51
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Towards a converged strategy for including microsolvation in reaction mechanism calculations. J Comput Aided Mol Des 2021; 35:473-492. [PMID: 33420644 DOI: 10.1007/s10822-020-00366-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/28/2020] [Indexed: 01/27/2023]
Abstract
A major part of chemical conversions is carried out in the fluid phase, where an accurate modeling of the involved reactions requires to also take into account solvation effects. Implicit solvation models often cover these effects with sufficient accuracy but can fail drastically when specific solvent-solute interactions are important. In those cases, microsolvation, i.e., the explicit inclusion of one or more solvent molecules, is a commonly used strategy. Nevertheless, microsolvation also introduces new challenges-a consistent workflow as well as strategies how to systematically improve prediction performance are not evident. For the COSMO and COSMO-RS solvation models, this work proposes a simple protocol to decide if microsolvation is needed and how the corresponding molecular model has to look like. To demonstrate the improved accuracy of the approach, specific application examples are presented and discussed, i.e., the computation of aqueous pKa values and a mechanistic study of the methanol mediated Morita-Baylis-Hillman reaction.
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52
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Loman JL, Makuvaza JT, Kokkin DL, Reid SA. Unraveling a trifecta of weak non-covalent interactions: The dissociation energy of the anisole-ammonia 1:1 complex. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2020.138106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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53
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Malloum A, Conradie J. Structures of water clusters in the solvent phase and relative stability compared to gas phase. Polyhedron 2021. [DOI: 10.1016/j.poly.2020.114856] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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54
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Evstropiev S, Nikonorov N, Saratovskii A, Dukelskii K, Vasilyev V, Karavaeva A, Soshnikov I. Photo-stimulated evolution of different structural forms of silver in solutions, composite and oxide coatings. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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55
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Koli AR, Yeole SD. Understanding the interactions between hydrogen-bonded complexes of xylose and water: Quantum Chemical Investigation. J CHEM SCI 2020. [DOI: 10.1007/s12039-020-1741-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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56
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57
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Infrared spectra of PEHA molecule and its resistance to oxidation in water and methanol media at 298.15 K: solvent cluster size dependency. J Mol Model 2020; 26:323. [PMID: 33123831 DOI: 10.1007/s00894-020-04584-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022]
Abstract
The present work investigates the infrared spectra and solvation free energies (SE) of PEHA ((E)-2-(Pyridin-2-yl) ethyl 3-(3,4-dihydroxyphenyl) acrylate) and their impact on the oxidation. The latter was examined through the ionization potential parameter (IP). These investigations were carried out by the DFT method at B3LYP/6-31G(d) for optimization and frequency calculations and corrected for BSSE. X3LYP/6-311++G(2d,2p) was employed for single-point energy calculations. Water and methanol cluster sizes were used for solvation through the explicit solvent model. Thus, the infrared spectra show that the overview frequencies of PEHA compare well with the experimental results. The intense infrared absorptions of complexes are due to the stretching of O-H bonds of solvent clusters in the range 2600-3850 cm-1. The binding energy per solvent molecule of complexes was calculated and shows that water and methanol clusters mimic the liquid state as from 5 to 10 solvent molecules. The SE of PEHA increases with the increase of the cluster size of water and methanol in the direction of the limit. The latter was censured by the solvation done using the combined explicit-implicit solvent model. As for IP parameter, the results are largely above the IP limit and lower than the IP from gas phase. Thus, water and methanol media have an effect of lowering the IP of PEHA compound. Consequently, both media favour the oxidation of PEHA molecule, which facilitates its metabolism in human organism.
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58
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Albuquerque JV, Shirsat RN. Prelude to Molecular Dynamics‐II: Investigation of Potential Energy Surfaces Using Gaussian Charge Models. ChemistrySelect 2020. [DOI: 10.1002/slct.202002418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Rajendra N. Shirsat
- School of Chemical Sciences Goa University, Taleigao Plateau Taleigao Goa. 403 206 India
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59
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Ahirwar MB, Gadre SR, Deshmukh MM. Direct and Reliable Method for Estimating the Hydrogen Bond Energies and Cooperativity in Water Clusters, W n, n = 3 to 8. J Phys Chem A 2020; 124:6699-6706. [PMID: 32786666 DOI: 10.1021/acs.jpca.0c05631] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
No direct method for estimating the individual O-H···O hydrogen bond (H-bond) energies in water clusters (Wn) exists in the literature. In this work, we propose such a direct method based on the molecular tailoring approach, which also enables the estimation of the cooperativity contributions. The calculated H-bond energies at MP2(full)/aug-cc-pVTZ and CCSD(T)/aug-cc-pVDZ levels for Wn, n = 3 to 8, agree well with one another and fall between 0.3 and 11.6 kcal mol-1 with the cooperativity contributions in the range of -1.2 and 7.0 kcal mol-1. For gauging the accuracy of our H-bond energies for a cluster, the H-bond energy sum is added to the sum of monomer energies, and the results are compared with the respective total energy. These two values agree with each other to within 8.3 mH (∼5 kcal mol-1), testifying the accuracy of our estimated H-bond energies. Further, these H-bond strengths show a good correlation with the respective O-H stretching frequencies and the molecular electron density values at the (3, -1) O-H···O H-bond critical point.
