been specifically invoked. The reactions discussed herein are organized to enable the reader to build an understanding of how halogen bonding might impact yield and chemoselectivity outcomes in reactions of iodonium ylides. Areas of focus include nucleophile σ-hole selectivity, and how ylide structural modifications and intramolecular halogen bonding (e.g., the ortho-effect) can improve ylide stability or solubility, and alter reaction outcomes.
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Affiliation(s)
- Carlee A Montgomery
- Department of Chemistry, University of Waterloo, 200 University Ave W., Waterloo, Ontario, N2L3G1, Canada
| | - Graham K Murphy
- Department of Chemistry, University of Waterloo, 200 University Ave W., Waterloo, Ontario, N2L3G1, Canada
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9
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Varadwaj PR, Varadwaj A, Marques HM, Yamashita K. Methylammonium Tetrel Halide Perovskite Ion Pairs and Their Dimers: The Interplay between the Hydrogen-, Pnictogen- and Tetrel-Bonding Interactions. Int J Mol Sci 2023; 24:10554. [PMID: 37445738 DOI: 10.3390/ijms241310554] [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: 05/07/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
The structural stability of the extensively studied organic-inorganic hybrid methylammonium tetrel halide perovskite semiconductors, MATtX3 (MA = CH3NH3+; Tt = Ge, Sn, Pb; X = Cl, Br, I), arises as a result of non-covalent interactions between an organic cation (CH3NH3+) and an inorganic anion (TtX3-). However, the basic understanding of the underlying chemical bonding interactions in these systems that link the ionic moieties together in complex configurations is still limited. In this study, ion pair models constituting the organic and inorganic ions were regarded as the repeating units of periodic crystal systems and density functional theory simulations were performed to elucidate the nature of the non-covalent interactions between them. It is demonstrated that not only the charge-assisted N-H···X and C-H···X hydrogen bonds but also the C-N···X pnictogen bonds interact to stabilize the ion pairs and to define their geometries in the gas phase. Similar interactions are also responsible for the formation of crystalline MATtX3 in the low-temperature phase, some of which have been delineated in previous studies. In contrast, the Tt···X tetrel bonding interactions, which are hidden as coordinate bonds in the crystals, play a vital role in holding the inorganic anionic moieties (TtX3-) together. We have demonstrated that each Tt in each [CH3NH3+•TtX3-] ion pair has the capacity to donate three tetrel (σ-hole) bonds to the halides of three nearest neighbor TtX3- units, thus causing the emergence of an infinite array of 3D TtX64- octahedra in the crystalline phase. The TtX44- octahedra are corner-shared to form cage-like inorganic frameworks that host the organic cation, leading to the formation of functional tetrel halide perovskite materials that have outstanding optoelectronic properties in the solid state. We harnessed the results using the quantum theory of atoms in molecules, natural bond orbital, molecular electrostatic surface potential and independent gradient models to validate these conclusions.
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Affiliation(s)
- Pradeep R Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
- School of Chemistry, Molecular Sciences Institute, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
| | - Helder M Marques
- School of Chemistry, Molecular Sciences Institute, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
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10
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Varadwaj PR, Varadwaj A, Marques HM, Yamashita K. The Tetrel Bond and Tetrel Halide Perovskite Semiconductors. Int J Mol Sci 2023; 24:6659. [PMID: 37047632 PMCID: PMC10094773 DOI: 10.3390/ijms24076659] [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: 02/26/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 04/05/2023] Open
Abstract
The ion pairs [Cs+•TtX3-] (Tt = Pb, Sn, Ge; X = I, Br, Cl) are the building blocks of all-inorganic cesium tetrel halide perovskites in 3D, CsTtX3, that are widely regarded as blockbuster materials for optoelectronic applications such as in solar cells. The 3D structures consist of an anionic inorganic tetrel halide framework stabilized by the cesium cations (Cs+). We use computational methods to show that the geometrical connectivity between the inorganic monoanions, [TtX3-]∞, that leads to the formation of the TtX64- octahedra and the 3D inorganic perovskite architecture is the result of the joint effect of polarization and coulombic forces driven by alkali and tetrel bonds. Depending on the nature and temperature phase of these perovskite systems, the Tt···X tetrel bonds are either indistinguishable or somehow distinguishable from Tt-X coordinate bonds. The calculation of the potential on the electrostatic surface of the Tt atom in molecular [Cs+•TtX3-] provides physical insight into why the negative anions [TtX3-] attract each other when in close proximity, leading to the formation of the CsTtX3 tetrel halide perovskites in the solid state. The inter-molecular (and inter-ionic) geometries, binding energies, and charge density-based topological properties of sixteen [Cs+•TtX3-] ion pairs, as well as some selected oligomers [Cs+•PbI3-]n (n = 2, 3, 4), are discussed.
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Affiliation(s)
- Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
| | - Helder M. Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
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11
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Saccone M, Cametti M, Metrangolo P, Pilati T, Resnati G, Terraneo G. Systematic Study of Podand Molecules for Synergistic Halogen and Hydrogen Bond-Driven Anion Recognition in the Solid State. Chem Asian J 2023; 18:e202201255. [PMID: 36715246 DOI: 10.1002/asia.202201255] [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: 12/16/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023]
Abstract
The increasing demand of species for the efficient capture and sensing of anions benefits from a systematic study of anion binding capabilities in the solid state. This work reports a detailed crystallographic study of ten structurally related podands and shows that these charged receptors bind anions with a combination of charge-assisted halogen and hydrogen bonds. Computational tools helped in highlighting the role of the different involved interaction and afforded possible design principles for the design of improved podands.
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Affiliation(s)
- Marco Saccone
- Dipartimento di Ingegneria, Università Degli Studi di Palermo, Viale Delle Scienze, Edificio 6, Palermo, 90128, Italy
| | - Massimo Cametti
- Dipartimento di Chimica Materiali e Ingegneria Chimica "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131, Milano, Italy
| | - Pierangelo Metrangolo
- Dipartimento di Chimica Materiali e Ingegneria Chimica "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131, Milano, Italy
| | - Tullio Pilati
- Dipartimento di Chimica Materiali e Ingegneria Chimica "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131, Milano, Italy
| | - Giuseppe Resnati
- Dipartimento di Chimica Materiali e Ingegneria Chimica "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131, Milano, Italy
| | - Giancarlo Terraneo
- Dipartimento di Chimica Materiali e Ingegneria Chimica "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131, Milano, Italy
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12
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Venkataramanan NS, Suvitha A, Sahara R, Kawazoe Y. Unveiling the gemcitabine drug complexation with cucurbit[n]urils (n = 6–8): a computational analysis. Struct Chem 2023. [DOI: 10.1007/s11224-023-02133-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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13
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Al-Faiyz YSS, Sarfaraz S, Yar M, Munsif S, Khan AA, Amin B, Sheikh NS, Ayub K. Efficient Detection of Nerve Agents through Carbon Nitride Quantum Dots: A DFT Approach. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:251. [PMID: 36678006 PMCID: PMC9864457 DOI: 10.3390/nano13020251] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 12/29/2022] [Accepted: 01/01/2023] [Indexed: 06/17/2023]
Abstract
V-series nerve agents are very lethal to health and cause the inactivation of acetylcholinesterase which leads to neuromuscular paralysis and, finally, death. Therefore, rapid detection and elimination of V-series nerve agents are very important. Herein, we have carried out a theoretical investigation of carbon nitride quantum dots (C2N) as an electrochemical sensor for the detection of V-series nerve agents, including VX, VS, VE, VG, and VM. Adsorption of V-series nerve agents on C2N quantum dots is explored at M05-2X/6-31++G(d,p) level of theory. The level of theory chosen is quite adequate in systems describing non-bonding interactions. The adsorption behavior of nerve agents is characterized by interaction energy, non-covalent interaction (NCI), Bader's quantum theory of atoms in molecules (QTAIM), frontier molecular orbital (FMO), electron density difference (EDD), and charge transfer analysis. The computed adsorption energies of the studied complexes are in the range of -12.93 to -17.81 kcal/mol, which indicates the nerve agents are physiosorbed onto C2N surface through non-covalent interactions. The non-covalent interactions between V-series and C2N are confirmed through NCI and QTAIM analysis. EDD analysis is carried out to understand electron density shifting, which is further validated by natural bond orbital (NBO) analysis. FMO analysis is used to estimate the changes in energy gap of C2N on complexation through HOMO-LUMO energies. These findings suggest that C2N surface is highly selective toward VX, and it might be a promising candidate for the detection of V-series nerve agents.
