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Ibrahim MA, Mahmoud AM, Shehata MN, Saeed RR, Moussa NA, Sayed SR, Abd El-Rahman MK, Shoeib T. σ-Hole Site-Based Interactions within Hypervalent Pnicogen, Halogen, and Aerogen-Bearing Molecules with Lewis Bases: A Comparative Study. ACS OMEGA 2024; 9:10391-10399. [PMID: 38463322 PMCID: PMC10918780 DOI: 10.1021/acsomega.3c08178] [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: 10/18/2023] [Revised: 01/02/2024] [Accepted: 01/22/2024] [Indexed: 03/12/2024]
Abstract
σ-Hole site-based interactions in the trigonal bipyramidal geometrical structure of hypervalent pnicogen, halogen, and aerogen-bearing molecules with pyridine and NCH Lewis bases (LBs) were comparatively examined. In this respect, the ZF5···, XF3O2···, and AeF2O3···LB complexes (where Z = As, Sb; X = Br, I; Ae = Kr, Xe; and LB = pyridine and NCH) were investigated. The electrostatic potential (EP) analysis affirmations outlined the occurrence of σ-holes on the systems under consideration with disparate magnitudes that increased according to the following order: AeF2O3 < XF3O2 < ZF5. In line with EP outcomes, the proficiency of σ-hole site-based interactions increased as the atomic size of the central atom increased with a higher favorability for the pyridine-based complexes over NCH-based ones. The interaction energy showed the most favorable negative values of -35.97, -44.53, and -56.06 kcal/mol for the XeF2O3···, IF3O2···, and SbF5···pyridine complexes, respectively. The preferentiality pattern of the studied interactions could be explained as a consequence of (i) the dramatic rearrangement of ZF5 molecules from the trigonal bipyramid geometry to the square pyramidal one, (ii) the significant and tiny deformation energy in the case of the interaction of XF3O2 molecules with pyridine and NCH, respectively, and (iii) the absence of geometrical deformation within the AeF2O3···pyridine and ···NCH complexes other than the XeF2O3···pyridine one. Quantum theory of atoms in molecules and noncovalent interaction index findings reveal the partially covalent nature of most of the investigated interactions. Symmetry-adapted perturbation theory affirmations declared that the electrostatic component was the driving force beyond the occurrence of the considered interactions. The obtained findings will help in improving our understanding of the effect of geometrical deformation on intermolecular interactions.
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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
| | - Asmaa M.M. Mahmoud
- 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
| | - Rehab R.A. Saeed
- 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
| | - Shaban R.M. Sayed
- Department
of Botany and Microbiology, College of Science,
King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - 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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2
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Aarabi M, Gholami S, Grabowski SJ. Double Centrosymmetric Si···π Tetrel Bonds as New Synthons─Evidence from Crystal Structures and DFT Calculations. J Phys Chem A 2023; 127:9995-10007. [PMID: 37975750 DOI: 10.1021/acs.jpca.3c06514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The crystal structure of bis((μ2-ethynylsilyloxo)-dichloro-aluminum), BEDCA, and a few related structures are characterized by the occurrence of tetrel bonds that link molecules. Particularly, centosymmetric dimers in such structures occur that are connected by two equivalent Si···π tetrel bonds. The dimer of BEDCA and dimers of other model species that similarly are linked by two equivalent Si···π tetrel bonds are analyzed theoretically. Some of the complexes calculated here are also characterized by the occurrence of triel bonds. Thus, ωB97XD/aug-cc-pVTZ calculations are performed and these DFT results are further supported by calculations with the use of other theoretical approaches: the quantum theory of atoms in molecules, QTAIM; the natural bond orbital, NBO; the energy decomposition analysis, EDA; and the noncovalent interactions method, NCI. The results show that the tetrel bonds analyzed here are rather weak, and they are not detected by the QTAIM approach; however, they are detected by other approaches, like NBO, for example. On the other hand, the triel bonds that occur in a few complexes discussed here are very strong and possess characteristics of covalent bonds.
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Affiliation(s)
- Mohammad Aarabi
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | - Samira Gholami
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | - Sławomir J Grabowski
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU & Donostia International Physics Center (DIPC) PK 1072, 20080 Donostia, Spain
- Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain
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3
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Ismail TM, Patkar D, Sajith PK, Deshmukh MM. Interplay of Hydrogen, Pnicogen, and Chalcogen Bonding in X(H 2O) n=1-5 (X = NO, NO +, and NO -) Complexes: Energetics Insights via a Molecular Tailoring Approach. J Phys Chem A 2023. [PMID: 38029408 DOI: 10.1021/acs.jpca.3c04181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Nitric oxide (NO) and its redox congeners (NO+ and NO-), designated as X, play vital roles in various atmospheric and biological events. Understanding the interaction between X and water is inevitable to explain the different reactions that occur during these events. The present study is a unified attempt to explore the noncovalent interactions in microhydrated networks of X using the MP2/aug-cc-pVTZ//MP2/6-311++G(d,p) level of theory. The interactions between X and water have been probed by the molecular electrostatic potential (MESP) by exploiting the features of the most positive (Vmax) and most negative potential (Vmin) sites. The individual energy and cooperativity contributions of various types of noncovalent interactions present in X(H2O)n=1-5 complexes are estimated with the help of a molecular tailoring-based approach (MTA-based). The MTA-based analysis reveals that among various possible interactions in NO(H2O)n complexes, the water···water hydrogen bonds (HBs) are the strongest. Neutral NO can form hydrogen and pnicogen bonds (PBs) with water depending on the orientation; however, such HBs and PBs are the weakest. On the other hand, in the NO+(H2O)n complexes, the NO+···water interactions that occur through PBs are the strongest; the next one is the chalcogen bonding (CB), and the water···water HBs are the weakest. In the case of the NO-(H2O)n complexes, the HB interactions via both N and O atoms of NO- and water molecules are the strongest ones. The strength of water···water HB interactions is also seen to increase with the increase in the number of water molecules in NO-(H2O)n. The present study exemplifies the applicability of MTA-based calculations for quantifying various types of individual noncovalent interactions and their interplay in microhydrated networks of NO and its related ions.
