1
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Zhou J, Jia S, Xue X, Skitnevskaya AD, Wang E, Wang X, Hao X, Zeng Q, Kuleff AI, Dorn A, Ren X. Revealing the Role of N Heteroatoms in Noncovalent Aromatic Interactions by Ultrafast Intermolecular Coulombic Decay. J Phys Chem Lett 2024; 15:1529-1538. [PMID: 38299504 DOI: 10.1021/acs.jpclett.3c02979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Despite the widely recognized importance of noncovalent interactions involving aromatic rings in many fields, our understanding of the underlying forces and structural patterns, especially the impact of heteroaromaticity, is still incomplete. Here, we investigate the relaxation processes that follow inner-valence ionization in a range of molecular dimers involving various combinations of benzene, pyridine, and pyrimidine, which initiate an ultrafast intermolecular Coulombic decay process. Multiparticle coincidence momentum spectroscopy, combined with ab initio calculations, enables us to explore the principal orientations of these fundamental dimers and, thus, to elucidate the influence of N heteroatoms on the relative preference of the aromatic π-stacking, H-bonding, and CH-π interactions and their dependence on the number of nitrogen atoms in the rings. Our studies reveal a sensitive tool for the structural imaging of molecular complexes and provide a more complete understanding of the effects of N heteroatoms on the noncovalent aromatic interactions at the molecular level.
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Affiliation(s)
- Jiaqi Zhou
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Shaokui Jia
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xiaorui Xue
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Anna D Skitnevskaya
- Laboratory of Quantum Chemistry, Irkutsk State University, Irkutsk 664003, Russia
| | - Enliang Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - Xing Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xintai Hao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Qingrui Zeng
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Alexander I Kuleff
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg 69120, Germany
| | - Alexander Dorn
- Max-Planck-Institut für Kernphysik, Heidelberg 69117, Germany
| | - Xueguang Ren
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
- Max-Planck-Institut für Kernphysik, Heidelberg 69117, Germany
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2
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Coufal R, Tošner Z, Drahoňovský D, Vohlídal J. Hemiacetal-based dynamic systems: a new mechanistic insight. Org Biomol Chem 2023; 21:6956-6968. [PMID: 37581612 DOI: 10.1039/d3ob00668a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
The formation of hemiacetals from pyrazine trifluoromethylketone as a model receptor and four simple alcohols was studied by using quantum chemical calculations and NMR spectroscopy. Free energy profiles for four types of mechanistic pathways were calculated and discussed with respect to kinetic and thermodynamic measurements. We show that hemiacetal formation is facilitated by an assisted proton transfer process via a pseudo eight-membered transition state which brings the theory and experiment into close agreement. Also, a newly proposed mechanistic pathway for hemiacetal formation via a five-membered transition state leading to zwitterionic intermediates is discussed. Direct proton transfer in a pseudo four-membered transition state can be ruled out due to the high energy of transition states with respect to other mechanistic pathways. We also show that in the case of hemiacetals, water and alcohol molecules cannot account sufficiently for the H-transfer process via six-membered transition states.
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Affiliation(s)
- Radek Coufal
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8/2030, 128 40 Prague 2, Czech Republic.
- Department of Science and Research, Faculty of Health Studies, Technical University of Liberec, Studentská 1402/2, 461 17 Liberec 1, Czech Republic
| | - Zdeněk Tošner
- NMR Laboratory, Faculty of Science, Charles University, Hlavova 8/2030, 128 40 Prague 2, Czech Republic
| | - Dušan Drahoňovský
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8/2030, 128 40 Prague 2, Czech Republic
| | - Jiří Vohlídal
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8/2030, 128 40 Prague 2, Czech Republic.
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3
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Mokhtar MS, Elbashir AA, Suliman FO. Spectroscopic and molecular simulation studies on the interaction of imazaquin herbicide with cucurbiturils (n = 6–8). J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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4
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Wolf S, Domes R, Merian A, Domes C, Frosch T. Parallelized Raman Difference Spectroscopy for the Investigation of Chemical Interactions. Anal Chem 2022; 94:10346-10354. [PMID: 35820661 DOI: 10.1021/acs.analchem.2c00222] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Raman spectroscopy provides an extremely high chemical selectivity. Raman difference spectroscopy is a technique to reveal even the smallest differences that occur due to weak interactions between substances and changes in the molecular structure. To enable parallelized and highly sensitive Raman difference spectroscopy in a microtiter-array, a diffractive optical element, a lens array, and a fiber bundle were integrated into a Raman spectroscopy setup in a unique fashion. The setup was evaluated with a microtiter-array containing pyridine-water complexes, and subwavenumber changes below the spectrometer's resolution could be resolved. The spectral changes were emphasized with two-dimensional correlation analysis. Density functional theory calculation and "atoms in molecule" analysis were performed to simulate the intermolecular long-range interactions between water and pyridine molecules and to get insight into the involved noncovalent interactions, respectively. It was found that by the addition of pyridine, the energy portion of hydrogen bonds to the total complexation energy between pyridine and water reduces. These results demonstrate the unique abilities of the new setup to investigate subtle changes due to biochemically important molecular interactions and opens new avenues to perform drug binding assays and to monitor highly parallelized chemical reactions.