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Affiliation(s)
- Mini Bharati Ahirwar
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, India
| | - Shridhar R Gadre
- Interdisciplinary School of Scientific Computing and Department of Chemistry, Savitribai Phule Pune University, Pune 411 007, India
| | - Milind M Deshmukh
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, India
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60
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Double stabilization of silver molecular clusters in thin films. RESEARCH ON CHEMICAL INTERMEDIATES 2020. [DOI: 10.1007/s11164-020-04189-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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61
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Koli AR, Yeole SD. Molecular hydration of carbohydrates: quantum chemical study of xylofuranose–(H2O)n clusters. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02634-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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62
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Chen WK, Zhang Y, Jiang B, Fang WH, Cui G. Efficient Construction of Excited-State Hessian Matrices with Machine Learning Accelerated Multilayer Energy-Based Fragment Method. J Phys Chem A 2020; 124:5684-5695. [DOI: 10.1021/acs.jpca.0c04117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yaolong Zhang
- Hefei National Laboratory for Physical Science at the Microscale, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bin Jiang
- Hefei National Laboratory for Physical Science at the Microscale, Department of Chemical Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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63
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Liu J, He X. Fragment-based quantum mechanical approach to biomolecules, molecular clusters, molecular crystals and liquids. Phys Chem Chem Phys 2020; 22:12341-12367. [PMID: 32459230 DOI: 10.1039/d0cp01095b] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To study large molecular systems beyond the system size that the current state-of-the-art ab initio electronic structure methods could handle, fragment-based quantum mechanical (QM) approaches have been developed over the past years, and proved to be efficient in dealing with large molecular systems at various ab initio levels. According to the fragmentation approach, a large molecular system can be divided into subsystems (fragments), and subsequently the property of the whole system can be approximately obtained by taking a proper combination of the corresponding terms of individual fragments. Therefore, the standard QM calculation of a large system could be circumvented by carrying out a series of calculations on small fragments, which significantly promotes computational efficiency. The electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method is one of the fragment-based QM approaches which has been developed by our research group in recent years. This Perspective presents the theoretical framework of this fragmentation method and its applications in biomolecules, molecular clusters, molecular crystals and liquids, including total energy calculation, protein-ligand/protein binding affinity prediction, geometry optimization, vibrational spectrum simulation, ab initio molecular dynamics simulation, and prediction of excited-state properties.
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Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
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64
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Krishnakumar P, Maity DK. A two level approach to predict minimum energy structures of higher hydrated clusters of oxalic acid. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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65
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Devi P, Bishnoi A, Fatma S. Synthesis, Spectroscopic Properties, and Quantum Mechanical Study of 5-Oxo-1-phenyl-4-(piperidin-1-ylmethyl)pyrrolidine-3-carboxylic Acid. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1070428020030173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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66
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Zins EL. Microhydration of a Carbonyl Group: How does the Molecular Electrostatic Potential (MESP) Impact the Formation of (H 2O) n:(R 2C═O)Complexes? J Phys Chem A 2020; 124:1720-1734. [PMID: 32049521 DOI: 10.1021/acs.jpca.9b09992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The presence of a carbonyl group in a molecule usually leads to the identification of a π-hole on the molecular electrostatic potential (MESP) of the species. How does this electrophilic site influence the formation of microhydrated complexes? To address this point, a panel of R2CO solutes with various MESPs was selected, and we identified the structures and properties of several complexes containing one, two, three and six water molecules. The following solutes were considered in the present study: H2CO, F2CO, Cl2CO,(NC)2CO and H2C═CO. Geometry optimizations and frequency calculations were carried out at the LC-ωPBE/6-311++G(d,p) level, with the GD3BJ empirical correction for dispersion. For a number of n water molecules around the R2CO solute, the structure and the features of the most stable (H2O)n:(R2CO) complexes are highly dependent on the MESP of the isolated R2CO solute. The formation of pi-hole bondings appears to play a decisive role in the initiation of a three-dimensional organization of water molecules around the solute.