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Affiliation(s)
- Thufail M Ismail
- Department of Chemistry, Farook College, Kozhikode, Kerala 673632, India
| | - Deepak Patkar
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, India
| | - Pookkottu K Sajith
- Department of Chemistry, Farook College, Kozhikode, Kerala 673632, India
| | - Milind M Deshmukh
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, India
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Jabłoński M. Bader's Topological Bond Path Does Not Necessarily Indicate Stabilizing Interaction-Proof Studies Based on the Ng@[3 n]cyclophane Endohedral Complexes. Molecules 2023; 28:6353. [PMID: 37687183 PMCID: PMC10490063 DOI: 10.3390/molecules28176353] [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: 07/27/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
According to Bader's quantum theory of atoms in molecules (QTAIM), the simultaneous presence of a bond path and the corresponding bond critical point between any two atoms is both a necessary and sufficient condition for the atoms to be bonded to one another. In principle, this means that this pair of atoms should make a stabilizing contribution to the molecular system. However, the multitude of so-called counterintuitive bond paths strongly suggests that this statement is not necessarily true. Particularly 'troublesome' are endohedral complexes, in which encapsulation-enforced proximity between the trapped guest (e.g., an atom) and the host's cage system usually 'produces' many counterintuitive bond paths. In the author's opinion, the best evidence to demonstrate the repulsive nature of the intra-cage guest⋯host interaction is the use of some trapping systems containing small escape channels and then showing that the initially trapped entity spontaneously escapes outside the host's cage during geometry optimization of the initially built guest@host endohedral complex. For this purpose, a group of 24 Ng@[3n]cyclophane (3≤n≤6) endohedral complexes is used. As a result, arguments are presented showing that Bader's topological bond path does not necessarily indicate a stabilizing interaction.
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Affiliation(s)
- Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100 Toruń, Poland
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5
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Lomas JS, Rosenberg RE. Cooperativity and intermolecular hydrogen bonding in donor‐acceptor complexes of phenol and polyhydroxybenzenes. J PHYS ORG CHEM 2023. [DOI: 10.1002/poc.4506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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The Ultrashort Spike-Ring Interaction in Substituted Iron Maiden Molecules. Molecules 2023; 28:molecules28052244. [PMID: 36903489 PMCID: PMC10004599 DOI: 10.3390/molecules28052244] [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: 02/06/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
The in forms of molecular iron maidens are known for their unique ultrashort interaction between the apical hydrogen atom or its small substituent and the surface of the benzene ring. It is generally believed that this forced ultrashort X⋯π contact is associated with high steric hindrance, which is responsible for specific properties of iron maiden molecules. The main aim of this article is to investigate the influence of significant charge enrichment or depletion of the benzene ring on the characteristics of the ultrashort C-X⋯π contact in iron maiden molecules. For this purpose, three strongly electron-donating (-NH2) or strongly electron-withdrawing (-CN) groups were inserted into the benzene ring of in-[34,10][7]metacyclophane and its halogenated (X = F, Cl, Br) derivatives. It is shown that, despite such extremely electron-donating or electron-accepting properties, the considered iron maiden molecules surprisingly reveal quite high resistance to changes in electronic properties.
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Freindorf M, McCutcheon M, Beiranvand N, Kraka E. Dihydrogen Bonding-Seen through the Eyes of Vibrational Spectroscopy. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010263. [PMID: 36615456 PMCID: PMC9822382 DOI: 10.3390/molecules28010263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/20/2022] [Accepted: 12/20/2022] [Indexed: 12/30/2022]
Abstract
In this work, we analyzed five groups of different dihydrogen bonding interactions and hydrogen clusters with an H3+ kernel utilizing the local vibrational mode theory, developed by our group, complemented with the Quantum Theory of Atoms-in-Molecules analysis to assess the strength and nature of the dihydrogen bonds in these systems. We could show that the intrinsic strength of the dihydrogen bonds investigated is primarily related to the protonic bond as opposed to the hydridic bond; thus, this should be the region of focus when designing dihydrogen bonded complexes with a particular strength. We could also show that the popular discussion of the blue/red shifts of dihydrogen bonding based on the normal mode frequencies is hampered from mode-mode coupling and that a blue/red shift discussion based on local mode frequencies is more meaningful. Based on the bond analysis of the H3+(H2)n systems, we conclude that the bond strength in these crystal-like structures makes them interesting for potential hydrogen storage applications.
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Latosińska JN, Latosińska M, Orzeszko A, Maurin JK. Synthesis and Crystal Structure of Adamantylated 4,5,6,7-Tetrahalogeno-1 H-benzimidazoles Novel Multi-Target Ligands (Potential CK2, M2 and SARS-CoV-2 Inhibitors); X-ray/DFT/QTAIM/Hirshfeld Surfaces/Molecular Docking Study. Molecules 2022; 28:molecules28010147. [PMID: 36615341 PMCID: PMC9822452 DOI: 10.3390/molecules28010147] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
A series of new congeners, 1-[2-(1-adamantyl)ethyl]-1H-benzimidazole (AB) and 1-[2-(1-adamantyl)ethyl]-4,5,6,7-tetrahalogeno-1H-benzimidazole (Hal=Cl, Br, I; tClAB, tBrAB, tIAB), have been synthesized and studied. These novel multi-target ligands combine a benzimidazole ring known to show antitumor activity and an adamantyl moiety showing anti-influenza activity. Their crystal structures were determined by X-ray, while intermolecular interactions were studied using topological Bader's Quantum Theory of Atoms in Molecules, Hirshfeld Surfaces, CLP and PIXEL approaches. The newly synthesized compounds crystallize within two different space groups, P-1 (AB and tIAB) and P21/c (tClAB and tBrAB). A number of intramolecular hydrogen bonds, C-H⋯Hal (Hal=Cl, Br, I), were found in all halogen-containing congeners studied, but the intermolecular C-H⋯N hydrogen bond was detected only in AB and tIAB, while C-Hal⋯π only in tClAB and tBrAB. The interplay between C-H⋯N and C-H⋯Hal hydrogen bonds and a shift from the strong (C-H⋯Cl) to the very weak (C-H⋯I) attractive interactions upon Hal exchange, supplemented with Hal⋯Hal overlapping, determines the differences in the symmetry of crystalline packing and is crucial from the biological point of view. The hypothesis about the potential dual inhibitor role of the newly synthesized congeners was verified using molecular docking and the congeners were found to be pharmaceutically attractive as Human Casein Kinase 2, CK2, inhibitors, Membrane Matrix 2 Protein, M2, blockers and Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2, inhibitors. The addition of adamantyl moiety seems to broaden and modify the therapeutic indices of the 4,5,6,7-tetrahalogeno-1H-benzimidazoles.
