1
|
Charry J, Tkatchenko A. van der Waals Radii of Free and Bonded Atoms from Hydrogen (Z = 1) to Oganesson (Z = 118). J Chem Theory Comput 2024; 20:7469-7478. [PMID: 39208255 PMCID: PMC11391583 DOI: 10.1021/acs.jctc.4c00784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Reliable numerical values of van der Waals (vdW) radii are required for constructing empirical force fields, vdW-inclusive density functional, and quantum-chemical methods, as well as for implicit solvent models. However, multiple definitions exist for vdW radii, involving either equilibrium or the closest contact distances between free or bonded atoms within molecules or crystals. For the paradigmatic case of the hydrogen atom, its reported vdW radius fluctuates between 2.15 and 3.70 Bohr depending on the definition, leading to a high uncertainty in calculations and different conceptual interpretations of noncovalent interactions. In this work, we systematically review different definitions and methodologies to establish the free and bonded vdW radii for hydrogen, based on equilibrium vdW distances in noncovalently bonded molecules, enveloping electron density cutoffs, noncovalent positron bonds in hydrogen anion dimer, vacuum virtual photon cloud caused by the hydrogen atom, and atomic dipole polarizability. By doing so, we show that the vdW radius of the free hydrogen atom is 3.16 ± 0.06 Bohr. By employing the most general and elegant definition of atomic vdW radius as a function of the atomic polarizability, we tabulate consistent values of vdW radii for all atoms in the periodic table up to Z = 118.
Collapse
Affiliation(s)
- Jorge Charry
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| |
Collapse
|
2
|
Wang S, Liu X, Zhang Y, Li S, Bo X, Wei L, Niu W, Wu H, Pu Y, Li F. Modifying electronic and optical properties of violet phosphorus through variable fluorine coverage. J Comput Chem 2024; 45:1737-1743. [PMID: 38622788 DOI: 10.1002/jcc.27369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/25/2024] [Accepted: 04/06/2024] [Indexed: 04/17/2024]
Abstract
We present a comprehensive investigation of the electronic properties of fluorinated monolayer violet phosphorus using first-principles calculations. Our results reveal a strong dependence of the electronic properties on the different fluorine coverages of fluorination. As the fluorine coverage increases, monolayer violet phosphorus undergoes a significant transition from a wide direct bandgap semiconductor to a narrow indirect bandgap semiconductor. Moreover, both semi-fluorinated and fully fluorinated monolayer violet phosphorus exhibit advantageous semiconducting characteristics, with a tunable bandgap of 0.50 ~ 1.04 eV under biaxial strain ranging from -6% to 6%. Notably, the fully fluorinated monolayer violet phosphorus demonstrates a higher coefficient of light absorption within the visible range. Therefore, our findings highlight the tunability of monolayer violet phosphorus properties through the absorption of various fluorine coverages, providing valuable insights for the design and development of novel semiconductor devices based on this material.
Collapse
Affiliation(s)
- Suen Wang
- School of Science & New Energy Technology Engineering Laboratory of Jiangsu Province, Nanjing University of Posts and Telecommunications (NJUPT), Nanjing, China
| | - Xiaoyu Liu
- School of Science & New Energy Technology Engineering Laboratory of Jiangsu Province, Nanjing University of Posts and Telecommunications (NJUPT), Nanjing, China
| | - Yang Zhang
- School of Science & New Energy Technology Engineering Laboratory of Jiangsu Province, Nanjing University of Posts and Telecommunications (NJUPT), Nanjing, China
| | - Shasha Li
- School of Science & New Energy Technology Engineering Laboratory of Jiangsu Province, Nanjing University of Posts and Telecommunications (NJUPT), Nanjing, China
| | - Xiangyan Bo
- School of Science & New Energy Technology Engineering Laboratory of Jiangsu Province, Nanjing University of Posts and Telecommunications (NJUPT), Nanjing, China
| | - Lujun Wei
- School of Science & New Energy Technology Engineering Laboratory of Jiangsu Province, Nanjing University of Posts and Telecommunications (NJUPT), Nanjing, China
| | - Wei Niu
- School of Science & New Energy Technology Engineering Laboratory of Jiangsu Province, Nanjing University of Posts and Telecommunications (NJUPT), Nanjing, China
| | - Hong Wu
- School of Science & New Energy Technology Engineering Laboratory of Jiangsu Province, Nanjing University of Posts and Telecommunications (NJUPT), Nanjing, China
| | - Yong Pu
- School of Science & New Energy Technology Engineering Laboratory of Jiangsu Province, Nanjing University of Posts and Telecommunications (NJUPT), Nanjing, China
| | - Feng Li
- School of Science & New Energy Technology Engineering Laboratory of Jiangsu Province, Nanjing University of Posts and Telecommunications (NJUPT), Nanjing, China
