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Ibrahim MAA, Shehata MNI, Abuelliel HAA, Moussa NAM, Sayed SRM, Ahmed MN, Abd El-Rahman MK, Dabbish E, Shoeib T. Hole interactions of aerogen oxides with Lewis bases: an insight into σ-hole and lone-pair-hole interactions. ROYAL SOCIETY OPEN SCIENCE 2023; 10:231362. [PMID: 38094266 PMCID: PMC10716657 DOI: 10.1098/rsos.231362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/03/2023] [Indexed: 01/11/2024]
Abstract
σ-Hole and lone-pair (lp)-hole interactions of aerogen oxides with Lewis bases (LB) were comparatively inspected in terms of quantum mechanics calculations. The ZOn ⋯ LB complexes (where Z = Kr and Xe, n = 1, 2, 3 and 4, and LB = NH3 and NCH) showed favourable negative interaction energies. The complexation features were explained in light of σ-hole and lp-hole interactions within optimum distances lower than the sum of the respective van der Waals radii. The emerging findings outlined that σ-hole interaction energies generally enhanced according to the following order: KrO4 ⋯ < KrO⋯ < KrO3⋯ < KrO2⋯LB and XeO4⋯ < XeO⋯ < XeO2⋯ < XeO3⋯LB complexes with values ranging from -2.23 to -12.84 kcal mol-1. Lp-hole interactions with values up to -5.91 kcal mol-1 were shown. Symmetry-adapted perturbation theory findings revealed the significant contributions of electrostatic forces accounting for 50-65% of the total attractive forces within most of the ZOn⋯LB complexes. The obtained observations would be useful for the understanding of hole interactions, particularly for the aerogen oxides, with application in supramolecular chemistry and crystal engineering.
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Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
- School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Mohammed N. I. Shehata
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Hassan A. A. Abuelliel
- 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, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Muhammad Naeem Ahmed
- Department of Chemistry, The University of Azad Jammu and Kashmir, Muzaffarabad 13100, Pakistan
| | - Mohamed K. Abd El-Rahman
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Eslam Dabbish
- Department of Chemistry, The American University in Cairo, New Cairo 11835, Egypt
| | - Tamer Shoeib
- Department of Chemistry, The American University in Cairo, New Cairo 11835, Egypt
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2
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Sajjad MA, Macgregor SA, Weller AS. A comparison of non-covalent interactions in the crystal structures of two σ-alkane complexes of Rh exhibiting contrasting stabilities in the solid state. Faraday Discuss 2023; 244:222-240. [PMID: 37096331 DOI: 10.1039/d3fd00009e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Non-covalent interactions surrounding the cationic Rh σ-alkane complexes within the crystal structures of [(Cy2PCH2CH2PCy2)Rh(NBA)][BArF4], [1-NBA][BArF4] (NBA = norbornane, C7H12; ArF = 3,5-(CF3)2C6H3), and [1-propane][BArF4] are analysed using Quantum Theory of Atoms in Molecules (QTAIM) and Independent Gradient Model approaches, the latter under a Hirshfeld partitioning scheme (IGMH). In both structures the cations reside in an octahedral array of [BArF4]- anions within which the [1-NBA]+ cation system exhibits a greater number of C-H⋯F contacts to the anions. QTAIM and IGMH analyses indicate these include the strongest individual atom-atom non-covalent interactions between the cation and the anion in these systems. The IGMH approach highlights the directionality of these C-H⋯F contacts that contrasts with the more diffuse C-H⋯π interactions. The accumulative effects of the latter lead to a more significant stabilizing contribution. IGMH %δGatom plots provide a particularly useful visual tool to identify key interactions and highlight the importance of a -{C3H6}- propylene moiety that is present within both the propane and NBA ligands (the latter as a truncated -{C3H4}- unit) and the cyclohexyl rings of the phosphine substituents. The potential for this to act as a privileged motif that confers stability on the crystal structures of σ-alkane complexes in the solid-state is discussed. The greater number of C-H⋯F inter-ion interactions in the [1-NBA][BArF4] system, coupled with more significant C-H⋯π interactions are all consistent with greater non-covalent stabilisation around the [1-NBA]+ cation. This is also supported by larger computed δGatom indices as a measure of cation-anion non-covalent interaction energy.