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Affiliation(s)
- Jolanta Natalia Latosińska
- Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland
- Correspondence: ; Tel.: +48-61-8295277
| | - Magdalena Latosińska
- Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland
| | - Andrzej Orzeszko
- Institute of Chemistry, Warsaw University of Life Sciences, 159C Nowoursynowska St., 02-787 Warsaw, Poland
| | - Jan Krzysztof Maurin
- National Medicines Institute, Chełmska 30/34, 00-750 Warsaw, Poland
- National Centre for Nuclear Research, Andrzeja Sołtana 7, 05-400 Otwock-Świerk, Poland
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9
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Leherte L, Bodart L, Wouters J, Vercauteren DP. Description of non-covalent interactions in benzyl chalcocyanate crystals from smoothed Cromer-Mann electron density distribution functions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:494003. [PMID: 36223781 DOI: 10.1088/1361-648x/ac99c9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
A well-known method to characterize non-covalent interactions consists in the topological analysis of electron density distribution (EDD) functions, complemented by the search for minima in the reduced density gradient (RDG) distributions. Here, we characterize intermolecular interactions occurring in crystals of benzyl chalcocyanate compounds through bond critical points (BCP) of the promolecular electron density (ED) built from the crystallographic Cromer-Mann parameters, at several smoothing levelst. The trajectories formed by thet-dependent BCP locations are interpreted in terms of the intermolecular interactions occurring within the crystal arrangements. Chalcogen…nitro BCPs are clearly present in the unsmoothed EDDs but are annihilated astincreases, while chalcogen…chalcogen BCPs appear and are among the only BCPs left at the highest smoothing level. The chalcogen bonds are differentiated from the other chalcogen interactions through the linear chalcogen…BCP…nitro geometry at low smoothing level and their more negative Laplacian values. The annihilation of CPs can be followed by the apparition of a RDG minimum, associated with a very weak interaction. Along the BCP trajectories, the Laplacian shows a progressive concentration of the ED in the intermolecular space within the crystals and adopts the most negative values at the shortest atom…atom separations. At the termination point of a BCP trajectory, the drastic increase of the ellipticity value illustrates the flattening of the EDD.
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Affiliation(s)
- Laurence Leherte
- Laboratory of Structural Biological Chemistry, Unit of Theoretical and Structural Physical Chemistry, Department of Chemistry, NAmur Research Institute for LIfe Sciences (NARILIS), Namur Institute of Structured Matter (NISM), NAmur MEdicine and Drug Innovation Center (NAMEDIC), University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Laurie Bodart
- Laboratory of Structural Biological Chemistry, Unit of Theoretical and Structural Physical Chemistry, Department of Chemistry, NAmur Research Institute for LIfe Sciences (NARILIS), Namur Institute of Structured Matter (NISM), NAmur MEdicine and Drug Innovation Center (NAMEDIC), University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Johan Wouters
- Laboratory of Structural Biological Chemistry, Unit of Theoretical and Structural Physical Chemistry, Department of Chemistry, NAmur Research Institute for LIfe Sciences (NARILIS), Namur Institute of Structured Matter (NISM), NAmur MEdicine and Drug Innovation Center (NAMEDIC), University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Daniel P Vercauteren
- Laboratory of Structural Biological Chemistry, Unit of Theoretical and Structural Physical Chemistry, Department of Chemistry, NAmur Research Institute for LIfe Sciences (NARILIS), Namur Institute of Structured Matter (NISM), NAmur MEdicine and Drug Innovation Center (NAMEDIC), University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
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10
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Scheiner S. On the reliability of atoms in molecules, noncovalent index, and natural bond orbital to identify and quantify noncovalent bonds. J Comput Chem 2022; 43:1814-1824. [DOI: 10.1002/jcc.26983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/03/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry Utah State University Logan Utah USA
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DFT–Assisted Structure Determination from Powder X-ray Diffraction Data of a New Zonisamide/ϵ-Caprolactam Cocrystal. CRYSTALS 2022. [DOI: 10.3390/cryst12081020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The crystal structure of a new zonisamide cocrystal, an anticonvulsant drug used to treat the symptoms of epilepsy and Parkinson’s disease, with ϵ-caprolactam is reported herein. The structure has been solved by direct space methodologies from powder X-ray diffraction data. The refinement of the structure was conducted by the Rietveld method assisted by the dispersion-corrected density-functional theory (D-DFT) calculations and periodic boundary conditions. Further analysis of the structure reveals several H-bonded synthons and self–assembled dimers that have been further analyzed by DFT calculations and other computational tools such as molecular electrostatic potential (MEP) surfaces and the quantum theory of “atom-in-molecules” (QTAIM).
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12
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Jabłoński M. The physical nature of the ultrashort spike-ring interaction in iron maiden molecules. J Comput Chem 2022; 43:1206-1220. [PMID: 35593685 DOI: 10.1002/jcc.26879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 11/08/2022]
Abstract
The so-called 'iron maiden' molecules belong to one of the most interesting subgroups of cyclophanes due to the presence of the ultrashort interaction between the CX apical bond and the benzene ring. This article presents an in-depth theoretical study of 16 'iron maiden' molecules, in which X = H, F, Cl or Br and the side chains are of various lengths and types: CSC, CSCC, CCC, and CCCC. It is shown that the H → F → Cl → Br substitution leads to a significant expansion of the 'iron maiden' molecule. Shorter chains lead to more pronounced effects, while insertion of sulfur atoms into the side chains lowers them. Structural changes are associated with an increase in energetic destabilization of X. Moreover, unlike for H, in the case of X = halogen, the out → in isomerization is energetically disadvantageous. The 'iron maiden' molecules are characterized by the presence of only three X⋯CAr bond paths. Particularly noteworthy are unusually large (even up to 32) values of the X⋯CAr bond ellipticity, which results from flat electron density distribution. The X⋯π interaction in each of the investigated 'iron maiden' molecule turned out to be multi-center, stabilizing and almost purely covalent in nature as indicated by the definitely dominant percentage (94.8%-101.6%) of the exchange-correlation energy. The spatial hindrance within the 'iron maiden' molecules appears to be not so much due to the X⋯π repulsion, but due to unfavorable steric interactions between X and the CC side bonds. It is also confirmed that some CH⋯HC interactions in aliphatic chains can be very weakly stabilizing.
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Affiliation(s)
- Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Toruń, Poland
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13
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Baykov SV, Semenov AV, Presnukhina SI, Novikov AS, Shetnev AA, Boyarskiy VP. Hydrogen vs. halogen bonding in crystals of 2,5-dibromothiophene-3-carboxylic acid derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Determining Repulsion in Cyclophane Cages. Molecules 2022; 27:molecules27133969. [PMID: 35807214 PMCID: PMC9268502 DOI: 10.3390/molecules27133969] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/15/2022] [Accepted: 06/18/2022] [Indexed: 02/01/2023] Open
Abstract
Superphane, i.e., [2.2.2.2.2.2](1,2,3,4,5,6)cyclophane, is a very convenient molecule in studying the nature of guest⋯host interactions in endohedral complexes. Nevertheless, the presence of as many as six ethylene bridges in the superphane molecule makes it practically impossible for the trapped entity to escape out of the superphane cage. Thus, in this article, I have implemented the idea of using the superphane derivatives with a reduced number of ethylene linkers, which leads to the [2n] cyclophanes where n<6. Seven such cyclophanes are then allowed to form endohedral complexes with noble gas (Ng) atoms (He, Ne, Ar, Kr). It is shown that in the vast majority of cases, the initially trapped Ng atom spontaneously escapes from the cyclophane cage, creating an exohedral complex. This is the best proof that the Ng⋯cyclophane interaction in endohedral complexes is indeed highly repulsive, i.e., destabilizing. Apart from the ‘sealed’ superphane molecule, endohedral complexes are only formed in the case of the smallest He atom. However, it has been shown that in these cases, the Ng⋯cyclophane interaction inside the cyclophane cage is nonbonding, i.e., repulsive. This highly energetically unfavorable effect causes the cyclophane molecule to ‘swell’.
