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Chen X, Wei C, Xie M, Hu Y. Single-Photon Ionization Induced New Covalent Bond Formation in Acrylonitrile(AN)-Pyrrole(Py) Clusters. J Phys Chem A 2023; 127:8272-8279. [PMID: 37769120 DOI: 10.1021/acs.jpca.3c02481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
The formation of nitrogen-containing organic compounds is crucial for understanding chemical evolution and the origin of life in the interstellar medium (ISM). In this study, we explore whether acrylonitrile (AN) and pyrrole (Py) can form new nitrogen-containing compounds after single-photon ionization in their gaseous clusters by vacuum ultraviolet (VUV)-infrared (IR) spectroscopy and theoretical calculations. The results show that a strong linear H-bond is formed in neutral AN-Py, while cyclic or bicyclic H-bonded networks are formed in the neutral AN-Py2 cluster. It is found that the structure containing a new C-C covalent bond between two moieties in (AN-Py)+ is formed besides the formation of H-bonded structures after AN-Py is ionized by VUV light. In (AN-Py2)+ cluster cations, new C-C or C-N covalent bonds tend to be formed between two Py, with (Py)2+ as the core in the cluster. The results reveal that new covalent bonds are more likely to be formed between two Py species when AN and Py are present in the cationic clusters. These results provide spectroscopic evidence of the formation of new nitrogen-containing organic compounds from AN and Py induced by VUV, which are helpful for our understanding of the formation of diverse prebiotic molecules in interstellar space.
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Affiliation(s)
- Xujian Chen
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Chengcheng Wei
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Min Xie
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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2
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Katsyuba SA, Spicher S, Gerasimova TP, Grimme S. Revisiting conformations of methyl lactate in water and methanol. J Chem Phys 2021; 155:024507. [PMID: 34266277 DOI: 10.1063/5.0057024] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The recently developed efficient protocols to implicit [Grimme et al., J. Phys. Chem. A 125, 4039-4054 (2021)] and explicit quantum mechanical modeling of non-rigid molecules in solution [Katsyuba et al., J. Phys. Chem. B 124, 6664-6670 (2020)] are applied to methyl lactate (ML). Building upon this work, a new combination scheme is proposed to incorporate solvation effects for the computation of infrared (IR) absorption spectra. Herein, Boltzmann populations calculated for implicitly solvated single conformers are used to weight the IR spectra of explicitly solvated clusters with a size of typically ten solvent molecules, i.e., accounting for the first solvation shell. It is found that in water and methanol, the most abundant conformers of ML are structurally modified relative to the gas phase, where the major form is ML1, in which the syn conformation of the -OH moiety is stabilized by a OH⋯O=C intramolecular hydrogen bond (HB). In solution, this syn conformation transforms to the gauche form because the intramolecular HB is disrupted by explicit water molecules that form intermolecular HBs with the hydroxyl and carbonyl groups. Similar changes induced by the gas-solution transition are observed for the minor conformers, ML2 and/or ML3, characterized by OH⋯OCH3 intramolecular HB in the gas phase. The relative abundance of ML1 is shown to decrease from ∼96% in gas to ∼51% in water and ∼92% in methanol. The solvent strongly influences frequencies, IR intensities, and normal modes, resulting in qualitatively different spectra compared to the gas phase. Some liquid-state conformational markers in the fingerprint region of IR spectra are revealed.