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Affiliation(s)
- Sebastian Wolf
- Leibniz Institute of Photonic Technology, Jena 07745, Germany
| | - Robert Domes
- Leibniz Institute of Photonic Technology, Jena 07745, Germany
| | - Andreas Merian
- Leibniz Institute of Photonic Technology, Jena 07745, Germany
| | - Christian Domes
- Leibniz Institute of Photonic Technology, Jena 07745, Germany
| | - Torsten Frosch
- Leibniz Institute of Photonic Technology, Jena 07745, Germany.,Abbe Center of Photonics, Friedrich Schiller University, Jena 07745, Germany.,Biophotonics and Biomedical Engineering Group, Technical University Darmstadt, Merckstraße 25, 64283 Darmstadt, Germany
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5
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Tan SL, Cardoso LNF, de Souza MVN, Wardell SMSV, Wardell JL, Tiekink ERT. Experimental and computational evidence for stabilising parallel, offset π[C(O)N(H)NC]⋯π(phenyl) interactions in acetohydrazide derivatives. CrystEngComm 2022. [DOI: 10.1039/d1ce01492g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stabilising π[C(O)N(H)NC]⋯π(phenyl) interactions are described.
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Affiliation(s)
- Sang Loon Tan
- Research Centre for Crystalline Materials, School of Medical and Life Sciences, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Laura N. F. Cardoso
- Instituto de Tecnologia em Fármacos Farmanguinhos, FIOCRUZ Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, Brazil
| | - Marcus V. N. de Souza
- Instituto de Tecnologia em Fármacos Farmanguinhos, FIOCRUZ Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, Brazil
| | | | - James L. Wardell
- Department of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen, AB24 3UE, Scotland, UK
| | - Edward R. T. Tiekink
- Research Centre for Crystalline Materials, School of Medical and Life Sciences, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
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6
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Tu D, Li J, Sun F, Yan H, Poater J, Solà M. Cage -···Cage - Interaction: Boron Cluster-Based Noncovalent Bond and Its Applications in Solid-State Materials. JACS AU 2021; 1:2047-2057. [PMID: 34841417 PMCID: PMC8611790 DOI: 10.1021/jacsau.1c00348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Carboranes are boron-carbon clusters with important applications in the fields of materials, catalysis, pharmaceuticals, etc. However, the noncovalent interactions that could determine the solid-state structures and properties of such boron clusters have rarely been investigated. Herein, inspired by the coordinate bond in metallacarborane or ferrocene, the boron cluster-based noncovalent interaction (denoted as cage-···cage- interaction) between two nido-carborane clusters was successfully realized by using a pyridinium-based molecular barrier. The X-ray diffraction studies uncover that the cage-···cage- interaction has a contacting distance of 5.4-7.0 Å from centroid to centroid in the systems reported here. Theoretical calculations validate the formation of the noncovalent interaction and disclose its repulsive bonding nature that is overcome thanks to the positively charged pyridinium-based framework. Interestingly, such bulk crystalline materials containing the cage-···cage- interaction show relevant properties such as full-color absorption in the visible light range and important photothermal effect, which are absent for the control compound without carboranes. This study may offer fundamental insights into the boron cluster-based noncovalent interactions and open a new research avenue to rationally design boron cluster-based materials.
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Affiliation(s)
- Deshuang Tu
- State
Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of
Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jiaxin Li
- State
Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of
Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Fangxiang Sun
- State
Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of
Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Hong Yan
- State
Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of
Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jordi Poater
- Departament
de Química Inorgànica i Orgànica & Institut
de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1-11, Barcelona 08028, Catalonia, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
| | - Miquel Solà
- Institut
de Química Computacional i Catàlisi and Departament
de Química, Universitat de Girona, C/Maria Aurèlia Capmany,
69, Girona 17003, Catalonia Spain
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7
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Hossain A, Dey A, Seth SK, Ray PP, Ortega-Castro J, Frontera A, Mukhopadhyay S. Anion-dependent structural variations and charge transport property analysis of 4′-(3-pyridyl)-4,2′:6′,4′′-terpyridinium salts. CrystEngComm 2021. [DOI: 10.1039/d1ce00248a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anion-dependent structural variations and charge transport analysis of three 4′-(3-pyridyl)-4,2′:6′,4′′-terpyridinium salts are reported. They exhibit pronounced photosensing behavior when illuminated using visible light.
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Affiliation(s)
- Anowar Hossain
- Department of Chemistry
- Jadavpur University
- Kolkata 700032
- India
| | - Arka Dey
- Department of Physics
- Jadavpur University
- Kolkata 700032
- India
| | | | | | | | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
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8
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Wu S, Wang X, Li Z, Zhang S, Xing F. Recent Advances in the Fabrication and Application of Graphene Microfluidic Sensors. MICROMACHINES 2020; 11:E1059. [PMID: 33265955 PMCID: PMC7760752 DOI: 10.3390/mi11121059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/13/2020] [Accepted: 11/28/2020] [Indexed: 02/07/2023]
Abstract
This review reports the progress of the recent development of graphene-based microfluidic sensors. The introduction of microfluidics technology provides an important possibility for the advance of graphene biosensor devices for a broad series of applications including clinical diagnosis, biological detection, health, and environment monitoring. Compared with traditional (optical, electrochemical, and biological) sensing systems, the combination of graphene and microfluidics produces many advantages, such as achieving miniaturization, decreasing the response time and consumption of chemicals, improving the reproducibility and sensitivity of devices. This article reviews the latest research progress of graphene microfluidic sensors in the fields of electrochemistry, optics, and biology. Here, the latest development trends of graphene-based microfluidic sensors as a new generation of detection tools in material preparation, device assembly, and chip materials are summarized. Special emphasis is placed on the working principles and applications of graphene-based microfluidic biosensors, especially in the detection of nucleic acid molecules, protein molecules, and bacterial cells. This article also discusses the challenges and prospects of graphene microfluidic biosensors.
