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Narayan J, Bezborah K. Recent advances in the functionalization, substitutional doping and applications of graphene/graphene composite nanomaterials. RSC Adv 2024; 14:13413-13444. [PMID: 38660531 PMCID: PMC11041312 DOI: 10.1039/d3ra07072g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/01/2024] [Indexed: 04/26/2024] Open
Abstract
Recently, graphene and graphene-based nanomaterials have emerged as advanced carbon functional materials with specialized unique electronic, optical, mechanical, and chemical properties. These properties have made graphene an exceptional material for a wide range of promising applications in biological and non-biological fields. The present review illustrates the structural modifications of pristine graphene resulting in a wide variety of derivatives. The significance of substitutional doping with alkali-metals, alkaline earth metals, and III-VII group elements apart from the transition metals of the periodic table is discussed. The paper reviews various chemical and physical preparation routes of graphene, its derivatives and graphene-based nanocomposites at room and elevated temperatures in various solvents. The difficulty in dispersing it in water and organic solvents make it essential to functionalize graphene and its derivatives. Recent trends and advances are discussed at length. Controlled reduction reactions in the presence of various dopants leading to nanocomposites along with suitable surfactants essential to enhance its potential applications in the semiconductor industry and biological fields are discussed in detail.
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Affiliation(s)
- Jyoti Narayan
- Synthetic Nanochemistry Laboratory, Department of Basic Sciences & Social Sciences, (Chemistry Division) School of Technology, North Eastern Hill University Shillong 793022 Meghalaya India
| | - Kangkana Bezborah
- Synthetic Nanochemistry Laboratory, Department of Basic Sciences & Social Sciences, (Chemistry Division) School of Technology, North Eastern Hill University Shillong 793022 Meghalaya India
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Rapacioli M, Buey MY, Spiegelman F. Addressing electronic and dynamical evolution of molecules and molecular clusters: DFTB simulations of energy relaxation in polycyclic aromatic hydrocarbons. Phys Chem Chem Phys 2024; 26:1499-1515. [PMID: 37933901 PMCID: PMC10793726 DOI: 10.1039/d3cp02852f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023]
Abstract
We present a review of the capabilities of the density functional based Tight Binding (DFTB) scheme to address the electronic relaxation and dynamical evolution of molecules and molecular clusters following energy deposition via either collision or photoabsorption. The basics and extensions of DFTB for addressing these systems and in particular their electronic states and their dynamical evolution are reviewed. Applications to PAH molecules and clusters, carbonaceous systems of major interest in astrochemical/astrophysical context, are reported. A variety of processes are examined and discussed such as collisional hydrogenation, fast collisional processes and induced electronic and charge dynamics, collision-induced fragmentation, photo-induced fragmentation, relaxation in high electronic states, electronic-to-vibrational energy conversion and statistical versus non-statistical fragmentation. This review illustrates how simulations may help to unravel different relaxation mechanisms depending on various factors such as the system size, specific electronic structure or excitation conditions, in close connection with experiments.
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Affiliation(s)
- Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| | - Maysa Yusef Buey
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| | - Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
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Kumar YB, Kumar N, Vaikundamani S, Nagamani S, Mahanta HJ, Sastry GM, Sastry GN. Analyzing the aromatic-aromatic interactions in proteins: A 2ID 2.0. Int J Biol Macromol 2023; 253:127207. [PMID: 37797858 DOI: 10.1016/j.ijbiomac.2023.127207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/09/2023] [Accepted: 09/30/2023] [Indexed: 10/07/2023]
Abstract
The Aromatic-Aromatic Interactions Database (A2ID) is a comprehensive repository dedicated to documenting aromatic-aromatic (π-π) networks observed in experimentally determined protein structures. The first version of A2ID was reported in 2011 [Int J Biol Macromol, 2011, 48, 540]. It has undergone a series of significant updates, leading to its current version, which focuses on the identification and analysis of 3,444,619 π-π networks from proteins. The geometrical parameters such as centroid-centroid distances (r) and interplanar angles (ϕ) were used to identify and characterize π-π networks. It was observed that among the 84,500 proteins with at least one aromatic π-π network, about 92.50 % of the instances are found to be either 2π (77.34 %) or 3π (15.23 %) networks. The analysis of interacting amino acid pairs in 2π networks indicated a dominance of PHE residues followed by TYR. The updated version of A2ID incorporates analysis of π-π networks based on SCOP2 and ECOD classifiers, in addition to the existing SCOP, CATH, and EC classifications. This expanded scope allows researchers to explore the characteristics and functional implications of π-π networks in protein structures from multiple perspectives. The current version of A2ID along with its extensive dataset and detailed geometric information is publicly accessible using https://acds.neist.res.in/a2idv2.
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Affiliation(s)
- Y Bhargav Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U. P., India
| | - Nandan Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - S Vaikundamani
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - Selvaraman Nagamani
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U. P., India
| | - Hridoy Jyoti Mahanta
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U. P., India
| | - G Madhavi Sastry
- Schrödinger Inc., HITEC City, Hyderabad, Telangana 500081, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U. P., India.
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Tang C, Saielli G, Wang Y. Influence of Anion Species on Liquid-Liquid Phase Separation in [EMIm +][X -]/Benzene Mixtures. J Phys Chem B 2023. [PMID: 38031410 DOI: 10.1021/acs.jpcb.3c06205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
When a molar excess of benzene is mixed with an ionic liquid (IL), liquid-liquid phase separation may appear with a pure liquid phase almost composed of only benzene molecules separated from a liquid clathrate phase with benzene molecules dissolved in the IL. Our previous study (J. Phys. Chem. B, 124, 7929, 2020) on long-chain IL/benzene systems has concluded that benzene molecules, as planar nonpolar ones, majorly dissolve in the IL nonpolar domains consisting of cationic alkyl side chains. Nevertheless, the above mechanism is inadequate for explaining the experimental observations that benzene can also dissolve in IL systems with very short alkyl side chains. In this study, by molecular dynamics simulation of the [EMIm+][X-]/benzene mixtures with X- being Cl-, NO3-, PF6-, or Tf2N-, we still observe liquid-liquid phase separation of the pure benzene phase from a liquid clathrate (mixed IL/benzene) phase where benzene molecules are almost equally distributed near imidazolium rings through π-stacking or near alkyl side chains. The anion species strongly influences the solubility of benzene and the ratio of the two liquid phases via the alteration of anionic charge density, which tunes the strength of the electrostatic interaction among ions and thus the probability of benzene molecules interacting with both imidazolium rings and alkyl side chains: a larger anionic charge density corresponds to a lower solubility of benzene.
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Affiliation(s)
- Chenyu Tang
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Giacomo Saielli
- CNR Institute on Membrane Technology, Unit of Padova, Via Marzolo, Padova 1-35131, Italy
- Department of Chemical Sciences, University of Padova, Via Marzolo, Padova 1-35131, Italy
| | - Yanting Wang
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Theoretical Interdisciplinary Sciences, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China
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Sussardi AN, Turner GF, Richardson JG, Spackman MA, Turley AT, McGonigal PR, Jones AC, Moggach SA. Tandem High-Pressure Crystallography-Optical Spectroscopy Unpacks Noncovalent Interactions of Piezochromic Fluorescent Molecular Rotors. J Am Chem Soc 2023; 145:19780-19789. [PMID: 37649399 DOI: 10.1021/jacs.3c05444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
To develop luminescent molecular materials with predictable and stimuli-responsive emission, it is necessary to correlate changes in their geometries, packing structures, and noncovalent interactions with the associated changes in their optical properties. Here, we demonstrate that high-pressure single-crystal X-ray diffraction can be combined with high-pressure UV-visible absorption and fluorescence emission spectroscopies to elucidate how subtle changes in structure influence optical outputs. A piezochromic aggregation-induced emitter, sym-heptaphenylcycloheptatriene (Ph7C7H), displays bathochromic shifts in its absorption and emission spectra at high pressure. Parallel X-ray measurements identify the pressure-induced changes in specific phenyl-phenyl interactions responsible for the piezochromism. Pairs of phenyl rings from neighboring molecules approach the geometry of a stable benzene dimer, while conformational changes alter intramolecular phenyl-phenyl interactions correlated with a relaxed excited state. This tandem crystallographic and spectroscopic analysis provides insights into how subtle structural changes relate to the photophysical properties of Ph7C7H and could be applied to a library of similar compounds to provide general structure-property relationships in fluorescent organic molecules with rotor-like geometries.