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Affiliation(s)
- M Arif Sajjad
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK.
| | - Stuart A Macgregor
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK.
| | - Andrew S Weller
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
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3
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Ibrahim MAA, Shehata MNI, Moussa NAM, Hemia RRA, Abd Elhafez HSM, Abd El-Rahman MK, Sayed SRM, Sidhom PA, Dabbish E, Shoeib T. Preferability of Molnupiravir, an Anti-COVID-19 Drug, toward Purine Nucleosides: A Quantum Mechanical Study. ACS OMEGA 2023; 8:27553-27565. [PMID: 37546583 PMCID: PMC10398865 DOI: 10.1021/acsomega.3c03215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/28/2023] [Indexed: 08/08/2023]
Abstract
Structural aspects of molnupiravir complexed with the RNA of the SARS-CoV-2 virus have been recently resolved inside the RNA-dependent RNA polymerase (RdRp), demonstrating the interactions of molnupiravir with purine nucleosides. However, the preference of molnupiravir to interact with one purine nucleoside over another has not been clearly investigated. Herein, the complexation of molnupiravir in its active form with guanosine and adenosine was compared, using sundry density functional theory calculations. The plausible tautomeric structures of the molnupiravir drug in complex with guanosine/adenosine were minutely scrutinized. The relative energy findings outlined the favorability of amino-molnupiravir···keto-amino-guanosine and imino-molnupiravir···amino-adenosine optimized complexes. According to the interaction (Eint) and binding (Ebind) energy values, higher preferential base-pairing of molnupiravir with guanosine over the adenosine one was recognized with Eint/Ebind values of -31.16/-21.81 and -13.93/-12.83 kcal/mol, respectively. This could be interpreted by the presence of three and two hydrogen bonds within the former and latter complexes, respectively. Observable changes in the electronic properties and global indices of reactivity of the studied complexes also confirmed the preferential binding within the studied complexes. The findings from the quantum theory of atoms in molecules and the noncovalent interaction index also support the partially covalent nature of the investigated interactions. For both complexes, changes in thermodynamic parameters outlined the spontaneous, exothermic, and nonrandom states of the inspected interactions. Inspecting the solvent effect on the studied interactions outlined more observable amelioration within the water medium compared with the gas one. These results would be a durable ground for the forthcoming studies concerned with the interactions of the molnupiravir drug with purine nucleosides.
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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
| | - Mohammed N. I. Shehata
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Nayra A. M. Moussa
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Randa R. A. Hemia
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Heba S. M. Abd Elhafez
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Mohamed K. Abd El-Rahman
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Shaban R. M. Sayed
- Department
of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Peter A. Sidhom
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt
| | - Eslam Dabbish
- Department
of Chemistry, The American University in
Cairo, New Cairo 11835, Egypt
| | - Tamer Shoeib
- Department
of Chemistry, The American University in
Cairo, New Cairo 11835, Egypt
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4
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Ibrahim MA, Saeed RR, Shehata MN, Mohamed EE, Soliman ME, Al-Fahemi JH, El-Mageed HA, Ahmed MN, Shawky AM, Moussa NA. Unexplored σ-hole and π-hole interactions in (X2CY)2 complexes (X = F, Cl; Y = O, S). J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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5
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Parker BF, Chatani N. Selective Nickel-Catalyzed Hydrodefluorination of Amides Using Sodium Borohydride. J Org Chem 2022; 87:9969-9976. [PMID: 35818824 DOI: 10.1021/acs.joc.2c00971] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrodefluorination selective to the ortho position to amides is accomplished under mild conditions using sodium borohydride and a nickel catalyst. The facile formation of a nickelacycle intermediate with a specific geometry ensures selectivity without the need for electronic directing groups, and fluorine atoms in other positions remain intact. This method avoids the use of stoichiometric silanes which are typical for most other defluorination reactions, resulting in virtually no organic waste byproducts.
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Affiliation(s)
- Bernard F Parker
- Department of Applied Chemistry, Faculty of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Naoto Chatani
- Department of Applied Chemistry, Faculty of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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6
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External Electric Field Effect on the Strength of σ-Hole Interactions: A Theoretical Perspective in Like⋯Like Carbon-Containing Complexes. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092963. [PMID: 35566307 PMCID: PMC9104924 DOI: 10.3390/molecules27092963] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/17/2022]
Abstract
For the first time, σ-hole interactions within like⋯like carbon-containing complexes were investigated, in both the absence and presence of the external electric field (EEF). The effects of the directionality and strength of the utilized EEF were thoroughly unveiled in the (F-C-F3)2, (F-C-H3)2, and (H-C-F3)2 complexes. In the absence of the EEF, favorable interaction energies, with negative values, are denoted for the (F-C-F3)2 and (H-C-F3)2 complexes, whereas the (F-C-H3)2 complex exhibits unfavorable interactions. Remarkably, the strength of the applied EEF exhibits a prominent role in turning the repulsive forces within the latter complex into attractive ones. The symmetrical nature of the considered like⋯like carbon-containing complexes eradicated the effect of directionality of the EEF. The quantum theory of atoms in molecules (QTAIM), and the noncovalent interaction (NCI) index, ensured the occurrence of the attractive forces, and also outlined the substantial contributions of the three coplanar atoms to the total strength of the studied complexes. Symmetry-adapted perturbation theory (SAPT) results show the dispersion-driven nature of the interactions.