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Jabłoński M. Endo- and exohedral complexes of superphane with cations. J Comput Chem 2022; 43:1120-1133. [PMID: 35470905 DOI: 10.1002/jcc.26874] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/28/2022] [Accepted: 04/01/2022] [Indexed: 11/07/2022]
Abstract
Quite recently it has been shown in a previous study that superphane, that is, [2.2.2.2.2.2](1,2,3,4,5,6)cyclophane, is a very convenient molecule in the study of endohedral complexes and especially in the study of the influence of the caged entity (i.e., guest) on the structure of the host molecule. This advantage results from the presence of two parallel benzene rings joined together by six quite flexible ethylene bridges (spacers). This article examines the energetic and structural properties of endo- and exohedral complexes of superphane with the following cations: H+ , Li+ , Na+ , K+ , Be2+ , Mg2+ , Ca2+ , B3+ , Al3+ , Ga3+ . The stability of endohedral complexes has been shown to be strongly dependent on the charge and radius of the caged cation. The inclusion of the cation inside the superphane molecule causes its 'swelling', which is manifested by an increase in the distance between the benzene rings and elongations of the ring and spacer C-C bonds. In the case of exohedral complexes, three forms are investigated: with the cation above the benzene ring, with the cation interacting with the superphane window in the equatorial position, and with the cation interacting with the center of the C-C spacer bond. The first of these forms has been shown to be preferred. The cation⋯acceptor distance depends on the cation radius. Among the cations investigated, H+ and Be2+ are particularly reactive and predisposed to induce significant structural changes in the superphane molecule, forming C-H bond or C-Be-C bridges, respectively.
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Affiliation(s)
- Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Toruń, Poland
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16
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Does the Presence of a Bond Path Really Mean Interatomic Stabilization? The Case of the Ng@Superphane (Ng = He, Ne, Ar, and Kr) Endohedral Complexes. Symmetry (Basel) 2021. [DOI: 10.3390/sym13122241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Using a fairly structurally flexible and, therefore, very suitable for this type of research, superphane molecule, we demonstrate that the inclusion of a noble gas atom (Ng = He, Ne, Ar, and Kr) inside it and, thus, the formation of the Ng@superphane endohedral complex, leads to its ‘swelling’. Positive values of both the binding and strain energies prove that encapsulation and in turn ‘swelling’ of the superphane molecule is energetically unfavorable and that the Ng⋯C interactions in the interior of the cage are destabilizing, i.e., repulsive. Additionally, negative Mayer Bond Orders indicate the antibonding nature of Ng⋯C contacts. This result in combination with the observed Ng⋯C bond paths shows that the presence of a bond path in the molecular graph does not necessarily prove interatomic stabilization. It is shown that the obtained conclusions do not depend on the computational methodology, i.e., the method and the basis set used. However, on the contrary, the number of bond paths may depend on the methodology. This is yet another disadvantageous finding that does not favor the treatment of bond paths on molecular graphs as indicators of chemical bonds. The Kr@superphane endohedral complex features one of the longest C–C bonds ever reported (1.753 Å).
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17
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Michalczyk M, Zierkiewicz W, Wysokiński R, Scheiner S. Triel bonds within anion ···anion complexes. Phys Chem Chem Phys 2021; 23:25097-25106. [PMID: 34751289 DOI: 10.1039/d1cp04296c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The ability of two anions to interact with one another is tested in the context of pairs of TrX4- homodimers, where Tr represents any of the triel atoms B, Al, Ga, In, or Tl, and X refers to a halogen substituent F, Cl, or Br. None of these pairs engage in a stable complex in the gas phase, but the situation reverses in water where the two monomers are held together by Tr⋯X triel bonds, complemented by stabilizing interactions between X atoms. Some of these bonds are quite strong, notably those involving TrF4-, with interaction energies surpassing 30 kcal mol-1. Others are very much weaker, with scarcely exothermic binding energies. The highly repulsive electrostatic interactions are counteracted by large polarization energies.
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Affiliation(s)
- Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Rafał Wysokiński
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.
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18
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Jabłoński M. Theoretical Study of N-Heterocyclic-Carbene-ZnX 2 (X = H, Me, Et) Complexes. MATERIALS 2021; 14:ma14206147. [PMID: 34683739 PMCID: PMC8539904 DOI: 10.3390/ma14206147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/24/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022]
Abstract
This article discusses the properties of as many as 30 carbene–ZnX2 (X = H, Me, Et) complexes featuring a zinc bond C⋯Zn. The group of carbenes is represented by imidazol-2-ylidene and its nine derivatives (labeled as IR), in which both hydrogen atoms of N-H bonds have been substituted by R groups with various spatial hindrances, from the smallest Me, iPr, tBu through Ph, Tol, and Xyl to the bulkiest Mes, Dipp, and Ad. The main goal is to study the relationship between type and size of R and X and both the strength of C⋯Zn and the torsional angle of the ZnX2 plane with respect to the plane of the imidazol-2-ylidene ring. Despite the considerable diversity of R and X, the range of dC⋯Zn is quite narrow: 2.12–2.20 Å. On the contrary, D0 is characterized by a fairly wide range of 18.5–27.4 kcal/mol. For the smallest carbenes, the ZnX2 molecule is either in the plane of the carbene or is only slightly twisted with respect to it. The twist angle becomes larger and more varied with the bulkier R. However, the value of this angle is not easy to predict because it results not only from the presence of steric effects but also from the possible presence of various interatomic interactions, such as dihydrogen bonds, tetrel bonds, agostic bonds, and hydrogen bonds. It has been shown that at least some of these interactions may have a non-negligible influence on the structure of the IR–ZnX2 complex. This fact should be taken into account in addition to the commonly discussed R⋯X steric repulsion.
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Affiliation(s)
- Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland
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19
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Methyl groups as widespread Lewis bases in noncovalent interactions. Nat Commun 2021; 12:5030. [PMID: 34413293 PMCID: PMC8376930 DOI: 10.1038/s41467-021-25314-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/29/2021] [Indexed: 11/08/2022] Open
Abstract
It is well known that, under certain conditions, C(sp3) atoms behave, via their σ-hole, as Lewis acids in tetrel bonding. Here, we show that methyl groups, when bound to atoms less electronegative than carbon, can counterintuitively participate in noncovalent interactions as electron density donors. Thousands of experimental structures are found in which methyl groups behave as Lewis bases to establish alkaline, alkaline earth, triel, tetrel, pnictogen, chalcogen and halogen bonds. Theoretical calculations confirm the high directionality and significant strength of the interactions that arise from a common pattern based on the electron density holes model. Moreover, despite the absence of lone pairs, methyl groups are able to transfer charge from σ bonding orbitals into empty orbitals of the electrophile to reinforce the attractive interaction.