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Affiliation(s)
- Yasair S. S. Al-Faiyz
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Sehrish Sarfaraz
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Muhammad Yar
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Sajida Munsif
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Adnan Ali Khan
- Centre for Computational Materials Science, University of Malakand, Chakdara 18800, Pakistan
- Department of Chemistry, University of Malakand, Chakdara 18800, Pakistan
| | - Bin Amin
- Department of Physics, Abbottabad University of Science & Technology, Abbottabad 22010, Pakistan
| | - Nadeem S. Sheikh
- Chemical Sciences, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong BE1410, Brunei
| | - Khurshid Ayub
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
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14
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Habib A, Metwally MM, Fahmy T, Sarhan A. Enhancement of optical and piezoelectric properties of P(Vinylidene fluoride-hexafluoropropylene)/N,N-Dimethyl-4-nitro-4-Stilbenamine composites for optoelectronic applications. POLYM-PLAST TECH MAT 2022. [DOI: 10.1080/25740881.2022.2086817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Affiliation(s)
- A. Habib
- Polymer Research Group, Physics Department, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - M. M. Metwally
- Chemistry Department, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - T. Fahmy
- Polymer Research Group, Physics Department, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - A. Sarhan
- Polymer Research Group, Physics Department, Faculty of Science, Mansoura University, Mansoura, Egypt
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15
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Varadwaj PR. Tetrel Bonding in Anion Recognition: A First Principles Investigation. Molecules 2022; 27:molecules27238449. [PMID: 36500544 PMCID: PMC9738195 DOI: 10.3390/molecules27238449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Twenty-five molecule-anion complex systems [I4Tt···X-] (Tt = C, Si, Ge, Sn and Pb; X = F, Cl, Br, I and At) were examined using density functional theory (ωB97X-D) and ab initio (MP2 and CCSD) methods to demonstrate the ability of the tetrel atoms in molecular entities, I4Tt, to recognize the halide anions when in close proximity. The tetrel bond strength for the [I4C···X-] series and [I4Tt···X-] (Tt = Si, Sn; X = I, At), was weak-to-moderate, whereas that in the remaining 16 complexes was dative tetrel bond type with very large interaction energies and short Tt···X close contact distances. The basis set superposition error corrected interaction energies calculated with the highest-level theory applied, [CCSD(T)/def2-TZVPPD], ranged from -3.0 to -112.2 kcal mol-1. The significant variation in interaction energies was realized as a result of different levels of tetrel bonding environment between the interacting partners at the equilibrium geometries of the complex systems. Although the ωB97X-D computed intermolecular geometries and interaction energies of a majority of the [I4Tt···X-] complexes were close to those predicted by the highest level of theory, the MP2 results were shown to be misleading for some of these systems. To provide insight into the nature of the intermolecular chemical bonding environment in the 25 molecule-anion complexes investigated, we discussed the charge-density-based topological and isosurface features that emanated from the application of the quantum theory of atoms in molecules and independent gradient model approaches, respectively.
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Affiliation(s)
- Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Tokyo 113-8656, Japan; or
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
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16
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Aetizaz M, Sarfaraz S, Ayub K. Interaction of Imidazolium based ionic liquid electrolytes with carbon nitride electrodes in supercapacitors; A step forward for understanding electrode-electrolyte interaction. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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17
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Definition of the Pnictogen Bond: A Perspective. INORGANICS 2022. [DOI: 10.3390/inorganics10100149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This article proposes a definition for the term “pnictogen bond” and lists its donors, acceptors, and characteristic features. These may be invoked to identify this specific subset of the inter- and intramolecular interactions formed by elements of Group 15 which possess an electrophilic site in a molecular entity.
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18
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Varadwaj A, Varadwaj PR, Marques HM, Yamashita K. The Pnictogen Bond, Together with Other Non-Covalent Interactions, in the Rational Design of One-, Two- and Three-Dimensional Organic-Inorganic Hybrid Metal Halide Perovskite Semiconducting Materials, and Beyond. Int J Mol Sci 2022; 23:8816. [PMID: 35955945 PMCID: PMC9369011 DOI: 10.3390/ijms23158816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
The pnictogen bond, a somewhat overlooked supramolecular chemical synthon known since the middle of the last century, is one of the promising types of non-covalent interactions yet to be fully understood by recognizing and exploiting its properties for the rational design of novel functional materials. Its bonding modes, energy profiles, vibrational structures and charge density topologies, among others, have yet to be comprehensively delineated, both theoretically and experimentally. In this overview, attention is largely centered on the nature of nitrogen-centered pnictogen bonds found in organic-inorganic hybrid metal halide perovskites and closely related structures deposited in the Cambridge Structural Database (CSD) and the Inorganic Chemistry Structural Database (ICSD). Focusing on well-characterized structures, it is shown that it is not merely charge-assisted hydrogen bonds that stabilize the inorganic frameworks, as widely assumed and well-documented, but simultaneously nitrogen-centered pnictogen bonding, and, depending on the atomic constituents of the organic cation, other non-covalent interactions such as halogen bonding and/or tetrel bonding, are also contributors to the stabilizing of a variety of materials in the solid state. We have shown that competition between pnictogen bonding and other interactions plays an important role in determining the tilting of the MX6 (X = a halogen) octahedra of metal halide perovskites in one, two and three-dimensions. The pnictogen interactions are identified to be directional even in zero-dimensional crystals, a structural feature in many engineered ordered materials; hence an interplay between them and other non-covalent interactions drives the structure and the functional properties of perovskite materials and enabling their application in, for example, photovoltaics and optoelectronics. We have demonstrated that nitrogen in ammonium and its derivatives in many chemical systems acts as a pnictogen bond donor and contributes to conferring stability, and hence functionality, to crystalline perovskite systems. The significance of these non-covalent interactions should not be overlooked, especially when the focus is centered on the rationale design and discovery of such highly-valued materials.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
| | - Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Helder M. Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
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19
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Peluso P, Chankvetadze B. Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers. Chem Rev 2022; 122:13235-13400. [PMID: 35917234 DOI: 10.1021/acs.chemrev.1c00846] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, I-07100 Sassari, Italy
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Avenue 3, 0179 Tbilisi, Georgia
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20
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Varadwaj A, Varadwaj PR, Marques HM, Yamashita K. The Pnictogen Bond: The Covalently Bound Arsenic Atom in Molecular Entities in Crystals as a Pnictogen Bond Donor. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113421. [PMID: 35684359 PMCID: PMC9181914 DOI: 10.3390/molecules27113421] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/08/2022] [Accepted: 05/17/2022] [Indexed: 12/04/2022]
Abstract
In chemical systems, the arsenic-centered pnictogen bond, or simply the arsenic bond, occurs when there is evidence of a net attractive interaction between the electrophilic region associated with a covalently or coordinately bound arsenic atom in a molecular entity and a nucleophile in another or the same molecular entity. It is the third member of the family of pnictogen bonds formed by the third atom of the pnictogen family, Group 15 of the periodic table, and is an inter- or intramolecular noncovalent interaction. In this overview, we present several illustrative crystal structures deposited into the Cambridge Structure Database (CSD) and the Inorganic Chemistry Structural Database (ICSD) during the last and current centuries to demonstrate that the arsenic atom in molecular entities has a significant ability to act as an electrophilic agent to make an attractive engagement with nucleophiles when in close vicinity, thereby forming σ-hole or π-hole interactions, and hence driving (in part, at least) the overall stability of the system’s crystalline phase. This overview does not include results from theoretical simulations reported by others as none of them address the signatory details of As-centered pnictogen bonds. Rather, we aimed at highlighting the interaction modes of arsenic-centered σ- and π-holes in the rationale design of crystal lattices to demonstrate that such interactions are abundant in crystalline materials, but care has to be taken to identify them as is usually done with the much more widely known noncovalent interactions in chemical systems, halogen bonding and hydrogen bonding. We also demonstrate that As-centered pnictogen bonds are usually accompanied by other primary and secondary interactions, which reinforce their occurrence and strength in most of the crystal structures illustrated. A statistical analysis of structures deposited into the CSD was performed for each interaction type As···D (D = N, O, S, Se, Te, F, Cl, Br, I, arene’s π system), thus providing insight into the typical nature of As···D interaction distances and ∠R–As···D bond angles of these interactions in crystals, where R is the remainder of the molecular entity.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Tokyo 113-8656, Japan;
- Correspondence: (A.V.); (P.R.V.)
| | - Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Tokyo 113-8656, Japan;
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
- Correspondence: (A.V.); (P.R.V.)
| | - Helder M. Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Tokyo 113-8656, Japan;
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21
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Varadwaj A, Varadwaj PR, Marques HM, Yamashita K. The Stibium Bond or the Antimony-Centered Pnictogen Bond: The Covalently Bound Antimony Atom in Molecular Entities in Crystal Lattices as a Pnictogen Bond Donor. Int J Mol Sci 2022; 23:4674. [PMID: 35563065 PMCID: PMC9099767 DOI: 10.3390/ijms23094674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 12/04/2022] Open
Abstract
A stibium bond, i.e., a non-covalent interaction formed by covalently or coordinately bound antimony, occurs in chemical systems when there is evidence of a net attractive interaction between the electrophilic region associated with an antimony atom and a nucleophile in another, or the same molecular entity. This is a pnictogen bond and are likely formed by the elements of the pnictogen family, Group 15, of the periodic table, and is an inter- or intra-molecular non-covalent interaction. This overview describes a set of illustrative crystal systems that were stabilized (at least partially) by means of stibium bonds, together with other non-covalent interactions (such as hydrogen bonds and halogen bonds), retrieved from either the Cambridge Structure Database (CSD) or the Inorganic Crystal Structure Database (ICSD). We demonstrate that these databases contain hundreds of crystal structures of various dimensions in which covalently or coordinately bound antimony atoms in molecular entities feature positive sites that productively interact with various Lewis bases containing O, N, F, Cl, Br, and I atoms in the same or different molecular entities, leading to the formation of stibium bonds, and hence, being partially responsible for the stability of the crystals. The geometric features, pro-molecular charge density isosurface topologies, and extrema of the molecular electrostatic potential model were collectively examined in some instances to illustrate the presence of Sb-centered pnictogen bonding in the representative crystal systems considered.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
| | - Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
| | - Helder M. Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
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22
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Ibrahim MAA, Moussa NAM, Saad SMA, Ahmed MN, Shawky AM, Soliman MES, Mekhemer GAH, Rady ASSM. σ-Hole and LP-Hole Interactions of Pnicogen···Pnicogen Homodimers under the External Electric Field Effect: A Quantum Mechanical Study. ACS OMEGA 2022; 7:11264-11275. [PMID: 35415328 PMCID: PMC8992284 DOI: 10.1021/acsomega.2c00176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
σ-Hole and lone-pair (lp)-hole interactions within σ-hole···σ-hole, σ-hole···lp-hole, and lp-hole···lp-hole configurations were comparatively investigated on the pnicogen···pnicogen homodimers (PCl3)2, for the first time, under field-free conditions and the influence of the external electric field (EEF). The electrostatic potential calculations emphasized the impressive versatility of the examined PCl3 monomers to participate in σ-hole and lp-hole pnicogen interactions. Crucially, the sizes of σ-hole and lp-hole were enlarged under the influence of the positively directed EEF and decreased in the case of reverse direction. Interestingly, the energetic quantities unveiled more favorability of the σ-hole···lp-hole configuration of the pnicogen···pnicogen homodimers, with significant negative interaction energies, than σ-hole···σ-hole and lp-hole···lp-hole configurations. Quantum theory of atoms in molecules and noncovalent interaction index analyses were adopted to elucidate the nature and origin of the considered interactions, ensuring their closed shell nature and the occurrence of attractive forces within the studied homodimers. Symmetry-adapted perturbation theory-based energy decomposition analysis alluded to the dispersion force as the main physical component beyond the occurrence of the examined interactions. The obtained findings would be considered as a fundamental underpinning for forthcoming studies pertinent to chemistry, materials science, and crystal engineering.
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Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Nayra A. M. Moussa
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Sherif M. A. Saad
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Muhammad Naeem Ahmed
- Department
of Chemistry, The University of Azad Jammu
and Kashmir, Muzaffarabad 13100, Pakistan
| | - Ahmed M. Shawky
- Science
and Technology Unit (STU), Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mahmoud E. S. Soliman
- Molecular
Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Gamal A. H. Mekhemer
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Al-shimaa S. M. Rady
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
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23
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Ibrahim MAA, Saeed RRA, Shehata MNI, Ahmed MN, Shawky AM, Khowdiary MM, Elkaeed EB, Soliman MES, Moussa NAM. Type I-IV Halogen⋯Halogen Interactions: A Comparative Theoretical Study in Halobenzene⋯Halobenzene Homodimers. Int J Mol Sci 2022; 23:3114. [PMID: 35328534 PMCID: PMC8953242 DOI: 10.3390/ijms23063114] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 01/25/2023] Open
Abstract
In the current study, unexplored type IV halogen⋯halogen interaction was thoroughly elucidated, for the first time, and compared to the well-established types I−III interactions by means of the second-order Møller−Plesset (MP2) method. For this aim, the halobenzene⋯halobenzene homodimers (where halogen = Cl, Br, and I) were designed into four different types, parodying the considered interactions. From the energetic perspective, the preference of scouted homodimers was ascribed to type II interactions (i.e., highest binding energy), whereas the lowest binding energies were discerned in type III interactions. Generally, binding energies of the studied interactions were observed to decline with the decrease in the σ-hole size in the order, C6H5I⋯IC6H5 > C6H5Br⋯BrC6H5 > C6H5Cl⋯ClC6H5 homodimers and the reverse was noticed in the case of type IV interactions. Such peculiar observations were relevant to the ample contributions of negative-belt⋯negative-belt interactions within the C6H5Cl⋯ClC6H5 homodimer. Further, type IV torsional trans → cis interconversion of C6H5X⋯XC6H5 homodimers was investigated to quantify the π⋯π contributions into the total binding energies. Evidently, the energetic features illustrated the amelioration of the considered homodimers (i.e., more negative binding energy) along the prolonged scope of torsional trans → cis interconversion. In turn, these findings outlined the efficiency of the cis configuration over the trans analog. Generally, symmetry-adapted perturbation theory-based energy decomposition analysis (SAPT-EDA) demonstrated the predominance of all the scouted homodimers by the dispersion forces. The obtained results would be beneficial for the omnipresent studies relevant to the applications of halogen bonds in the fields of materials science and crystal engineering.
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Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt; (R.R.A.S.); (M.N.I.S.); (N.A.M.M.)
| | - Rehab R. A. Saeed
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt; (R.R.A.S.); (M.N.I.S.); (N.A.M.M.)
| | - Mohammed N. I. Shehata
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt; (R.R.A.S.); (M.N.I.S.); (N.A.M.M.)
| | - Muhammad Naeem Ahmed
- Department of Chemistry, The University of Azad Jammu and Kashmir, Muzaffarabad 13100, Pakistan;
| | - Ahmed M. Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Manal M. Khowdiary
- Chemistry Department, Faculty of Applied Science, Umm Al-Qura University, Al-Lith Branch, Makkah 24211, Saudi Arabia;
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh 13713, Saudi Arabia;
| | - Mahmoud E. S. Soliman
- Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Nayra A. M. Moussa
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt; (R.R.A.S.); (M.N.I.S.); (N.A.M.M.)