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Wang W, Liu CD, Fan CC, Fu XB, Jing CQ, Jin ML, You YM, Zhang W. Rational Design of 2D Metal Halide Perovskites with Low Congruent Melting Temperature and Large Melt-Processable Window. J Am Chem Soc 2024; 146:9272-9284. [PMID: 38517743 DOI: 10.1021/jacs.4c00768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
Metal halide perovskites (MHPs) have garnered significant attention due to their distinctive optical and electronic properties, coupled with excellent processability. However, the thermal characteristics of these materials are often overlooked, which can be harnessed to cater to diverse application scenarios. We showcase the efficacy of lowering the congruent melting temperature (Tm) of layered 2D MHPs by employing a strategy that involves the modification of flexible alkylammonium through N-methylation and I-substitution. Structural-property analysis reveals that the N-methylation and I-substitution play pivotal roles in reducing hydrogen bond interactions between the organic components and inorganic parts, lowering the rotational symmetry number of the cation and restricting the residual motion of the cations. Additional I···I interactions enhance intermolecular interactions and lead to improved molten stability, as evidenced by a higher viscosity. The 2D MHPs discussed in this study exhibit low Tm and wide melt-processable windows, e.g., (DMIPA)2PbI4 showcasing a low Tm of 98 °C and large melt-processable window of 145 °C. The efficacy of the strategy was further validated when applied to bromine-substituted 2D MHPs. Lowering the Tm and enhancing the molten stability of the MHPs hold great promise for various applications, including glass formation, preparation of high-quality films for photodetection, and fabrication of flexible devices.
Collapse
Affiliation(s)
- Wei Wang
- Jiangsu Key Laboratory for Science and Applications of Molecular Ferroelectrics and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Cheng-Dong Liu
- Jiangsu Key Laboratory for Science and Applications of Molecular Ferroelectrics and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chang-Chun Fan
- Jiangsu Key Laboratory for Science and Applications of Molecular Ferroelectrics and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Xiao-Bin Fu
- Department of Molten Salt Chemistry and Engineering, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Chang-Qing Jing
- Jiangsu Key Laboratory for Science and Applications of Molecular Ferroelectrics and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Ming-Liang Jin
- Jiangsu Key Laboratory for Science and Applications of Molecular Ferroelectrics and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yu-Meng You
- Jiangsu Key Laboratory for Science and Applications of Molecular Ferroelectrics and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Wen Zhang
- Jiangsu Key Laboratory for Science and Applications of Molecular Ferroelectrics and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| |
Collapse
|
5
|
Roos G, Murray JS. Probing intramolecular interactions using molecular electrostatic potentials: changing electron density contours to unveil both attractive and repulsive interactions. Phys Chem Chem Phys 2024; 26:7592-7601. [PMID: 38362927 DOI: 10.1039/d3cp06005e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
We focus on intramolecular interactions, using the electrostatic potential plotted on iso-density surfaces to lead the way. We show that plotting the electrostatic potential on varying iso-density envelopes much closer to the nuclei than the commonly used 0.001 a.u. contour can reveal the driving forces for such interactions, whether they be stabilizing or destabilizing. Our approach involves optimizing the structures of molecules exhibiting intramolecular interactions and then finding the contour of the electronic density which allows the interacting atoms to be separated; we call this the nearly-touching contour. The electrostatic potential allows then to identify the intramolecular interactions as either attractive or repulsive. The discussed 1,5- and 1,6-intramolecular interactions in o-bromophenol and o-nitrophenol are attractive, while the interactions between terminal methyl hydrogens in diethyl disulfides (as shown recently) and those between the closest hydrogens in planar biphenyl and phenanthrene are clearly repulsive in nature. For the attractive 1,4-interactions in trinitromethane and chlorotrinitromethane, and the 1,3-S⋯N and the 1,4-Si⋯N interactions in the ClH2Si(CH2)nNH2 series, the lack of (3,-1) bond critical points has often been cited as reason to not identify such interactions as attractive in nature. Here, by looking at the nearly-touching contours we see that bond critical points are neither necessary nor sufficient for attractive interactions, as others have pointed out, and in some instances also pointing to repulsive interactions, as the examples of planar biphenyl and phenanthrene discussed in this work show.