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Affiliation(s)
- Sergey A Katsyuba
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Centre of RAS, Arbuzov st. 8, 420088 Kazan, Russia
| | - Sebastian Spicher
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Tatiana P Gerasimova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Centre of RAS, Arbuzov st. 8, 420088 Kazan, Russia
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, 53115 Bonn, Germany
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3
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Sun F, Xie M, Zhang Y, Song W, Sun X, Hu Y. Spectroscopic evidence of the C-N covalent bond formed between two interstellar molecules (ISM): acrylonitrile and ammonia. Phys Chem Chem Phys 2021; 23:9672-9678. [PMID: 33616131 DOI: 10.1039/d0cp06274j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Acrylonitrile (AN) and ammonia (NH3) are two important nitrogen-containing interstellar molecules in outer space, especially on Titan. Herein, we measured infrared (IR) spectra of neutral and cationic AN-NH3 complexes by VUV single-photon ionization combined with time-of-flight mass spectrometry. On combining IR spectra with the theoretical calculations, we found that the molecules prefer to form a single-ring cyclic H-bonded structure in the neutral AN-NH3 and (AN)2-NH3 clusters. However, after ionization of AN-NH3 and (AN)2-NH3 clusters, a new C-N-covalent bond is confirmed to form directly between AN and NH3, without any energy barrier in the cationic complexes. Moreover, in the ionized (AN)2-NH3 cluster, the covalent C-N bond prefers to form between AN and NH3 rather than the two AN groups. These results provide spectroscopic evidence of AN forming a new molecule with NH3, induced by VUV radiation. The formation of the new C-N bond broadens our knowledge on the evolution of the prebiotic nitrogen-containing molecules in space.
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Affiliation(s)
- Fufei Sun
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China.
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4
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Theoretical studies on the electronic and optoelectronic properties of DNA/RNA hybrid-metal complexes. Polyhedron 2021. [DOI: 10.1016/j.poly.2020.115015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Frandsen BN, Deal AM, Lane JR, Vaida V. Lactic Acid Spectroscopy: Intra- and Intermolecular Interactions. J Phys Chem A 2020; 125:218-229. [PMID: 33377780 DOI: 10.1021/acs.jpca.0c09341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lactic acid, a relevant molecule in biology and the environment, is an α-hydroxy acid with a high propensity to form hydrogen bonds, both internally and to other hydrogen-bond-accepting molecules. This work includes the novel recording of infrared spectra of gas-phase lactic acid using Fourier transform infrared spectroscopy, and the vibrational absorption features of lactic acid are assigned with the aid of computationally simulated vibrational spectra with anharmonic corrections. Theoretical chemistry methods are used to relate intramolecular hydrogen-bond strengths to the relative stability of lactic acid conformers. The formation of hydrogen-bonded lactic acid dimers and 1:1 water complexes is investigated by simulated vibrational spectra and calculated thermodynamic parameters for the lactic acid monomer and dimer and its water complex in the gas phase. The results of this study are discussed in the context of environmental chemistry with an emphasis on indoor environments.
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Affiliation(s)
- Benjamin N Frandsen
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States.,Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, UCB 216, Boulder, Colorado 80309, United States
| | - Alexandra M Deal
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States.,Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, UCB 216, Boulder, Colorado 80309, United States
| | - Joseph R Lane
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Veronica Vaida
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States.,Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, UCB 216, Boulder, Colorado 80309, United States
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6
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Li Y, Song W, Jiang N, Zhang Z, Xie M, Hu Y. Structural rearrangement of the acrylonitrile (AN) cluster in the gas phase under VUV one-photon radiation explored by mass-selected infrared spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 226:117620. [PMID: 31610467 DOI: 10.1016/j.saa.2019.117620] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/27/2019] [Accepted: 10/06/2019] [Indexed: 06/10/2023]
Abstract
Acrylonitrile (AN), one of the most abundant nitriles in space, is considered to closely relate to the formation of interstellar prebiotic nitrogen-containing aromatics. Herein, we measured the vibrational spectra of acrylonitrile cluster cations (AN)2,3+ in a supersonic jet using infrared (IR) dissociation with vacuum-ultraviolet (VUV) photoionization and time-of-flight mass spectroscopy. Interestingly, the observed IR spectra demonstrate that a new molecular ion [Formula: see text] , is generated from the dimer and trimer of AN upon VUV single-photo ionization. Calculation results reveal that the new molecular cations can be generated through a relative low energy barrier after ionization of the neutral (AN)2. However, the reaction pathways are barrierless for the trimer, in which the third solvent AN acts as a catalyst. The mechanisms of those reactions also have been discussed in detail. This study contributes to a deeper understanding of ion-molecule reaction in gas-phase and the quest for the formation of prebiotic N -containing molecules in the outer space.