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Affiliation(s)
- Alif N Sussardi
- School of Chemistry, The University of Edinburgh, Edinburgh EH9 3FL, U.K
| | - Gemma F Turner
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia
| | | | - Mark A Spackman
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia
| | - Andrew T Turley
- Department of Chemistry, Durham University, Durham DH1 3LE, U.K
| | - Paul R McGonigal
- Department of Chemistry, Durham University, Durham DH1 3LE, U.K
- School of Chemistry, The University of York, York YO10 5DD, U.K
| | - Anita C Jones
- School of Chemistry, The University of Edinburgh, Edinburgh EH9 3FL, U.K
| | - Stephen A Moggach
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia
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Palluccio TD, Germain ME, Marazzi M, Temprado M, Silvia JS, Müller P, Cummins CC, Davis JV, Serafim LF, Captain B, Hoff CD, Rybak-Akimova EV. Binding of Nitriles and Isonitriles to V(III) and Mo(III) Complexes: Ligand vs Metal Controlled Mechanism. Inorg Chem 2023. [PMID: 37377337 DOI: 10.1021/acs.inorgchem.3c00595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
The synthesis and structures of nitrile complexes of V(N[tBu]Ar)3, 2 (Ar = 3,5-Me2C6H3), are described. Thermochemical and kinetic data for their formation were determined by variable temperature Fourier transform infrared (FTIR), calorimetry, and stopped-flow techniques. The extent of back-bonding from metal to coordinated nitrile indicates that electron donation from the metal to the nitrile plays a less prominent role for 2 than for the related complex Mo(N[tBu]Ar)3, 1. Kinetic studies reveal similar rate constants for nitrile binding to 2, but the activation parameters depend critically on the nature of R in RCN. Activation enthalpies range from 2.9 to 7.2 kcal·mol-1, and activation entropies from -9 to -28 cal·mol-1·K-1 in an opposing manner. Density functional theory (DFT) calculations provide a plausible explanation supporting the formation of a π-stacking interaction between a pendant arene of the metal anilide of 2 and the arene substituent on the incoming nitrile in favorable cases. Data for ligand binding to 1 do not exhibit this range of activation parameters and are clustered in a small area centered at ΔH‡ = 5.0 kcal·mol-1 and ΔS‡ = -26 cal·mol-1·K-1. Computational studies are in agreement with the experimental data and indicate a stronger dependence on electronic factors associated with the change in spin state upon ligand binding to 1.
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Affiliation(s)
- Taryn D Palluccio
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Meaghan E Germain
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Marco Marazzi
- Departamento de Química Analítica, Química Física e Ingeniería Química, Grupo de Reactividad y Estructura Molecular (RESMOL), Universidad de Alcalá, Alcalá de Henares, Madrid 28805, Spain
- Instituto de Investigación Química 'Andrés M. del Río'' (IQAR), Universidad de Alcalá, Alcalá de Henares, Madrid 28805, Spain
| | - Manuel Temprado
- Departamento de Química Analítica, Química Física e Ingeniería Química, Grupo de Reactividad y Estructura Molecular (RESMOL), Universidad de Alcalá, Alcalá de Henares, Madrid 28805, Spain
- Instituto de Investigación Química 'Andrés M. del Río'' (IQAR), Universidad de Alcalá, Alcalá de Henares, Madrid 28805, Spain
| | - Jared S Silvia
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Peter Müller
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher C Cummins
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jack V Davis
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Leonardo F Serafim
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Burjor Captain
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Carl D Hoff
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Elena V Rybak-Akimova
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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Abstract
One of the several possibilities offered by the interesting clathrate hydrates is the opportunity to encapsulate several atoms or molecules, in such a way that more efficient storage materials could be explored or new molecules that otherwise do not exist could be created. These types of applications are receiving growing attention from technologists and chemists, given the future positive implications that they entail. In this context, we investigated the multiple cage occupancy of helium clathrate hydrates, to establish stable novel hydrate structures or ones similar to those predicted previously by experimental and theoretical studies. To this purpose, we analyzed the feasibility of including an increased number of He atoms inside the small (D) and large (H) cages of the sII structure through first-principles properly assessed density functional approaches. On the one hand, we have computed energetic and structural properties, in which we examined the guest-host and guest-guest interactions in both individual and two-adjacent clathrate-like sII cages by means of binding and evaporation energies. On the other hand, we have carried out a thermodynamical analysis on the stability of such He-containing hydrostructures in terms of changes in enthalpy, ΔH, Gibbs free energy, ΔG, and entropy, ΔS, during their formation process at various temperature and pressure values. In this way, we have been able to make a comparison with experiments, reaffirming the ability of computational DFT approaches to describe such weak guest-host interactions. In principle, the most stable structure involves the encapsulation of one and four He atoms inside the D and H sII cages, respectively; however, more He atoms could be entrapped under lower temperature and/or higher pressure thermodynamic conditions. We foresee such accurate computational quantum chemistry approaches contributing to the current emerging machine-learning model development.
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Affiliation(s)
- Raquel Yanes-Rodríguez
- Institute of Fundamental Physics (IFF-CSIC), CSIC, Serrano 123, 28006 Madrid, Spain.
- Doctoral Programme in Theoretical Chemistry and Computational Modelling, Doctoral School, Universidad Autónoma de Madrid, Spain
| | - Rita Prosmiti
- Institute of Fundamental Physics (IFF-CSIC), CSIC, Serrano 123, 28006 Madrid, Spain.
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R A C Lima CF, Mague JT, Du Y, Pascal RA, Santos LMNBF. How great is the stabilization of crowded polyphenylbiphenyls by London dispersion? Phys Chem Chem Phys 2023; 25:13359-13375. [PMID: 37145056 DOI: 10.1039/d2cp05085d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Decaphenylbiphenyl (1) and 2,2',4,4',6,6'-hexaphenylbiphenyl (2) are bulky molecules expected to be greatly destabilized by steric crowding. Herein, through a combined experimental and computational approach, we evaluate the molecular energetics of crowded biphenyls. This is complemented by the study of phase equilibria for 1 and 2. Compound 1 shows a rich phase behavior, displaying an unusual interconversion between two polymorphs. Surprisingly, the polymorph with distorted molecules of C1 symmetry is found to have the highest melting point and to be the one that is preferentially formed. The thermodynamic results also indicate that the polymorph displaying the more regular D2 molecular geometry has larger heat capacity and is probably the more stable at lower temperatures. The melting and sublimation data clearly reveal the weakening of cohesive forces in crowded biphenyls due to the lower molecular surface area. The experimental quantification of the intramolecular interactions in 1 and 2 indicated, using homodesmotic reactions, a molecular stabilization of about 30 kJ mol-1. We attribute the origin of this stabilization in both compounds to the existence of two parallel-displaced π⋯π interactions between the ortho-phenyl substituents on each side of the central biphenyl. Computational calculations with dispersion-corrected DFT methods underestimate the stabilization in 1, unless the steric crowding is well balanced in a homodesmotic scheme. This work demonstrates that London dispersion forces are important in crowded aromatic systems, making these molecules considerably more stable than previously thought.
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Affiliation(s)
- Carlos F R A C Lima
- CIQUP, Institute of Molecular Sciences (IMS), Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, rua do Campo Alegre s/n, 4169-007 Porto, Portugal.
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
| | - Yuchen Du
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
| | - Robert A Pascal
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
| | - Luís M N B F Santos
- CIQUP, Institute of Molecular Sciences (IMS), Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, rua do Campo Alegre s/n, 4169-007 Porto, Portugal.
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Feng JY, Lee YP, Hsu PJ, Kuo JL, Ebata T. Structures of (Pyrazine) 2 and (Pyrazine)(Benzene) Dimers Investigated with Infrared-Vacuum Ultraviolet Spectroscopy and Quantum-Chemical Calculations: Competition among π-π, CH···π, and CH···N Interactions. J Phys Chem A 2023; 127:4291-4301. [PMID: 37145887 DOI: 10.1021/acs.jpca.3c01767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The structures of a pyrazine dimer (pyrazine)2 and (pyrazine)(benzene) hetero-dimer cooled in a supersonic beam were investigated by the measurement of the infrared spectra in the C-H stretching region with infrared-vacuum ultraviolet (IR-VUV) spectroscopy and quantum-chemical calculations. The stabilization energy calculation at the CCSD(T)/aug-cc-pVTZ level of theory predicted three isomers for (pyrazine)2 and three for (pyrazine)(benzene) with energy within 6 kJ/mol. Among them, the cross-displaced π-π stacked structure is the most stable in both dimers. In the observed IR spectra, both dimers exhibited two intense bands near 3065 cm-1, with intervals of 8 cm-1 in (pyrazine)2 and 11 cm-1 in (pyrazine)(benzene), while only one band appeared in the monomer. For (pyrazine)(benzene), we also measured the IR spectrum of (pyrazine)(benzene-d6), where the interval of the two bands was unchanged. The analysis of the observed IR spectra with anharmonic calculations suggested the coexistence of three isomers of (pyrazine)2 and (pyrazine)(benzene) in a supersonic jet. For (pyrazine)2, the two isomers which were previously assigned to the H-bonded planar and the π-π stacked structures respectively were reassigned to the cross-displaced π-π stacked and T-shaped structures, respectively. In addition, the quantum chemical calculation and IR-VUV spectral measurement suggested the coexistence of the H-bonded planar isomer in the jet. For (pyrazine)(benzene), the IR spectrum of the (pyrazine) site showed a similar spectral pattern to that of (pyrazine)2, especially the split at ∼3065 cm-1. However, the anharmonic analysis suggested that they are assigned to the different vibrational motions of (pyrazine). The anharmonic vibrational analysis is essential to associate the observed IR spectra with the correct structures of the dimer.