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24
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Varadwaj PR, Varadwaj A, Marques HM, Yamashita K. The Phosphorus Bond, or the Phosphorus-Centered Pnictogen Bond: The Covalently Bound Phosphorus Atom in Molecular Entities and Crystals as a Pnictogen Bond Donor. Molecules 2022; 27:molecules27051487. [PMID: 35268588 PMCID: PMC8911988 DOI: 10.3390/molecules27051487] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/16/2022] [Accepted: 02/16/2022] [Indexed: 02/07/2023] Open
Abstract
The phosphorus bond in chemical systems, which is an inter- or intramolecular noncovalent interaction, occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a covalently or coordinately bonded phosphorus atom in a molecular entity and a nucleophile in another, or the same, molecular entity. It is the second member of the family of pnictogen bonds, formed by the second member of the pnictogen family of the periodic table. In this overview, we provide the reader with a snapshot of the nature, and possible occurrences, of phosphorus-centered pnictogen bonding in illustrative chemical crystal systems drawn from the ICSD (Inorganic Crystal Structure Database) and CSD (Cambridge Structural Database) databases, some of which date back to the latter part of the last century. The illustrative systems discussed are expected to assist as a guide to researchers in rationalizing phosphorus-centered pnictogen bonding in the rational design of molecular complexes, crystals, and materials and their subsequent characterization.
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Affiliation(s)
- Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, University of Tokyo 7-3-1, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
- Correspondence:
| | - Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, University of Tokyo 7-3-1, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
| | - Helder M. Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, University of Tokyo 7-3-1, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
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Chalcogen Bonding in the Molecular Dimers of WCh 2 (Ch = S, Se, Te): On the Basic Understanding of the Local Interfacial and Interlayer Bonding Environment in 2D Layered Tungsten Dichalcogenides. Int J Mol Sci 2022; 23:ijms23031263. [PMID: 35163185 PMCID: PMC8835845 DOI: 10.3390/ijms23031263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 01/28/2023] Open
Abstract
Layered two-dimensional transition metal dichalcogenides and their heterostructures are of current interest, owing to the diversity of their applications in many areas of materials nanoscience and technologies. With this in mind, we have examined the three molecular dimers of the tungsten dichalcogenide series, (WCh2)2 (Ch = S, Se, Te), using density functional theory to provide insight into which interactions, and their specific characteristics, are responsible for the interfacial/interlayer region in the room temperature 2H phase of WCh2 crystals. Our calculations at various levels of theory suggested that the Te···Te chalcogen bonding in (WTe2)2 is weak, whereas the Se···Se and S···S bonding interactions in (WSe2)2 and (WS2)2, respectively, are of the van der Waals type. The presence and character of Ch···Ch chalcogen bonding interactions in the dimers of (WCh2)2 are examined with a number of theoretical approaches and discussed, including charge-density-based approaches, such as the quantum theory of atoms in molecules, interaction region indicator, independent gradient model, and reduced density gradient non-covalent index approaches. The charge-density-based topological features are shown to be concordant with the results that originate from the extrema of potential on the electrostatic surfaces of WCh2 monomers. A natural bond orbital analysis has enabled us to suggest a number of weak hyperconjugative charge transfer interactions between the interacting monomers that are responsible for the geometry of the (WCh2)2 dimers at equilibrium. In addition to other features, we demonstrate that there is no so-called van der Waals gap between the monolayers in two-dimensional layered transition metal tungsten dichalcogenides, which are gapless, and that the (WCh2)2 dimers may be prototypes for a basic understanding of the physical chemistry of the chemical bonding environments associated with the local interfacial/interlayer regions in layered 2H-WCh2 nanoscale systems.
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Chalcogen···Chalcogen Bonding in Molybdenum Disulfide, Molybdenum Diselenide and Molybdenum Ditelluride Dimers as Prototypes for a Basic Understanding of the Local Interfacial Chemical Bonding Environment in 2D Layered Transition Metal Dichalcogenides. INORGANICS 2022. [DOI: 10.3390/inorganics10010011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
An attempt was made, using computational methods, to understand whether the intermolecular interactions in the dimers of molybdenum dichalcogenides MoCh2 (Ch = chalcogen, element of group 16, especially S, Se and Te) and similar mixed-chalcogenide derivatives resemble the room temperature experimentally observed interactions in the interfacial regions of molybdenites and their other mixed-chalcogen derivatives. To this end, MP2(Full)/def2-TVZPPD level electronic structure calculations on nine dimer systems, including (MoCh2)2 and (MoChCh′2)2 (Ch, Ch′ = S, Se and Te), were carried out not only to demonstrate the energetic stability of these systems in the gas phase, but also to reproduce the intermolecular geometrical properties that resemble the interfacial geometries of 2D layered MoCh2 systems reported in the crystalline phase. Among the six DFT functionals (single and double hybrids) benchmarked against MP2(full), it was found that the double hybrid functional B2PLYPD3 has some ability to reproduce the intermolecular geometries and binding energies. The intermolecular geometries and binding energies of all nine dimers are discussed, together with the charge density topological aspects of the chemical bonding interactions that emerge from the application of the quantum theory of atoms in molecules (QTAIM), the isosurface topology of the reduced density gradient noncovalent index, interaction region indicator and independent gradient model (IGM) approaches. While the electrostatic surface potential model fails to explain the origin of the S···S interaction in the (MoS2)2 dimer, we show that the intermolecular bonding interactions in all nine dimers examined are a result of hyperconjugative charge transfer delocalizations between the lone-pair on (Ch/Ch′) and/or the π-orbitals of a Mo–Ch/Ch′ bond of one monomer and the dπ* anti-bonding orbitals of the same Mo–Ch/Ch′ bond in the second monomer during dimer formation, and vice versa. The HOMO–LUMO gaps calculated with the MN12-L functional were 0.9, 1.0, and 1.1 eV for MoTe2, MoSe2 and MoS2, respectively, which match very well with the solid-state theoretical (SCAN-rVV10)/experimental band gaps of 0.75/0.88, 0.90/1.09 and 0.93/1.23 eV of the corresponding systems, respectively. We observed that the gas phase dimers examined are perhaps prototypical for a basic understanding of the interfacial/inter-layer interactions in molybdenum-based dichalcogenides and their derivatives.