Collapse
Affiliation(s)
- Goedele Roos
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Jane S Murray
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA.
| |
Collapse
|
6
|
Murray JS. The Formation of σ-Hole Bonds: A Physical Interpretation. Molecules 2024; 29:600. [PMID: 38338346 PMCID: PMC10856353 DOI: 10.3390/molecules29030600] [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: 12/28/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
This paper discusses two quite different computational experiments relating to the formation of σ-hole bonds A···B. The first involves looking at the complex at equilibrium and finding the contour X of the electronic density which allows the iso-density envelopes of A and B to be nearly touching. This contour increases, becoming closer to the nuclei, as the strength of the interaction increases. The second experiment involves allowing A and B to approach each other, with the aim of finding the distance at which their 0.001 a.u. iso-density envelopes are nearly merging into one envelope. What is found in the second experiment may be somewhat surprising, in that the ratio of the distance between interacting atoms at this nearly merging point-divided by the sum of the van der Waals radii of these atoms-covers a narrow range, typically between 1.2 and 1.3. It is intriguing to note that for the dataset presented, approaching molecules attracted to each other appear to do so unknowing of the strength of their ultimate interaction. This second experiment also supports the notion that one should expect favorable interactions, in some instances, to have close contacts significantly greater than the sums of the van der Waals radii.
Collapse
Affiliation(s)
- Jane S Murray
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA
| |
Collapse
|
7
|
Stoy A, Jürgensen M, Millidoni C, Berthold C, Ramler J, Martínez S, Buchner MR, Lichtenberg C. Bismuth in Dynamic Covalent Chemistry: Access to a Bowl-Type Macrocycle and a Barrel-Type Heptanuclear Complex Cation. Angew Chem Int Ed Engl 2023; 62:e202308293. [PMID: 37522394 DOI: 10.1002/anie.202308293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/01/2023]
Abstract
Dynamic covalent chemistry (DCvC) is a powerful and widely applied tool in modern synthetic chemistry, which is based on the reversible cleavage and formation of covalent bonds. One of the inherent strengths of this approach is the perspective to reversibly generate in an operationally simple approach novel structural motifs that are difficult or impossible to access with more traditional methods and require multiple bond cleaving and bond forming steps. To date, these fundamentally important synthetic and conceptual challenges in the context of DCvC have predominantly been tackled by exploiting compounds of lighter p-block elements, even though heavier p-block elements show low bond dissociation energies and appear to be ideally suited for this approach. Here we show that a dinuclear organometallic bismuth compound, containing BiMe2 groups that are connected by a thioxanthene linker, readily undergoes selective and reversible cleavage of its Bi-C bonds upon exposure to external stimuli. The exploitation of DCvC in the field of organometallic heavy p-block chemistry grants access to unprecedented macrocyclic and barrel-type oligonuclear compounds.
Collapse
Affiliation(s)
- Andreas Stoy
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Str. 4, 35032, Marburg, Germany
| | - Malte Jürgensen
- Institute of Inorganic Chemistry, Julius-Maximilians-University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Christina Millidoni
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Str. 4, 35032, Marburg, Germany
| | - Chantsalmaa Berthold
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Str. 4, 35032, Marburg, Germany
| | - Jacqueline Ramler
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Str. 4, 35032, Marburg, Germany
| | - Sebastián Martínez
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Str. 4, 35032, Marburg, Germany
| | - Magnus R Buchner
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Str. 4, 35032, Marburg, Germany
| | - Crispin Lichtenberg
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Str. 4, 35032, Marburg, Germany
| |
Collapse
|
8
|
Liang H, Bi X, Chen H, He T, Lin Y, Zhang Y, Ma K, Feng W, Ma Z, Long G, Li C, Kan B, Zhang H, Rakitin OA, Wan X, Yao Z, Chen Y. A rare case of brominated small molecule acceptors for high-efficiency organic solar cells. Nat Commun 2023; 14:4707. [PMID: 37543678 PMCID: PMC10404295 DOI: 10.1038/s41467-023-40423-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023] Open
Abstract
Given that bromine possesses similar properties but extra merits of easily synthesizing and polarizing comparing to homomorphic fluorine and chlorine, it is quite surprising very rare high-performance brominated small molecule acceptors have been reported. This may be caused by undesirable film morphologies stemming from relatively larger steric hindrance and excessive crystallinity of bromides. To maximize the advantages of bromides while circumventing weaknesses, three acceptors (CH20, CH21 and CH22) are constructed with stepwise brominating on central units rather than conventional end groups, thus enhancing intermolecular packing, crystallinity and dielectric constant of them without damaging the favorable intermolecular packing through end groups. Consequently, PM6:CH22-based binary organic solar cells render the highest efficiency of 19.06% for brominated acceptors, more excitingly, a record-breaking efficiency of 15.70% when further thickening active layers to ~500 nm. By exhibiting such a rare high-performance brominated acceptor, our work highlights the great potential for achieving record-breaking organic solar cells through delicately brominating.