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7
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Ibrahim MAA, Moussa NAM, Saad SMA, Ahmed MN, Shawky AM, Soliman MES, Mekhemer GAH, Rady ASSM. σ-Hole and LP-Hole Interactions of Pnicogen···Pnicogen Homodimers under the External Electric Field Effect: A Quantum Mechanical Study. ACS OMEGA 2022; 7:11264-11275. [PMID: 35415328 PMCID: PMC8992284 DOI: 10.1021/acsomega.2c00176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
σ-Hole and lone-pair (lp)-hole interactions within σ-hole···σ-hole, σ-hole···lp-hole, and lp-hole···lp-hole configurations were comparatively investigated on the pnicogen···pnicogen homodimers (PCl3)2, for the first time, under field-free conditions and the influence of the external electric field (EEF). The electrostatic potential calculations emphasized the impressive versatility of the examined PCl3 monomers to participate in σ-hole and lp-hole pnicogen interactions. Crucially, the sizes of σ-hole and lp-hole were enlarged under the influence of the positively directed EEF and decreased in the case of reverse direction. Interestingly, the energetic quantities unveiled more favorability of the σ-hole···lp-hole configuration of the pnicogen···pnicogen homodimers, with significant negative interaction energies, than σ-hole···σ-hole and lp-hole···lp-hole configurations. Quantum theory of atoms in molecules and noncovalent interaction index analyses were adopted to elucidate the nature and origin of the considered interactions, ensuring their closed shell nature and the occurrence of attractive forces within the studied homodimers. Symmetry-adapted perturbation theory-based energy decomposition analysis alluded to the dispersion force as the main physical component beyond the occurrence of the examined interactions. The obtained findings would be considered as a fundamental underpinning for forthcoming studies pertinent to chemistry, materials science, and crystal engineering.
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Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Nayra A. M. Moussa
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Sherif M. A. Saad
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Muhammad Naeem Ahmed
- Department
of Chemistry, The University of Azad Jammu
and Kashmir, Muzaffarabad 13100, Pakistan
| | - Ahmed M. Shawky
- Science
and Technology Unit (STU), Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mahmoud E. S. Soliman
- Molecular
Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Gamal A. H. Mekhemer
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Al-shimaa S. M. Rady
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
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8
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Jana K, Pramanik U, Ingle KS, Maity R, Mukherjee S, Nayak SK, Chandra Debnath S, Maity T, Maity S, Chandra Samanta B. Copper(II) complexes with NNN and NNO Schiff base ligands as efficient photodegradation agents for methylene blue, preferential BSA binder and biomaterial transplants. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2021.113565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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Al-Wahaibi LH, Rahul B, Mohamed AAB, Abdelbaky MSM, Garcia-Granda S, El-Emam AA, Percino MJ, Thamotharan S. Supramolecular Self-Assembly Built by Weak Hydrogen, Chalcogen, and Unorthodox Nonbonded Motifs in 4-(4-Chlorophenyl)-3-[(4-fluorobenzyl)sulfanyl]-5-(thiophen-2-yl)-4 H-1,2,4-triazole, a Selective COX-2 Inhibitor: Insights from X-ray and Theoretical Studies. ACS OMEGA 2021; 6:6996-7007. [PMID: 33748613 PMCID: PMC7970574 DOI: 10.1021/acsomega.0c06287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 02/22/2021] [Indexed: 11/28/2022]
Abstract
![]()
A selective triazole-based
COX-2 inhibitor, 4-(4-chlorophenyl)-3-[(4-fluorobenzyl)sulfanyl]-5-(thiophen-2-yl)-4H-1,2,4-triazole, C19H13ClFN3S2, has been synthesized, and its crystal structure was
determined at 150 K. Single-crystal X-ray diffraction analysis revealed
that the thiophene ring was disordered over two orientations. The
crystal structure is stabilized by weak hydrogen and chalcogen bonds
and unorthodox F···π and S···C(π)
contacts. These noncovalent interactions cooperatively generate the
supramolecular self-assembly in the crystalline state. The Hirshfeld
surface and its associated two-dimensional (2D)-fingerprint plots
were obtained to analyze the role of different noncovalent interactions
in the crystal packing. Further, the enrichment ratio was obtained
from different atom···atom pairs to calculate the propensity
of these pairs to form noncovalent interactions. The strength of different
dimeric motifs formed in the crystal structure and lattice energies
was calculated by the PIXEL method. Furthermore, the topological analysis
of the charge density of intermolecular interactions was described.