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Sarfaraz S, Yar M, Ans M, Gilani MA, Ludwig R, Hashmi MA, Hussain M, Muhammad S, Ayub K. Computational investigation of a covalent triazine framework (CTF-0) as an efficient electrochemical sensor. RSC Adv 2022; 12:3909-3923. [PMID: 35425404 PMCID: PMC8981076 DOI: 10.1039/d1ra08738j] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/15/2022] [Indexed: 12/12/2022] Open
Abstract
In the current study, a covalent triazine framework (CTF-0) was evaluated as an electrochemical sensor against industrial pollutants i.e., O3, NO, SO2, SO3, and CO2. The deep understanding of analytes@CTF-0 complexation was acquired by interaction energy, NCI, QTAIM, SAPT0, EDD, NBO and FMO analyses. The outcome of interaction energy analyses clearly indicates that all the analytes are physiosorbed onto the CTF-0 surface. NCI and QTAIM analysis were employed to understand the nature of the non-covalent interactions. Furthermore, SAPT0 analysis revealed that dispersion has the highest contribution towards total SAPT0 energy. In NBO analysis, the highest charge transfer is obtained in the case of SO3@CTF-0 (−0.167 e−) whereas the lowest charge transfer is observed in CO2@CTF-0. The results of NBO charge transfer are also verified through EDD analysis. FMO analysis revealed that the highest reduction in the HOMO–LUMO energy gap is observed in the case of O3 (5.03 eV) adsorption onto the CTF-0 surface, which indicates the sensitivity of CTF-0 for O3 analytes. We strongly believe that these results might be productive for experimentalists to tailor a highly sensitive electrochemical sensor using covalent triazine-based frameworks (CTFs). In the current study, a covalent triazine framework (CTF-0) was evaluated as an electrochemical sensor against industrial pollutants i.e., O3, NO, SO2, SO3, and CO2.![]()
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Affiliation(s)
- Sehrish Sarfaraz
- Department of Chemistry, COMSATS University, Abbottabad Campus, KPK, Pakistan, 22060
| | - Muhammad Yar
- Department of Chemistry, COMSATS University, Abbottabad Campus, KPK, Pakistan, 22060
| | - Muhammad Ans
- Department of Chemistry, University of Agriculture Faisalabad, 38000, Faisalabad, Pakistan
| | - Mazhar Amjad Gilani
- Department of Chemistry, COMSATS University Islamabad, Lahore Campus, 54600, Pakistan
| | - Ralf Ludwig
- Universität Rostock, Institut für Chemie, Abteilung für Physikalische Chemie, Dr.-Lorenz-Weg 1, 18059 Rostock, Germany
- Leibniz-Institut für Katalyse an der Universität Rostock, Albert-Einstein-Strasse 29a, 18059 Rostock, Germany
| | - Muhammad Ali Hashmi
- Department of Chemistry, Division of Science & Technology, University of Education, 54770 Lahore, Pakistan
| | - Masroor Hussain
- Department of Data Science, Ghulam Ishaq Khan Institute of Engineering Sciences and Technology, Topi, KPK, Pakistan
| | - Shabbir Muhammad
- Department of Chemistry, College of Science, King Khalid University, P. O. Box 9004, Abha, 61413, Saudi Arabia
| | - Khurshid Ayub
- Department of Chemistry, COMSATS University, Abbottabad Campus, KPK, Pakistan, 22060
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28
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Topaloğlu Aksoy B, Dedeoglu B, Zorlu Y, Ayhan MM, Çoşut B. Exploring halogen⋯halogen interactions in supramolecular self-assemblies of BODIPY networks. CrystEngComm 2022. [DOI: 10.1039/d2ce00776b] [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
In this study, the efficiency of halogen⋯halogen interactions to control supramolecular assemblies of boron dipyrromethene (BODIPY) (B1–B5) derivatives was explored.
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Affiliation(s)
| | - Burcu Dedeoglu
- Department of Chemistry, Gebze Technical University, Gebze, Kocaeli, 41400, Türkiye
| | - Yunus Zorlu
- Department of Chemistry, Gebze Technical University, Gebze, Kocaeli, 41400, Türkiye
| | - Mehmet Menaf Ayhan
- Department of Chemistry, Gebze Technical University, Gebze, Kocaeli, 41400, Türkiye
| | - Bünyemin Çoşut
- Department of Chemistry, Gebze Technical University, Gebze, Kocaeli, 41400, Türkiye
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29
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Lipkowski P, Kozłowska J, Bartkowiak W. A Look at the Spatial Confining Effect on the Molecular Electrostatic Potential (MEP)-A Case Study of the HF and BrCN Molecules. Molecules 2021; 26:5924. [PMID: 34641468 PMCID: PMC8512269 DOI: 10.3390/molecules26195924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 11/16/2022] Open
Abstract
In this theoretical study, we report on the molecular electrostatic potential (MEP) of titled molecules confined by repulsive potentials of cylindrical symmetry mimicking a topology. Our calculations show that the spatial restriction significantly changes the picture of the MEP of molecules in a quantitative and qualitative sense. In particular, the drastic changes in the MEP as a function of the strength of spatial confinement are observed for the BrCN molecule. This preliminary study is the first step in the investigation of the behavior of the MEP of molecular systems under orbital compression.
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Affiliation(s)
| | | | - Wojciech Bartkowiak
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland; (P.L.); (J.K.)
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30
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Ibrahim MAA, Moussa NAM, Soliman MES, Moustafa MF, Al-Fahemi JH, El-Mageed HRA. On the Potentiality of X-T-X 3 Compounds (T = C, Si, and Ge, and X = F, Cl, and Br) as Tetrel- and Halogen-Bond Donors. ACS OMEGA 2021; 6:19330-19341. [PMID: 34337270 PMCID: PMC8320108 DOI: 10.1021/acsomega.1c03183] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/08/2021] [Indexed: 05/08/2023]
Abstract
The versatility of the X-T-X3 compounds (where T = C, Si, and Ge, and X = F, Cl, and Br) to participate in tetrel- and halogen-bonding interactions was settled out, at the MP2/aug-cc-pVTZ level of theory, within a series of configurations for (X-T-X3)2 homodimers. The electrostatic potential computations ensured the remarkable ability of the investigated X-T-X3 monomers to participate in σ-hole halogen and tetrel interactions. The energetic findings significantly unveil the favorability of the tetrel···tetrel directional configuration with considerable negative binding energies over tetrel···halogen, type III halogen···halogen, and type II halogen···halogen analogs. Quantum theory of atoms in molecules and noncovalent interaction analyses were accomplished to disclose the nature of the tetrel- and halogen-bonding interactions within designed configurations, giving good correlations between the total electron densities and binding energies. Further insight into the binding energy physical meanings was invoked through using symmetry-adapted perturbation theory-based energy decomposition analysis, featuring the dispersion term as the most prominent force beyond the examined interactions. The theoretical results were supported by versatile crystal structures which were characterized by the same type of interactions. Presumably, the obtained findings would be considered as a solid underpinning for future supramolecular chemistry, materials science, and crystal engineering studies, as well as a fundamental linchpin for a better understanding of the biological activities of chemicals.
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Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Nayra A. M. Moussa
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Mahmoud E. S. Soliman
- Molecular
Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Mahmoud F. Moustafa
- Department
of Biology, College of Science, King Khalid
University, Abha 9004, Saudi Arabia
- Department
of Botany and Microbiology, Faculty of Science, South Valley University, Qena 83523, Egypt
| | - Jabir H. Al-Fahemi
- Chemistry
Department, Faculty of Applied Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - H. R. Abd El-Mageed
- Micro-Analysis,
Environmental Research and Community Affairs Center (MAESC), Faculty
of Science, Beni-Suef University, Beni-Suef 62511, Egypt
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31
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Solel E, Ruth M, Schreiner PR. London Dispersion Helps Refine Steric A-Values: The Halogens. J Org Chem 2021; 86:7701-7713. [PMID: 33988377 DOI: 10.1021/acs.joc.1c00767] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Halogens are rarely considered as dispersion energy donors for organic reaction design. Here, we re-examine one of the textbook examples for assessing steric hindrance, the A-value, and demonstrate that even in this system, halogens cannot be treated solely as classic repulsive hard spheres. A significant part of the steric demand of the halogens is compensated by attractive London dispersion (LD) interactions, explaining the experimental lack of a clear trend when going down the halogens' row. Beyond monohalogenated cyclohexanes, dihalo- and perhalocyclohexanes also show significant LD interactions. We also explored several other small organic systems containing halogens. Our findings show that organic chemists should treat halogens as possible sources of LD interactions in reaction design, as these atoms can change the landscape of the potential energy surface and reverse trends of conformer stabilities and reaction selectivities.