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20
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Molecular Tailoring Approach for the Estimation of Intramolecular Hydrogen Bond Energy. Molecules 2021; 26:molecules26102928. [PMID: 34069140 PMCID: PMC8155843 DOI: 10.3390/molecules26102928] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/29/2022] Open
Abstract
Hydrogen bonds (HBs) play a crucial role in many physicochemical and biological processes. Theoretical methods can reliably estimate the intermolecular HB energies. However, the methods for the quantification of intramolecular HB (IHB) energy available in the literature are mostly empirical or indirect and limited only to evaluating the energy of a single HB. During the past decade, the authors have developed a direct procedure for the IHB energy estimation based on the molecular tailoring approach (MTA), a fragmentation method. This MTA-based method can yield a reliable estimate of individual IHB energy in a system containing multiple H-bonds. After explaining and illustrating the methodology of MTA, we present its use for the IHB energy estimation in molecules and clusters. We also discuss the use of this method by other researchers as a standard, state-of-the-art method for estimating IHB energy as well as those of other noncovalent interactions.
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21
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Altun Z, Bleda EA, Trindle C. Focal Point Evaluation of Energies for Tautomers and Isomers for 3-Hydroxy-2-Butenamide: Evaluation of Competing Internal Hydrogen Bonds of Types -OH…O=, -OH…N, -NH…O=, and CH…X (X=O and N). Molecules 2021; 26:molecules26092623. [PMID: 33946257 PMCID: PMC8124485 DOI: 10.3390/molecules26092623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/22/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022] Open
Abstract
The title compound is a small molecule with many structural variations; it can illustrate a variety of internal hydrogen bonds, among other noncovalent interactions. Here we examine structures displaying hydrogen bonding between carbonyl oxygen and hydroxyl H; between carbonyl oxygen and amino H; hydroxyl H and amino N; hydroxyl O and amino H. We also consider H-bonding in its tautomer 2-oxopropanamide. By extrapolation algorithms applied to Hartree-Fock and correlation energies as estimated in HF, MP2, and CCSD calculations using the cc-pVNZ correlation-consistent basis sets (N = 2, 3, and 4) we obtain reliable relative energies of the isomeric forms. Assuming that such energy differences may be attributed to the presence of the various types of hydrogen bonding, we attempt to infer relative strengths of types of H-bonding. The Atoms in Molecules theory of Bader and the Local Vibrational Modes analysis of Cremer and Kraka are applied to this task. Hydrogen bonds are ranked by relative strength as measured by local stretching force constants, with the stronger =O…HO- > NH…O= > -OH…N well separated from a cluster > NH…O= ≈ >NH…OH ≈ CH…O= of comparable and intermediate strength. Weaker but still significant interactions are of type CH…N which is stronger than CH…OH.
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Affiliation(s)
- Zikri Altun
- Physics Department, Marmara University, Göztepe Kampus, Istanbul 34772, Turkey; (Z.A.); (E.A.B.)
| | - Erdi Ata Bleda
- Physics Department, Marmara University, Göztepe Kampus, Istanbul 34772, Turkey; (Z.A.); (E.A.B.)
| | - Carl Trindle
- Chemistry Department, University of Virginia, Charlottesville, VA 22902, USA
- Correspondence: ; Tel.: +1-4347709197
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22
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Jabłoński M. Study of Beryllium, Magnesium, and Spodium Bonds to Carbenes and Carbodiphosphoranes. Molecules 2021; 26:2275. [PMID: 33920004 PMCID: PMC8071025 DOI: 10.3390/molecules26082275] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/09/2021] [Accepted: 04/11/2021] [Indexed: 11/17/2022] Open
Abstract
The aim of this article is to present results of theoretical study on the properties of C⋯M bonds, where C is either a carbene or carbodiphosphorane carbon atom and M is an acidic center of MX2 (M = Be, Mg, Zn). Due to the rarity of theoretical data regarding the C⋯Zn bond (i.e., the zinc bond), the main focus is placed on comparing the characteristics of this interaction with C⋯Be (beryllium bond) and C⋯Mg (magnesium bond). For this purpose, theoretical studies (ωB97X-D/6-311++G(2df,2p)) have been performed for a large group of dimers formed by MX2 (X = H, F, Cl, Br, Me) and either a carbene ((NH2)2C, imidazol-2-ylidene, imidazolidin-2-ylidene, tetrahydropyrymid-2-ylidene, cyclopropenylidene) or carbodiphosphorane ((PH3)2C, (NH3)2C) molecule. The investigated dimers are characterized by a very strong charge transfer effect from either the carbene or carbodiphosphorane molecule to the MX2 one. This may even be over six times as strong as in the water dimer. According to the QTAIM and NCI method, the zinc bond is not very different than the beryllium bond, with both featuring a significant covalent contribution. However, the zinc bond should be definitely stronger if delocalization index is considered.
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Affiliation(s)
- Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń, Poland
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23
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Kumar N, Saha S, Sastry GN. Towards developing a criterion to characterize non-covalent bonds: a quantum mechanical study. Phys Chem Chem Phys 2021; 23:8478-8488. [DOI: 10.1039/d0cp05689h] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chemical bonds are central to chemistry, biology, and allied fields, but still, the criterion to characterize an interaction as a non-covalent bond has not been studied rigorously.
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Affiliation(s)
- Nandan Kumar
- Centre for Molecular Modeling
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Soumen Saha
- Centre for Molecular Modeling
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- Nagoya University
| | - G. Narahari Sastry
- Centre for Molecular Modeling
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- Academy of Scientific and Innovative Research (AcSIR)
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24
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Jabłoński M. A Critical Overview of Current Theoretical Methods of Estimating the Energy of Intramolecular Interactions. Molecules 2020; 25:molecules25235512. [PMID: 33255559 PMCID: PMC7728086 DOI: 10.3390/molecules25235512] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 11/16/2022] Open
Abstract
This article is probably the first such comprehensive review of theoretical methods for estimating the energy of intramolecular hydrogen bonds or other interactions that are frequently the subject of scientific research. Rather than on a plethora of numerical data, the main focus is on discussing the theoretical rationale of each method. Additionally, attention is paid to the fact that it is very often possible to use several variants of a particular method. Both of the methods themselves and their variants often give wide ranges of the obtained estimates. Attention is drawn to the fact that the applicability of a particular method may be significantly limited by various factors that disturb the reliability of the estimation, such as considerable structural changes or new important interactions in the reference system.