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Affiliation(s)
- Yujian Li
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, South China Normal University, Guangzhou, 510631, PR China
| | - Wentao Song
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, South China Normal University, Guangzhou, 510631, PR China
| | - Ningjing Jiang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, South China Normal University, Guangzhou, 510631, PR China
| | - Zhaoli Zhang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, South China Normal University, Guangzhou, 510631, PR China
| | - Min Xie
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, South China Normal University, Guangzhou, 510631, PR China.
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, South China Normal University, Guangzhou, 510631, PR China.
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7
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Yang S, Garner AC, Wallis JD. N–H⋯O hydrogen bonding to the alkoxy oxygen of a carboxylic ester group: crystal structures of methyl 2,6-diaminobenzoate and its derivatives. CrystEngComm 2020. [DOI: 10.1039/d0ce00495b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecules with hydrogen bonds from amino groups to both oxygens of a carboxylic ester are described, and other examples of hydrogen bonding to an ester's alkoxy oxygen atom are highlighted.
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Affiliation(s)
- Songjie Yang
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
| | | | - John D. Wallis
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
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8
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Srivastava R. Interactions, electronic and optical properties of nanographene–peptide complexes: a theoretical study. RSC Adv 2020; 10:38654-38662. [PMID: 35517564 PMCID: PMC9057264 DOI: 10.1039/d0ra07961h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 10/09/2020] [Indexed: 12/22/2022] Open
Abstract
We studied the interaction of planar phenylalanine (phe), tryptophan (try), tyrosine (tyr); amide asparagine (asn) and glutamine (gln); arginine (arg) side-chains, charged histidine (his-c) and charged lysine (lys-c) side-chains on a nanographene (g) surface by Density Functional theory (DFT) and Time Dependent Density Functional Theory (TDDFT). The occupied number of states by the system at each energy level and relative contribution of a particular atom/orbital has been studied by Density of States (DOS) and Partial Density of States (PDOS) respectively. Atom-in Molecules (AIM) analysis and non-covalent interaction (NCI) PLOT are used to study the interactions in these complexes. The absorption spectra and HOMO–LUMO (HL) gaps are quantitatively analysed to study the correlation between the optical properties of the studied complexes. The HL gap of peptides is larger than the HL gap of graphene–peptide complexes, indicating strong interactions. All the peptides interact from the above the nanographene surfaces. garg, glys-c, gtry and gtyr complexes have smaller bond distance as compared to gasn, ggln, ghis-c and gphe complexes. AIM analysis and (NCI) PLOT showed noncovalent interactions for these complexes. TDDFT calculations indicated the applicability of these complexes as biosensors. We studied interactions of planar phenylalanine, tryptophan, tyrosine; amide asparagine and glutamine; arginine side-chains, charged histidine and charged lysine side-chains on a nanographene surface by density functional theory and time dependent density functional theory.![]()
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Affiliation(s)
- Ruby Srivastava
- CSIR-Centre for Cellular and Molecular Biology
- Hyderabad
- India
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9
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Dutta B, Chowdhury J. Existence of dimeric hydroxylamine-O-sulfonic acid: Experimental observations aided by ab initio, DFT, Car-Parrinello and Born – Oppenheimer on the fly dynamics. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.136645] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Kjaersgaard A, Lane JR, Kjaergaard HG. Room Temperature Gibbs Energies of Hydrogen-Bonded Alcohol Dimethylselenide Complexes. J Phys Chem A 2019; 123:8427-8434. [DOI: 10.1021/acs.jpca.9b06855] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexander Kjaersgaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Joseph R. Lane
- School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Henrik G. Kjaergaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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11
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Zhang J, Li X. Intramolecular hydrogen bonding, π-π stacking interactions, and substituent effects of 8-hydroxyquinoline derivative supermolecular structures: a theoretical study. J Mol Model 2019; 25:241. [DOI: 10.1007/s00894-019-4140-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/14/2019] [Indexed: 10/26/2022]
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12
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Investigation of intramolecular hydrogen bonding in conjunction with cation-π interactions in complexes involving 4-substituted-8-hydroxyquinolines. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.01.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Møller KH, Bates KH, Kjaergaard HG. The Importance of Peroxy Radical Hydrogen-Shift Reactions in Atmospheric Isoprene Oxidation. J Phys Chem A 2019; 123:920-932. [DOI: 10.1021/acs.jpca.8b10432] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kristian H. Møller