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Affiliation(s)
- Jun-Ying Feng
- Department of Applied Chemistry and Institute for Molecular Science, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Yuan-Pern Lee
- Department of Applied Chemistry and Institute for Molecular Science, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
- Center for Emergent Functional Matter Sciences, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106319, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106319, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
- International Graduate Program of Molecular Science and Technology (NTU-MST), National Taiwan University, Taipei 10617 Taiwan
| | - Takayuki Ebata
- Department of Applied Chemistry and Institute for Molecular Science, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
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Mitani T, Tsurumaki E, Toyota S. Structures and Supramolecular Properties of Inclusion Complexes of Anthracene-Triptycene Nanocages with Fullerene Guests and Their Dynamic Motion as Molecular Gyroscopes. Chemistry 2023; 29:e202203462. [PMID: 36460616 DOI: 10.1002/chem.202203462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/04/2022]
Abstract
Three derivatives of macrocyclic cage compounds consisting of diarylanthracene and triptycene units were synthesized. These nanocages formed host-guest complexes with C60 and other fullerene guests as confirmed by 1 H NMR and fluorescence spectroscopy. The association constant of the mesityl and 2,4,6-tributoxyphenyl derivatives with C60 was determined to be 2.2 × 104 L mol-1 , which was larger than that of the pentafluorophenyl derivative. Direct experimental evidence of the complexation was obtained by X-ray diffraction analysis: the guest C60 molecule was included in the cavity via multipoint CH⋅⋅⋅π interactions. Dynamic disorders of the included C60 molecule in variable-temperature X-ray analysis indicated uniaxial motion, such as gyroscopic motion. The unique dynamic behavior of the spherical C60 rotor anchored by the cage stator via CH⋅⋅⋅π interactions in the crystal, as well as substituent effects on the association properties, are discussed with the aid of DFT calculations.
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Affiliation(s)
- Takuji Mitani
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Eiji Tsurumaki
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Shinji Toyota
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
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12
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Herman KM, Aprà E, Xantheas SS. A critical comparison of CH⋯π versus π⋯π interactions in the benzene dimer: obtaining benchmarks at the CCSD(T) level and assessing the accuracy of lower scaling methods. Phys Chem Chem Phys 2023; 25:4824-4838. [PMID: 36692338 DOI: 10.1039/d2cp04335a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We have established CCSD(T)/CBS (Complete Basis Set) limits for 3 stationary points on the benzene dimer potential energy surface, corresponding to the π⋯π (parallel displaced or PD(C2h), minimum) and CH⋯π (T-shaped or T(C2v), transition state) and tilted T-shaped (or TT(Cs), minimum) bonding scenarios considering both the structure and binding energy. The CCSD(T)/CBS binding energies are -2.65 ± 0.02 (PD), -2.74 ± 0.03 (T), and -2.83 ± 0.01 kcal mol-1 (TT). To this end, the CH⋯π is ∼0.2 kcal mol-1 stronger than the π⋯π interaction, whereas the tilting of the CH donating benzene molecule with respect to the other benzene is worth 0.1 kcal mol-1. As previously discussed in the literature, the MP2 level of theory does not provide a close match for either the energy or structure, yet the SCS-MP2 yields structures in excellent agreement with respect to the CCSD(T) result. It is found that the SCS-MI-MP2 also gives optimized structures very close to SCS-MP2 (within ∼0.01 Å of the benchmark). Despite the closer match in structure, the spin-biased MP2 methods (SCS-, SCS-MI-, and SOS-MP2) incorrectly predict the relative stabilities of the isomers. That said, none of the spin biased MP2 methods offers a good compromise between energy and structure for the systems examined. Finally, the CCSD(T)/CBS benchmarks were used to assess the performance of 13 DFT functionals selected from different rungs of Jacob's ladder. Several functionals such as TPSS-D3, B3LYP-D3, B97-D, B97-D3, and B2PLYP-D3 provided a good description of the binding energies for both CH⋯π and π⋯π interactions, yielding values within 6% of the CCSD(T)/CBS benchmark values. Unlike the MP2 methods, these functionals correctly predict the relative stability of the PD(C2h) and T(C2v) dimers. Further, we find that there is no systematic improvement as Jacob's ladder is ascended (increased complexity of functional). The best functionals that result in a good compromise between structure and energy accuracy are B97-D3 and B2PLYP-D3 for both the CH⋯π and π⋯π interaction. Despite the impressive performance of these functionals, a challenge that remains is ensuring the transferability of these density functionals in accurately describing the interaction between dimers of larger aromatic molecules, the latter requiring high-level benchmarks for these systems.
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Affiliation(s)
- Kristina M Herman
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - Edoardo Aprà
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA. .,Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, WA, 99352, USA
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13
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El Harrar T, Gohlke H. Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. J Chem Inf Model 2023; 63:281-298. [PMID: 36520535 DOI: 10.1021/acs.jcim.2c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data are available describing the energetic effects of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of >1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol-1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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14
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Li E, Lyu CK, Chen C, Xie H, Zhang J, Lam JWY, Tang BZ, Lin N. On-surface synthesis and spontaneous segregation of conjugated tetraphenylethylene macrocycles. Commun Chem 2022; 5:174. [PMID: 36697742 PMCID: PMC9814618 DOI: 10.1038/s42004-022-00794-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Creating conjugated macrocycles has attracted extensive research interest because their unique chemical and physical properties, such as conformational flexibility, intrinsic inner cavities and aromaticity/antiaromaticity, make these systems appealing building blocks for functional supramolecular materials. Here, we report the synthesis of four-, six- and eight-membered tetraphenylethylene (TPE)-based macrocycles on Ag(111) via on-surface Ullmann coupling reactions. The as-synthesized macrocycles are spontaneously segregated on the surface and self-assemble as large-area two-dimensional mono-component supramolecular crystals, as characterized by scanning tunneling microscopy (STM). We propose that the synthesis benefits from the conformational flexibility of the TPE backbone in distinctive multi-step reaction pathways. This study opens up opportunities for exploring the photophysical properties of TPE-based macrocycles.
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Affiliation(s)
- En Li
- grid.24515.370000 0004 1937 1450Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Cheng-Kun Lyu
- grid.24515.370000 0004 1937 1450Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Chengyi Chen
- grid.24515.370000 0004 1937 1450Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Huilin Xie
- grid.24515.370000 0004 1937 1450Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Jianyu Zhang
- grid.24515.370000 0004 1937 1450Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Jacky Wing Yip Lam
- grid.24515.370000 0004 1937 1450Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Ben Zhong Tang
- grid.24515.370000 0004 1937 1450Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China ,grid.10784.3a0000 0004 1937 0482School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong China
| | - Nian Lin
- grid.24515.370000 0004 1937 1450Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
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15
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Jansen C, Assahub N, Spieß A, Liang J, Schmitz A, Xing S, Gökpinar S, Janiak C. The Complexity of Comparative Adsorption of C 6 Hydrocarbons (Benzene, Cyclohexane, n-Hexane) at Metal-Organic Frameworks. Nanomaterials (Basel) 2022; 12:3614. [PMID: 36296804 PMCID: PMC9610754 DOI: 10.3390/nano12203614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The relatively stable MOFs Alfum, MIL-160, DUT-4, DUT-5, MIL-53-TDC, MIL-53, UiO-66, UiO-66-NH2, UiO-66(F)4, UiO-67, DUT-67, NH2-MIL-125, MIL-125, MIL-101(Cr), ZIF-8, ZIF-11 and ZIF-7 were studied for their C6 sorption properties. An understanding of the uptake of the larger C6 molecules cannot simply be achieved with surface area and pore volume (from N2 sorption) but involves the complex micropore structure of the MOF. The maximum adsorption capacity at p p0-1 = 0.9 was shown by DUT-4 for benzene, MIL-101(Cr) for cyclohexane and DUT-5 for n-hexane. In the low-pressure range from p p0-1 = 0.1 down to 0.05 the highest benzene uptake is given by DUT-5, DUT-67/UiO-67 and MIL-101(Cr), for cyclohexane and n-hexane by DUT-5, UiO-67 and MIL-101(Cr). The highest uptake capacity at p p0-1 = 0.02 was seen with MIL-53 for benzene, MIL-125 for cyclohexane and DUT-5 for n-hexane. DUT-5 and MIL-101(Cr) are the MOFs with the widest pore window openings/cross sections but the low-pressure uptake seems to be controlled by a complex combination of ligand and pore-size effect. IAST selectivities between the three binary mixtures show a finely tuned and difficult to predict interplay of pore window size with (critical) adsorptive size and possibly a role of electrostatics through functional groups such as NH2.
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Affiliation(s)
- Christian Jansen
- Institut für Anorganische Chemie und Strukturchemie, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | - Nabil Assahub
- Institut für Anorganische Chemie und Strukturchemie, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | - Alex Spieß
- Institut für Anorganische Chemie und Strukturchemie, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | - Jun Liang
- Institut für Anorganische Chemie und Strukturchemie, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | - Alexa Schmitz
- Institut für Anorganische Chemie und Strukturchemie, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | - Shanghua Xing
- Institut für Anorganische Chemie und Strukturchemie, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | - Serkan Gökpinar
- Microtrac Retsch GmbH, Retsch-Allee 1-5, D-42781 Haan, Germany
| | - Christoph Janiak
- Institut für Anorganische Chemie und Strukturchemie, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
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16
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Ahamed SS, Mahanta H, Paul AK. An advanced bath model to simulate association followed by ensuing dissociation dynamics of benzene + benzene system: a comparative study of gas and condensed phase results. Phys Chem Chem Phys 2022; 24:23825-23839. [PMID: 36164966 DOI: 10.1039/d2cp02483g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of the environment (N2 molecules) on the association followed by the ensuing dissociation reaction of benzene + benzene system is studied here with the help of a new code setup. Chemical dynamics simulations are performed to investigate this reaction in vacuum as well as in a bath of 1000 N2 molecules, equilibrated at 300 K. Bath densities of 20 and 324 kg m-3 are considered with a few results from the latter density. The simulations are performed at three different excitation temperatures of benzene, namely, 1000, 1500, and 2000 K, with an impact parameter range of 0-12 Å for both vacuum and bath models. Higher association probabilities and hence, higher temperature dependent association rate constants are obtained in the condensed phase. In the condensed phase, when a trajectory takes a longer time for the monomers to associate, the associated complex is formed with a longer lifetime and provides a lower rate of ensuing dissociation. Higher association rate and lower dissociation rate in condensed phase dynamics are due to the energy transfer process. Hence, the energy transfer phenomenon plays a decisive role in the association/dissociation dynamics, which is completely ignored in the same reaction when studied in vacuum.