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Affiliation(s)
- Emilie-Laure Zins
- De la Molécule aux Nano-Objets: Réactivité, Interactions Spectroscopies, MONARIS, CNRS, Sorbonne Université, 75005, Paris, France
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67
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Xu J, Deng G, Wang YT, Guo HY, Kalhor P, Yu ZW. Local Acid Strength of Solutions and Its Quantitative Evaluation Using Excess Infrared Nitrile Probes. J Phys Chem Lett 2020; 11:1007-1012. [PMID: 31958952 DOI: 10.1021/acs.jpclett.9b03804] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We propose the concept of local acidity in condensed-phase chemistry in this work. The feature is demonstrated in trifluoroethanol (TFE) by employing two Fourier-transform infrared spectroscopy (FTIR) nitrile probes, acetonitrile (CH3CN) and benzonitrile (PhCN). Specifically, three positive excess peaks were found in the binary systems composed of TFE and a probe using excess spectroscopy. To characterize the local acidity quantitatively, we have tried to correlate the wavenumbers of the positive excess peaks of the probes and the pKa values in water of a series of XH-containing compounds (X = O, N, and C). Good linear relationships were discovered. Accordingly, three different pKa values of TFE were determined based on the three positive excess infrared peaks, which are attributed to the monomer, dimer, and trimer of TFE with the help of quantum-chemical calculations. The concept of local acidity and its quantitative evaluation enrich our knowledge of acid-base chemistry and will shed light on a better understanding of microstructures of solutions.
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Affiliation(s)
- Jing Xu
- MOE Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology, Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China
| | - Geng Deng
- MOE Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology, Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China
| | - Yu-Tian Wang
- MOE Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology, Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China
| | - Hao-Yue Guo
- MOE Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology, Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China
| | - Payam Kalhor
- MOE Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology, Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China
| | - Zhi-Wu Yu
- MOE Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology, Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China
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68
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Malloum A, Fifen JJ, Conradie J. Large-Sized Ammonia Clusters and Solvation Energies of the Proton in Ammonia. J Comput Chem 2020; 41:21-30. [PMID: 31568565 DOI: 10.1002/jcc.26071] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/19/2019] [Accepted: 08/28/2019] [Indexed: 01/10/2023]
Abstract
The absolute solvation energies (free energies and enthalpies) of the proton in ammonia are used to compute the pKa of species embedded in ammonia. They are also used to compute the solvation energies of other ions in ammonia. Despite their importance, it is not possible to determine experimentally the solvation energies of the proton in a given solvent. We propose in this work a direct approach to compute the solvation energies of the proton in ammonia from large-sized neutral and protonated ammonia clusters. To undertake this investigation, we performed a geometry optimization of neutral and protonated ammonia 30-mer, 40-mer, and 50 mer to locate stable structures. These structures have been fully optimized at both APFD/6-31++g(d,p) and M06-2X/6-31++g(d,p) levels of theory. An infrared spectroscopic study of these structures has been provided to assess the reliability of our investigation. Using these structures, we have computed the absolute solvation free energy and the absolute solvation enthalpy of the proton in ammonia. It comes out that the absolute solvation free energy of the proton in ammonia is calculated to be -1192 kJ mol-1 , whereas the absolute solvation enthalpy is evaluated to be -1214 kJ mol-1 . © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Alhadji Malloum
- Department of Chemistry, University of the Free State, Bloemfontein, 9300, South Africa
| | - Jean J Fifen
- Department of Physics, Faculty of Science, The University of Ngaoundere, 454, Ngaoundere, Cameroon
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, Bloemfontein, 9300, South Africa
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69
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Malloum A, Fifen JJ, Conradie J. Exploration of the potential energy surfaces of small ethanol clusters. Phys Chem Chem Phys 2020; 22:13201-13213. [DOI: 10.1039/d0cp01393e] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The potential energy surfaces of small ethanol clusters, from dimer to pentamer, have been thoroughly explored using two different levels of theory. There is a clear relative energy gap between cyclic, linear and branched cyclic structures.
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Affiliation(s)
- Alhadji Malloum
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
- Department of Physics
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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70
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Chen WK, Fang WH, Cui G. Integrating Machine Learning with the Multilayer Energy-Based Fragment Method for Excited States of Large Systems. J Phys Chem Lett 2019; 10:7836-7841. [PMID: 31786927 DOI: 10.1021/acs.jpclett.9b03113] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In this work we have combined machine learning techniques with our recently developed multilayer energy-based fragment method for studying excited states of large systems. The photochemically active and inert regions are separately treated with the complete active space self-consistent field method and the trained models. This method is demonstrated to provide accurate energies and gradients leading to essentially the same excited-state potential energy surfaces and nonadiabatic dynamics compared with full ab initio results. Furthermore, in conjunction with the use of machine learning models, this method is highly parallel and exhibits low-scaling computational cost. Finally, the present work could encourage the marriage of machine learning with fragment-based electronic structure methods to explore photochemistry of large systems.