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Kelvin H. Bates
- Center for the Environment, Harvard University, 29 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Henrik G. Kjaergaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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14
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Verevkin SP, Emel'yanenko VN, Pimerzin AA, Yermalayeu AV. How much different are thermochemical properties of enantiomers and their racemates? Thermochemical properties of enantiopure and racemate of methyl- and butyl lactates. J Chem Phys 2018; 149:054506. [PMID: 30089383 DOI: 10.1063/1.5029433] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
This work is a contribution to the molecular understanding of the thermodynamic properties of the chiral compounds. A comprehensive thermochemical study of the liquid enantiopure and racemate pairs of optically active alkyl lactates has been performed. Vapor pressures of DL-(±)-, L-(-)-methyl-, and DL-(±)-, L-(-)-n-butyl esters of lactic acid were measured by the transpiration method. The liquid phase standard molar enthalpies of formation of these esters were measured by using the high-precision combustion calorimetry. The standard molar enthalpies of vaporization of alkyl lactates at 298.15 K were derived from vapor pressure temperature dependencies. Thermochemical data of these compounds were collected, evaluated, and tested for internal and external consistency. The high-level G4 quantum-chemical method was used for mutual validation of the experimental and theoretical gas phase enthalpies of formation of alkyl lactates. A critical review of the available thermochemical data for the liquid and crystalline enantiopure and racemate pairs of optically active compounds has been performed. Useful general trends in energetics of sublimation, vaporization, and formation of optically active compounds have been revealed. This knowledge is required for evaluation of new and already available experimental data for the chiral compounds, and it can be helpful to assess volatility or feasibility of processes to separate enantiomers.
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Affiliation(s)
- Sergey P Verevkin
- Department of Physical Chemistry, Institute of Chemistry, University of Rostock, 18059 Rostock, Germany
| | | | - Andrey A Pimerzin
- Chemical Department, Samara State Technical University, 443100 Samara, Russia
| | - Andrei V Yermalayeu
- Department of Physical Chemistry, Institute of Chemistry, University of Rostock, 18059 Rostock, Germany
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15
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A series of cocrystals formed by 2,3-dimethylpyrazine bridging various aromatic acids through hydrogen bonds: Synthesis, structural characterization and synthon discussion. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.03.105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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16
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Varadwaj A, Varadwaj PR, Marques HM, Yamashita K. A DFT assessment of some physical properties of iodine-centered halogen bonding and other non-covalent interactions in some experimentally reported crystal geometries. Phys Chem Chem Phys 2018; 20:15316-15329. [PMID: 29796486 DOI: 10.1039/c8cp01085d] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A set of six binary complexes that feature iodine-centered halogen bonding, extracted from structures deposited in the Cambridge Structure Database, has been examined computationally using density functional theory calculations with the M06-2X global hybrid, and dispersion corrected B3LYP-D3 and B97-D3, to determine their equilibrium geometries, binding energies and electronic properties. The results show that gas phase calculations are very informative in evaluating what occurs in the solid state, even though these calculations ignore the importance of lattice packing and counter ion effects. The calculated binding energies for the non-covalent interactions responsible for these complexes lie between -4.15 and -7.48 kcal mol-1 (M06-2X), which enables us to characterize them as weak-to-moderate in strength. The basis set superposition error energies are calculated to vary between 0.60 and 2.42 kcal mol-1 for all the complexes examined, even though an all-electron QZP basis set used in the analysis was of quadrupole-ζ (plus polarization) quality. Dispersion is found to have a profound effect on the binding energy of some of these complexes, and was estimated to be as large as 5.0 kcal mol-1. For one complex, the crystal geometry could not be precisely reproduced using a gas phase calculation. While both halogen- and hydrogen-bonding interactions were found competitive, they cooperate with each other to determine the stable configuration of the binary complex. The molecular electrostatic surface potential, quantum theory of atoms in molecules, and reduced density gradient non-covalent Interaction models were utilized to arrive at a fundamental understanding of the various inter- and intra-molecular molecular interactions involved, as well as some other previously-overlooked non-covalent interactions that emerge in the modelling.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, 113-8656, Japan.