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Affiliation(s)
- Shigang Wu
- School of Materials Science and Engineering, Shandong University of Technology, Zibo 255049, China;
| | - Xin Wang
- School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255049, China; (X.W.); (S.Z.)
| | - Zongwen Li
- School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255049, China; (X.W.); (S.Z.)
| | - Shijie Zhang
- School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255049, China; (X.W.); (S.Z.)
| | - Fei Xing
- School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255049, China; (X.W.); (S.Z.)
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9
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Tripathi S, Hossain A, Seth SK, Mukhopadhyay S. Quantitative insights into the crystal structure of a mixed-ligand Co(III) complex: Experimental and theoretical studies. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128207] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Carter-Fenk K, Herbert JM. Electrostatics does not dictate the slip-stacked arrangement of aromatic π-π interactions. Chem Sci 2020; 11:6758-6765. [PMID: 34094127 PMCID: PMC8159364 DOI: 10.1039/d0sc02667k] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Benzene dimer has long been an archetype for π-stacking. According to the Hunter–Sanders model, quadrupolar electrostatics favors an edge-to-face CH⋯π geometry but competes with London dispersion that favors cofacial π-stacking, with a compromise “slip-stacked” structure emerging as the minimum-energy geometry. This model is based on classical electrostatics, however, and neglects charge penetration. A fully quantum-mechanical analysis, presented here, demonstrates that electrostatics actually exerts very little influence on the conformational landscape of (C6H6)2. Electrostatics also cannot explain the slip-stacked arrangement of C6H6⋯C6F6, where the sign of the quadrupolar interaction is reversed. Instead, the slip-stacked geometry emerges in both systems due to competition between dispersion and Pauli repulsion, with electrostatics as an ambivalent spectator. This revised interpretation helps to rationalize the persistence of offset π-stacking in larger polycyclic aromatic hydrocarbons and across the highly varied electrostatic environments that characterize π–π interactions in proteins. According to the Hunter–Sanders model, geometries in π–π systems arise from competition between quadrupolar electrostatics (favoring an edge-to-face geometry) and London dispersion (favoring stacking), but this model misrepresents the molecular physics.![]()
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Affiliation(s)
- Kevin Carter-Fenk
- Department of Chemistry & Biochemistry, The Ohio State University Columbus OH USA
| | - John M Herbert
- Department of Chemistry & Biochemistry, The Ohio State University Columbus OH USA
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11
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Melikova SM, Voronin AP, Panek J, Frolov NE, Shishkina AV, Rykounov AA, Tretyakov PY, Vener MV. Interplay of π-stacking and inter-stacking interactions in two-component crystals of neutral closed-shell aromatic compounds: periodic DFT study. RSC Adv 2020; 10:27899-27910. [PMID: 35519116 PMCID: PMC9055576 DOI: 10.1039/d0ra04799f] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/13/2020] [Indexed: 01/19/2023] Open
Abstract
This paper bridges the gap between high-level ab initio computations of gas-phase models of 1 : 1 arene–arene complexes and calculations of the two-component (binary) organic crystals using atom–atom potentials. The studied crystals consist of electron-rich and electron-deficient compounds, which form infinite stacks (columns) of heterodimers. The sublimation enthalpy of crystals has been evaluated by DFT periodic calculations, while intermolecular interactions have been characterized by Bader analysis of the periodic electronic density. The consideration of aromatic compounds without a dipole moment makes it possible to reveal the contribution of quadrupole–quadrupole interactions to the π-stacking energy. These interactions are significant for heterodimers formed by arenes with more than 2 rings, with absolute values of the traceless quadrupole moment (Qzz) larger than 10 D Å. The further aggregation of neighboring stacks is due to the C–H⋯F interactions in arene/perfluoroarene crystals. In crystals consisting of arene and an electron-deficient compound such as pyromellitic dianhydride, aggregation occurs due to the C–H⋯O interactions. The C–H⋯F and C–H⋯O inter-stacking interactions make the main contribution to the sublimation enthalpy, which exceeds 150 kJ mol−1 for the two-component crystals formed by arenes with more than 2 rings. The interplay of π-stacking and inter-stacking interactions in two-component organic crystals without conventional hydrogen bonds.![]()
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12
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Patkowski K. Recent developments in symmetry‐adapted perturbation theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1452] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Konrad Patkowski
- Department of Chemistry and Biochemistry Auburn University Auburn Alabama
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13
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Chou TC, Cheng JF, Gholap AR, Huang JJK, Chen JC, Huang JK, Tseng JC. Aromatization-driven Grob-fragmentation approach toward polyazaacenes. Synthesis and amination of multi-functionalized diazapentacenes. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.130689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Gurdal Y. Aromatic versus aliphatic thiols on Au(111) surface: a DFT exploration of adsorption registry and electronic structure. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1663844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yeliz Gurdal
- Department of Bioengineering, Adana Alparslan Turkes Science and Technology University, Adana, Turkey
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15
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Andrić JM, Antonijević IS, Janjić GV, Zarić SD. Influence of hydrogen bonds on edge-to-face interactions between pyridine molecules. J Mol Model 2018; 24:60. [PMID: 29464387 DOI: 10.1007/s00894-017-3570-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/14/2017] [Indexed: 11/30/2022]
Abstract
Edge-to-face interactions between two pyridine molecules and the influence of simultaneous hydrogen bonding of one or both of the pyridines to water on those interactions were studied by analyzing data from ab initio calculations. The results show that the edge-to-face interactions of pyridine dimers that are hydrogen bonded to water are generally stronger than those of non-H-bonded pyridine dimers, especially when the donor pyridine forms a hydrogen bond. The binding energy of the most stable edge-to-face interacting H-bonded pyridine dimer is -5.05 kcal/mol, while that for the most stable edge-to-face interacting non-H-bonded pyridine dimer is -3.64 kcal/mol. The interaction energy data obtained in this study cannot be explained solely by the differences in electrostatic potential between pyridine and the pyridine-water dimer. However, the calculated cooperative effect can be predicted using electrostatic potential maps.