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Affiliation(s)
- Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
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25
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26
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Abstract
The fundamental underpinnings of noncovalent bonds are presented, focusing on the σ-hole interactions that are closely related to the H-bond. Different means of assessing their strength and the factors that control it are discussed. The establishment of a noncovalent bond is monitored as the two subunits are brought together, allowing the electrostatic, charge redistribution, and other effects to slowly take hold. Methods are discussed that permit prediction as to which site an approaching nucleophile will be drawn, and the maximum number of bonds around a central atom in its normal or hypervalent states is assessed. The manner in which a pair of anions can be held together despite an overall Coulombic repulsion is explained. The possibility that first-row atoms can participate in such bonds is discussed, along with the introduction of a tetrel analog of the dihydrogen bond.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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27
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Lomas JS, Rosenberg RE, Brémond E. Cooperativity in a cycloalkane-1,2/1,3-polyol corona: Topological hydrogen bonding in 1,2-diol motifs. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:957-968. [PMID: 32529717 DOI: 10.1002/mrc.5065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/06/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
A corona, consisting of 18 carbon atoms bearing 12 hydroxy groups in a continuous hydrogen-bonded chain, is built up by alternating degenerate conformations of alternating alkane-1,2-diol and 1,3-diol motifs. Geometries, proton nuclear magnetic resonance shifts and interaction energies for the dodecahydroxycyclo-octadecane and selected fragments are determined by density functional calculations at the B3LYP/6-311+G(d,p) level. Cooperative effects of O-H⋯O-H bonding are evident from the simple juxtaposition of these two motifs with a common OH group in butane-1,2,4-triol conformers. Bracketing a 1,2-diol motif with two 1,3-diol motifs in hexane-1,3,4,6-tetrol leads to a structure in which the 1,2-diol motif displays a bond critical point for hydrogen bonding. This is associated with enhancement of the shift of the hydrogen-bonded OH proton and of the corresponding H⋯O interaction energy. The full corona has a complete outer ring of O-H⋯O-H bond paths, and an inner ring of bond paths, due to C-H⋯H-C hydrogen-hydrogen bonding, which result in a central ring critical point. The topological O-H⋯O-H hydrogen bond, never seen in simple alkane-1,2-diols, is associated with cooperative enhancement of the H⋯O interaction energy, but this is not a necessary condition for a bond path: values for topological C-H⋯H-C hydrogen-hydrogen bonds can be as low as -0.4 kcal mol-1 .
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Affiliation(s)
- John S Lomas
- ITODYS, CNRS, Université de Paris, Paris, France
| | | | - Eric Brémond
- ITODYS, CNRS, Université de Paris, Paris, France
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28
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Scheiner S. Versatility of the Cyano Group in Intermolecular Interactions. Molecules 2020; 25:E4495. [PMID: 33007991 PMCID: PMC7582283 DOI: 10.3390/molecules25194495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 11/17/2022] Open
Abstract
Several cyano groups are added to an alkane, alkene, and alkyne group so as to construct a Lewis acid molecule with a positive region of electrostatic potential in the area adjoining these substituents. Although each individual cyano group produces only a weak π-hole, when two or more such groups are properly situated, they can pool their π-holes into one much more intense positive region that is located midway between them. A NH3 base is attracted to this site, where it forms a strong noncovalent bond to the Lewis acid, amounting to as much as 13.6 kcal/mol. The precise nature of the bonding varies a bit from one complex to the next but typically contains a tetrel bond to the C atoms of the cyano groups or the C atoms of the linkage connecting the C≡N substituents. The placement of the cyano groups on a cyclic system like cyclopropane or cyclobutane has a mild weakening effect upon the binding. Although F is comparable to C≡N in terms of electron-withdrawing power, the replacement of cyano by F substituents substantially weakens the binding with NH3.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Logan, UT 84322-0300, USA
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29
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Abstract
The question as to whether the F atom can engage in a halogen bond (XB) remains unsettled. This issue is addressed via density functional theory calculations which pair a wide range of organic and inorganic F-acids with various sorts of Lewis bases. From an energetic perspective, perfluorinated hydrocarbons with sp, sp2, or sp3 C-hybridization are unable to form an XB with an N-base, but a very weak bond can be formed if electron-withdrawing C≡N substituents are added to the acid. There is little improvement for inorganic acids O2NF, FOF, ClF, BrF, SiF4, or GeF4, but F2 is capable of a stronger XB of up to 5 kcal/mol. These results are consistent with a geometric criterion, which compares the intermolecular equilibrium distance with the sum of atomic van der Waals radii. The intensity of the σ-hole on the F atom has predictive value in that a Vs,max of at least 10-15 kcal/mol is required for XB formation. Adding a positive charge to the Lewis acid enhances the strength of any XB and even more so if the base is anionic. The acid-base interaction induces a contraction of the r(AF) covalent bond in the acid in most cases and a deshielding of the NMR signal of the F nucleus.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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30
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Anisimov AA, Ananyev IV. Interatomic exchange-correlation interaction energy from a measure of quantum theory of atoms in molecules topological bonding: A diatomic case. J Comput Chem 2020; 41:2213-2222. [PMID: 32731310 DOI: 10.1002/jcc.26390] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 01/01/2023]
Abstract
The potential relations between the measure of topological interatomic bonding-integrals of electron density with respect to internuclear axis over the corresponding quantum theory of atoms in molecules (QTAIM)-defined interatomic surface (IAS)-and interatomic exchange-correlation contributions from the interacting quantum atoms approach are discussed. The quantum chemical computations of 38 equilibrium diatomic systems at different levels of theory (HF, MP2, MP4SDQ, and CCSD) are invoked to support abstract considerations. Parameters of excellent correlations between IAS integrals and interatomic exchange-correlation energy are found by the optimization. The performance of these trends depends on the accuracy of the electronic correlation treatment. The resulting trends are a unique feature of equilibrium states, whereas more complicated dependencies are explored for several systems at non-equilibrium conditions. The relations of established trends with other IAS-based estimations of strength of bonding interactions between topological atoms and issues explored for multiatomic systems are briefly discussed.
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Affiliation(s)
- Aleksei A Anisimov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, Moscow, 119991, GSP-1, Russia
| | - Ivan V Ananyev
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, Moscow, 119991, GSP-1, Russia.,National Research University Higher School of Economics, Miasnitskaya Str. 20, Moscow, 101000, Russia
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31
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Ibrahim MAA, Mahmoud AHM, Moussa NAM. Comparative investigation of ±σ–hole interactions of carbon-containing molecules with Lewis bases, acids and di-halogens. CHEMICAL PAPERS 2020. [DOI: 10.1007/s11696-020-01187-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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32
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Delouche T, Mokrai R, Roisnel T, Tondelier D, Geffroy B, Nyulászi L, Benkő Z, Hissler M, Bouit PA. Naphthyl-Fused Phosphepines: Luminescent Contorted Polycyclic P-Heterocycles. Chemistry 2020; 26:1856-1863. [PMID: 31799704 DOI: 10.1002/chem.201904490] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Indexed: 11/12/2022]
Abstract
This article presents the synthesis of a new family of naphthyl-fused phosphepines through Ni-mediated C-C coupling. Interestingly, the chlorophosphine oxide intermediate shows strong resistance toward oxidation/hydrolysis owing to a combination of steric hindrance and pnictogen interactions. However, it can undergo substitution reactions under specific conditions. The optical/redox properties and the electronic structure of these new π-systems were studied experimentally (UV/Vis absorption, emission, cyclic voltammetry) and computationally (TD-DFT calculations, NICS investigation). Taking advantage of the luminescence of these derivatives, a blue-emitting OLED has been prepared, highlighting that these novel π-conjugated P-heterocycles appear to be promising building blocks for solid-state lighting applications.