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17
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Sheng X, Jiang X, Zhao H, Wan D, Liu Y, Ngwenya CA, Du L. FTIR study of hydrogen bonding interaction between fluorinated alcohol and unsaturated esters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 198:239-247. [PMID: 29549865 DOI: 10.1016/j.saa.2018.03.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/25/2018] [Accepted: 03/08/2018] [Indexed: 06/08/2023]
Abstract
The 1:1 complexes of two unsaturated esters with 2,2,2-trifluoroethanol (TFE) were investigated experimentally and computationally. The experimental observations of the spectral shifts of the OH-stretching vibrational transitions were obtained at 113cm-1 for TFE-methyl acrylate (MA) and 92cm-1 for TFE-vinyl acetate (VA). There are three docking sites in the two unsaturated esters for the incoming TFE. The predicted red shifts of the OH-stretching vibrational transitions were found to be larger for the OH⋯OC hydrogen bonded conformer than those for the OH⋯π and OH⋯O ones. The binding energies further prove that the OH⋯OC hydrogen bonded conformers are the most stable ones. On the basis of the DFT calculations as well as previous works, the carbonyl group is the best docking site for TFE. Furthermore, the thermodynamic equilibrium constants of TFE-MA and TFE-VA were obtained at 0.28 and 0.15 by combining the experimental spectra data and the DFT calculations. Consequently, the Gibbs free energies of formation were determined to be 3.2 and 4.8kJmol-1 for TFE-MA and TFE-VA, respectively. The quantum theory of atoms in molecules (AIM) and generalized Kohn-Sham energy decomposition analysis (GKS-EDA) were carried out for further characterization of the hydrogen bonding interactions. GKS-EDA shows an "electrostatic" dominated hydrogen bonding character for the OH⋯OC hydrogen bonds.
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Affiliation(s)
- Xia Sheng
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China
| | - Xiaotong Jiang
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100 Jinan, China
| | - Hailiang Zhao
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China; Environment Research Institute, Shandong University, Shanda South Road 27, 250100 Jinan, China
| | - Dongjin Wan
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China
| | - Yongde Liu
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China
| | - Cleopatra Ashley Ngwenya
- College of Chemistry, Chemical and Environmental Engineering, Henan University of Technology, Lianhua Street 100, 450001 Zhengzhou, China
| | - Lin Du
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100 Jinan, China.
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18
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Palchowdhury S, Bhargava BL. Solvation of Methyl Lactate in Water: Molecular Dynamics Studies. J Phys Chem B 2018; 122:2113-2120. [DOI: 10.1021/acs.jpcb.7b12248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sourav Palchowdhury
- School of Chemical Sciences, National Institute of Science Education & Research-Bhubaneswar, HBNI, P.O. Jatni, Khurda, Odisha 752050, India
| | - B. L. Bhargava
- School of Chemical Sciences, National Institute of Science Education & Research-Bhubaneswar, HBNI, P.O. Jatni, Khurda, Odisha 752050, India
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19
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Jin S, Hu Y, Wang P, Zhan H, Lu Q, Liu F, Sheng L. Hydrogen bonding and dominant conformations of hydrated sugar analogue complexes using tetrahydrofurfuryl alcohol as the model sugar molecule. Phys Chem Chem Phys 2018; 20:7351-7360. [DOI: 10.1039/c7cp07935d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water molecules, which serve as both hydrogen bond donors and acceptors, have been found to influence the conformational landscape of gas-phase phenyl-β-d-glucopyranoside.