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Affiliation(s)
- Ephrath Solel
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Marcel Ruth
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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32
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Ibrahim MAA, Ahmed OAM, El-Taher S, Al-Fahemi JH, Moussa NAM, Moustafa H. Cospatial σ-Hole and Lone Pair Interactions of Square-Pyramidal Pentavalent Halogen Compounds with π-Systems: A Quantum Mechanical Study. ACS OMEGA 2021; 6:3319-3329. [PMID: 33553949 PMCID: PMC7860235 DOI: 10.1021/acsomega.0c05795] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 01/13/2021] [Indexed: 05/08/2023]
Abstract
In the spirit of the mounting interest in noncovalent interactions, the present study was conducted to scrutinize a special type that simultaneously involved both σ-hole and lone pair (lp) interactions with aromatic π-systems. Square-pyramidal pentavalent halogen-containing molecules, including X-Cl-F4, F-Y-F4, and F-I-X4 compounds (where X = F, Cl, Br, and I and Y = Cl, Br, and I) were employed as σ-hole/lp donors. On the other hand, benzene (BZN) and hexafluorobenzene (HFB) were chosen as electron-rich and electron-deficient aromatic π-systems, respectively. The investigation relied upon a variety of quantum chemical calculations that complement each other. The results showed that (i) the binding energy of the X-Y-F4···BZN complexes increased (i.e., more negative) as the Y atom had a larger magnitude of σ-hole, contrary to the pattern of X-Y-F4···HFB complexes; (ii) the interaction energies of X-Y-F4···BZN complexes were dominated by both dispersion and electrostatic contributions, while dispersive interactions dominated X-Y-F4···HFB complexes; and (iii) the X4 atoms in F-I-X4···π-system complexes governed the interaction energy pattern: the larger the X4 atoms were, the greater the interaction energies were, for the same π-system. The results had illuminating facets in regard to the rarely addressed cases of the σ-hole/lp contradictory scene.
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Affiliation(s)
| | - Ossama A. M. Ahmed
- Chemistry
Department, Faculty of Science, Minia University, Minia 61519, Egypt
- Department
of Chemistry, Faculty of Science, Cairo
University, Giza 12613, Egypt
| | - Sabry El-Taher
- Department
of Chemistry, Faculty of Science, Cairo
University, Giza 12613, Egypt
| | - Jabir H. Al-Fahemi
- Chemistry
Department, Faculty of Applied Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Nayra A. M. Moussa
- Chemistry
Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Hussein Moustafa
- Department
of Chemistry, Faculty of Science, Cairo
University, Giza 12613, Egypt
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33
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Zarechnaya OM, Anisimov AA, Belov EY, Burakov NI, Kanibolotsky AL, Mikhailov VA. Polycentric binding in complexes of trimethylamine- N-oxide with dihalogens. RSC Adv 2021; 11:6131-6145. [PMID: 35423161 PMCID: PMC8694807 DOI: 10.1039/d0ra08165e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/13/2021] [Indexed: 02/01/2023] Open
Abstract
Dihalogens readily interact with trimethylamine-N-oxide under ambient conditions. Accordingly, herein, stable 1 : 1 adducts were obtained in the case of iodine chloride and iodine bromide. The crystal and molecular structure of the trimethylamine-N-oxide-iodine chloride adduct was solved. Furthermore, the geometry and electronic structure of the trimethylamine-N-oxide-dihalogen complexes were studied computationally. Only molecular ensembles were found in the global minimum for the 1 : 1 stoichiometry. The O⋯X-Y halogen bond is the main factor for the thermodynamic stability of these complexes. Arguments for electrostatic interactions as the driving force for this noncovalent interaction were discussed. Also, the equilibrium structures are additionally stabilised by weak C-H⋯X hydrogen bonds. Consequently, formally monodentate ligands are bound in a polycentric manner.
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Affiliation(s)
- Olga M Zarechnaya
- L.M. Litvinenko Institute of Physical Organic and Coal Chemistry R. Luxemburg St., 70 Donetsk Ukraine
| | - Aleksei A Anisimov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences 28 Vavilov St. 119991 Moscow Russia
- D.I. Mendeleev Russian Chemical Technological University 9 Miusskaya Sq. 125047 Moscow Russia
| | - Eugenii Yu Belov
- L.M. Litvinenko Institute of Physical Organic and Coal Chemistry R. Luxemburg St., 70 Donetsk Ukraine
| | - Nikolai I Burakov
- L.M. Litvinenko Institute of Physical Organic and Coal Chemistry R. Luxemburg St., 70 Donetsk Ukraine
| | | | - Vasilii A Mikhailov
- L.M. Litvinenko Institute of Physical Organic and Coal Chemistry R. Luxemburg St., 70 Donetsk Ukraine
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34
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Ibrahim MAA, Telb EMZ. Comparison of ±σ-hole and ±R˙-hole interactions formed by tetrel-containing complexes: a computational study. RSC Adv 2021; 11:4011-4021. [PMID: 35424365 PMCID: PMC8694216 DOI: 10.1039/d0ra09564h] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/11/2021] [Indexed: 11/21/2022] Open
Abstract
For the first time, unconventional ±R˙-hole interactions were unveiled in tetrel-containing complexes. The nature and characteristics of ±R˙-hole interactions were explored relative to their ±σ-hole counterparts for ˙TF3⋯ and W-T-F3⋯B/R˙/A complexes (where T = C, Si, and Ge, W = H and F, B = Lewis bases, R˙ = free radicals, and A = Lewis acids). In an effort to thoroughly investigate such interactions, a plethora of quantum mechanical calculations, including molecular electrostatic potential (MEP), maximum positive electrostatic potential (V s,max), point-of-charge (PoC), interaction energy, symmetry adapted perturbation theory (SAPT), and reduced density gradient-noncovalent interaction (RDG-NCI) calculations, were applied. The most notable findings to emerge from this study are that (i) from the electrostatic perspective, the molecular stabilization energies of ˙TF3 and W-T-F3 monomers became more negative as the Lewis basicity increased, (ii) the most stable complexes were observed for the ones containing Lewis bases, forming -σ-hole and -R˙-hole interactions, and the interaction energies systematically increased in the order H-T-F3⋯B < ˙TF3⋯B < F-T-F3⋯B, (iii) contrariwise, the +σ-hole and +R˙-hole interactions with Lewis acids are more energetically favorable in the order F-T-F3⋯A < ˙TF3⋯A < H-T-F3⋯A, and (iv) generally, the dispersion force plays a key role in stabilizing the tetrel-containing complexes, jointly with the electrostatic and induction forces for the interactions with Lewis bases and acids, respectively. Concretely, the findings presented in this paper add to our understanding of the characteristics and nature of such intriguing interactions.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Ebtisam M Z Telb
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
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35
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Ibrahim MAA, Saad SMA, Al-Fahemi JH, Mekhemer GAH, Ahmed SA, Shawky AM, Moussa NAM. External electric field effects on the σ-hole and lone-pair hole interactions of group V elements: a comparative investigation. RSC Adv 2021; 11:4022-4034. [PMID: 35424345 PMCID: PMC8694126 DOI: 10.1039/d0ra09765a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/31/2020] [Indexed: 11/21/2022] Open
Abstract
σ-hole and lone-pair (lp) hole interactions of trivalent pnicogen-bearing (ZF3) compounds were comparatively scrutinized, for the first time, under field-free and external electric field (EEF) conditions. Conspicuously, the sizes of the σ-hole and lp-hole were increased by applying an EEF along the positive direction, while the sizes of both holes decreased through the reverse EEF direction. The MP2 energetic calculations of ZF3⋯FH/NCH complexes revealed that σ-holes exhibited more impressive interaction energies compared to the lp-holes. Remarkably, the strengths of σ-hole and lp-hole interactions evolved with the increment of the positive value of the considered EEF; i.e., the interaction energy increased as the utilized EEF value increased. Unexpectedly, under field-free conditions, nitrogen-bearing complexes showed superior strength for their lp-hole interactions than phosphorus-bearing complexes. However, the reverse picture was exhibited for the interaction energies of nitrogen- and phosphorus-bearing complexes interacting within lp-holes by applying the high values of a positively directed EEF. These results significantly demonstrate the crucial influence of EEF on the strength of σ-hole and lp-hole interactions, which in turn leads to an omnipresent enhancement for variable fields, including biological simulations and material science.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Sherif M A Saad
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Jabir H Al-Fahemi
- Chemistry Department, Faculty of Applied Sciences, Umm Al-Qura University Makkah 21955 Saudi Arabia
| | - Gamal A H Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Saleh A Ahmed
- Chemistry Department, Faculty of Applied Sciences, Umm Al-Qura University Makkah 21955 Saudi Arabia
- Chemistry Department, Faculty of Science, Assiut University Assiut 71516 Egypt
| | - Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University Makkah 21955 Saudi Arabia
- Central Laboratory for Micro-analysis, Minia University Minia 61519 Egypt
| | - Nayra A M Moussa