A CSD survey of C–H···F hydrogen bond, C–S···Cl
chalcogen bond, and unorthodox nonbonded contacts (F···π
and S···C(π)) is presented. The title compound
possesses selective inhibitory activity against human COX-2 enzyme
rather than COX-1. The quantum mechanics (QM) polarized ligand docking
analysis was used to predict the binding pose and study the title
compound’s selectivity against COX-1/2 enzymes.
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Affiliation(s)
- Lamya H. Al-Wahaibi
- Department of Chemistry, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Bavanandan Rahul
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur 613 401, India
| | - Ahmed A. B. Mohamed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mohammed S. M. Abdelbaky
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, Oviedo University-CINN, Oviedo 33006, Spain
| | - Santiago Garcia-Granda
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, Oviedo University-CINN, Oviedo 33006, Spain
| | - Ali A. El-Emam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - M. Judith Percino
- Unidad de Polímeros y Electrónica Orgánica, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Val3-Ecocampus Valsequillo, Independencia O2 Sur 50, San Pedro Zacachimalpa, Puebla C.P. 72960, Mexico
| | - Subbiah Thamotharan
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur 613 401, India
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10
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2,2-Dimethyl-3-[(4-methylphenyl)sulfonyl]-2,3-dihydro-1,3,2-benzoxazasilole: synthesis, properties, and structure. Russ Chem Bull 2021. [DOI: 10.1007/s11172-021-3097-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Investigation of intermolecular interactions in fluoro/trifluoromethyl derivatives of benzoylferrocene. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Hathwar VR, Bhowal R, Chopra D. Insights from electron density analysis into the charge transfer mechanism in a photoluminescent cocrystal of phenanthrene and tetrafluoro-1,4-benzoquinone. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Grudova MV, Gil DM, Khrustalev VN, Nikitina EV, Sinelshchikova AA, Grigoriev MS, Kletskov AV, Frontera A, Zubkov FI. Synthesis, X-ray characterization and theoretical study of 3 a,6:7,9 a-diepoxybenzo[ de]isoquinoline derivatives: on the importance of F⋯O interactions. NEW J CHEM 2020. [DOI: 10.1039/d0nj04328a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This manuscript reports the synthesis, X-ray characterization and theoretical study of 3a,6:7,9a-diepoxybenzo[de]isoquinoline derivatives focusing on the importance of F···O interactions.
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Affiliation(s)
- Mariya V. Grudova
- Faculty of Science, Peoples’ Friendship University of Russia (RUDN University)
- Moscow 117198
- Russian Federation
| | - Diego M. Gil
- INBIOFAL (CONICET – UNT), Instituto de Química Orgánica. Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán
- San Miguel de Tucumán
- Argentina
| | - Victor N. Khrustalev
- Faculty of Science, Peoples’ Friendship University of Russia (RUDN University)
- Moscow 117198
- Russian Federation
- N. D. Zelinsky Institute of Organic Chemistry of RAS
- 119991 Moscow
| | - Eugeniya V. Nikitina
- Faculty of Science, Peoples’ Friendship University of Russia (RUDN University)
- Moscow 117198
- Russian Federation
| | - Anna A. Sinelshchikova
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences
- Moscow 119071
- Russian Federation
| | - Mikhail S. Grigoriev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences
- Moscow 119071
- Russian Federation
| | - Alexey V. Kletskov
- Faculty of Science, Peoples’ Friendship University of Russia (RUDN University)
- Moscow 117198
- Russian Federation
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears
- 07122 Palma de Mallorca (Baleares)
- Spain
| | - Fedor I. Zubkov
- Faculty of Science, Peoples’ Friendship University of Russia (RUDN University)
- Moscow 117198
- Russian Federation
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14
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Mahesha, Hema MK, Karthik CS, Pampa KJ, Mallu P, Lokanath NK. Solvent induced mononuclear and dinuclear mixed ligand Cu( ii) complex: structural diversity, supramolecular packing polymorphism and molecular docking studies. NEW J CHEM 2020. [DOI: 10.1039/d0nj03567j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Phenolate bridged dinuclear and solvent induced mononuclear supramolecular isomers of Cu(ii) complex have been reported to explore the structural diversity and their antibacterial activity supported by molecular docking studies.