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Affiliation(s)
- Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , People's Republic of China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , People's Republic of China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , People's Republic of China
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71
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Lomas JS. Relationships between NMR shifts and interaction energies in biphenyls, alkanes, aza-alkanes, and oxa-alkanes with X─H … H─Y and X─H … Z (X, Y = C or N; Z = N or O) hydrogen bonding. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:1121-1135. [PMID: 31218728 DOI: 10.1002/mrc.4900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 06/09/2023]
Abstract
Hydrogen-hydrogen C─H… H─C bonding between the bay-area hydrogens in biphenyls, and more generally in congested alkanes, very strained polycyclic alkanes, and cis-2-butene, has been investigated by calculation of proton nuclear magnetic resonance (NMR) shifts and atom-atom interaction energies. Computed NMR shifts for all protons in the biphenyl derivatives correlate very well with experimental data, with zero intercept, unit slope, and a root mean square deviation of 0.06 ppm. For some congested alkanes, there is generally good agreement between computed values for a selected conformer and the experimental data, when it is available. In both cases, the shift of a given proton or pair of protons tends to increase with the corresponding interaction energy. Computed NMR shift differences for methylene protons in polycyclic alkanes, where one is involved in a very short contact ("in") and the other is not ("out"), show a rough correlation with the corresponding C─H… H─C exchange energies. The "in" and "in,in" isomers of selected aza- and diaza-cycloalkanes, respectively, are X─H… H─N hydrogen bonded, whereas the "out" and "in,out" isomers display X─H… N hydrogen bonds (X = C or N). Oxa-alkanes and the "in" isomers of aza-oxa-alkanes are X─H… O hydrogen bonded. There is a very good general correlation, including both N─H… H─Y (Y = C or N) and N─H… Z (Z = N or O) interactions, for NH proton shifts against the exchange energy. For "in" CH protons, the data for the different C─H… H─Y and C─H… Z interactions are much more dispersed and the overall shift/exchange energy correlation is less satisfactory.
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Affiliation(s)
- John S Lomas
- Interfaces, Traitements, Organisation et Dynamique des Systèmes (CNRS UMR-7086), Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
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72
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Yang H, Wong MW. Automatic Conformational Search of Transition States for Catalytic Reactions Using Genetic Algorithm. J Phys Chem A 2019; 123:10303-10314. [DOI: 10.1021/acs.jpca.9b09543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Hui Yang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Ming Wah Wong
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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73
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Chen WK, Fang WH, Cui G. A multi-layer energy-based fragment method for excited states and nonadiabatic dynamics. Phys Chem Chem Phys 2019; 21:22695-22699. [PMID: 31595910 DOI: 10.1039/c9cp04842a] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We developed a multi-layer energy-based fragment (MLEBF) method within the many-body energy expansion framework. It supplies accurate energies and gradients, and accurately reproduces excited-state topological structures. Moreover, MLEBF-based nonadiabatic dynamics simulations give nearly the same results compared with full ab initio ones. The present work could stimulate developing energy-based fragment methods for photochemistry of large systems.
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Affiliation(s)
- Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
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74
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Ahuja P, Molayem M, Gadre SR. Electrostatics-Assisted Building-Up Procedure for Capturing Energy Minima of Metal Clusters: Test Case of Ag n Clusters. J Phys Chem A 2019; 123:7872-7880. [PMID: 31433180 DOI: 10.1021/acs.jpca.9b05601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Global geometry optimization of metal clusters is an important problem in nanophysics. The starting geometries of the clusters generated with empirical or other model potentials are generally optimized further by density functional theory (DFT)-based energy minimization. For this purpose, several algorithms such as simulated annealing, genetic algorithms, basin hopping, etc. are used. Our building-up procedure generates putative lower-energy structures of metal (M) clusters, Mn+1, Mn+2, etc., by anchoring one or more metal atoms in the vicinity of the minima of the molecular electrostatic potential (MESP) of Mn. Here, we report an application of this method to Agn clusters, for 5 ≤ n ≤ 20, followed up by DFT-based geometry optimization, generating several lower-energy structures than those reported in the literature. New low-energy isomers are obtained by applying the same procedure to the test case of mixed-metal clusters, NinAgm, for n + m = 4 and 5. In conclusion, our MESP-based building-up procedure offers a new general methodology for generating lower-energy geometries of metal clusters.