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Affiliation(s)
- Sk Samir Ahamed
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, Meghalaya, India.
| | - Himashree Mahanta
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, Meghalaya, India.
| | - Amit K Paul
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, Meghalaya, India.
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Zhou J, Yu X, Luo S, Xue X, Jia S, Zhang X, Zhao Y, Hao X, He L, Wang C, Ding D, Ren X. Triple ionization and fragmentation of benzene trimers following ultrafast intermolecular Coulombic decay. Nat Commun 2022; 13. [PMID: 36088449 PMCID: PMC9464219 DOI: 10.1038/s41467-022-33032-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/25/2022] [Indexed: 11/25/2022] Open
Abstract
Intermolecular interactions involving aromatic rings are ubiquitous in biochemistry and they govern the properties of many organic materials. Nevertheless, our understanding of the structures and dynamics of aromatic clusters remains incomplete, in particular for systems beyond the dimers, despite their high presence in many macromolecular systems such as DNA and proteins. Here, we study the fragmentation dynamics of benzene trimer that represents a prototype of higher-order aromatic clusters. The trimers are initially ionized by electron-collision with the creation of a deep-lying carbon 2s−1 state or one outer-valence and one inner-valence vacancies at two separate molecules. The system can thus relax via ultrafast intermolecular decay mechanisms, leading to the formation of C\documentclass[12pt]{minimal}
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\begin{document}$${}_{6}{{{{{{{{{\rm{H}}}}}}}}}_{6}}^{+}$$\end{document}6H6+ trications and followed by a concerted three-body Coulomb explosion. Triple-coincidence ion momentum spectroscopy, accompanied by ab-initio calculations and further supported by strong-field laser experiments, allows us to elucidate the details on the fragmentation dynamics of benzene trimers. Higher-order aromatic clusters are prevalent in biochemical systems, but a full understanding of their structural and dynamical properties is lacking. Here, the authors demonstrate that inner-valence ionization can induce ultrafast relaxation and further fragmentation mechanisms in benzene trimers.
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18
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Wang HR, Zhang C, Sun CG, Hu BC, Ju XH. Nitrogen-rich polycyclic pentazolate salts as promising energetic materials: theoretical investigating. J Mol Model 2022; 28:299. [PMID: 36066673 DOI: 10.1007/s00894-022-05128-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/27/2022] [Indexed: 10/14/2022]
Abstract
Pentazolate (cyclo-N5-) salts are nitrogen-rich compounds with great development potential as energetic materials due to their full nitrogen anion. However, the densities of available N5- salts are generally low, which seriously lowers their performances. It is necessary to screen out cyclo-N5- salts with high density. To this end, eight new non-metallic cyclo-N5- salts based on fused heterocycle were designed. -NH2, -NO2, and -O- groups were introduced into the compounds to adjust and improve the detonation performance and impact sensitivity of cyclo-N5- salts. By theoretical calculations and Hirshfeld surface analyses, the densities, heats of formation, detonation performance, sensitivities, and crystal structures of the title compounds were predicted, and the contribution of hydrogen bond as well as π-π stacking to the stability of cyclo-N5- salt was revealed. The results indicate that the densities of title compounds are higher than 1.85 g cm‒3, and the sensitivities of these compounds are predicted to be lower than that of HMX. The detonation properties of a (D = 9.47 km s-1, P = 41.21 GPa) and d (D = 9.44 km s-1, P = 40.26 GPa) are better than those of HMX. These mean that using fused ring as a cation and introducing proper substituents are an effective method to improve cyclo-N5- salt's density and balance the detonation performance and sensitivity.
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Fu H, Wang B, Zhu D, Zhou Z, Bao S, Qu X, Guo Y, Ling L, Zheng S, Duan P, Mao J, Schmidt-Rohr K, Tao S, Alvarez PJJ. Mechanism for selective binding of aromatic compounds on oxygen-rich graphene nanosheets based on molecule size/polarity matching. Sci Adv 2022; 8:eabn4650. [PMID: 35905181 PMCID: PMC9337764 DOI: 10.1126/sciadv.abn4650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Selective binding of organic compounds is the cornerstone of many important industrial and pharmaceutical applications. Here, we achieved highly selective binding of aromatic compounds in aqueous solution and gas phase by oxygen-enriched graphene oxide (GO) nanosheets via a previously unknown mechanism based on size matching and polarity matching. Oxygen-containing functional groups (predominately epoxies and hydroxyls) on the nongraphitized aliphatic carbons of the basal plane of GO formed highly polar regions that encompass graphitic regions slightly larger than the benzene ring. This facilitated size match-based interactions between small apolar compounds and the isolated aromatic region of GO, resulting in high binding selectivity relative to larger apolar compounds. The interactions between the functional group(s) of polar aromatics and the epoxy/hydroxyl groups around the isolated aromatic region of GO enhanced binding selectivity relative to similar-sized apolar aromatics. These findings provide opportunities for precision separations and molecular recognition enabled by size/polarity match-based selectivity.
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Affiliation(s)
- Heyun Fu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Jiangsu 210023, China
| | - Bingyu Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Jiangsu 210023, China
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Jiangsu 210094, China
| | - Dongqiang Zhu
- Key Laboratory of the Ministry of Education for Earth Surface Processes, School of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Zhicheng Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Jiangsu 210023, China
| | - Shidong Bao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Jiangsu 210023, China
| | - Xiaolei Qu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Jiangsu 210023, China
| | - Yong Guo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Jiangsu 210098, China
| | - Lan Ling
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Shourong Zheng
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Jiangsu 210023, China
| | - Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jingdong Mao
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA
| | | | - Shu Tao
- Key Laboratory of the Ministry of Education for Earth Surface Processes, School of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Pedro J. J. Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
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20
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He E, Tu K, Cheng J, Wang Y, Lu H, Zhang L, Cheng Z. Synthesis and Phase Behavior of (Semifluorinated Alkane)‐based Side‐Chain Liquid Crystalline Copolymers. Macromol Rapid Commun 2022; 43:e2200266. [DOI: 10.1002/marc.202200266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/16/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Enjie He
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis College of Chemistry Chemical Engineering and Materials Science Soochow University Suzhou 215123 China
| | - Kai Tu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis College of Chemistry Chemical Engineering and Materials Science Soochow University Suzhou 215123 China
| | - Jiannan Cheng
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis College of Chemistry Chemical Engineering and Materials Science Soochow University Suzhou 215123 China
| | - Yuxue Wang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis College of Chemistry Chemical Engineering and Materials Science Soochow University Suzhou 215123 China
| | - Huanjun Lu
- Jiangsu Key Laboratory of Micro and Nano Heat Fluid Flow Technology and Energy Application School of Physical Science and Technology Suzhou University of Science and Technology Suzhou 215009 China
| | - Lifen Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis College of Chemistry Chemical Engineering and Materials Science Soochow University Suzhou 215123 China
| | - Zhenping Cheng
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application Suzhou Key Laboratory of Macromolecular Design and Precision Synthesis College of Chemistry Chemical Engineering and Materials Science Soochow University Suzhou 215123 China
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21
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Gao Y, Dong B, Wen K, Zhao Y. The role of intermolecular interactions of aromatic sandwich dimer ligands for the half-titanocene catalysts: Theoretical study. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Mallick S, Zhou Y, Chen X, Tan YN, Meng M, Cao L, Qin Y, He ZC, Cheng T, Zhu GY, Liu CY. A Single Solvating Benzene Molecule Decouples the Mixed-valence Complex through Intermolecular Orbital Interactions. iScience 2022; 25:104365. [PMID: 35620431 PMCID: PMC9126792 DOI: 10.1016/j.isci.2022.104365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/10/2022] [Accepted: 05/02/2022] [Indexed: 11/19/2022] Open
Abstract
Characterization of covalency of intermolecular interactions in the van der Waals distance limit remains challenging because the interactions between molecules are weak, dynamic, and not measurable. Herein, we approach this issue in a series of supramolecular mixed-valence (MV) donor(D)-bridge(B)-acceptor(A) systems consisting of two bridged Mo2 units with a C6H6 molecule encapsulated, as characterized by the X-ray crystal structures. Comparative analysis of the intervalence charge transfer spectra in benzene and dichloromethane substantiates the strong electronic decoupling effect of the solvating C6H6 molecule that breaks down the dielectric solvation theory. Ab initio and DFT calculations unravel that the intermolecular orbital overlaps between the complex bridge and the C6H6 molecule alter the electronic states of the D-B-A molecule through intermolecular nuclear dynamics. This work exemplifies that site-specific intermolecular interaction can be exploited to control the chemical property of supramolecular systems and to elucidate the functionalities of side-chains in biological systems. Decoupling mixed-valence complexes by an encapsulated benzene molecule Demonstrating intermolecular orbital interactions in the van der Waals distances Illustrating interplay between intermolecular electronic and nuclear degrees of freedom