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Affiliation(s)
- Mahesha
- Department of Studies in Physics
- University of Mysore
- Mysuru-570 006
- India
| | - M. K. Hema
- Department of Studies in Physics
- University of Mysore
- Mysuru-570 006
- India
| | - C. S. Karthik
- Department of Chemistry
- SJCE
- JSS Science and Technology University
- Mysuru-570 006
- India
| | - K. J. Pampa
- Department of Biotechnology
- University of Mysore
- Mysuru-570 006
- India
| | - P. Mallu
- Department of Chemistry
- SJCE
- JSS Science and Technology University
- Mysuru-570 006
- India
| | - N. K. Lokanath
- Department of Studies in Physics
- University of Mysore
- Mysuru-570 006
- India
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15
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Nikonov AY, Sterkhova IV, Serykh VY, Kolyvanov NA, Lazareva NF. Synthesis and structural features of N-[(2-(trimethylsilyl)oxy)phenyl]-arylsulfonamides. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.07.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Mondal PK, T A, Rao V, Chopra D. Crystal structure analysis of the biologically active drug mol-ecule riluzole and riluzolium chloride. Acta Crystallogr E Crystallogr Commun 2019; 75:1084-1089. [PMID: 31417770 PMCID: PMC6690469 DOI: 10.1107/s2056989019009022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 06/24/2019] [Indexed: 11/17/2022]
Abstract
This study is an investigation into the crystal structure of the biologically active drug mol-ecule riluzole [RZ, 6-(tri-fluoro-meth-oxy)-1,3-benzo-thia-zol-2-amine], C8H5F3N2OS, and its derivative, the riluzolium chloride salt [RZHCl, 2-amino-6-(tri-fluoro-meth-oxy)-1,3-benzo-thia-zol-3-ium chloride], C8H6F3N2OS+·Cl-. In spite of repeated efforts to crystallize the drug, its crystal structure has not been reported to date, hence the current study provides a method for obtaining crystals of both riluzole and its corresponding salt, riluzolium hydro-chloride. The salt was obtained by grinding HCl with the drug and crystallizing the obtained solid from di-chloro-methane. The crystals of riluzole were obtained in the presence of l-glutamic acid and d-glutamic acid in separate experiments. In the crystal structure of RZHCl, the -OCF3 moiety is perpendicular to the mol-ecular plane containing the riluzolium ion, as can be seen by the torsion angle of 107.4 (3)°. In the case of riluzole, the torsion angles of the four different mol-ecules in the asymmetric unit show that in three cases the tri-fluoro-meth-oxy group is perpendicular to the riluzole mol-ecular plane and only in one mol-ecule does the -OCF3 group lie in the same mol-ecular plane. The crystal structure of riluzole primarily consists of strong N-H⋯N hydrogen bonds along with weak C-H⋯F, C-H⋯S, F⋯F, C⋯C and C⋯S inter-actions, while that of its salt is stabilized by strong [N-H]+⋯Cl- and weak C-H⋯Cl-, N-H⋯S, C-H⋯F, C⋯C, S⋯N and S⋯Cl- inter-actions.
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Affiliation(s)
- Pradip Kumar Mondal
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal, Bhauri, Bhopal 462066, India
| | - Athulbabu T
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal, Bhauri, Bhopal 462066, India
| | - Varun Rao
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal, Bhauri, Bhopal 462066, India
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal, Bhauri, Bhopal 462066, India
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17
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Abstract
In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specific examples, that halogen bonds do not always follow the strict Type-II topology, and the occurrence of Type-I and -III halogen-centered contacts in crystals is very difficult to predict. In many instances, Type-I halogen-centered contacts appear simultaneously with Type-II halogen bonds. We employed the Independent Gradient Model, a recently proposed electron density approach for probing strong and weak interactions in molecular domains, to show that this is a very useful tool in unraveling the chemistry of halogen-assisted noncovalent interactions, especially in the weak bonding regime. Wherever possible, we have attempted to connect some of these results with those reported previously. Though useful for studying interactions of reasonable strength, IUPAC’s proposed “less than the sum of the van der Waals radii” criterion should not always be assumed as a necessary and sufficient feature to reveal weakly bound interactions, since in many crystals the attractive interaction happens to occur between the midpoint of a bond, or the junction region, and a positive or negative site.