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Affiliation(s)
- Jelena M Andrić
- Innovation Center of the Faculty of Chemistry, Studentski trg 12-16, Belgrade, Serbia
| | - Ivana S Antonijević
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade, Serbia
| | - Goran V Janjić
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade, Serbia
| | - Snežana D Zarić
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia. .,Department of Chemistry, Texas A & M University at Qatar, P.O. Box 23874, Doha, Qatar.
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16
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Anichini C, Czepa W, Pakulski D, Aliprandi A, Ciesielski A, Samorì P. Chemical sensing with 2D materials. Chem Soc Rev 2018; 47:4860-4908. [DOI: 10.1039/c8cs00417j] [Citation(s) in RCA: 342] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
During the last decade, two-dimensional materials (2DMs) have attracted great attention due to their unique chemical and physical properties, which make them appealing platforms for diverse applications in sensing of gas, metal ions as well as relevant chemical entities.
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Affiliation(s)
| | - Włodzimierz Czepa
- Faculty of Chemistry
- Adam Mickiewicz University
- 61614 Poznań
- Poland
- Centre for Advanced Technologies
| | | | | | | | - Paolo Samorì
- Université de Strasbourg
- CNRS
- ISIS
- 67000 Strasbourg
- France
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17
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Das A. Synthesis, X-ray crystallographic studies, DFT calculations and nanostructural features of annulated imidazo[4,5-b]pyridine derivatives. SYNTHETIC COMMUN 2017. [DOI: 10.1080/00397911.2017.1381882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Aniruddha Das
- University College of Science, Technology and Agriculture, University of Calcutta, Kolkata, India
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18
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Sierański T. Discovering the stacking landscape of a pyridine-pyridine system. J Mol Model 2017; 23:338. [PMID: 29124340 PMCID: PMC5680376 DOI: 10.1007/s00894-017-3496-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/09/2017] [Indexed: 10/24/2022]
Abstract
Extremely extensive calculations of potential energy surfaces for the parallel-displaced configuration of pyridine dimer systems have been carried out using a dispersion-corrected density functional. Instead of focusing on stationary geometries these calculations provide much deeper insight into the "landscape" of the interaction energies of the particular systems-one can learn how the pyridine dimer stability changes along with various geometrical parameters. Other calculations such as natural bond orbital and energy decomposition have also been applied. The interplay of two significant factors, electrostatic forces and electron correlation effects, have been evaluated. The role of π···π interactions in the stacked pyridine systems has also been confirmed, and surprisingly, this happened to be true even for the geometries where the formation of C-H···π interactions might be proposed instead. The combination of many different methods has revealed the complexity of the stacking interactions. Apart from providing a "literal new look" into pyridine interaction patterns another picture has emerged. A stacking interaction in a pyridine dimer system is perceived as a combination of many different sources of the interaction energy, including orbital ones, and this is true for many different geometries.
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Affiliation(s)
- Tomasz Sierański
- Institute of General and Ecological Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland.