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Affiliation(s)
- Suman Mallick
- Department of Chemistry, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Yuli Zhou
- Department of Chemistry, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Xiaoli Chen
- Department of Chemistry, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Ying Ning Tan
- Department of Chemistry, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Miao Meng
- Department of Chemistry, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
- Corresponding author
| | - Lijiu Cao
- Department of Chemistry, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Yi Qin
- Department of Chemistry, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Zi Cong He
- Department of Chemistry, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Tao Cheng
- Department of Chemistry, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Guang Yuan Zhu
- Department of Chemistry, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
| | - Chun Y. Liu
- Department of Chemistry, Jinan University, 601 Huang-Pu Avenue West, Guangzhou 510632, China
- Corresponding author
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23
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Xiao LY, Zhang LX, Kang YN, Yin YY, Yuan ZY, Ma T, Li LX, Luo CY, Liu Y, He YM, Bie LJ. Single‐Crystal‐to‐Single‐Crystal (SCSC) Transformation of a Binuclear Cadmium (II) Complex to a Discrete Mononuclear Cadmium (II) Complex. Z Anorg Allg Chem 2022. [DOI: 10.1002/zaac.202100159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Le-Xi Zhang
- Tianjin University of Technology School of Materials Science and Engineering 391 Binshui Xidao, Xiqing District 300384 Tianjin CHINA
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24
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Ren X, Zhou J, Wang E, Yang T, Xu Z, Sisourat N, Pfeifer T, Dorn A. Ultrafast energy transfer between π-stacked aromatic rings upon inner-valence ionization. Nat Chem 2022; 14:232-8. [PMID: 34931045 DOI: 10.1038/s41557-021-00838-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 10/18/2021] [Indexed: 11/08/2022]
Abstract
Non-covalently bound aromatic systems are ubiquitous and govern the physicochemical properties of various organic materials. They are important to many phenomena of biological and technological relevance, such as protein folding, base-pair stacking in nucleic acids, molecular recognition and self-assembly, DNA-drug interactions, crystal engineering and organic electronics. Nevertheless, their molecular dynamics and chemical reactivity, particularly in electronic excited states, are not fully understood. Here, we observe intermolecular Coulombic decay in benzene dimers, (C6H6)2-the simplest prototypes of noncovalent π-π interactions between aromatic systems. Intermolecular Coulombic decay is initiated by a carbon 2s vacancy state produced by electron-impact ionization and proceeds through ultrafast energy transfer between the benzene molecules. As a result, the dimer relaxes with the emission of a further low-energy electron (<10 eV) and a pair of C6H6+ cations undergoing Coulomb explosion. Coincident fragment-ion and electron momentum spectroscopy, accompanied by ab initio calculations, enables us to elucidate the dynamical details of this ultrafast relaxation process.
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25
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Mahanta H, Paul AK. Dynamical Behavior of Aromatic Trimer Complexes in Unimolecular Dissociation Reaction at High Temperatures. Case Studies on C 6H 6-C 6F 6-C 6H 6 and C 6H 6 Trimer Complexes. J Phys Chem A 2022; 126:259-271. [PMID: 34994202 DOI: 10.1021/acs.jpca.1c09073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The intramolecular vibrational energy redistribution (IVR) dynamics during unimolecular dissociation of aromatic trimers at high temperatures is the primary interest of this study. Chemical dynamics simulations are performed for the unimolecular dissociation of benzene-hexafluorobenzene-benzene (Bz-HFB-Bz) and benzene trimer (Bz-trimer) complexes at a temperature range of 1000-2000 K. Partial dissociation of both the complexes is observed, which leads to a dimer and a monomer in the dynamics. However, the probability of such dissociation was found much lower in the case of the Bz-trimer, which further decreases with the increase of temperature. The rate of partial dissociation of Bz-HFB-Bz is faster at 1500, 1800, and 2000 K, whereas the rate of complete dissociation of the Bz-trimer is significantly faster than Bz-HFB-Bz at all temperatures. This is just the opposite of the corresponding dimer's dissociation, where benzene-hexafluorobenzene (Bz-HFB) dissociates at a faster rate than the benzene dimer (Bz-dimer). Thus, the dissociation dynamics of the trimer is different than that of the dimer. Simulations with excited intramolecular and intermolecular modes of the trimer complexes reveal that energy flows from intermolecular to intramolecular modes of Bz-HFB-Bz more freely than the Bz-trimer, and the dissociation process becomes slower for the former. Calculated activation energies for both types of dynamics are much lower than the corresponding binding energies, which may be due to the anharmonicity. The Arrhenius equation with an anharmonic correction factor is considered to recalculate the activation energy and pre-exponential factor.
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Affiliation(s)
- Himashree Mahanta
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, Meghalaya, India
| | - Amit Kumar Paul
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, Meghalaya, India
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26
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Fedyanin IV. Control of supramolecular chirality in co-crystals of achiral molecules via stacking interactions and hydrogen bonding. CrystEngComm 2022. [DOI: 10.1039/d2ce00081d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An approach is proposed to obtain non-centrosymmetric crystal structures using co crystallization of specific achiral molecules. The co-formers, donors and acceptors of electron density, are selected in such a way...
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27
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Kumar K, Pandey P, Kant R, Bhattacharya S. Synthesis and Structural Studies of Cu(I) Methylthiosalicylate Complexes and their Catalytic Application in Thiol-Yne Click Reaction. NEW J CHEM 2022. [DOI: 10.1039/d2nj02722d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three complexes of Cu(I), [Cu(PPh3)2(mts)] (1), [Cu(dppf)(mts)] (2), [Cu(dppe)(mts)]2 (3) (mts = methylthiosalicylate; dppf = dipheylphosphinoferrocene; dppe = diphenylphosphinoethane) have been synthesized and characterized. Complexes 1 and 2 have monomeric...
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28
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Kumar K, Agrahari AK, Pratap R, Tiwari VK, Bhattacharya S. Synthesis and structural features of a series of Cu( i) furan-2-thiocarboxylate complexes: efficient “click” catalysts for the synthesis of glycoconjugates and glycocluster. NEW J CHEM 2022. [DOI: 10.1039/d2nj03433f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of phosphinecopper(i) thiocarboxylates have been synthesized and characterized structurally. These complexes act as efficient catalysts for the 'click' azide–alkyne cycloaddition leading to glycoconjugates and a glycocluster.
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Affiliation(s)
- Krishna Kumar
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi-221005, India
| | - Anand K. Agrahari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi-221005, India
| | - Rajesh Pratap
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi-221005, India
| | - Vinod K. Tiwari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi-221005, India
| | - Subrato Bhattacharya
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi-221005, India
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29
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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30
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Yanes-Rodríguez R, Prosmiti R. Assessment of DFT approaches in noble gas clathrate-like clusters: stability and thermodynamics. Phys Chem Chem Phys 2021; 24:1475-1485. [PMID: 34935011 DOI: 10.1039/d1cp04935f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have assessed the performance and accuracy of different wavefunction-based electronic structure methods, such as DFMP2 and domain-based local pair-natural orbital (DLPNO-CCSD(T)), as well as a variety of density functional theory (DFT) approaches on He@(H2O)N cage systems. We have selected representative clathrate-like structures corresponding to the building blocks present in each of the sI, sII and sH natural gas clathrate hydrates, and we have carefully studied the interaction between a He atom with each of their individual cages. We reported well-converged DFMP2 and DLPNO-CCSD(T) reference data, together with interaction and cohesive energies of four different density functionals (two GGA, revPBE and PW86PBE, and two hybrids, B3LYP and PBE0), including diverse dispersion correction schemes (D3(0), D3(BJ), D4 and XDM) for both He-filled and empty clathrate-like cages. After the analysis of the results, we came to the conclusion that the PW86PBE functional, with both XDM and D4 corrections, and the PBE0-D4 functional present reasonably adequate approaches to describe the guest-host noncovalent interactions that take place in such He clathrate hydrates. Taking into account that the He@sII is the only helium clathrate that scientists have been able to synthesize recently, we have performed a thermodynamic study on the individual 512 and 51264 cages present in the sII crystal. We determined the change in enthalpy, ΔH, and in Gibbs free energy, ΔG, at various temperatures and pressures, and we found out that in the range of experimental conditions the reactions associated with the encapsulation of the He atom inside the cages are exothermic and spontaneous. Finally, we highlighted the importance of an accurate description of the interaction in He@water mixtures, as a crucial component in construction of reliable data-driven models.
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Affiliation(s)
- Raquel Yanes-Rodríguez
- Institute of Fundamental Physics (IFF-CSIC), CSIC, Serrano 123, 28006 Madrid, Spain. .,Doctoral Programme in Theoretical Chemistry and Computational Modelling, Doctoral School, Universidad Autónoma de Madrid, Spain
| | - Rita Prosmiti
- Institute of Fundamental Physics (IFF-CSIC), CSIC, Serrano 123, 28006 Madrid, Spain.