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18
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Hirai Y, Ferreira da Rosa PP, Nakanishi T, Kitagawa Y, Fushimi K, Seki T, Ito H, Hasegawa Y. Structural Manipulation of Triboluminescent Lanthanide Coordination Polymers by Side-Group Alteration. Inorg Chem 2018; 57:14653-14659. [PMID: 30422642 DOI: 10.1021/acs.inorgchem.8b02367] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Novel Eu(III) coordination polymers with furan-based bridging ligands [Eu(hfa)3(Cy)] n and [Eu(hfa)3(Tol)] n (hfa: hexafluoroacetylacetonato, Cy: 2,5-bis(dicyclohexylphosphoryl)furan), Tol: 2,5-bis(di- p-tolylphosphoryl)furan) are reported. The rigidity of assembly steric structures was controlled by intermolecular interactions through the side groups in bridging ligands. They exhibited one of the best performances (thermal stability above 320 °C and external photoluminescence quantum yields of up to 71%) among reported lanthanide(III) compounds. The triboluminescence activity was demonstrated to be dependent on the mechanical stability of the coordination polymers, which was proportional to the number of hydrogen atoms in the side groups. The second example of a large TL/PL spectral difference in [Tb,Eu(hfa)3(Tol)] n also revealed discrete photophysical processes under the conditions of grinding and UV irradiation.
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Affiliation(s)
- Yuichi Hirai
- PPSM, ENS Cachan, CNRS , Université Paris-Saclay , 61 Avenue du Président Wilson , Cachan 94230 , France
| | | | - Takayuki Nakanishi
- Faculty of Industrial Science and Technology , Tokyo University of Science , 6-3-1, Niijuku , Katsushika-ku, Tokyo 125-8585 , Japan
| | - Yuichi Kitagawa
- Faculty of Engineering , Hokkaido University , Kita-13 Jo, Nishi-8 Chome , Sapporo , Hokkaido 060-8628 , Japan
| | - Koji Fushimi
- Faculty of Engineering , Hokkaido University , Kita-13 Jo, Nishi-8 Chome , Sapporo , Hokkaido 060-8628 , Japan
| | - Tomohiro Seki
- Faculty of Engineering , Hokkaido University , Kita-13 Jo, Nishi-8 Chome , Sapporo , Hokkaido 060-8628 , Japan
| | - Hajime Ito
- Faculty of Engineering , Hokkaido University , Kita-13 Jo, Nishi-8 Chome , Sapporo , Hokkaido 060-8628 , Japan
| | - Yasuchika Hasegawa
- Faculty of Engineering , Hokkaido University , Kita-13 Jo, Nishi-8 Chome , Sapporo , Hokkaido 060-8628 , Japan
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19
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Shukla R, Nayak SK, Chopra D, Reddy MK, Guru Row T. Observation of 3D isostructurality in halogen substituted N -benzoyl- N -phenylbenzamides. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Varadwaj A, Varadwaj PR, Marques HM, Yamashita K. Revealing Factors Influencing the Fluorine-Centered Non-Covalent Interactions in Some Fluorine-Substituted Molecular Complexes: Insights from First-Principles Studies. Chemphyschem 2018; 19:1486-1499. [PMID: 29569853 DOI: 10.1002/cphc.201800023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Indexed: 01/13/2023]
Abstract
We examine the equilibrium structure and properties of six fully or partially fluorinated hydrocarbons and several of their binary complexes using computational methods. In the monomers, the electrostatic surface of the fluorine is predicted to be either entirely negative or weakly positive. However, its lateral sites are always negative. This enables the fluorine to display an anisotropic distribution of charge density on its electrostatic surface. While this is the electrostatic surface scenario of the fluorine atom, its negative sites in some of these monomers are shown to have the potential to engage in attractive engagements with the negative site(s) on the same atom in another molecule of the same type, or a molecule of a different type, to form bimolecular complexes. This is revealed by analyzing the results of current state-of-the-art computational approaches such as DFT, together with those obtained from the quantum theory of atoms in molecules, molecular electrostatic surface potential and symmetry adapted perturbation theories. We demonstrate that the intermolecular interaction energy arising in part from the universal London dispersion, which has been underappreciated for decades, is an essential factor in explaining the attraction between the negative sites, although energy arising from polarization strengthens the extent of the intermolecular interactions in these complexes.