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19
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Ninković DB, Malenov DP, Petrović PV, Brothers EN, Niu S, Hall MB, Belić MR, Zarić SD. Unexpected Importance of Aromatic-Aliphatic and Aliphatic Side Chain-Backbone Interactions in the Stability of Amyloids. Chemistry 2017; 23:11046-11053. [DOI: 10.1002/chem.201701351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Dragan B. Ninković
- Science Program; Texas A&M University at Qatar; Texas A&M Engineering Building, Education City Doha Qatar
- Innovation Center; Department of Chemistry; University of Belgrade; Studentski trg 12-16 11000 Belgrade Serbia
| | - Dušan P. Malenov
- Department of Chemistry; University of Belgrade; Studentski trg 12-16 11000 Belgrade Serbia
| | - Predrag V. Petrović
- Science Program; Texas A&M University at Qatar; Texas A&M Engineering Building, Education City Doha Qatar
- Innovation Center; Department of Chemistry; University of Belgrade; Studentski trg 12-16 11000 Belgrade Serbia
| | - Edward N. Brothers
- Science Program; Texas A&M University at Qatar; Texas A&M Engineering Building, Education City Doha Qatar
| | - Shuqiang Niu
- Department of Chemistry; Texas A&M University; College Station TX 77843-3255 USA
| | - Michael B. Hall
- Department of Chemistry; Texas A&M University; College Station TX 77843-3255 USA
| | - Milivoj R. Belić
- Science Program; Texas A&M University at Qatar; Texas A&M Engineering Building, Education City Doha Qatar
| | - Snežana D. Zarić
- Science Program; Texas A&M University at Qatar; Texas A&M Engineering Building, Education City Doha Qatar
- Department of Chemistry; University of Belgrade; Studentski trg 12-16 11000 Belgrade Serbia
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20
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Mitra M, Hossain A, Manna P, Choudhury SR, Kaenket S, Helliwell M, Bauzá A, Frontera A, Mukhopadhyay S. Melamine-mediated self-assembly of a Cu(II)–methylmalonate complex assisted by π+–π+ and anti-electrostatic H-bonding interactions. J COORD CHEM 2017. [DOI: 10.1080/00958972.2016.1277709] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Monojit Mitra
- Department of Chemistry, Jadavpur University, Kolkata, India
| | - Anowar Hossain
- Department of Chemistry, Jadavpur University, Kolkata, India
| | | | | | - Surasak Kaenket
- School of Chemistry, The University of Manchester, Manchester, UK
| | | | - Antonio Bauzá
- Departament de Química, Universitat de les Illes Balears, Palma (Baleares), Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Palma (Baleares), Spain
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21
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Halberstadt AL. Pharmacology and Toxicology of N-Benzylphenethylamine ("NBOMe") Hallucinogens. Curr Top Behav Neurosci 2017; 32:283-311. [PMID: 28097528 DOI: 10.1007/7854_2016_64] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Serotonergic hallucinogens induce profound changes in perception and cognition. The characteristic effects of hallucinogens are mediated by 5-HT2A receptor activation. One class of hallucinogens are 2,5-dimethoxy-substituted phenethylamines, such as the so-called 2C-X compounds 2,5-dimethoxy-4-bromophenethylamine (2C-B) and 2,5-dimethoxy-4-iodophenethylamine (2C-I). Addition of an N-benzyl group to phenethylamine hallucinogens produces a marked increase in 5-HT2A-binding affinity and hallucinogenic potency. N-benzylphenethylamines ("NBOMes") such as N-(2-methoxybenzyl)-2,5-dimethoxy-4-iodophenethylamine (25I-NBOMe) show subnanomolar affinity for the 5-HT2A receptor and are reportedly highly potent in humans. Several NBOMEs have been available from online vendors since 2010, resulting in numerous cases of toxicity and multiple fatalities. This chapter reviews the structure-activity relationships, behavioral pharmacology, metabolism, and toxicity of members of the NBOMe hallucinogen class. Based on a review of 51 cases of NBOMe toxicity reported in the literature, it appears that rhabdomyolysis is a relatively common complication of severe NBOMe toxicity, an effect that may be linked to NBOMe-induced seizures, hyperthermia, and vasoconstriction.
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Affiliation(s)
- Adam L Halberstadt
- Department of Psychiatry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0804, USA.
- Research Service, VA San Diego Healthcare System, San Diego, CA, USA.
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22
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Very Strong Parallel Interactions Between Two Saturated Acyclic Groups Closed with Intramolecular Hydrogen Bonds Forming Hydrogen-Bridged Rings. CRYSTALS 2016. [DOI: 10.3390/cryst6040034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Sredojević DN, Petrović PV, Janjić GV, Brothers EN, Hall MB, Zarić SD. The stacking interactions of bipyridine complexes: the influence of the metal ion type on the strength of interactions. J Mol Model 2016; 22:30. [PMID: 26757913 DOI: 10.1007/s00894-015-2888-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/10/2015] [Indexed: 11/26/2022]
Abstract
The strength of the stacking interactions in the bipy complexes of nickel, palladium, and platinum, [M(CN)2 bipy]2 (M = Ni, Pd, Pt), was calculated using the ωB97xD/def2-TZVP method. The results show that for all considered geometries, interactions are the strongest for platinum, and weakest for nickel complexes, as a result of higher dispersion contributions of platinum over the palladium and nickel complexes. It was also shown that strength of interactions considerably rises with an increase of the stacking overlap area. As a consequence of the favorable electrostatic term, the strength of interactions also rises when metal atom and cyano ligands are involved in the overlap with bipy ligand. The strongest interaction was calculated in the platinum complex, for the geometry that has overlap of metal and cyano ligands with bipy ligand with an energy of -39.80 kcal mol(-1). The energies for similar geometries of palladium and nickel complexes are -34.60 and -32.45 kcal mol(-1). These energies, remarkably, exceed the strength of the stacking interactions between organic aromatic molecules. These results can be of importance in all systems with stacking interactions, from materials to biomolecules.
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Affiliation(s)
- Dušan N Sredojević
- Department of Chemistry, Texas A&M University at Qatar, P.O. Box 23874, Doha, Qatar
- Innovation Center, Department of Chemistry, Studentski trg 12-16, 11000, Belgrade, Serbia
| | - Predrag V Petrović
- Department of Chemistry, Texas A&M University at Qatar, P.O. Box 23874, Doha, Qatar
- Innovation Center, Department of Chemistry, Studentski trg 12-16, 11000, Belgrade, Serbia
| | - Goran V Janjić
- Institute of Chemistry, Technology and Metallurgy, Njegoseva 12, University of Belgrade, P.O.B. 473, 11001, Belgrade, Serbia
| | - Edward N Brothers
- Department of Chemistry, Texas A&M University at Qatar, P.O. Box 23874, Doha, Qatar
| | - Michael B Hall
- Department of Chemistry, Texas A&M University College Station, Texas, TX, 77843-3255, USA
| | - Snežana D Zarić
- Department of Chemistry, Texas A&M University at Qatar, P.O. Box 23874, Doha, Qatar.