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Affiliation(s)
- Prateek Ahuja
- Department of Chemical Sciences , IISER Mohali , Sector-81, Mohali 140306 , India
| | - Mohammad Molayem
- Physical and Theoretical Chemistry , Saarland University , Saarbrücken 66123 , Germany
| | - Shridhar R Gadre
- Interdisciplinary School of Scientific Computing and Department of Chemistry , Savitribai Phule Pune University , Pune 411007 , India
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75
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Cametti M, Valkonen A, Rissanen K. Entrapment of a linear water pentamer into a uranyl-salophen dimer in the solid state. Supramol Chem 2019. [DOI: 10.1080/10610278.2019.1632458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Massimo Cametti
- Department of Chemistry, Materials and Chemical Engineering"Giulio Natta", Politecnico di Milano, Milano, Italy
| | - Arto Valkonen
- Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Kari Rissanen
- Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
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76
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Kulkarni AD. Molecular Hydration of Carbonic Acid: Ab Initio Quantum Chemical and Density Functional Theory Investigation. J Phys Chem A 2019; 123:5504-5516. [PMID: 31244117 DOI: 10.1021/acs.jpca.9b01122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular hydration of carbonic acid (H2CO3) is investigated in terms of bonding patterns in H2CO3···(H2O) n [ n = 1-4] hydrogen-bonded clusters within ab initio quantum chemical and density functional theory (DFT) frameworks. Successive addition of water molecules to H2CO3···H2O entails elongation of O-H (hydroxyl) bond as well as contraction of specific intermolecular hydrogen bonds signifying hydration of carbonic acid; these structural features get markedly enhanced under the continuum solvation framework. A comparison between the structurally similar clusters H2CO3···(H2O) n and HCOOH···(H2O) n [ n = 1-3] brings out the structural stability of the former. The present investigation in conjunction with the binding energy behavior of approaching water molecule(s) should serve as a precursor for pathways exploring aqueous dissociation of H2CO3 for larger clusters, as well as development of force-field potentials for acid dissociation process.
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Affiliation(s)
- Anant D Kulkarni
- Solid State and Structural Chemistry Unit , Indian Institute of Science , Bangalore 560012 , India
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77
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Zhang H, Wu H, Jia Y, Geng L, Luo Z, Fu H, Yao J. An integrated instrument of DUV-IR photoionization mass spectrometry and spectroscopy for neutral clusters. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:073101. [PMID: 31370508 DOI: 10.1063/1.5108994] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/10/2019] [Indexed: 06/10/2023]
Abstract
We have developed an integrated instrument combining deep ultraviolet laser ionization mass spectrometry (DUV-LIMS) and infrared multiphoton dissociation (IR-MPD) spectroscopy, abbreviated as DUV-IR. The 177.3 nm DUV laser (7 eV single-photon energy) has short pulse duration (15 ps) and appropriate pulse energy (∼20 µJ), which is found to be highly efficient for low-fragment photoionization of neutral metal clusters and molecules. A home-made cluster source is designed with an adjustable formation channel suitable for the generation of different cluster series. The well-aligned components of the reflection time-of-flight mass spectrometer, as well as the coaxial design of DUV laser and molecular beam, bring forth high sensitivity and high resolution of the DUV-LIMS. Taking these advantages, well-resolved neutral Vn (n = 1-43) and (Benzene)n (n = 1-25) clusters have been generated free of fragmentation. In addition to the generation and detection of neutral clusters, a fast-flow reaction tube is also designed downstream of the cluster source allowing to study their reactivity. In particular, a broad-range tunable IR laser (1.3-16 µm) is coupled with the DUV laser to attain IR-MPD spectroscopic analysis. This integrated system offers a general protocol to prepare various clusters to study their gas-phase reactivity and to determine their structures.
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Affiliation(s)
- Hanyu Zhang
- Beijing National Laboratory of Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Haiming Wu
- Beijing National Laboratory of Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Yuhan Jia
- Beijing National Laboratory of Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Lijun Geng
- Beijing National Laboratory of Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Zhixun Luo
- Beijing National Laboratory of Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Hongbing Fu
- Beijing National Laboratory of Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Jiannian Yao
- Beijing National Laboratory of Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
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78
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Gupta AK, Thapa B, Raghavachari K. Exploring Reaction Energy Profiles Using the Molecules-in-Molecules Fragmentation-Based Approach. J Chem Theory Comput 2019; 15:3991-4002. [PMID: 31181886 DOI: 10.1021/acs.jctc.9b00152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Molecules-in-Molecules (MIM) fragmentation-based approach has been successfully used in previous studies to obtain the energies, optimized geometries, and spectroscopic properties of large molecular systems. The present work delineates a protocol to study the potential energy profiles for multistep chemical reactions using the MIM methodology. In a complex multistep chemical reaction, the fragmentation scheme needs to be changed as the reacting species transition into a new reaction step, resulting in a discontinuity in the potential energy curve of the reaction. In our approach, the fragmentation scheme for a particular step in a reaction is chosen on the basis of the nature of the bonding changes associated with that step. Thus, the reactant, transition state, and product are treated consistently throughout the reaction step, leading to an accurate energy barrier for that step. The discontinuity now occurs in describing the energies of reaction intermediates at the transition point between two reaction steps that are treated by two different fragmentation schemes. To address this issue, we propose a systematic procedure for obtaining continuous potential energy curves that are least shifted from their initial positions. The corrected MIM potential energy curves are continuous with activation energies preserved. Following this approach, energy profiles of complex reactions involving large molecular species can be obtained at high levels of theory with a reasonable computational cost.