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku, Japan 113-8656, and CREST-JST, 7 Gobancho, Chiyoda-ku, Tokyo, Japan 102-0076
| | - Pradeep R Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku, Japan 113-8656, and CREST-JST, 7 Gobancho, Chiyoda-ku, Tokyo, Japan 102-0076
| | - 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, Hongo, Bunkyo-ku, Japan 113-8656, and CREST-JST, 7 Gobancho, Chiyoda-ku, Tokyo, Japan 102-0076
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21
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Shukla R, Nayak SK, Chopra D, Reddy MK, Guru Row TN. Quantitative investigation of intermolecular interactions in dimorphs of 3-Chloro-N-(2-fluorophenyl)benzamide and 2-Iodo-N-(4- bromophenyl)benzamide. J CHEM SCI 2018. [DOI: 10.1007/s12039-018-1444-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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22
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Bojarska J, Remko M, Fruziński A, Maniukiewicz W. The experimental and theoretical landscape of a new antiplatelet drug ticagrelor: Insight into supramolecular architecture directed by C H⋯F, π⋯π and C H⋯π interactions. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.10.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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23
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Venkatesan P, Cerón M, Thamotharan S, Robles F, Percino MJ. Quantitative analysis of weak non-covalent interactions in (Z)-3-(4-halophenyl)-2-(pyridin-2/3/4-yl)acrylonitriles. CrystEngComm 2018. [DOI: 10.1039/c7ce02096a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A detailed experimental and theoretical investigation on the intermolecular interactions in (Z)-3-(4-halophenyl)-2-(pyridin-2/3/4-yl)acrylonitriles is reported and different π staking motifs observed in these structures.
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Affiliation(s)
- Perumal Venkatesan
- Laboratorio de Polímeros
- Centro de Química
- Instituto de Ciencias
- Benemérita Universidad Autónoma de Puebla
- Complejo de Ciencias
| | - Margarita Cerón
- Laboratorio de Polímeros
- Centro de Química
- Instituto de Ciencias
- Benemérita Universidad Autónoma de Puebla
- Complejo de Ciencias
| | - Subbiah Thamotharan
- Biomolecular Crystallography Laboratory
- Department of Bioinformatics
- School of Chemical and Biotechnology
- SASTRA Deemed University
- Thanjavur 613 401
| | - Fernando Robles
- Laboratorio Nacional del Sureste de México
- BUAP
- C.P. 72500 Puebla
- Mexico
| | - M. Judith Percino
- Laboratorio de Polímeros
- Centro de Química
- Instituto de Ciencias
- Benemérita Universidad Autónoma de Puebla
- Complejo de Ciencias
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24
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Omorodion H, Palenzuela M, Ruether M, Twamley B, Platts JA, Baker RJ. A rationally designed perfluorinated host for the extraction of PFOA from water utilising non-covalent interactions. NEW J CHEM 2018. [DOI: 10.1039/c7nj03026f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Three hosts for the encapsulation of perfluorooctanoic acid have been synthesized. The host:guest complexes have been characterized by multinuclear NMR spectroscopy in solution and the solid state.