Collapse
Affiliation(s)
- Huazhe Liang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, The Centre of Nanoscale Science and Technology and Key Laboratory of Functional Polymer Materials, Renewable Energy Conversion and Storage Center (RECAST), College of Chemistry, Nankai University, 300071, Tianjin, China
| | - Xingqi Bi
- State Key Laboratory and Institute of Elemento-Organic Chemistry, The Centre of Nanoscale Science and Technology and Key Laboratory of Functional Polymer Materials, Renewable Energy Conversion and Storage Center (RECAST), College of Chemistry, Nankai University, 300071, Tianjin, China
| | - Hongbin Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, The Centre of Nanoscale Science and Technology and Key Laboratory of Functional Polymer Materials, Renewable Energy Conversion and Storage Center (RECAST), College of Chemistry, Nankai University, 300071, Tianjin, China
| | - Tengfei He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, The Centre of Nanoscale Science and Technology and Key Laboratory of Functional Polymer Materials, Renewable Energy Conversion and Storage Center (RECAST), College of Chemistry, Nankai University, 300071, Tianjin, China
| | - Yi Lin
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Center for Advanced Low-dimension Materials, College of Materials Science and Engineering, Donghua University, 201620, Shanghai, China
| | - Yunxin Zhang
- School of Materials Science and Engineering, National Institute for Advanced Materials, Renewable Energy Conversion and Storage Center (RECAST), Nankai University, 300350, Tianjin, China
| | - Kangqiao Ma
- State Key Laboratory and Institute of Elemento-Organic Chemistry, The Centre of Nanoscale Science and Technology and Key Laboratory of Functional Polymer Materials, Renewable Energy Conversion and Storage Center (RECAST), College of Chemistry, Nankai University, 300071, Tianjin, China
| | - Wanying Feng
- State Key Laboratory and Institute of Elemento-Organic Chemistry, The Centre of Nanoscale Science and Technology and Key Laboratory of Functional Polymer Materials, Renewable Energy Conversion and Storage Center (RECAST), College of Chemistry, Nankai University, 300071, Tianjin, China
| | - Zaifei Ma
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Center for Advanced Low-dimension Materials, College of Materials Science and Engineering, Donghua University, 201620, Shanghai, China
| | - Guankui Long
- School of Materials Science and Engineering, National Institute for Advanced Materials, Renewable Energy Conversion and Storage Center (RECAST), Nankai University, 300350, Tianjin, China
| | - Chenxi Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, The Centre of Nanoscale Science and Technology and Key Laboratory of Functional Polymer Materials, Renewable Energy Conversion and Storage Center (RECAST), College of Chemistry, Nankai University, 300071, Tianjin, China
| | - Bin Kan
- School of Materials Science and Engineering, National Institute for Advanced Materials, Renewable Energy Conversion and Storage Center (RECAST), Nankai University, 300350, Tianjin, China
| | - Hongtao Zhang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, The Centre of Nanoscale Science and Technology and Key Laboratory of Functional Polymer Materials, Renewable Energy Conversion and Storage Center (RECAST), College of Chemistry, Nankai University, 300071, Tianjin, China
| | - Oleg A Rakitin
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Xiangjian Wan
- State Key Laboratory and Institute of Elemento-Organic Chemistry, The Centre of Nanoscale Science and Technology and Key Laboratory of Functional Polymer Materials, Renewable Energy Conversion and Storage Center (RECAST), College of Chemistry, Nankai University, 300071, Tianjin, China
| | - Zhaoyang Yao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, The Centre of Nanoscale Science and Technology and Key Laboratory of Functional Polymer Materials, Renewable Energy Conversion and Storage Center (RECAST), College of Chemistry, Nankai University, 300071, Tianjin, China.
| | - Yongsheng Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, The Centre of Nanoscale Science and Technology and Key Laboratory of Functional Polymer Materials, Renewable Energy Conversion and Storage Center (RECAST), College of Chemistry, Nankai University, 300071, Tianjin, China.