- Department of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia.
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Chen X, Han S, Wang R, Li Y. Four supramolecular isomers of dichloridobis(1,10-phenanthroline)cobalt(II): synthesis, structure characterization and isomerization. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2016; 72:6-13. [PMID: 26742821 DOI: 10.1107/s2053229615022779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/28/2015] [Indexed: 11/10/2022]
Abstract
Crystal engineering can be described as the understanding of intermolecular interactions in the context of crystal packing and the utilization of such understanding to design new solids with desired physical and chemical properties. Free-energy differences between supramolecular isomers are generally small and minor changes in the crystallization conditions may result in the occurrence of new isomers. The study of supramolecular isomerism will help us to understand the mechanism of crystallization, a very central concept of crystal engineering. Two supramolecular isomers of dichloridobis(1,10-phenanthroline-κ(2)N,N')cobalt(II), [CoCl2(C12H8N2)2], i.e. (IA) (orthorhombic) and (IB) (monoclinic), and two supramolecular isomers of dichloridobis(1,10-phenanthroline-κ(2)N,N')cobalt(II) N,N-dimethylformamide monosolvate, [CoCl2(C12H8N2)2]·C3H7NO, i.e. (IIA) (orthorhombic) and (IIB) (monoclinic), were synthesized in dimethylformamide (DMF) and structurally characterized. Of these, (IA) and (IIA) have been prepared and structurally characterized previously [Li et al. (2007). Acta Cryst. E63, m1880-m1880; Cai et al. (2008). Acta Cryst. E64, m1328-m1329]. We found that the heating rate is a key factor for the crystallization of (IA) or (IB), while the temperature difference is responsible for the crystallization of (IIA) or (IIB). Based on the crystallization conditions, isomerization behaviour, the KPI (Kitajgorodskij packing index) values and the density data, (IB) and (IIA) are assigned as the thermodynamic and stable kinetic isomers, respectively, while (IA) and (IIB) are assigned as the metastable kinetic products. The 1,10-phenanthroline (phen) ligands interact with each other through offset face-to-face (OFF) π-π stacking in (IB) and (IIB), but by edge-to-face (EF) C-H...π interactions in (IA) and (IIA). Meanwhile, the DMF molecules in (IIB) connect to neighbouring [CoCl2(phen)2] units through two C-H...Cl hydrogen bonds, whereas there are no obvious interactions between DMF molecules and [CoCl2(phen)2] units in (IIA). Since OFF π-π stacking is generally stronger than EF C-H...π interactions for transition-metal complexes with nitrogen-containing aromatic ligands, (IIA) is among the uncommon examples that are stable and densely packed but that do not following Etter's intermolecular interaction hierarchy.
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Affiliation(s)
- Xiaocui Chen
- College of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, People's Republic of China
| | - Shumin Han
- College of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, People's Republic of China
| | - Ruiyao Wang
- Department of Chemistry, Xi'an Jiaotong-Liverpool University, 111 Ren Ai Road, Suzhou 215123, People's Republic of China
| | - Yuan Li
- College of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, People's Republic of China
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Tokoro Y, Ohtsuka N, Toh A, Fukuzawa SI. Synthesis and Structure of N-Hetero-ortho-phenylene Hexamers Containing 2,3-Substituted Pyridine Moieties. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501270] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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The Bright Future of Unconventional σ/π-Hole Interactions. Chemphyschem 2015; 16:2496-517. [DOI: 10.1002/cphc.201500314] [Citation(s) in RCA: 475] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Indexed: 01/25/2023]
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Qin H, Zhou T, Yang S, Xing D. Fluorescence Quenching Nanoprobes Dedicated to In Vivo Photoacoustic Imaging and High-Efficient Tumor Therapy in Deep-Seated Tissue. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:2675-2686. [PMID: 25656695 DOI: 10.1002/smll.201403395] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 12/22/2014] [Indexed: 06/04/2023]
Abstract
Photoacoustic imaging (PAI) and photoacoustic (PA) therapy have promising applications for treating tumors. It is known that the utilization of high-absorption-coefficient probes can selectively enhance the PAI target contrast and PA tumor therapy efficiency in deep-seated tissue. Here, the design of a probe with the highest availability of optical-thermo conversion by using graphene oxide (GO) and dyes via π-π stacking interactions is reported. The GO serves as a base material for loading dyes and quenching dye fluorescence via fluorescence resonance energy transfer (FRET), with the one purpose of maximum of PA efficiency. Experiments verify that the designed fluorescence quenching nanoprobes can produce stronger PA signals than the sum of the separate signals generated in the dye and the GO. Potential applications of the fluorescence quenching nanoprobes are demonstrated, dedicating to enhance PA contrast of targets in deep-seated tissues and tumors in living mice. PA therapy efficiency both in vitro and in vivo by using the fluorescence quenching nanoprobes is found to be higher than with the commonly used PA therapy agents. Taken together, quenching dye fluorescence via FRET will provide a valid means for developing high-efficiency PA probes. Fluorescence quenching nanoprobes are likely to become a promising candidate for deep-seated tumor imaging and therapy.