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Affiliation(s)
| | - Miguel Palenzuela
- School of Chemistry
- University of Dublin
- Trinity College
- Dublin 2
- Ireland
| | - Manuel Ruether
- School of Chemistry
- University of Dublin
- Trinity College
- Dublin 2
- Ireland
| | - Brendan Twamley
- School of Chemistry
- University of Dublin
- Trinity College
- Dublin 2
- Ireland
| | | | - Robert J. Baker
- School of Chemistry
- University of Dublin
- Trinity College
- Dublin 2
- Ireland
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25
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San LK, Spisak SN, Dubceac C, Deng SHM, Kuvychko IV, Petrukhina MA, Wang X, Popov AA, Strauss SH, Boltalina OV. Experimental and DFT Studies of the Electron‐Withdrawing Ability of Perfluoroalkyl (R
F
) Groups: Electron Affinities of PAH(R
F
)
n
Increase Significantly with Increasing R
F
Chain Length. Chemistry 2017; 24:1441-1447. [DOI: 10.1002/chem.201704868] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Long K. San
- Department of Chemistry Colorado State University Fort Collins Colorado 80523 USA
| | - Sarah N. Spisak
- Department of Chemistry University at Albany, State University of New York Albany New York 12222 USA
| | - Cristina Dubceac
- Department of Chemistry University at Albany, State University of New York Albany New York 12222 USA
| | - Shihu H M. Deng
- Physical Sciences Division Pacific Northwest National Laboratory MS K8 88, P.O. Box 999 Richland Washington 99352 USA
| | - Igor V. Kuvychko
- Department of Chemistry Colorado State University Fort Collins Colorado 80523 USA
| | - Marina A. Petrukhina
- Department of Chemistry University at Albany, State University of New York Albany New York 12222 USA
| | - Xue‐Bin Wang
- Physical Sciences Division Pacific Northwest National Laboratory MS K8 88, P.O. Box 999 Richland Washington 99352 USA
| | - Alexey A. Popov
- Department of Electrochemistry and Conducting Polymers Liebniz Institute for Solid State and Materials Research Dresden 01069 Germany
| | - Steven H. Strauss
- Department of Chemistry Colorado State University Fort Collins Colorado 80523 USA
| | - Olga V. Boltalina
- Department of Chemistry Colorado State University Fort Collins Colorado 80523 USA
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26
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Koiso N, Kitagawa Y, Nakanishi T, Fushimi K, Hasegawa Y. Eu(III) Chiral Coordination Polymer with a Structural Transformation System. Inorg Chem 2017; 56:5741-5747. [DOI: 10.1021/acs.inorgchem.7b00337] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Naoyuki Koiso
- TOSOH Corporation, 2743-1, Hayakawa, Ayase, Kanagawa 252-1123, Japan
| | - Yuichi Kitagawa
- Faculty of Engineering, Hokkaido University, Kita-13 Jo, Nishi-8 Chome, Kita-ku, Sapporo,
Hokkaido 060-8628, Japan
| | - Takayuki Nakanishi
- Faculty of Engineering, Hokkaido University, Kita-13 Jo, Nishi-8 Chome, Kita-ku, Sapporo,
Hokkaido 060-8628, Japan
| | - Koji Fushimi
- Faculty of Engineering, Hokkaido University, Kita-13 Jo, Nishi-8 Chome, Kita-ku, Sapporo,
Hokkaido 060-8628, Japan
| | - Yasuchika Hasegawa
- Faculty of Engineering, Hokkaido University, Kita-13 Jo, Nishi-8 Chome, Kita-ku, Sapporo,
Hokkaido 060-8628, Japan
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27
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Shukla R, Mohan T, Vishalakshi B, Chopra D. Synthesis, crystal structure and theoretical analysis of intermolecular interactions in two biologically active derivatives of 1,2,4-triazoles. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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28
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Pitts CR, Siegler MA, Lectka T. Intermolecular Aliphatic C–F···H–C Interaction in the Presence of “Stronger” Hydrogen Bond Acceptors: Crystallographic, Computational, and IR Studies. J Org Chem 2017; 82:3996-4000. [DOI: 10.1021/acs.joc.7b00268] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cody Ross Pitts
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Maxime A. Siegler
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Thomas Lectka
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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29
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On the molecular and supramolecular properties of N,N′-disubstituted iminoisoindolines: Synthesis, spectroscopy, X-ray structure and Hirshfeld surface analyses, and DFT calculations of two (E)-N,N′-bis(aryl)iminoisoindolines (aryl = 2-tert-butylphenyl or perfluorophenyl). J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.10.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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30
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Shukla R, Saeed A, Simpson J, Chopra D. Quantitative investigation of C–H⋯π and other intermolecular interactions in a series of crystalline N-(substituted phenyl)-2-naphthamide derivatives. CrystEngComm 2017. [DOI: 10.1039/c7ce01310h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we have investigated the nature and characteristics of different intermolecular interactions present in a series of sevenN-(substituted phenyl)-2-naphthamides.
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Affiliation(s)
- Rahul Shukla
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- IISER Bhopal
- Bhopal 462066
- India
| | - Aamer Saeed
- Department of Chemistry
- Quaid-i-Azam University-45320
- Islamabad
- Pakistan
| | - Jim Simpson
- Department of Chemistry
- University of Otago
- Dunedin 9054
- New Zealand
| | - Deepak Chopra
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- IISER Bhopal
- Bhopal 462066
- India
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31
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Shukla R, Khan I, Ibrar A, Simpson J, Chopra D. Complex electronic interplay of σ-hole and π-hole interactions in crystals of halogen substituted 1,3,4-oxadiazol-2(3H)-thiones. CrystEngComm 2017. [DOI: 10.1039/c7ce00678k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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