| |
Collapse
|
9
|
Otte F, Kleinheider J, Grabe B, Hiller W, Busse F, Wang R, Kreienborg NM, Merten C, Englert U, Strohmann C. Gauging the Strength of the Molecular Halogen Bond via Experimental Electron Density and Spectroscopy. ACS OMEGA 2023; 8:21531-21539. [PMID: 37360450 PMCID: PMC10286298 DOI: 10.1021/acsomega.3c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/19/2023] [Indexed: 06/28/2023]
Abstract
Strong and weak halogen bonds (XBs) in discrete aggregates involving the same acceptor are addressed by experiments in solution and in the solid state. Unsubstituted and perfluorinated iodobenzenes act as halogen donors of tunable strength; in all cases, quinuclidine represents the acceptor. NMR titrations reliably identify the strong intermolecular interactions in solution, with experimental binding energies of approx. 7 kJ/mol. Interaction of the σ hole at the halogen donor iodine leads to a redshift in the symmetric C-I stretching vibration; this shift reflects the interaction energy in the halogen-bonded adducts and may be assessed by Raman spectroscopy in condensed phase even for weak XBs. An experimental picture of the electronic density for the XBs is achieved by high-resolution X-ray diffraction on suitable crystals. Quantum theory of atoms in molecules (QTAIM) analysis affords the electron densities and energy densities in the bond critical points of the halogen bonds and confirms stronger interaction for the shorter contacts. For the first time, the experimental electron density shows a significant effect on the atomic volumes and Bader charges of the quinuclidine N atoms, the halogen-bond acceptor: strong and weak XBs are reflected in the nature of their acceptor atom. Our experimental findings at the acceptor atom match the discussed effects of halogen bonding and thus the proposed concepts in XB activated organocatalysis.
Collapse
Affiliation(s)
- Felix Otte
- Inorganic
Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Johannes Kleinheider
- Inorganic
Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Bastian Grabe
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Wolf Hiller
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Franziska Busse
- Inorganic
Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Ruimin Wang
- Inorganic
Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
- Institute
of Molecular Science, Shanxi University, Wucheng Road 92, 030006 Taiyuan, P. R. China
| | - Nora M. Kreienborg
- Organic Chemistry
II, Ruhr University Bochum, Universitätstraße 150, 44801 Bochum, Germany
| | - Christian Merten
- Organic Chemistry
II, Ruhr University Bochum, Universitätstraße 150, 44801 Bochum, Germany
| | - Ulli Englert
- Inorganic
Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
- Institute
of Molecular Science, Shanxi University, Wucheng Road 92, 030006 Taiyuan, P. R. China
| | - Carsten Strohmann
- Inorganic
Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| |
Collapse
|
10
|
Roles of Hydrogen, Halogen Bonding and Aromatic Stacking in a Series of Isophthalamides. Symmetry (Basel) 2023. [DOI: 10.3390/sym15030738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
The synthesis and spectroscopic characterisation of six bis(5-X-pyridine-2-yl)isophthalamides (X = H, F, Br, Cl, I, NO2) are reported, together with five crystal structure analyses (for X = H, F to I). The isophthalamides span a range of conformations as syn/anti (H-DIP; I-DIP), anti/anti- (F-DIP; Br-DIP) and with both present in ratio 2:1 in Cl-DIP. The essentially isostructural F-DIP and Br-DIP molecules (using strong amide…amide interactions) aggregate into 2D molecular sheets that align with either F/H or Br atoms at the sheet surfaces (interfaces), respectively. Sheets are linked by weak C-H⋯F contacts in F-DIP and by Br⋯Br halogen bonding interactions as a ‘wall of bromines’ at the Br atom rich interfaces in Br-DIP. Cl-DIP is an unusual crystal structure incorporating both syn/anti and anti/anti molecular conformations in the asymmetric unit (Z’ = 3). The I-DIP•½(H2O) hemihydrate structure has a water molecule residing on a twofold axis between two I-DIPs and has hydrogen and N⋯I (Nc = 0.88) halogen bonding. The hydrate is central to an unusual synthon and involved in six hydrogen bonding interactions/contacts. Contact enrichment analysis on the Hirshfeld surface demonstrates that F-DIP, Cl-DIP and Br-DIP have especially over-represented halogen···halogen interactions. With the F-DIP, Cl-DIP and Br-DIP molecules having an elongated skeleton, the formation of layers of halogen atoms in planes perpendicular to the long unit cell axis occurs in the crystal packings. All six DIPs were analysed by ab initio calculations and conformational analysis; comparisons are made between their minimized structures and the five crystal structures. In addition, physicochemical properties are compared and assessed.