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Affiliation(s)
- Huan Qin
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Ting Zhou
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Sihua Yang
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Da Xing
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
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28
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Ray S, Das A. Studies on the π–π stacking features of imidazole units present in a series of 5-amino-1-alkylimidazole-4-carboxamides. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.02.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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29
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Tian G, Li H, Ma W, Wang Y. Substituent Effects in π-Stacking of Histidine on Functionalized-SWNT and Graphene. COMPUT THEOR CHEM 2015; 1062:44-49. [PMID: 25914869 DOI: 10.1016/j.comptc.2015.03.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adsorptions of histidine on the functionalized (10,0) single-walled carbon nanotube (SWNT) and graphene were investigated using density function theory methods, M05-2x and DFT-D. The results show that the binding of the histidine ring to the functionalized SWNT is weaker than that to the pristine SWNT for both singlet and triplet complexes, regardless of the electron-donating (-OH, -NH2) or electron-withdrawing (-COOH) character and their attached sites. The present decreased binding is opposite to the well-known enhanced binding in the substituted benzene dimers. Since the atoms of the histidine are distant from the substituent atoms by over 6Å, there would be no direct interaction between histidine and the substituent as in the case of the substituted benzene systems. The decreased binding can be mainly driven by the aromaticity of the functionalized SWNT. The nucleus-independent chemical shift (NICS) index analysis for the functionalized SWNTs in deed shows that local aromaticity of SWNT is decreased because of the electron redistribution induced by functional groups, and the π-π stacking between the histidine ring and functionalized-SWNT is therefore decreased as compared to the pristine SWNT. However, the above trend does not remain for the binding between the histidine and graphene. The binding of the histidine to the functionalized graphene with -OH and -NH2 is just slightly weaker than that to the pristine graphene, while its binding to COOH-SWNT becomes a little bit stronger.
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Affiliation(s)
- Ge Tian
- School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, Jinan, Shandong 250353, China ; Department of Natural Science, Albany State University, Albany, GA 31705, USA
| | - Huifang Li
- Department of Natural Science, Albany State University, Albany, GA 31705, USA ; Department of Chemistry, Gannan Normal University, GanZhou, JiangXi 341000, China
| | - Wanyong Ma
- School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, Jinan, Shandong 250353, China
| | - Yixuan Wang
- Department of Natural Science, Albany State University, Albany, GA 31705, USA
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Albrecht M, Yi H, Pan F, Valkonen A, Rissanen K. Connecting Electron-Deficient and Electron-Rich Aromatics to Support Intermolecular Interactions in Crystals. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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31
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Karthikeyan S, Lee JY. Tuning the C–X…π interaction of benzene–chloroacetylene complexes by aromatic substitutions. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.04.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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32
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Kheirjou S, Fattahi A, Hashemi MM. The intramolecular cation–π interaction of some aryl amines and its drastic influence on the basicity of them: AIM and NBO analysis. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Ninković DB, Andrić JM, Malkov SN, Zarić SD. What are the preferred horizontal displacements of aromatic–aromatic interactions in proteins? Comparison with the calculated benzene–benzene potential energy surface. Phys Chem Chem Phys 2014; 16:11173-7. [DOI: 10.1039/c3cp54474e] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Stacking interactions of phenylalanine residues show preference for large offsets (3.5–5.0 Å), while the calculations show substantially strong interactions, of about −2.0 kcal mol−1.
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Affiliation(s)
| | - Jelena M. Andrić
- Innovation center of the Department of Chemistry
- 11000 Belgrade, Serbia
| | - Saša N. Malkov
- Department of Mathematics
- University of Belgrade
- 11000 Belgrade, Serbia
| | - Snežana D. Zarić
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
- Department of Chemistry
- Texas A & M University at Qatar
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Janjić GV, Ninković DB, Zarić SD. Influence of supramolecular structures in crystals on parallel stacking interactions between pyridine molecules. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2013; 69:389-394. [PMID: 23873064 DOI: 10.1107/s2052519213013961] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/20/2013] [Indexed: 06/02/2023]
Abstract
Parallel stacking interactions between pyridines in crystal structures and the influence of hydrogen bonding and supramolecular structures in crystals on the geometries of interactions were studied by analyzing data from the Cambridge Structural Database (CSD). In the CSD 66 contacts of pyridines have a parallel orientation of molecules and most of these pyridines simultaneously form hydrogen bonds (44 contacts). The geometries of stacked pyridines observed in crystal structures were compared with the geometries obtained by calculations and explained by supramolecular structures in crystals. The results show that the mean perpendicular distance (R) between pyridine rings with (3.48 Å) and without hydrogen bonds (3.62 Å) is larger than that calculated, because of the influence of supramolecular structures in crystals. The pyridines with hydrogen bonds show a pronounced preference for offsets of 1.25-1.75 Å, close to the position of the calculated minimum (1.80 Å). However, stacking interactions of pyridines without hydrogen bonds do not adopt values at or close to that of the calculated offset. This is because stacking interactions of pyridines without hydrogen bonds are less strong, and they are more susceptible to the influence of supramolecular structures in crystals. These results show that hydrogen bonding and supramolecular structures have an important influence on the geometries of stacked pyridines in crystals.