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Affiliation(s)
- Thomas Delouche
- CNRS, ISCR-UMR 6226, Université Rennes, 35000, Rennes, France
| | - Réka Mokrai
- CNRS, ISCR-UMR 6226, Université Rennes, 35000, Rennes, France.,Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellert ter 4, 1111, Budapest, Hungary
| | - Thierry Roisnel
- CNRS, ISCR-UMR 6226, Université Rennes, 35000, Rennes, France
| | - Denis Tondelier
- LPICM, CNRS, Ecole Polytechnique, IPParis, 91128, Palaiseau, France
| | - Bernard Geffroy
- LICSEN, NIMBE, CEA, CNRS, CEA Saclay, Université Paris-Saclay, 91191, Gif-sur-Yvette Cedex, France
| | - László Nyulászi
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellert ter 4, 1111, Budapest, Hungary.,MTA-BME Computation Driven Chemistry Research Group, Szt. Gellert ter 4, 1111, Budapest, Hungary
| | - Zoltán Benkő
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellert ter 4, 1111, Budapest, Hungary
| | - Muriel Hissler
- CNRS, ISCR-UMR 6226, Université Rennes, 35000, Rennes, France
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33
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Jabłoński M, Krygowski TM. Study of the influence of intermolecular interaction on classical and reverse substituent effects in para-substituted phenylboranes. NEW J CHEM 2020. [DOI: 10.1039/d0nj01334j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The substituent effect and the reverse substituent effect in para-substituted phenylboranes and the influence of the intermolecular interaction of H⋯B type with either silane or methylsilane on the latter of these effects are extensively studied.
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Affiliation(s)
- Mirosław Jabłoński
- Faculty of Chemistry
- Nicolaus Copernicus University in Toruń
- 87-100 Toruń
- Poland
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34
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Scheiner S. The ditetrel bond: noncovalent bond between neutral tetrel atoms. Phys Chem Chem Phys 2020; 22:16606-16614. [DOI: 10.1039/d0cp03068f] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The ability of a tetrel atom to serve in the capacity of electron donor in a σ-hole noncovalent bond is tested by quantum calculations.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry
- Utah State University Logan
- Logan
- USA
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35
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Oliveira VP, Marcial BL, Machado FBC, Kraka E. Metal-Halogen Bonding Seen through the Eyes of Vibrational Spectroscopy. MATERIALS 2019; 13:ma13010055. [PMID: 31861904 PMCID: PMC6982077 DOI: 10.3390/ma13010055] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 12/09/2019] [Accepted: 12/15/2019] [Indexed: 11/17/2022]
Abstract
Incorporation of a metal center into halogen-bonded materials can efficiently fine-tune the strength of the halogen bonds and introduce new electronic functionalities. The metal atom can adopt two possible roles: serving as halogen acceptor or polarizing the halogen donor and acceptor groups. We investigated both scenarios for 23 metal–halogen dimers trans-M(Y2)(NC5H4X-3)2 with M = Pd(II), Pt(II); Y = F, Cl, Br; X = Cl, Br, I; and NC5H4X-3 = 3-halopyridine. As a new tool for the quantitative assessment of metal–halogen bonding, we introduced our local vibrational mode analysis, complemented by energy and electron density analyses and electrostatic potential studies at the density functional theory (DFT) and coupled-cluster single, double, and perturbative triple excitations (CCSD(T)) levels of theory. We could for the first time quantify the various attractive contacts and their contribution to the dimer stability and clarify the special role of halogen bonding in these systems. The largest contribution to the stability of the dimers is either due to halogen bonding or nonspecific interactions. Hydrogen bonding plays only a secondary role. The metal can only act as halogen acceptor when the monomer adopts a (quasi-)planar geometry. The best strategy to accomplish this is to substitute the halo-pyridine ring with a halo-diazole ring, which considerably strengthens halogen bonding. Our findings based on the local mode analysis provide a solid platform for fine-tuning of existing and for design of new metal–halogen-bonded materials.
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Affiliation(s)
- Vytor P. Oliveira
- Departamento de Química, Instituto Tecnológico de Aeronáutica (ITA), São José dos Campos, 12228-900 São Paulo, Brazil; (V.P.O.); (F.B.C.M.)
| | - Bruna L. Marcial
- Núcleo de Química, Instituto Federal Goiano (IF Goiano), Campus Morrinhos, 75650-000 Goiás, Brazil;
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica (ITA), São José dos Campos, 12228-900 São Paulo, Brazil; (V.P.O.); (F.B.C.M.)
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA
- Correspondence: ; Tel.: +1-214-768-2611
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Bifurcated Triel Bonds—Hydrides and Halides of 1,2-Bis(Dichloroboryl)Benzene and 1,8-Bis(Dichloroboryl)Naphthalene. CRYSTALS 2019. [DOI: 10.3390/cryst9100503] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
MP2/aug-cc-pVTZ calculations were performed on hydrides, fluorides, and chlorides of 1,8-bis(dichloroboryl)naphthalene and 1,2-bis(dichloroboryl)benzene. The theoretical analysis of BHB−, BFB−, and BClB− arrangements occurring in these complexes and classified as bifurcated triel bonds was partly based on decomposition of the energy of interaction. The latter was carried out for structures optimized using the DFT method. The complexes analyzed were characterized by a partly covalent character of the links to the hydride and halide anions; these anions strongly influenced the geometry of the complexes. The boron centers’ links for the neutral 1,8-bis(dichloroboryl)naphthalene and 1,2-bis(dichloroboryl)benzene molecules were characterized by approximately trigonal and planar configurations, while for anionic complexes, tetrahedral configurations were observed. The crystal structures of compounds related to species calculated here were found in the Cambridge Structural Database (CSD).