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Affiliation(s)
- Shan Jin
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Pengchao Wang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Huaqi Zhan
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Qiao Lu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Fuyi Liu
- National Synchrotron Radiation Laboratory
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Liusi Sheng
- National Synchrotron Radiation Laboratory
- University of Science and Technology of China
- Hefei
- P. R. China
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Holcomb M, Adhikary R, Zimmermann J, Romesberg FE. Topological Evidence of Previously Overlooked Ni+1–H···Ni H-Bonds and Their Contribution to Protein Structure and Stability. J Phys Chem A 2017; 122:446-450. [DOI: 10.1021/acs.jpca.7b11013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew Holcomb
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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21
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Wang P, Hu Y, Zhan H, Chen J, Jin S, Song W, Li Y. Vibrational spectroscopy of the mass-selected tetrahydrofurfuryl alcohol monomers and its dimers in gas phase using IR depletion and VUV single photon ionization. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 185:63-68. [PMID: 28544895 DOI: 10.1016/j.saa.2017.04.089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/22/2017] [Accepted: 04/30/2017] [Indexed: 06/07/2023]
Abstract
Tetrahydrofurfuryl alcohol (THFA, C5H10O2) is a close chemical analog of the sugar rings present in the phosphate-deoxyribose backbone structure of the nucleic acids. In present report, the infrared (IR) spectra of the size-selected THFA monomer and its dimer have been investigated in a pulsed supersonic jet using infrared-vacuum ultraviolet (VUV) ionization. Herein, the laser light at 118nm wavelength served as the source of "soft" ionization in a time-of-flight mass spectrometer. The IR features for the monomers located at 3622cm-1 can be assigned to the intramolecular hydrogen bonding stretch vibrations mainly referring to A and C conformers. Compared with the monomer, however, characteristic peaks for the dimer centered at 3415 and 3453cm-1, red shifted 207 and 169cm-1, respectively, were associated with the intermolecular hydrogen bonding stretch vibrations. Combined with the quantum-chemical calculations, the dimer in the gas phase preferred cyclic AC conformer stabled by forming two strong intermolecular hydrogen bonds, which shown the high hydrogen bond selectivity in the cluster. The conclusions drawn from the role played in the conformational flexibility by the hydroxyl and ether groups may be extended to other biomolecules.
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Affiliation(s)
- Pengchao Wang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China.
| | - Huaqi Zhan
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
| | - Jiaxin Chen
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
| | - Shan Jin
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
| | - Wentao Song
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
| | - Yujian Li
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
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22
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Zhao H, Tang S, Du L. Hydrogen bond docking site competition in methyl esters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 181:122-130. [PMID: 28351818 DOI: 10.1016/j.saa.2017.03.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 03/07/2017] [Accepted: 03/17/2017] [Indexed: 06/06/2023]
Abstract
The OH⋯O hydrogen bonds in the 2,2,2-trifluoroethanol (TFE)-methyl ester complexes in the gas phase have been investigated by FTIR spectroscopy and DFT calculations. Methyl formate (MF), methyl acetate (MA), and methyl trifluoroacetate (MTFA) were chosen as the hydrogen bond acceptors. A dominant inter-molecular hydrogen bond was formed between the OH group of TFE and different docking sites in the methyl esters (carbonyl oxygen or ester oxygen). The competition of the two docking sites decides the structure and spectral properties of the complexes. On the basis of the observed red shifts of the OH-stretching transition with respect to the TFE monomer, the order of the hydrogen bond strength can be sorted as TFE-MA (119cm-1)>TFE-MF (93cm-1)>TFE-MTFA (44cm-1). Combining the experimental infrared spectra with the DFT calculations, the Gibbs free energies of formation were determined to be 1.5, 4.5 and 8.6kJmol-1 for TFE-MA, TFE-MF and TFE-MTFA, respectively. The hydrogen bonding in the MTFA complex is much weaker than those of the TFE-MA and TFE-MF complexes due to the effect of the CF3 substitution on MTFA, while the replacement of an H atom with a CH3 group in methyl ester only slightly increases the hydrogen bond strength. Topological analysis and localized molecular orbital energy decomposition analysis was also applied to compare the interactions in the complexes.
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Affiliation(s)
- Hailiang Zhao
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China
| | - Shanshan Tang
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China
| | - Lin Du
- Environment Research Institute, Shandong University, Shanda South Road 27, 250100, Shandong, China.