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Affiliation(s)
- Ankur Kumar Gupta
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Bishnu Thapa
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Krishnan Raghavachari
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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79
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Khire SS, Gadre SR. Pragmatic Many-Body Approach for Economic MP2 Energy Estimation of Molecular Clusters. J Phys Chem A 2019; 123:5005-5011. [PMID: 31117601 DOI: 10.1021/acs.jpca.9b03481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We propose a procedure, within the many-body analysis (MBA) framework, for an economic yet accurate estimation of the correlated method-based energies of large molecular clusters employing Dunning's augmented basis sets. The basis of the procedure is to segregate the Hartree-Fock ( EHF) and correlation energy ( EC) estimations. EHF is found to differ by tens of millihartrees (mH) from its full-calculation (FC) counterpart on truncating the MBA expansion at the two-body (MBA-2) level. On the contrary, EC is estimated with smaller error on modest hardware with limited computation time at the (MBA-2) level. In view of this, we adopt a pragmatic method wherein the EHF (accurate to five decimal places) is taken from the FC, whereas EC is estimated at the MBA-2 level. This method is applied to a variety of medium to large molecular clusters at the MP2 level. Preliminary results at the CCSD(T) level for (H2O)16 and (H2O)17 are also reported with tremendous savings in wall-clock time and resources. The typical errors in MP2 and CCSD(T) energies per monomer are up to 0.1 and 0.2 mH, respectively. Thus the present method, balancing accuracy and computational economy, opens a way for estimating energies of large molecular clusters using correlated theories with large basis sets.
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Affiliation(s)
- Subodh S Khire
- Interdisciplinary School of Scientific Computing , Savitribai Phule Pune University , Pune 411007 , India
| | - Shridhar R Gadre
- Interdisciplinary School of Scientific Computing , Savitribai Phule Pune University , Pune 411007 , India
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80
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Jana G, Jha R, Pan S, Chattaraj PK. Microsolvation of lithium–phosphorus double helix: a DFT study. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2462-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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81
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Makuvaza JT, Kokkin DL, Loman JL, Reid SA. C-H/π and C-H-O Interactions in Concert: A Study of the Anisole-Methane Complex using Resonant Ionization and Velocity Mapped Ion Imaging. J Phys Chem A 2019; 123:2874-2880. [PMID: 30860841 DOI: 10.1021/acs.jpca.9b01020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Noncovalent forces such as hydrogen bonding, halogen bonding, π-π stacking, and C-H/π and C-H/O interactions hold the key to such chemical processes as protein folding, molecular self-assembly, and drug-substrate interactions. Invaluable insight into the nature and strength of these forces continues to come from the study of isolated molecular clusters. In this work, we report on a study of the isolated anisole-methane complex, where both C-H/π and C-H/O interactions are possible, using a combination of theory and experiments that include mass-selected two-color resonant two-photon ionization spectroscopy, two-color appearance potential (2CAP) measurements, and velocity mapped ion imaging (VMI). Using 2CAP and VMI, we derive the binding energies of the complex in ground, excited, and cation radical states. The experimental values from the two methods are in excellent agreement, and they are compared with selected theoretical values calculated using density functional theory and ab initio methods. The optimized ground-state cluster geometry, which is consistent with the experimental observations, shows methane sitting above the ring, interacting with anisole via both C-H/π and C-H/O interactions, and this dual mode of interaction is reflected in a larger ground-state binding energy as compared with the prototypical benzene-methane system.