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31
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Badorrek J, Walter M. Computational study on noncovalent interactions between (n, n) single-walled carbon nanotubes and simple lignin model-compounds. J Comput Chem 2021; 43:340-348. [PMID: 34893979 DOI: 10.1002/jcc.26794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 11/10/2022]
Abstract
Composites of carbon nanotubes (CNTs) and lignin are promising and potentially cheap precursors of-to this day-expensive carbon fibers. Since the control of the CNT-lignin interface is crucial to maximize fiber performance, it is imperative to understand the fundamental noncovalent interactions between lignin and CNT. In the present study a density functional theory study is conducted to investigate the fundamental noncovalent interaction strength between metallic (n, n) single-walled CNT (SWCNT) and simple lignin model molecules. In particular, the respective adsorption energies are used to gauge the strength of interaction classes (ππ interaction, CHπ hydrogen bonding and OH-related hydrogen bonding. From the data, substituent-dependent interaction trends as well as class- and curvature-dependent interaction trends are derived. Overall, we find that most of the interaction strength trends appear to be strongly influenced by geometry: flat orientation of the test molecules relative to the (n, n) SWCNT surface and small (n, n) SWCNT curvature-that is, large diameter enhances the CHπ and ππ interactions.
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Affiliation(s)
- Jan Badorrek
- Freiburger Materialforschungszentrum, Freiburg im Breisgau, Germany
| | - Michael Walter
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), Universität Freiburg, Freiburg im Breisgau, Germany.,Cluster of Excellence livMatS @ FIT, Freiburg im Breisgau, Germany.,Fraunhofer IWM, Freiburg im Breisgau, Germany
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32
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Igarashi M, Nozawa T, Matsumoto T, Yagihashi F, Kikuchi T, Sato K. Parallel-stacked aromatic molecules in hydrogen-bonded inorganic frameworks. Nat Commun 2021; 12:7025. [PMID: 34893610 PMCID: PMC8664825 DOI: 10.1038/s41467-021-27324-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/11/2021] [Indexed: 12/02/2022] Open
Abstract
By precisely constructing molecules and assembling these into well-defined supramolecular structures, novel physical properties and functionalities can be realized, and new areas of the chemical space can be accessed. In both materials science and biology, a deeper understanding of the properties and exploitation of the reversible character of weak bonds and interactions, such as hydrogen bonds and π–π interactions, is anticipated to lead to the development of materials with novel properties and functionalities. We apply the hydrogen-bonded organic frameworks (HOFs) strategy to inorganic materials science using the cubic octamer of orthosilicic acid, [Si8O12][OH]8, as a building block, and find that various types of hydrogen-bonded inorganic frameworks (HIFs). We succeed in parallel π-stacking pure benzene, thiophene, selenophene, p-benzoquinone, thiophene·p-benzoquinone, and benzene·p-benzoquinone polymers infinitely. These polymers interact via their π-systems by taking advantage of the flexible pores of the three-dimensional nano-honeycomb HIFs, which consist of periodic wide and narrow segments. Hydrogen-bonded inorganic frameworks are porous structures that may lead to novel materials with unprecedented properties and functionalities. Here the authors report the solid-state structures of orthosilicic acid-based hydrogen-bonded inorganic frameworks that can encapsulate small unsaturated cyclic molecules such as benzene, which are found stacked in parallel.
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Affiliation(s)
- Masayasu Igarashi
- Interdisciplinary Research Center for Catalytic Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, 305-8565, Japan.
| | - Takeshi Nozawa
- Interdisciplinary Research Center for Catalytic Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, 305-8565, Japan
| | - Tomohiro Matsumoto
- Interdisciplinary Research Center for Catalytic Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, 305-8565, Japan
| | - Fujio Yagihashi
- Interdisciplinary Research Center for Catalytic Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, 305-8565, Japan
| | - Takashi Kikuchi
- Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima-shi, Tokyo, 196-8666, Japan
| | - Kazuhiko Sato
- Interdisciplinary Research Center for Catalytic Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, 305-8565, Japan.
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33
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Ruiz E, Gueye T, Masson C, Varenne C, Pauly A, Brunet J, Ndiaye AL. Macrocycle-Functionalized RGO for Gas Sensors for BTX Detection Using a Double Transduction Mode. Chemosensors 2021; 9:346. [DOI: 10.3390/chemosensors9120346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
To fabricate mass and resistive sensors based on reduced graphene oxide (RGO), we investigated the functionalization of RGO by tetra tert-butyl phthalocyanine (PcH2tBu), which possesses a macroring and tert-butyl peripheral groups. Herein, we present the gas sensor responses of the functionalized RGO toward benzene, toluene, and xylene (BTX) vapors. The RGO was obtained by the reduction of graphene oxide (GO) using citrate as a reducing agent, while the functionalization was achieved non-covalently by simply using ultrasonic and heating treatment. The sensor devices based on both QCM (quartz crystal microbalance) and resistive transducers were used simultaneously to understand the reactivity. Both the GO and the RGO showed less sensitivity to BTX vapors, while the RGO/PcH2tBu presented enhanced sensor responses. These results show that the p-network plays a very important role in targeting BTX vapors. The resistive response analysis allowed us to state that the RGO is a p-type semiconductor and that the interaction is governed by charge transfer, while the QCM response profiles allowed use to determine the differences between the BTX vapors. Among BTX, benzene shows the weakest sensitivity and a reactivity in the higher concentration range (>600 ppm). The toluene and xylene showed linear responses in the range of 100–600 ppm.
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34
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Kannengießer JF, Briesenick M, Meier D, Huch V, Morgenstern B, Kickelbick G. Synthesis and Hydrogen-Bond Patterns of Aryl-Group Substituted Silanediols and -triols from Alkoxy- and Chlorosilanes. Chemistry 2021; 27:16461-16476. [PMID: 34545975 PMCID: PMC9297978 DOI: 10.1002/chem.202102729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Indexed: 12/01/2022]
Abstract
Organosilanols typically show a high condensation tendency and only exist as stable isolable molecules under very specific steric and electronic conditions at the silicon atom. In the present work, various novel representatives of this class of compounds were synthesized by hydrolysis of alkoxy‐ or chlorosilanes. Phenyl, 1‐naphthyl, and 9‐phenanthrenyl substituents at the silicon atom were applied to systematically study the influence of the aromatic substituents on the structure and reactivity of the compounds. Chemical shifts in 29Si NMR spectroscopy in solution, correlated well with the expected electronic situation induced by the substitution pattern on the Si atom. 1H NMR studies allowed the detection of strong intermolecular hydrogen bonds. Single‐crystal X‐ray structures of the alkoxides and the chlorosilanes are dominated by π‐π interactions of the aromatic systems, which are substituted by strong hydrogen bonding interactions representing various structural motifs in the respective silanol structures.
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Affiliation(s)
- Jan-Falk Kannengießer
- Inorganic Solid-State Chemistry, Saarland University Campus, Building C4 1, 66123, Saarbrücken, Germany
| | - Max Briesenick
- Inorganic Solid-State Chemistry, Saarland University Campus, Building C4 1, 66123, Saarbrücken, Germany
| | - Dennis Meier
- Inorganic Solid-State Chemistry, Saarland University Campus, Building C4 1, 66123, Saarbrücken, Germany
| | - Volker Huch
- Inorganic Solid-State Chemistry, Saarland University Campus, Building C4 1, 66123, Saarbrücken, Germany
| | - Bernd Morgenstern
- Inorganic Solid-State Chemistry, Saarland University Campus, Building C4 1, 66123, Saarbrücken, Germany
| | - Guido Kickelbick
- Inorganic Solid-State Chemistry, Saarland University Campus, Building C4 1, 66123, Saarbrücken, Germany
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35
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Zhao Q. Substituent effects on the regium-π stacking interactions between Au 6 cluster and substituted benzene. J Mol Model 2021; 27:328. [PMID: 34687368 DOI: 10.1007/s00894-021-04944-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/07/2021] [Indexed: 11/27/2022]
Abstract
The regium-π stacking interactions in the Au6···PhX (X = H, CH3, OH, OCH3, NH2, F, Cl, Br, CN, NO2) complexes are studied using quantum chemical methods. The present study focuses on the different effects of electron-donating and electron-withdrawing substituent. The structure and binding strength of the complexes are examined. The interactions between Au6 cluster and various substituted benzene become strengthened relative to the Au6···benzene complex. The interaction region indicator analysis was performed, and the interaction region and interaction between the substituent and Au6 cluster are discussed. It is found that the substituent effects on the regium-π stacking interactions between Au6 cluster and substituted benzene are different from π···π interactions of benzene dimer. Energy decomposition analysis was carried out to study the nature of regium-π stacking interactions, and the substituent effects are mainly reflected on the electrostatic interaction and dispersion.
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36
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Patmanidis I, Alessandri R, de Vries AH, Marrink SJ. Comparing Dimerization Free Energies and Binding Modes of Small Aromatic Molecules with Different Force Fields. Molecules 2021; 26:molecules26196069. [PMID: 34641613 PMCID: PMC8512883 DOI: 10.3390/molecules26196069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/25/2021] [Accepted: 09/26/2021] [Indexed: 11/16/2022] Open
Abstract
Dimerization free energies are fundamental quantities that describe the strength of interaction of different molecules. Obtaining accurate experimental values for small molecules and disentangling the conformations that contribute most to the binding can be extremely difficult, due to the size of the systems and the small energy differences. In many cases, one has to resort to computational methods to calculate such properties. In this work, we used molecular dynamics simulations in conjunction with metadynamics to calculate the free energy of dimerization of small aromatic rings, and compared three models from popular online servers for atomistic force fields, namely G54a7, CHARMM36 and OPLS. We show that, regardless of the force field, the profiles for the dimerization free energy of these compounds are very similar. However, significant care needs to be taken when studying larger molecules, since the deviations from the trends increase with the size of the molecules, resulting in force field dependent preferred stacking modes; for example, in the cases of pyrene and tetracene. Our results provide a useful background study for using topology builders to model systems which rely on stacking of aromatic moieties, and are relevant in areas ranging from drug design to supramolecular assembly.