Collapse
|
11
|
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: 2.0] [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.
Collapse
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
| |
Collapse
|
12
|
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.
Collapse
|
13
|
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: 1.0] [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.
Collapse
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
| |
Collapse
|
14
|
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: 57] [Impact Index Per Article: 28.5] [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.
Collapse
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
| |
Collapse
|
15
|
Synthesis, crystal structure and theoretical calculation of di-n-butyltin (IV) carboxylate based on m-nitrobenzaldehyde oxime acetic acid. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
16
|
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: 1.5] [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.
Collapse
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;
| |
Collapse
|
17
|
Lowing the energy loss of organic solar cells by molecular packing engineering via multiple molecular conjugation extension. Sci China Chem 2022. [DOI: 10.1007/s11426-022-1264-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
18
|
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: 1.5] [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.
Collapse
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.)
| |
Collapse
|
19
|
Miller DK, Chernyshov IY, Torubaev YV, Rosokha SV. From weak to strong interactions: structural and electron topology analysis of the continuum from the supramolecular chalcogen bonding to covalent bonds. Phys Chem Chem Phys 2022; 24:8251-8259. [PMID: 35320823 DOI: 10.1039/d1cp05441d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The relationship between covalent and supramolecular bonding, and the criteria of the assignments of different interactions were explored via the review of selenium and tellurium containing structures in the Cambridge Structural Database and their computational analysis using Quantum Theory of Atoms in Molecules (QTAIM). This combined study revealed continuums of the interatomic Se⋯Br and Te⋯I distances, dCh⋯X, in the series of associations from the sums of the van der Waals radii of these atoms (rCh + rX) to their covalent bond lengths. The electron densities, ρ(r), at Bond Critical Points (BCPs) along the chalcogen bond paths increased gradually from about 0.01 a.u. common for the non-covalent interactions to about 0.1 a.u. typical for the covalent bonds. The log ρ(r) values fell on the same linear trend line when plotted against normalized interatomic distances, RXY = dCh⋯X/(rCh + rX). The transition from the positive to negative values of the energy densities, H(r), at the BCPs (related to a changeover of essentially non-covalent into partially covalent interactions) were observed at RXY ≈ 0.80. Synchronous changes of bonding characteristics with RXY (similar to that found earlier in the halogen-bonded systems) designated normalized interatomic separation as a critical factor determining the nature of these bondings. The uninterrupted continuums of Te⋯I and Se⋯Br bond lengths and BCPs' characteristics signified an intrinsic link between limiting types of bonding involving chalcogen atoms and between covalent and supramolecular bonding in general.
Collapse
Affiliation(s)
- Daniel K Miller
- Chemistry Department, Ball State University, Muncie, IN, 47306, USA.
| | - Ivan Yu Chernyshov
- TheoMat group, ChemBio Cluster, ITMO University, Lomonosova 9, St. Petersburg, 191002, Russia
| | - Yury V Torubaev
- N.S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, GSP-1, L eninsky prospect, 31, Moscow, 119991, Russia
| | - Sergiy V Rosokha
- Chemistry Department, Ball State University, Muncie, IN, 47306, USA.
| |
Collapse
|
20
|
Te⋯N secondary-bonding interactions in tellurium crystals: Supramolecular aggregation patterns and a comparison with their lighter congeners. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214397] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
21
|
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: 5.0] [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.
Collapse
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.)
| |
Collapse
|
22
|
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: 2.5] [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.
Collapse
|
23
|
Kinzhalov MA, Ivanov DM, Melekhova AA, Bokach NA, Gomila RM, Frontera A, Kukushkin VY. Chameleonic Metal-bound Isocyanides: π-Donating CuI-center Imparts a Nucleophilicity to the Isocyanide Carbon toward Halogen Bonding. Inorg Chem Front 2022. [DOI: 10.1039/d2qi00034b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the structures of the isostructural cocrystals [CuI3(CNXyl)3]·CHX3 (X = Br, I), two adjacent CuI-bound isocyanide groups, whose carbon lone pairs are blocked by the ligation, exhibit nucleophilic properties induced...