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Affiliation(s)
- James T Makuvaza
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - Damian L Kokkin
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - John L Loman
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - Scott A Reid
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
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82
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Jesus WS, Prudente FV, Marques JMC. Microsolvation of Li+ in a Mixture of Argon and Krypton: Unveiling the Most Stable Structures of the Clusters. J Phys Chem A 2019; 123:2867-2873. [DOI: 10.1021/acs.jpca.9b00960] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wanderson S. Jesus
- Instituto de Física, Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Frederico V. Prudente
- Instituto de Física, Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
| | - Jorge M. C. Marques
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
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83
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Malloum A, Fifen JJ, Dhaouadi Z, Nana Engo SG, Conradie J. Structures, relative stability and binding energies of neutral water clusters, (H2O)2–30. NEW J CHEM 2019. [DOI: 10.1039/c9nj01659g] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have revised the structures of neutral water clusters, (H2O)n=2–30, with the affordable M06-2X functional, presenting up to 25 isomers for each cluster size.
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Affiliation(s)
- Alhadji Malloum
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Zoubeida Dhaouadi
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Tunis
- Tunisia
| | - Serge Guy Nana Engo
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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84
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Gavezzotti A, Lo Presti L. Dynamic simulation of liquid molecular nanoclusters: structure, stability and quantification of internal (pseudo)symmetries. NEW J CHEM 2019. [DOI: 10.1039/c8nj05825c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In a few hours on a standard laptop, AA-CLP MD correctly reproduces the thermodynamic properties of bulk liquids and provides information on the nanoscale dynamics of liquid nanoclusters.
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Affiliation(s)
| | - Leonardo Lo Presti
- Department of Chemistry
- University of Milano
- Milano
- Italy
- Istituto di Scienze e Tecnologie Molecolari
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85
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Kumar CK, Deval Sathiyashivan S, Masram DT, Jose KVJ, Sathiyendiran M. Experimental and theoretical investigation of intramolecular cooperativity in cyclic benzene trimer motif. RSC Adv 2019; 9:753-760. [PMID: 35517582 PMCID: PMC9059549 DOI: 10.1039/c8ra06647g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/18/2018] [Indexed: 12/04/2022] Open
Abstract
A series of new symmetrical tripodal molecules 1a–4b with a central benzene scaffold substituted with methyl/ethyl groups and three benzimidazolyl units having a bithiophene/biphenyl/5-alkylthiophene motif at the 2-position via a –CH2– unit were synthesized and characterized by elemental analysis, HR-MS, and NMR spectroscopy. NMR spectral data reveal that all molecules adopt a cyclic benzene trimer (CBT) using three benzimidazolyl units. Intramolecular cooperative edge-to-face C–H⋯π interactions stabilize the CBT motif in solution and are strong in ethyl substituted molecules (1b–4b) compared to methyl substituted (1a–4a) ones. However, the strength of the CBT unit in the tripodal molecule is independent of the length of the substituent at the 2-position of the benzimidazolyl unit. The relative 1H NMR chemical shift calculated at the MPW1PW91/6-311+G(d,p) level of theory corroborates the experimental values, and the calculations predict the distribution of the structures into syn isomers. The relative change in the NMR chemical shift is justified by the relative change in the magnitude of the (3,+3) critical point (CP) in the molecular electrostatic potential (MESP) topography. Also, a linear correlation of the intramolecular C–H⋯π interactions evaluated at M062X/6-311+G(d,p) with the relative NMR chemical shift suggest the latter as a measure of intramolecular cooperativity. A family of biaryl/alkylthiophene (R–R) benzimidazolyl-based tripodal molecules with cyclic benzene trimer (CBT) motif was synthesized and studied by NMR spectroscopy and MPW1PW91/6-311+G(d,p) theory.![]()
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86
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Kuznetsov VV. Simulation of Pyramidal Inversion of Nitrogen in Tetrahydro-1,3-Oxazines in Polar Medium. J STRUCT CHEM+ 2018. [DOI: 10.1134/s0022476618060173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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87
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Louarn E, Asri-Idlibi AM, Leprovost J, Héninger M, Mestdagh H. Evidence of Reactivity in the Membrane for the Unstable Monochloramine during MIMS Analysis. SENSORS 2018; 18:s18124252. [PMID: 30513986 PMCID: PMC6308428 DOI: 10.3390/s18124252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 11/21/2022]
Abstract
Membrane Inlet Mass Spectrometry (MIMS) was used to analyze monochloramine solutions (NH2Cl) and ammonia solutions in a compact FTICR. Chemical ionization enables identification and quantification of the products present in the permeate. The responses of protonated monochloramine and ammonium increase linearly with the solution concentration. The enrichments were respectively 1.2 and 5.5. Pervaporation is dependent on pH and only the basic form of ammonia NH3 pervaporates through the membrane. Unexpectedly, the small ammonia molecule permeated very slowly. It could be due to interactions with water molecules inside the membrane that create clusters. Moreover, NH2Cl solutions, in addition to the NH3Cl+ signal, presented a strong NH4+ signal at m/z 18.034. Ammonia presence in the low-pressure zone before ionization is probable as NH4+ was detected with all the precursors used, particularly CF3+ and trimethylbenzene that presents a proton affinity higher than monochloramine. Ammonia may be formed inside the membrane due to the fact that NH2Cl is unstable and may react with the water present in the membrane. Those results highlight the need for caution when dealing with chloramines in MIMS and more generally with unstable molecules.