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23
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Møller KH, Tram CM, Kjaergaard HG. Side-by-Side Comparison of Hydroperoxide and Corresponding Alcohol as Hydrogen-Bond Donors. J Phys Chem A 2017; 121:2951-2959. [DOI: 10.1021/acs.jpca.7b01323] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kristian H. Møller
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Camilla Mia Tram
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Henrik G. Kjaergaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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24
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Zhan H, Hu Y, Wang P, Chen J. Dominant conformer of tetrahydropyran-2-methanol and its clusters in the gas phase explored by the use of VUV photoionization and vibrational spectroscopy. J Chem Phys 2017; 146:134303. [DOI: 10.1063/1.4979298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Huaqi Zhan
- MOE Key laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, People’s Republic of China
| | - Yongjun Hu
- MOE Key laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, People’s Republic of China
| | - Pengchao Wang
- MOE Key laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, People’s Republic of China
| | - Jiaxin Chen
- MOE Key laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, People’s Republic of China
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25
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Schrøder SD, Hansen AS, Wallberg JH, Nielsen AR, Du L, Kjaergaard HG. The weak fundamental NH-stretching transition in amines. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 173:201-206. [PMID: 27664544 DOI: 10.1016/j.saa.2016.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 08/30/2016] [Accepted: 09/01/2016] [Indexed: 06/06/2023]
Abstract
Absolute intensities of NH-stretching fundamental and overtone transitions of gas phase aniline, methylamine, ethylamine, cyclopropylamine, methylethylamine, diethylamine and pyrrolidine have been measured with long path length conventional absorption spectroscopy. To support the assignments of NH-stretching transitions, transition frequencies and intensities were calculated with the local mode model using ab initio calculated local mode parameters and dipole moment functions obtained at the CCSD(T)-F12a/VDZ-F12 level of theory. For aniline, the absolute intensities of the NH-stretching transitions show the typical decrease of approximately an order of magnitude for each successive vibrational excitation. For methylamine, ethylamine, cyclopropylamine, methylethylamine, diethylamine and pyrrolidine, the observed absolute intensities of the fundamental NH-stretching transition is weak and of similar strength or even weaker than the corresponding first overtone transition. Characteristic for the amines with a normal fundamental intensity is a conjugated double bond next to the amine group.
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Affiliation(s)
- Sidsel D Schrøder
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen Ø DK-2100, Denmark
| | - Anne S Hansen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen Ø DK-2100, Denmark
| | - Jens H Wallberg
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen Ø DK-2100, Denmark
| | - Anne R Nielsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen Ø DK-2100, Denmark
| | - Lin Du
- Environment Research Institute, Shandong University, Shanda South Road 27, Jinan, Shandong, China
| | - Henrik G Kjaergaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen Ø DK-2100, Denmark.
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26
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Zhan H, Hu Y, Wang P, Chen J. Molecular structures of gas-phase neutral morpholine and its monohydrated complexes: experimental and theoretical approaches. RSC Adv 2017. [DOI: 10.1039/c6ra26582k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Morpholine (NH(CH2CH2)2O) is a typical six-membered aliphatic heterocyclic compound.
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Affiliation(s)
- Huaqi Zhan
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Pengchao Wang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Jiaxin Chen
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
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27
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Wang P, Hu Y, Zhan H, Chen J. Gas-phase conformational preference of the smallest saccharide (glycolaldehyde) and its hydrated complexes with bridged hydrogen bonding. RSC Adv 2017. [DOI: 10.1039/c6ra26965f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Glycoaldehyde (GA, HOCH2CHO) is the simplest sugar unit of the carbohydrates and the only sugar to have been detected in interstellar space to date.
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Affiliation(s)
- Pengchao Wang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Huaqi Zhan
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Jiaxin Chen
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
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28
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Tang S, Zhao H, Du L. Hydrogen bonding in alcohol–ethylene oxide and alcohol–ethylene sulfide complexes. RSC Adv 2016. [DOI: 10.1039/c6ra16205c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The O–H⋯O and O–H⋯S hydrogen bonds are of similar strength in the corresponding alcohol–EO and alcohol–ES complexes.
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Affiliation(s)
- Shanshan Tang
- Environment Research Institute
- Shandong University
- China
| | - Hailiang Zhao
- Environment Research Institute
- Shandong University
- China
| | - Lin Du
- Environment Research Institute
- Shandong University
- China
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