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Affiliation(s)
- Ilias Patmanidis
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands; (I.P.); (R.A.); (A.H.d.V.)
| | - Riccardo Alessandri
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands; (I.P.); (R.A.); (A.H.d.V.)
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Alex H. de Vries
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands; (I.P.); (R.A.); (A.H.d.V.)
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands; (I.P.); (R.A.); (A.H.d.V.)
- Correspondence:
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37
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Telychko M, Wang L, Hsu CH, Li G, Peng X, Song S, Su J, Chuang FC, Wu J, Wong MW, Lu J. Tailoring long-range superlattice chirality in molecular self-assemblies via weak fluorine-mediated interactions. Phys Chem Chem Phys 2021; 23:21489-21495. [PMID: 34550130 DOI: 10.1039/d1cp02996g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Controllable fabrication of enantiospecific molecular superlattices is a matter of imminent scientific and technological interest. Herein, we demonstrate that long-range superlattice chirality in molecular self-assemblies can be tailored by tuning the interplay of weak intermolecular non-covalent interactions between hexaphenylbenzene-based enantiomers. By means of high-resolution scanning tunneling microscopy measurements, we demonstrate that the functionalization of a hexaphenylbenzene-based molecule with fluorine (F) atoms leads to the formation of molecular self-assemblies with distinct long-range chiral recognition patterns. We employed density functional theory calculations to quantify F-mediated lone pair F⋯π, C-H⋯F, and F⋯F interactions attributed to the distinct enantiospecific molecular self-organizations. Our findings underpin a viable route to fabricate long-range chiral recognition patterns in supramolecular assemblies by engineering the weak non-covalent intermolecular interactions.
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Affiliation(s)
- Mykola Telychko
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Lulu Wang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Chia-Hsiu Hsu
- Department of Physics, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan.,Physics Division, National Center for Theoretical Sciences, Taipei, 10617, Taiwan.
| | - Guangwu Li
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Xinnan Peng
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Shaotang Song
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Jie Su
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Feng-Chuan Chuang
- Department of Physics, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan.,Physics Division, National Center for Theoretical Sciences, Taipei, 10617, Taiwan.
| | - Jishan Wu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Ming Wah Wong
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
| | - Jiong Lu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore. .,Centre for Advanced 2D Materials (CA2DM), National University of Singapore, 6 Science Drive 2, Singapore 117546, Singapore
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38
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Abstract
A systematic study of arene-perfluoroarene interactions in solution is presented. Using a combination of NMR titration experiments, X-ray crystallography, and computational analysis, we analyze the effects of fluorination, substituents, ring size, and solvation on the arene-perfluoroarene interaction. We find that fluorination, extension of the π systems, and enhancement of solvent polarity greatly stabilize the stacking energy up to 3 orders of magnitude (Ka = <1 to 6000 M-1), with the highest Ka achieved for the interaction of water-soluble variants of perfluoronaphthalene and anthracene in buffered D2O (pD = 12). Combining computational and experimental results, we conclude that this impressive binding energy is a result of enthalpically favorable electrostatic and dispersion interactions as well as the entropically driven hydrophobic effect. The enhanced understanding of arene-perfluoroarene interactions in aqueous solution sets the stage for the implementation of this abiotic intermolecular interaction in biology and medicine.
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Affiliation(s)
- Ga Young Lee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Elizabeth Hu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Arnold L Rheingold
- Department of Chemistry and Biochemistry, University of California, San Diego, California 92093, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Ellen M Sletten
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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39
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Aichi M, Hafied M, Dibi A. THEORETICAL STUDY OF PENTAVALENT HALOSILICONATES:
STRUCTURE AND CHARGE DELOCALIZATION. J STRUCT CHEM+ 2021. [DOI: 10.1134/s0022476621060020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Zheng K, Li D, Jiang L, Li X, Xie C, Feng L, Qin J, Qian S, Pang Q. Revisiting stacking interactions in tetrathiafulvalene and selected derivatives using tight-binding quantum chemical calculations and local coupled-cluster method. Acta Crystallogr B Struct Sci Cryst Eng Mater 2021; 77:311-320. [PMID: 34096512 DOI: 10.1107/s2052520621003085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
The engineering of supramolecular architectures needs accurate descriptions of the intermolecular interactions in crystal structures. Tetrathiafulvalene (TTF) is an effective building block used in the construction of promising functional materials. The parallel packing of the neutral TTF-TTF system was studied previously using the high-level quantum chemical method, advancing it as a valuable model system. The recently developed tight-binding quantum chemical method GFN2-xTB and local coupled-cluster method DLPNO-CCSD(T) were used to investigate the stacking interactions of TTF and selected derivatives deposited in the Cambridge Structural Database. Using the interaction energy of the TTF-TTF dimer calculated at the CCSD(T)/CBS level as the reference, the accuracies of the two methods are investigated. The energy decomposition analysis within the DLPNO-CCSD(T) framework reveals the importance of dispersion interaction in the TTF-related stacking systems. The dispersion interaction density plot vividly shows the magnitude and distribution of the dispersion interaction, providing a revealing insight into the stacking interactions in crystal structures. The results show that the GFN2-xTB and DLPNO-CCSD(T) methods could achieve accuracy at an affordable computational cost, which would be valuable in understanding the nature of parallel stacking in supramolecular systems.
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Affiliation(s)
- Kang Zheng
- School of Life Sciences, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
| | - Danping Li
- School of Life Sciences, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
| | - Liu Jiang
- School of Life Sciences, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
| | - Xiaowei Li
- School of Materials Science and Engineering, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
| | - Changjian Xie
- School of Life Sciences, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
| | - Ling Feng
- School of Life Sciences, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
| | - Jie Qin
- School of Life Sciences, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
| | - Shaosong Qian
- School of Life Sciences, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
| | - Qiuxiang Pang
- School of Life Sciences, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
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41
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Singh S, Hsu PJ, Kuo JL, Patwari GN. Dipole moment enhanced π-π stacking in fluorophenylacetylenes is carried over from gas-phase dimers to crystal structures propagated through liquid like clusters. Phys Chem Chem Phys 2021; 23:9938-9947. [PMID: 33908511 DOI: 10.1039/d1cp00279a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The aggregates of monofluorinated phenylacetylenes in the gas-phase, investigated using the IR-UV double resonance spectroscopic method in combination with extensive structural search and electronic structure calculations, reveal the formation of liquid-like clusters with a π-stacked dimeric core. The structural assignment based on the IR spectra in the acetylenic and aromatic C-H stretching regions suggests that, unlike the parent non-fluorinated phenylacetylene, the substitution of a F atom on the phenyl ring increases the dipole moment, leading to robustness in the formation of a ππ stacked dimer, which propagates incorporating C-Hπ_{Ar/Ac} and C-HF interactions involving both acetylenic and aromatic C-H groups. The structural evolution of fluorophenylacetylene aggregates in the gas phase shows marginal effects due to fluorine atom position on the phenyl ring, with substitution in the para-position tending towards phenylacetylene. The present study signifies that the ππ stacked dimers act as a nucleus for the growth of higher clusters to which other molecular units are added predominantly via the {Ar}_C-Hπ_{Ar} type of interaction and the dominant interactions present in the crystal structures gradually emerge with increasing cluster size. Based on these features, gas-phase clusters of fluorophenylacetylene are hypothesized as "liquid-like clusters" acting as intermediates in the generation of various polymorphic forms starting from a ππ stacked dimer as the core molecular unit.
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Affiliation(s)
- Sumitra Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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42
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Abstract
The benzene-ethene and parallel-displaced (PD) benzene-benzene dimers are the most fundamental systems involving π-π stacking interactions. Several high-level ab initio investigations calculated the binding energies of these dimers using the coupled-cluster with singles, doubles, and quasi-perturbative triple excitations [CCSD(T)] method at the complete basis set [CBS] limit using various approaches such as reduced virtual orbital spaces and/or MP2-based basis set corrections. Here, we obtain CCSDT(Q) binding energies using a Weizmann-3-type approach. In particular, we extrapolate the self-consistent field (SCF), CCSD, and (T) components using large heavy-atom augmented Gaussian basis sets [namely, SCF/jul-cc-pV{5,6}Z, CCSD/jul-cc-pV{Q,5}Z, and (T)/jul-cc-pV{T,Q}Z]. We consider post-CCSD(T) contributions up to CCSDT(Q), inner-shell, scalar-relativistic, and Born-Oppenheimer corrections. Overall, our best relativistic, all-electron CCSDT(Q) binding energies are ∆Ee,all,rel = 1.234 (benzene-ethene) and 2.550 (benzene-benzene PD), ∆H0 = 0.949 (benzene-ethene) and 2.310 (benzene-benzene PD), and ∆H298 = 0.130 (benzene-ethene) and 1.461 (benzene-benzene PD) kcal mol-1. Important conclusions are reached regarding the basis set convergence of the SCF, CCSD, (T), and post-CCSD(T) components. Explicitly correlated calculations are used as a sanity check on the conventional binding energies. Overall, post-CCSD(T) contributions are destabilizing by 0.028 (benzene-ethene) and 0.058 (benzene-benzene) kcal mol-1, and thus, they cannot be neglected if sub-chemical accuracy is sought (i.e., errors below 0.1 kcal mol-1). CCSD(T)/aug-cc-pwCVTZ core-valence corrections increase the binding energies by 0.018 (benzene-ethene) and 0.027 (benzene-benzene PD) kcal mol-1. Scalar-relativistic and diagonal Born-Oppenheimer corrections are negligibly small. We use our best CCSDT(Q) binding energies to evaluate the performance of MP2-based, CCSD-based, and lower-cost composite ab initio procedures for obtaining these challenging π-π stacking binding energies.