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
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36
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Investigation of intermolecular interactions in fluoro/trifluoromethyl derivatives of benzoylferrocene. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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37
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Alkorta I, Elguero J, Trujillo C, Sánchez-Sanz G. Interaction between Trinuclear Regium Complexes of Pyrazolate and Anions, a Computational Study. Int J Mol Sci 2020; 21:E8036. [PMID: 33126636 PMCID: PMC7663457 DOI: 10.3390/ijms21218036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 01/27/2023] Open
Abstract
The geometry, energy and electron density properties of the 1:1, 1:2 and 1:3 complexes between cyclic (Py-M)3 (M = Au, Ag and Cu) and halide ions (F-, Cl- and Br-) were studied using Møller Plesset (MP2) computational methods. Three different configurations were explored. In two of them, the anions interact with the metal atoms in planar and apical dispositions, while in the last configuration, the anions interact with the CH(4) group of the pyrazole. The energetic results for the 1:2 and 1:3 complexes are a combination of the specific strength of the interaction plus a repulsive component due to the charge:charge coulombic term. However, stable minima structures with dissociation barriers for the anions indicate that those complexes are stable and (Py-M)3 can hold up to three anions simultaneously. A search in the CSD confirmed the presence of (Pyrazole-Cu)3 systems with two anions interacting in apical disposition.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain;
| | - José Elguero
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain;
| | - Cristina Trujillo
- Trinity Biomedical Sciences Institute, School of Chemistry, Trinity Dublin College, D02 R590 Dublin 2, Ireland;
| | - Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal Quay, Dublin 2, Ireland
- School of Chemistry, University College Dublin, Belfield, D02 HP83 Dublin 4, Ireland
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Factors Impacting σ- and π-Hole Regions as Revealed by the Electrostatic Potential and Its Source Function Reconstruction: The Case of 4,4'-Bipyridine Derivatives. Molecules 2020; 25:molecules25194409. [PMID: 32992941 PMCID: PMC7582854 DOI: 10.3390/molecules25194409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 02/08/2023] Open
Abstract
Positive electrostatic potential (V) values are often associated with σ- and π-holes, regions of lower electron density which can interact with electron-rich sites to form noncovalent interactions. Factors impacting σ- and π-holes may thus be monitored in terms of the shape and values of the resulting V. Further precious insights into such factors are obtained through a rigorous decomposition of the V values in atomic or atomic group contributions, a task here achieved by extending the Bader-Gatti source function (SF) for the electron density to V. In this article, this general methodology is applied to a series of 4,4'-bipyridine derivatives containing atoms from Groups VI (S, Se) and VII (Cl, Br), and the pentafluorophenyl group acting as a π-hole. As these molecules are characterized by a certain degree of conformational freedom due to the possibility of rotation around the two C-Ch bonds, from two to four conformational motifs could be identified for each structure through conformational search. On this basis, the impact of chemical and conformational features on σ- and π-hole regions could be systematically evaluated by computing the V values on electron density isosurfaces (VS) and by comparing and dissecting in atomic/atomic group contributions the VS maxima (VS,max) values calculated for different molecular patterns. The results of this study confirm that both chemical and conformational features may seriously impact σ- and π-hole regions and provide a clear analysis and a rationale of why and how this influence is realized. Hence, the proposed methodology might offer precious clues for designing changes in the σ- and π-hole regions, aimed at affecting their potential involvement in noncovalent interactions in a desired way.
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39
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Ibrahim MAA, Moussa NAM. Unconventional Type III Halogen···Halogen Interactions: A Quantum Mechanical Elucidation of σ-Hole···σ-Hole and Di-σ-Hole Interactions. ACS OMEGA 2020; 5:21824-21835. [PMID: 32905309 PMCID: PMC7469378 DOI: 10.1021/acsomega.0c02887] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/04/2020] [Indexed: 05/08/2023]
Abstract
Herein, two unconventional type III halogen···halogen interactions, namely, σ-hole···σ-hole and di-σ-hole interactions, were reported in a series of halogenated complexes. In type III, the A-halogen···halogen angles are typically equal to 180°, and the occurrence of σ-hole on halogen atoms is mandatory. Using diverse quantum mechanical calculations, it was demonstrated that the occurrence of such interactions with binding energies varied from -0.35 to -1.30 kcal/mol. Symmetry-adapted perturbation theory-based energy decomposition analysis (SAPT-EDA) revealed that type III interactions are dominated by dispersion forces, while electrostatic forces are unfavorable. Cambridge Structure Database (CSD) survey unveiled the experimental evidence for the manifestation of σ-hole···σ-hole interactions in crystal structures. This work might be deemed as a foundation for a vast number of forthcoming crystal engineering and materials science studies.
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Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry
Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Nayra A. M. Moussa
- Computational Chemistry Laboratory, Chemistry
Department, Faculty of Science, Minia University, Minia 61519, Egypt
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40
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Ibrahim MAA, Telb EMZ. σ-Hole and Lone-Pair Hole Interactions in Chalcogen-Containing Complexes: A Comparative Study. ACS OMEGA 2020; 5:21631-21640. [PMID: 32905338 PMCID: PMC7469375 DOI: 10.1021/acsomega.0c02362] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/04/2020] [Indexed: 05/07/2023]
Abstract
The potentiality of sp3-hybridized chalcogen-containing molecules to participate in lone-pair (lp) hole interactions was reported for the first time. lp hole interactions were characterized and compared to σ-hole ones for OF2 and SF2 molecules as a case study. Various quantum mechanical calculations, including molecular electrostatic potential (MEP), maximum positive electrostatic potential (V s,max), point of charge (PoC), symmetry-adapted perturbation theory (SAPT), quantum theory of atoms in molecule (QTAIM), and reduced density gradient-noncovalent interaction (RDG-NCI) calculations, were carried out. The more significant findings to emerge from this study are the following: (i) the V s,max calculation was proved to be an unreliable method to determine the precise σ-hole and lp hole locations. (ii) The maximum positive electrostatic potential of the σ hole and lp hole was found to be at the F-Chal···PoC angle (θ) of 180° and at the centroid of XYlp plane, respectively. (iii) Lewis basicity has a significant effect on the strength of σ-hole and lp hole interactions. (iv) The studied molecules more favorably interact with Lewis bases via the σ hole compared to the lp hole, and (v) stabilization of the σ-hole and lp hole interactions stems from the electrostatic and dispersion forces, respectively.
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Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory,
Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Ebtisam M. Z. Telb
- Computational Chemistry Laboratory,
Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
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41
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Marsan ES, Bayse CA. Halogen Bonding Interactions of Polychlorinated Biphenyls and the Potential for Thyroid Disruption. Chemistry 2020; 26:5200-5207. [PMID: 31849117 PMCID: PMC8812442 DOI: 10.1002/chem.201903904] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/13/2019] [Indexed: 11/21/2023]
Abstract
Polychlorinated biphenyl (PCB) flame retardants are persistent pollutants and inhibit neurodevelopment, particularly in the early stages of life. Halogen bonding (XB) to the iodothyronine deiodinases (Dio) that modulate thyroid hormones (THs) is a potential mechanism for endocrine disruption. Cl⋅⋅⋅Se XB interactions of PCBs with SeMe- , a small model of the Dio active site selenocysteine, are compared with previous results on polybrominated diphenylethers (PBDEs) and THs using density functional theory. PCBs generally display weaker XB interactions compared to PBDEs and THs, consistent with the dependence of XB strength on the size of the halogen (I>Br>Cl). PCBs also do not meet a proposed energy threshold for substrates to undergo dehalogenation, suggesting they may behave as competitive inhibitors of Dio in addition to other mechanisms of endocrine disruption. XB interactions in PCBs are position-dependent, with ortho interactions slightly more favorable than meta and para interactions, suggesting that PCBs may have a greater effect on certain classes of Dio. Flexibility of PCBs around the biphenyl C-C bond is limited by ortho substitutions relative to the biphenyl linkage, which may contribute to the ability to inhibit Dio and other TH-related proteins.