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Affiliation(s)
- Goran V Janjić
- ICTM, University of Belgrade, Njegoševa 12, Belgrade 11000, Serbia
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Abstract
Fundamental features of biomolecules, such as their structure, solvation, and crystal packing and even the docking of drugs, rely on noncovalent interactions. Theory can help elucidate the nature of these interactions, and energy component analysis reveals the contributions from the various intermolecular forces: electrostatics, London dispersion terms, induction (polarization), and short-range exchange-repulsion. Symmetry-adapted perturbation theory (SAPT) provides one method for this type of analysis. In this Account, we show several examples of how SAPT provides insight into the nature of noncovalent π-interactions. In cation-π interactions, the cation strongly polarizes electrons in π-orbitals, leading to substantially attractive induction terms. This polarization is so important that a cation and a benzene attract each other when placed in the same plane, even though a consideration of the electrostatic interactions alone would suggest otherwise. SAPT analysis can also support an understanding of substituent effects in π-π interactions. Trends in face-to-face sandwich benzene dimers cannot be understood solely in terms of electrostatic effects, especially for multiply substituted dimers, but SAPT analysis demonstrates the importance of London dispersion forces. Moreover, detailed SAPT studies also reveal the critical importance of charge penetration effects in π-stacking interactions. These effects arise in cases with substantial orbital overlap, such as in π-stacking in DNA or in crystal structures of π-conjugated materials. These charge penetration effects lead to attractive electrostatic terms where a simpler analysis based on atom-centered charges, electrostatic potential plots, or even distributed multipole analysis would incorrectly predict repulsive electrostatics. SAPT analysis of sandwich benzene, benzene-pyridine, and pyridine dimers indicates that dipole/induced-dipole terms present in benzene-pyridine but not in benzene dimer are relatively unimportant. In general, a nitrogen heteroatom contracts the electron density, reducing the magnitude of both the London dispersion and the exchange-repulsion terms, but with an overall net increase in attraction. Finally, using recent advances in SAPT algorithms, researchers can now perform SAPT computations on systems with 200 atoms or more. We discuss a recent study of the intercalation complex of proflavine with a trinucleotide duplex of DNA. Here, London dispersion forces are the strongest contributors to binding, as is typical for π-π interactions. However, the electrostatic terms are larger than usual on a fractional basis, which likely results from the positive charge on the intercalator and its location between two electron-rich base pairs. These cation-π interactions also increase the induction term beyond those of typical noncovalent π-interactions.
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Affiliation(s)
- C. David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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Wu J, Zhang D, Chen L, Li J, Wang J, Ning C, Yu N, Zhao F, Chen D, Chen X, Chen K, Jiang H, Liu H, Liu D. Discovery and Mechanism Study of SIRT1 Activators that Promote the Deacetylation of Fluorophore-Labeled Substrate. J Med Chem 2013; 56:761-80. [DOI: 10.1021/jm301032j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | | | | | - Jianneng Li
- School of Life Sciences, Fudan
University, Shanghai 200433, China
| | | | - Chengqing Ning
- Institute of Molecular Design and Drug
Discovery, School of Pharmaceutical Sciences, Central South University,
Changsha 410078, Hunan, China
| | - Niefang Yu
- Institute of Molecular Design and Drug
Discovery, School of Pharmaceutical Sciences, Central South University,
Changsha 410078, Hunan, China
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Manna P, Seth SK, Mitra M, Das A, Singh NJ, Choudhury SR, Kar T, Mukhopadhyay S. A successive layer-by-layer assembly of supramolecular frameworks driven by a novel type of face-to-face π+–π+ interactions. CrystEngComm 2013. [DOI: 10.1039/c3ce41230j] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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38
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Seth SK, Manna P, Singh NJ, Mitra M, Jana AD, Das A, Choudhury SR, Kar T, Mukhopadhyay S, Kim KS. Molecular architecture using novel types of non-covalent π-interactions involving aromatic neutrals, aromatic cations and π-anions. CrystEngComm 2013. [DOI: 10.1039/c2ce26577j] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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39
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Ninković DB, Andrić JM, Zarić SD. Parallel Interactions at Large Horizontal Displacement in Pyridine-Pyridine and Benzene-Pyridine Dimers. Chemphyschem 2012; 14:237-43. [DOI: 10.1002/cphc.201200607] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Indexed: 11/11/2022]
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40
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Georgakilas V, Otyepka M, Bourlinos AB, Chandra V, Kim N, Kemp KC, Hobza P, Zboril R, Kim KS. Functionalization of graphene: covalent and non-covalent approaches, derivatives and applications. Chem Rev 2012; 112:6156-214. [PMID: 23009634 DOI: 10.1021/cr3000412] [Citation(s) in RCA: 1826] [Impact Index Per Article: 152.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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41
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Snyder SE, Huang BS, Chu YW, Lin HS, Carey JR. The Effects of Substituents on the Geometry of π-π Interactions. Chemistry 2012; 18:12663-71. [DOI: 10.1002/chem.201202253] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Indexed: 11/07/2022]
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42
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Theoretical study of different substituent benzenes and benzene dimers blue-shifted hydrogen bonds. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2011.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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43
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Das LK, Park SW, Cho SJ, Ghosh A. An unprecedented “linear-bent” isomerism in tri-nuclear Cu2IIZnII complexes with a salen type di-Schiff base ligand. Dalton Trans 2012; 41:11009-17. [DOI: 10.1039/c2dt31011b] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Kim KS, Karthikeyan S, Singh NJ. How Different Are Aromatic π Interactions from Aliphatic π Interactions and Non-π Stacking Interactions? J Chem Theory Comput 2011; 7:3471-7. [DOI: 10.1021/ct200586g] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kwang S. Kim
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
| | - S. Karthikeyan
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
| | - N. Jiten Singh
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
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