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Affiliation(s)
- Amir Karton
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Jan M L Martin
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Reḥovot, Israel
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43
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Domingos SR, Pérez C, Kreienborg NM, Merten C, Schnell M. Dynamic chiral self-recognition in aromatic dimers of styrene oxide revealed by rotational spectroscopy. Commun Chem 2021; 4:32. [PMID: 36697526 PMCID: PMC9814401 DOI: 10.1038/s42004-021-00468-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/01/2021] [Indexed: 01/28/2023] Open
Abstract
Chiral molecular recognition is a pivotal phenomenon in biomolecular science, governed by subtle balances of intermolecular forces that are difficult to quantify. Non-covalent interactions involving aromatic moieties are particularly important in this realm, as recurring motifs in biomolecular aggregation. In this work, we use high-resolution broadband rotational spectroscopy to probe the dynamic conformational landscape enclosing the self-pairing topologies of styrene oxide, a chiral aromatic system. We reach a definite assignment of four homochiral and two heterochiral dimers using auxiliary quantum chemistry calculations as well as structure-solving methods based on experimental isotopic information. A complete picture of the dimer conformational space is obtained, and plausible routes for conformational relaxation are derived. Molecular structures are discussed in terms of conformational flexibility, the concerted effort of weak intermolecular interactions, and their role in the expression of the molecular fit.
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Affiliation(s)
- Sérgio R. Domingos
- grid.7683.a0000 0004 0492 0453Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, Hamburg, 22607 Germany ,grid.8051.c0000 0000 9511 4342Present Address: CFisUC, Department of Physics, University of Coimbra, Coimbra, 3004-516 Portugal
| | - Cristóbal Pérez
- grid.7683.a0000 0004 0492 0453Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, Hamburg, 22607 Germany
| | - Nora M. Kreienborg
- grid.5570.70000 0004 0490 981XRuhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, Bochum, 44801 Germany
| | - Christian Merten
- grid.5570.70000 0004 0490 981XRuhr-Universität Bochum, Fakultät für Chemie und Biochemie, Organische Chemie II, Universitätsstraße 150, Bochum, 44801 Germany
| | - Melanie Schnell
- grid.7683.a0000 0004 0492 0453Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, Hamburg, 22607 Germany ,grid.9764.c0000 0001 2153 9986Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, Kiel, 24118 Germany
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44
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Rui Y, Zuo Y, Yang L, Xu J, Wei Y, Yi Z. Molecular dynamics and spectral analysis for the binding of methoxylated polybrominated diphenyl ethers to lysozyme. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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45
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Pirgheibi M, Mohammadi M, Khanmohammadi A. A comparative study of interplay effects between the cation-π and intramolecular hydrogen bond interactions in the various complexes of methyl salicylate with Mn+, Fe2+, Co+, Ni2+, Cu+, and Zn2+ cations. Struct Chem 2021; 32:1529-39. [DOI: 10.1007/s11224-021-01728-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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46
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Veljković IS, Kretić DS, Veljković DŽ. Geometrical and energetic characteristics of Se⋯Se interactions in crystal structures of organoselenium molecules. CrystEngComm 2021. [DOI: 10.1039/d1ce00129a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Combined crystallographic and quantum chemical study was performed to reveal the nature of selenium–selenium interactions in the crystal structures of organoselenium compounds.
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Affiliation(s)
- Ivana S. Veljković
- University of Belgrade – Institute of Chemistry
- Technology and Metallurgy – National Institute of the Republic of Serbia
- 11000 Belgrade
- Serbia
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47
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Abstract
The σ-hole⋯σ-hole stacking interaction, an unrecognized type of noncovalent interaction, has been found to be present in large quantities in the Cambridge Structural Database. In the σ-hole⋯σ-hole stacking interaction, each of the two interacting σ-holes has the dual electron donor/electron acceptor character; when one σ-hole acts as an electron donor, the other σ-hole acts as an electron acceptor, and vice versa. The σ-hole⋯σ-hole stacking interaction is clearly different from the σ-hole bond in which the charge transfer occurs mainly from the electron donor to the σ-hole. Energy component analysis shows that the σ-hole⋯σ-hole stacking interaction is dominated by the dispersion energy, which is similar to the nature of the aromatic stacking interaction between unsaturated molecules or the σ⋯σ stacking interaction between saturated molecules.
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Affiliation(s)
- Yu Zhang
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang 471934, China
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang 471934, China
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48
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Abstract
The nature of π-π interactions has long been debated. The term "π-stacking" is considered by some to be a misnomer, in part because overlapping π-electron densities are thought to incur steric repulsion, and the physical origins of the widely-encountered "slip-stacked" motif have variously been attributed to either sterics or electrostatics, in competition with dispersion. Here, we use quantum-mechanical energy decomposition analysis to investigate π-π interactions in supramolecular complexes of polycyclic aromatic hydrocarbons, ranging in size up to realistic models of graphene, and for comparison we perform the same analysis on stacked complexes of polycyclic saturated hydrocarbons, which are cyclohexane-based analogues of graphane. Our results help to explain the short-range structure of liquid hydrocarbons that is inferred from neutron scattering, trends in melting-point data, the interlayer separation of graphene sheets, and finally band gaps and observation of molecular plasmons in graphene nanoribbons. Analysis of intermolecular forces demonstrates that aromatic π-π interactions constitute a unique and fundamentally quantum-mechanical form of non-bonded interaction. Not only do stacked π-π architectures enhance dispersion, but quadrupolar electrostatic interactions that may be repulsive at long range are rendered attractive at the intermolecular distances that characterize π-stacking, as a result of charge penetration effects. The planar geometries of aromatic sp2 carbon networks lead to attractive interactions that are "served up on a molecular pizza peel", and adoption of slip-stacked geometries minimizes steric (rather than electrostatic) repulsion. The slip-stacked motif therefore emerges not as a defect induced by electrostatic repulsion but rather as a natural outcome of a conformational landscape that is dominated by van der Waals interactions (dispersion plus Pauli repulsion), and is therefore fundamentally quantum-mechanical in its origins. This reinterpretation of the forces responsible for π-stacking has important implications for the manner in which non-bonded interactions are modeled using classical force fields, and for rationalizing the prevalence of the slip-stacked π-π motif in protein crystal structures.
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Affiliation(s)
- Kevin Carter-Fenk
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA.
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49
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Zhang L, He L, Wang Q, Tang Q, Liu F. Theoretical and experimental studies of a novel electrochemical sensor based on molecularly imprinted polymer and GQDs-PtNPs nanocomposite. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105196] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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50
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Ahamed SS, Kim H, Paul AK, West NA, Winner JD, Donzis DA, North SW, Hase WL. Comparison of intermolecular energy transfer from vibrationally excited benzene in mixed nitrogen-benzene baths at 140 K and 300 K. J Chem Phys 2020; 153:144116. [PMID: 33086796 DOI: 10.1063/5.0021293] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Gas phase intermolecular energy transfer (IET) is a fundamental component of accurately explaining the behavior of gas phase systems in which the internal energy of particular modes of molecules is greatly out of equilibrium. In this work, chemical dynamics simulations of mixed benzene/N2 baths with one highly vibrationally excited benzene molecule (Bz*) are compared to experimental results at 140 K. Two mixed bath models are considered. In one, the bath consists of 190 N2 and 10 Bz, whereas in the other bath, 396 N2 and 4 Bz are utilized. The results are compared to results from 300 K simulations and experiments, revealing that Bz*-Bz vibration-vibration IET efficiency increased at low temperatures consistent with longer lived "chattering" collisions at lower temperatures. In the simulations, at the Bz* excitation energy of 150 kcal/mol, the averaged energy transferred per collision, ⟨ΔEc⟩, for Bz*-Bz collisions is found to be ∼2.4 times larger in 140 K than in 300 K bath, whereas this value is ∼1.3 times lower for Bz*-N2 collisions. The overall ⟨ΔEc⟩, for all collisions, is found to be almost two times larger at 140 K compared to the one obtained from the 300 K bath. Such an enhancement of IET efficiency at 140 K is qualitatively consistent with the experimental observation. However, the possible reasons for not attaining a quantitative agreement are discussed. These results imply that the bath temperature and molecular composition as well as the magnitude of vibrational energy of a highly vibrationally excited molecule can shift the overall timescale of rethermalization.
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Affiliation(s)
- Sk Samir Ahamed
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, India
| | - Hyunsik Kim
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
| | - Amit K Paul
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong 793003, India
| | - Niclas A West
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, USA
| | - Joshua D Winner
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, USA
| | - Diego A Donzis
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, USA
| | - Simon W North
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, USA
| | - William L Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, USA
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