Collapse
|
24
|
Fierro A, Matthies DJ, Cassels BK, Jaque P, Zapata-Torres G. 5-HT 2 Receptor Subfamily and the Halogen Bond Promise. J Chem Inf Model 2021; 61:5001-5012. [PMID: 34617740 DOI: 10.1021/acs.jcim.1c00466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The binding of C-4-halogenated 1-(4-X-2,5-dimethoxyphenyl)-2-aminopropane (DOX) serotonin agonist psychedelics at all three 5-HT2 receptor subtypes is up to two orders of magnitude stronger for X = Cl, Br, or I (but not F) than when C-4 bears a hydrogen atom and more than expected from their hydrophobicities. Our docking and molecular dynamics simulations agree with the fact that increasing the polarizability of halogens results in halogen-oxygen distances to specific backbone C═O groups, and C-X···O angles, in ranges expected for halogen bonds (XBs), which could contribute to the high affinities observed. Good linear correlations are found for each receptor type, indicating that the binding pocket-ligand affinity is enhanced as the XB interaction becomes stronger (i.e., I ≈ Br > Cl > F). It is also striking to note how the linear equations unveil that the receptor's response on the strength of the XB interaction is quite similar among 5-HT2A and 5-HT2C, whereas the 5-HT2B's sensitivity is less. The calculated dipole polarizabilities in the binding pocket of the receptors reflect the experimental affinity values, indicating that less-polarizable and harder binding sites are more prone to XB formation.
Collapse
Affiliation(s)
- Angélica Fierro
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Douglas J Matthies
- Unidad de Gráfica Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone 1007, Independencia, Santiago 8380494, Chile
| | - Bruce K Cassels
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Pablo Jaque
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone 1007, Independencia, Santiago 8380492, Chile
| | - Gerald Zapata-Torres
- Unidad de Gráfica Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone 1007, Independencia, Santiago 8380494, Chile
| |
Collapse
|
25
|
Taponen AI, Ayadi A, Lahtinen MK, Oyarzabal I, Bonhommeau S, Rouzières M, Mathonière C, Tuononen HM, Clérac R, Mailman A. Room-Temperature Magnetic Bistability in a Salt of Organic Radical Ions. J Am Chem Soc 2021; 143:15912-15917. [PMID: 34547207 DOI: 10.1021/jacs.1c07468] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Cocrystallization of 7,7',8,8'-tetracyanoquinodimethane radical anion (TCNQ-•) and 3-methylpyridinium-1,2,3,5-dithiadiazolyl radical cation (3-MepyDTDA+•) afforded isostructural acetonitrile (MeCN) or propionitrile (EtCN) solvates containing cofacial π dimers of homologous components. Loss of lattice solvent from the diamagnetic solvates above 366 K affords a high-temperature paramagnetic phase containing discrete TCNQ-• and weakly bound π dimers of 3-MepyDTDA+•, as evidenced by X-ray diffraction methods and magnetic susceptibility measurements. Below 268 K, a first-order phase transition occurs, leading to a low-temperature diamagnetic phase with TCNQ-• σ dimer and π dimers of 3-MepyDTDA+•. This study reveals the first example of cooperative interactions between two different organic radical ions leading to magnetic bistability, and these results are central to the future design of multicomponent functional molecular materials.
Collapse
Affiliation(s)
- Anni I Taponen
- NanoScience Centre, Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Awatef Ayadi
- NanoScience Centre, Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Manu K Lahtinen
- NanoScience Centre, Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Itziar Oyarzabal
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR5031, F-33600 Pessac, France.,BCMaterials, Basque Center for Materials, Applications and Nanostructures, UPV/EHU Science Park, ES-48940 Leioa, Spain.,IKERBASQUE, Basque Foundation for Science, ES-48009 Bilbao, Spain
| | | | - Mathieu Rouzières
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR5031, F-33600 Pessac, France
| | - Corine Mathonière
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR5031, F-33600 Pessac, France
| | - Heikki M Tuononen
- NanoScience Centre, Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Rodolphe Clérac
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR5031, F-33600 Pessac, France
| | - Aaron Mailman
- NanoScience Centre, Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| |
Collapse
|
26
|
Tiekink ER. Supramolecular aggregation patterns featuring Se⋯N secondary-bonding interactions in mono-nuclear selenium compounds: A comparison with their congeners. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214031] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
27
|
Abstract
It follows from the Schrödinger equation that the forces operating within molecules and molecular complexes are Coulombic, which necessarily entails both electrostatics and polarization. A common and important class of molecular complexes is due to π-holes. These are molecular regions of low electronic density that are perpendicular to planar portions of the molecular frameworks. π-Holes often have positive electrostatic potentials associated with them, which result in mutually polarizing attractive forces with negative sites such as lone pairs, π electrons or anions. In many molecules, π-holes correspond to a flattening of the electronic density surface but in benzene derivatives and in polyazines the π-holes are craters above and below the rings. The interaction energies of π-hole complexes can be expressed quite well in terms of regression relationships that account for both the electrostatics and the polarization. There is a marked gradation in the interaction energies, from quite weak (about -2 kcal mol-1) to relatively strong (about -40 kcal mol-1). Gradations are also evident in the ratios of the intermolecular separations to the sums of the respective van der Waals radii and in the gradual transition of the π-hole atoms from trigonal to quasi-tetrahedral configurations. These trends are consistent with the concept that chemical interactions form a continuum, from very weak to very strong.