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Honacker C, Kappelt B, Jabłoński M, Hepp A, Layh M, Rogel F, Uhl W. Aluminium Functionalized Germanes: Intramolecular Activation of Ge–H Bonds, Formation of a Dihydrogen Bond and Facile Hydrogermylation of Unsaturated Substrates. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201900543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Christian Honacker
- Institut für Anorganische und Analytische Chemie Universität Münster Corrensstraße 30 48149 Münster Germany
| | - Benedikt Kappelt
- Institut für Anorganische und Analytische Chemie Universität Münster Corrensstraße 30 48149 Münster Germany
| | - Mirosław Jabłoński
- Department of Quantum Chemistry Faculty of Chemistry Nicolaus Copernicus University in Toruń 7, Gagarina St. 87‐100 Toruń Poland
| | - Alexander Hepp
- Institut für Anorganische und Analytische Chemie Universität Münster Corrensstraße 30 48149 Münster Germany
| | - Marcus Layh
- Institut für Anorganische und Analytische Chemie Universität Münster Corrensstraße 30 48149 Münster Germany
| | - Friedhelm Rogel
- Institut für Anorganische und Analytische Chemie Universität Münster Corrensstraße 30 48149 Münster Germany
| | - Werner Uhl
- Institut für Anorganische und Analytische Chemie Universität Münster Corrensstraße 30 48149 Münster Germany
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Alternative trajectories of electron density to plot the atomic connectivity graph in the region of nondirectional interactions. Russ Chem Bull 2019. [DOI: 10.1007/s11172-019-2560-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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On the ability of pnicogen atoms to engage in both σ and π-hole complexes. Heterodimers of ZF 2C 6H 5 (Z = P, As, Sb, Bi) and NH 3. J Mol Model 2019; 25:152. [PMID: 31069527 DOI: 10.1007/s00894-019-4031-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/07/2019] [Indexed: 01/11/2023]
Abstract
When bound to a pair of F atoms and a phenyl ring, a pyramidal pnicogen (Z) atom can form a pnicogen bond wherein an NH3 base lies opposite one F atom. In addition to this σ-hole complex, the ZF2C6H5 molecule can distort in such a way that the NH3 approaches on the opposite side to the lone pair on Z, where there is a so-called π-hole. The interaction energies of these π-hole dimers are roughly 30 kcal/mol, much larger than the equivalent quantities for the σ-hole complexes, which are only 4-13 kcal/mol. On the other hand, this large interaction energy is countered by the considerable deformation energy required for the Lewis acid to adopt the geometry necessary to form the π-hole complex. The overall energetics of the complexation reaction are thus more exothermic for the σ-hole dimers than for the π-hole dimers.
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Sarkar R, Kundu TK. Nonbonding interaction analyses on PVDF/[BMIM][BF 4] complex system in gas and solution phase. J Mol Model 2019; 25:131. [PMID: 31025122 DOI: 10.1007/s00894-019-4020-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/29/2019] [Indexed: 11/24/2022]
Abstract
The present study provides a detailed quantum chemical description of the physicochemical interactions between poly-vinylidene fluoride (PVDF) and 1-butyl-3-methyl-imidazolium tetrafluoro borate ([BMIM][BF4]) ionic liquid (IL). Geometry optimization and frequency calculations are carried out for four monomer units of α- and β-PVDF, [BMIM][BF4], and PVDF/[BMIM][BF4] using dispersion corrected density functional theory. The effects of solvation on the systems under study are demonstrated for three polar aprotic solvents, namely tetra-hydrofuran (THF), acetone, and n,n-dimethyl formamide (DMF) using the integral equation formalism polarizable continuum model (IEFPCM). Calculated negative solvation free energy values suggest solution phase stability of the systems under study. Binding and interaction energies for β-PVDF/IL are found higher in magnitude than those for α-PVDF/IL. The nonbonding interaction phenomenon of β-PVDF/[BMIM][BF4] is elucidated on the basis of natural bond orbital (NBO), Bader's quantum theory of atoms in molecules (QTAIM), delocalization indices, Hirshfeld surface, and reduced density gradient (RDG) analyses. Both anions and cations of ionic liquids are found to show weak van der Waals interaction with PVDF molecule but the anion ([BF4]-)/PVDF interaction is found to be stronger than cation ([BMIM]+)/PVDF interaction. Inter-unit C-H⋯F type hydrogen bonds are found to show improper (causing blue shifts in vibrational frequencies) nature. Frontier molecular orbital analysis is carried out, and different chemical parameters like electronegativity, chemical potential, chemical hardness and softness, and electrophilicity index are calculated using Koopmans' theorem. Thermochemical calculations are also performed, and the variation in different standard thermodynamic parameters with temperature is formulated. Graphical abstract (a) Hirshfeld surface mapped onto electron density and (b) NCI isosurfaces showing inter-unit interactions of β-PVDF/[BMIM][BF4].
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Affiliation(s)
- Ranjini Sarkar
- Department of Metallurgical and Materials Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - T K Kundu
- Department of Metallurgical and Materials Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.
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Jabłoński M. On the Uselessness of Bond Paths Linking Distant Atoms and on the Violation of the Concept of Privileged Exchange Channels. ChemistryOpen 2019; 8:497-507. [PMID: 31019875 PMCID: PMC6470636 DOI: 10.1002/open.201900109] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Indexed: 11/09/2022] Open
Abstract
We refer to frequently used determinants suggesting dominant interactions between distant atoms in various dimers. First of all, we show, against the still-prevailling opinion, that, in general, bond paths have nothing in common with dominant intermolecular interactions and therefore they are useless in such cases. Quite the contrary, reliable information about dominant intermolecular interactions can be obtained by means of electrostatic potential maps, which very convincingly explain mutual orientation of molecules in a dimer. For the first time, numerous examples of interactions that violate both the concept of privileged exchange channels proposed by Pendás and his collaborators as well as inequalities obtained by Tognetti and Joubert for the β parameter related to secondary interactions are presented. The possible cause of this violation is suggested. We also show that the so-called counterintuitive bond paths result from quite natural behavior of the electron density gradient vector, i. e. searching for those areas of space that are characterized by large values of electron density or the most expanded its distributions.
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Affiliation(s)
- Mirosław Jabłoński
- Department of Quantum Chemistry, Faculty of ChemistryNicolaus Copernicus University in Toruń7-Gagarina St.87-100ToruńPoland
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Affiliation(s)
- Mirosław Jabłoński
- Department of Quantum Chemistry, Faculty of ChemistryNicolaus Copernicus University in Toruń 7‐Gagarina St. Toruń 87‐100 Poland
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Cooperative Effects in Weak Interactions: Enhancement of Tetrel Bonds by Intramolecular Hydrogen Bonds. Molecules 2019; 24:molecules24020308. [PMID: 30654469 PMCID: PMC6359400 DOI: 10.3390/molecules24020308] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/08/2019] [Accepted: 01/09/2019] [Indexed: 12/02/2022] Open
Abstract
A series of silyl and germanium complexes containing halogen atoms (fluorine and chlorine atoms) and exhibiting tetrel bonds with Lewis bases were analyzed by means of Møller-Plesset computational theory. Binding energies of germanium derivatives were more negative than silicon ones. Amongst the different Lewis bases utilized, ammonia produced the strongest tetrel bonded complexes in both Ge and Si cases, and substitution of the F atom by Cl led to stronger complexes with an ethylene backbone. However, with phenyl backbones, the fluorosilyl complexes were shown to be less stable than the chlorosilyl ones, but the opposite occurred for halogermanium complexes. In all the cases studied, the presence of a hydroxyl group enhanced the tetrel bond. That effect becomes more remarkable when an intramolecular hydrogen bond between the halogen and the hydrogen atom of the hydroxyl group takes places.
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