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Affiliation(s)
- Eric S Marsan
- Department of Chemistry and Biochemistry, Old Dominion University, 1 Old Dominion University, Norfolk, VA, 23529, USA
| | - Craig A Bayse
- Department of Chemistry and Biochemistry, Old Dominion University, 1 Old Dominion University, Norfolk, VA, 23529, USA
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42
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Orangi N, Eskandari K. Fluorine as a Lewis acid: A symmetry‐adapted perturbation theory based on density functional theory and interacting quantum atoms study of noncovalent interactions in the NCF⋯NH
3
complex. J Comput Chem 2020; 41:1598-1605. [DOI: 10.1002/jcc.26202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 03/06/2020] [Accepted: 03/18/2020] [Indexed: 11/11/2022]
Affiliation(s)
| | - Kiamars Eskandari
- Department of ChemistryIsfahan University of Technology Isfahan Iran
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43
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Hoffmann G, Tognetti V, Joubert L. Electrophilicity Indices and Halogen Bonds: Some New Alternatives to the Molecular Electrostatic Potential. J Phys Chem A 2020; 124:2090-2101. [DOI: 10.1021/acs.jpca.9b10233] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Guillaume Hoffmann
- Normandy University, COBRA UMR 6014 & FR 3038, Université de Rouen INSA Rouen, CNRS, 1 rue Tesniére 76821 Mont St Aignan. Cedex, France
| | - Vincent Tognetti
- Normandy University, COBRA UMR 6014 & FR 3038, Université de Rouen INSA Rouen, CNRS, 1 rue Tesniére 76821 Mont St Aignan. Cedex, France
| | - Laurent Joubert
- Normandy University, COBRA UMR 6014 & FR 3038, Université de Rouen INSA Rouen, CNRS, 1 rue Tesniére 76821 Mont St Aignan. Cedex, France
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44
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Towards an unified chemical model of secondary bonding. J Mol Model 2020; 26:62. [DOI: 10.1007/s00894-019-4283-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/19/2019] [Indexed: 11/27/2022]
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Abstract
The CH3Cl molecule has been used in several studies as an example purportedly to demonstrate that while Cl is weakly negative, a positive potential can be induced on its axial surface by the electric field of a reasonably strong Lewis base (such as O=CH2). The induced positive potential then has the ability to attract the negative site of the Lewis base, thus explaining the importance of polarization leading to the formation of the H3C–Cl···O=CH2 complex. By examining the nature of the chlorine’s surface in CH3Cl using the molecular electrostatic surface potential (MESP) approach, with MP2/aug-cc-pVTZ, we show that this view is not correct. The results of our calculations demonstrate that the local potential associated with the axial surface of the Cl atom is inherently positive. Therefore, it should be able to inherently act as a halogen bond donor. This is shown to be the case by examining several halogen-bonded complexes of CH3Cl with a series of negative sites. In addition, it is also shown that the lateral portions of Cl in CH3Cl features a belt of negative electrostatic potential that can participate in forming halogen-, chalcogen-, and hydrogen-bonded interactions. The results of the theoretical models used, viz. the quantum theory of atoms in molecules; the reduced density gradient noncovalent index; the natural bond orbital analysis; and the symmetry adapted perturbation theory show that Cl-centered intermolecular bonding interactions revealed in a series of 18 binary complexes do not involve a polarization-induced potential on the Cl atom.
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46
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Bijina PV, Suresh CH. Molecular Electrostatic Potential Reorganization Theory to Describe Positive Cooperativity in Noncovalent Trimer Complexes. J Phys Chem A 2020; 124:2231-2241. [DOI: 10.1021/acs.jpca.9b11538] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Padinjare Veetil Bijina
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, Kerala695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Cherumuttathu H. Suresh
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, Kerala695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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47
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X-ray diffraction and QTAIM calculations of the non-covalent intermolecular fluorine-fluorine interactions in tris(trifluoroacetylacetonato)-manganese(III). J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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48
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Rossi E, De Santis M, Sorbelli D, Storchi L, Belpassi L, Belanzoni P. Spin-orbit coupling is the key to unraveling intriguing features of the halogen bond involving astatine. Phys Chem Chem Phys 2020; 22:1897-1910. [PMID: 31912075 DOI: 10.1039/c9cp06293a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The effect of spin-orbit coupling (SOC) on the halogen bond involving astatine has been investigated using state-of-the-art two- and four-component relativistic calculations. Adducts between Cl-X (X = Cl, Br, I and At) and ammonia have been selected to establish a trend on going down the periodic table. The SOC influence has been explored not only on the geometric and energetic features that can be used to characterize the halogen bond strength but also on the three main contributions to it that are the charge transfer, the "σ-hole" (i.e. the localized region with a net positive electrostatic potential at the halogen site) and the "polar flattening" (which is related to the effective shape of the halogen site). A surprisingly large increase of the Cl-At dipole moment, due to the inclusion of SOC, has been worked out using four-component CCSD(T) reference calculations, indicating that this bond is significantly more ionic than one may predict. Due to the SOC effect, which induces a peculiar charge accumulation on the At side in the Cl-At dimer, a weakening of the astatine-mediated halogen bond occurs arising from the (i) reduced amount of charge transfer, (ii) decrease of the polar flattening and (iii) lowering of the short-range Coulomb potential. The analysis of the electronic structure of the Cl-At moiety allows for a rationalization of the SOC effects on all the considered features of the halogen bond, including an unprecedented unsymmetrical charge back-donation from Cl-At to ammonia.
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Affiliation(s)
- Elisa Rossi
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy.
| | - Matteo De Santis
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy.
| | - Diego Sorbelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy.
| | - Loriano Storchi
- CNR Institute of Chemical Science and Technologies "Giulio Natta" (CNR-SCITEC), via Elce di Sotto 8, 06123 Perugia, Italy. and Dipartimento di Farmacia, Università G. D'Annunzio, via dei Vestini 31, 66100 Chieti, Italy
| | - Leonardo Belpassi
- CNR Institute of Chemical Science and Technologies "Giulio Natta" (CNR-SCITEC), via Elce di Sotto 8, 06123 Perugia, Italy. and Consortium for Computational Molecular and Materials Sciences (CMS)2, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Paola Belanzoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy. and CNR Institute of Chemical Science and Technologies "Giulio Natta" (CNR-SCITEC), via Elce di Sotto 8, 06123 Perugia, Italy. and Consortium for Computational Molecular and Materials Sciences (CMS)2, via Elce di Sotto 8, 06123 Perugia, Italy
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49
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Wang R, Cheng Z, Li Q, McDowell SA. Regular/abnormal variation in the strength and nature of the halogen bond between H
2
Te and the dihalogens: Prominent effect of methyl substituents. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.5468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ruijing Wang
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical EngineeringYantai University Yantai 264005 China
| | - Ziyi Cheng
- Institute of Functional Materials and Molecular Imaging, Key Laboratory of Emergency and Trauma, Ministry of Education, College of Emergency and TraumaHainan Medical University Haikou 571199 China
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical EngineeringYantai University Yantai 264005 China
| | - Sean A.C. McDowell
- Department of Biological and Chemical SciencesThe University of the West Indies Cave Hill Campus Barbados
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50
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Hou M, Zhu Y, Li Q, Scheiner S. Tuning the Competition between Hydrogen and Tetrel Bonds by a Magnesium Bond. Chemphyschem 2020; 21:212-219. [DOI: 10.1002/cphc.201901076] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 12/04/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Mingchang Hou
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical EngineeringYantai University Yantai 264005 China
| | - Yifan Zhu
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical EngineeringYantai University Yantai 264005 China
| | - Qingzhong Li
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical EngineeringYantai University Yantai 264005 China
| | - Steve Scheiner
- Department of Chemistry and BiochemistryUtah State University Logan UT 84322-0300 USA
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