Collapse
Affiliation(s)
- Peter Politzer
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA.
| | | | | |
Collapse
|
28
|
Characterising Supramolecular Architectures in Crystals Featuring I⋯Br Halogen Bonding: Persistence of X⋯X’ Secondary-Bonding in Their Congeners. CRYSTALS 2021. [DOI: 10.3390/cryst11040433] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The Cambridge Structural Database was surveyed for crystals featuring I⋯Br secondary-bonding in their supramolecular assemblies occurring independently of other obvious supramolecular synthons and devoid of other halogen bonding interactions. In all, 41 crystals satisfied these criteria, with nine examples of zero-dimensional aggregation (uniformly two-molecule aggregates) and 30 one-dimensional chains of varying topology (linear, zigzag and helical). There is one example each of two- and three-dimensional patterns. Type-I, type-II and intermediate bonding situations are apparent; for type-II bonding, the ratio of iodide:bromide functioning as the electrophile is 2:1. Most molecules participated, on average, in one I⋯Br contact, although smaller numbers of half (zero-dimensional) or two contacts (two- and three-dimensional) were observed. The propensity of the formation of related halogen bonding interactions in congeners of the 41 investigated crystals was also studied. Congeners were apparent for 11 crystals, with seven of these exhibiting isostructural relationships, in terms of space-group symmetry and unit-cell parameters. Isostructural relationships do not ensure the formation of analogous aggregation patterns, particularly and in accord with expectation, for the lighter halides. When formed, often distinct aggregation patterns are observed despite the isostructural relationships. Hetero-atomic halogen bonding offers surprises and opportunities in crystal engineering endeavours.
Collapse
|
29
|
Otte F, Kleinheider J, Hiller W, Wang R, Englert U, Strohmann C. Weak yet Decisive: Molecular Halogen Bond and Competing Weak Interactions of Iodobenzene and Quinuclidine. J Am Chem Soc 2021; 143:4133-4137. [PMID: 33687197 DOI: 10.1021/jacs.1c00239] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The halogen bonded adduct between the commonly used constituents quinuclidine and iodobenzene is based on a single weak nitrogen-iodine contact, and the isolation of this adduct was initially unexpected. Iodobenzene does not contain any electron-withdrawing group and therefore represents an unconventional halogen bond donor. Based on excellent diffraction data of high resolution, an electron density study was successfully accomplished and confirmed one of the longest N···I molecular halogen bonds with a distance of 2.9301(4) Å. The topological analysis identified the XB as a directional but weak σ hole interaction and revealed secondary contacts between peripheral regions of opposite charge. These additional contacts and their competition with a nitrogen-based interaction were confirmed by NOESY experiments in solution. Integration enabled us to determine the relative NOE ratios and provided insight regarding the existing interactions.
Collapse
Affiliation(s)
- Felix Otte
- TU Dortmund University, Inorganic Chemistry, Otto-Hahn-Str. 6, D-44227, Dortmund, Germany
| | - Johannes Kleinheider
- TU Dortmund University, Inorganic Chemistry, Otto-Hahn-Str. 6, D-44227, Dortmund, Germany
| | - Wolf Hiller
- TU Dortmund University, Inorganic Chemistry, Otto-Hahn-Str. 6, D-44227, Dortmund, Germany.,TU Dortmund University, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, D-44227, Dortmund, Germany
| | - Ruimin Wang
- RWTH Aachen University, Inorganic Chemistry, Landoltweg 1, D-52056, Aachen, Germany.,Shanxi University, Institute of Molecular Science, Wucheng Road 92, 030006, Taiyuan, P. R. China
| | - Ulli Englert
- RWTH Aachen University, Inorganic Chemistry, Landoltweg 1, D-52056, Aachen, Germany.,Shanxi University, Institute of Molecular Science, Wucheng Road 92, 030006, Taiyuan, P. R. China
| | - Carsten Strohmann
- TU Dortmund University, Inorganic Chemistry, Otto-Hahn-Str. 6, D-44227, Dortmund, Germany
| |
Collapse
|