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Affiliation(s)
- Essyllt Louarn
- Laboratoire de Chimie Physique, UMR 8000, CNRS et Université Paris Sud, 91405 Orsay, France.
| | | | - Julien Leprovost
- AlyXan, Centre Hoche, 3 rue Condorcet, Avenue 91260 Juvisy-sur-Orge, France.
| | - Michel Héninger
- Laboratoire de Chimie Physique, UMR 8000, CNRS et Université Paris Sud, 91405 Orsay, France.
| | - Hélène Mestdagh
- Laboratoire de Chimie Physique, UMR 8000, CNRS et Université Paris Sud, 91405 Orsay, France.
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88
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Debnath S, Sengupta A, Jose KVJ, Raghavachari K. Fragment-Based Approaches for Supramolecular Interaction Energies: Applications to Foldamers and Their Complexes with Anions. J Chem Theory Comput 2018; 14:6226-6239. [DOI: 10.1021/acs.jctc.8b00525] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sibali Debnath
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Arkajyoti Sengupta
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - K. V. Jovan Jose
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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89
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Meng S, Duan A, Xue J, Zheng X, Zhao Y. UV-Vis, Fluorescence, and Resonance Raman Spectroscopic and Density Functional Theoretical Studies on 3-Amino-1,2,4-triazole: Microsolvation and Solvent-Dependent Nonadiabatic Excited State Decay in Solution. J Phys Chem A 2018; 122:8530-8538. [PMID: 30295485 DOI: 10.1021/acs.jpca.8b07384] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The microsolvation and photophysics of 3-amino-1,2,4-triazole (3AT) after excitation to the light-absorbing S2(nπ*) state were studied by using resonance Raman spectroscopy and single component artificial force-induced reaction (SC-AFIR) in a global reaction route mapping (GRRM) strategy. The vibrational spectra were assigned on the basis of experimental data and density functional theory (DFT) calculations. The resonance Raman spectra of 3AT were measured to probe the excited state structural dynamics in the Franck-Condon region. The conformations of 3AT(CH3CN)1, 3AT(CH3OH)2, and 3AT(H2O)2 clusters were determined by combining vibrational spectrum experiments and B3LYP/6-311++G(d,p) computations. DFT calculations were carried out to obtain the minimal excitation energies of the lower-lying singlet excited states, and the curve-crossing points. It was revealed that the short-time structural dynamics of 3AT were dominated by the N-N stretching coordinates. An excited state decay mechanism is proposed: 3AT is initially excited to the S2(nπ*) state, then the conical intersection (CI) of the S2(nπ*)/S1(ππ*) potential energy surfaces is crossed, and 3AT then decays to the lower solvent-dependent excited state S1(ππ*). It subsequently returns to the S0 state, accompanied by a large Stokes fluorescence shift, which was interpreted as the stabilized S1(ππ*) excited state bonding to several water molecules via intermolecular hydrogen bonding.
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Affiliation(s)
- Shuang Meng
- Department of Chemistry and Engineering Research Center for Eco-dyeing and Finishing of Textiles, Key Laboratory of Advanced Textiles Materials and Manufacture Technology, Ministry of Education , Zhejiang Sci-Tech University , Hangzhou 310018 , China
| | - Aimin Duan
- Department of Chemistry and Engineering Research Center for Eco-dyeing and Finishing of Textiles, Key Laboratory of Advanced Textiles Materials and Manufacture Technology, Ministry of Education , Zhejiang Sci-Tech University , Hangzhou 310018 , China
| | - Jiadan Xue
- Department of Chemistry and Engineering Research Center for Eco-dyeing and Finishing of Textiles, Key Laboratory of Advanced Textiles Materials and Manufacture Technology, Ministry of Education , Zhejiang Sci-Tech University , Hangzhou 310018 , China
| | - Xuming Zheng
- Department of Chemistry and Engineering Research Center for Eco-dyeing and Finishing of Textiles, Key Laboratory of Advanced Textiles Materials and Manufacture Technology, Ministry of Education , Zhejiang Sci-Tech University , Hangzhou 310018 , China
| | - Yanying Zhao
- Department of Chemistry and Engineering Research Center for Eco-dyeing and Finishing of Textiles, Key Laboratory of Advanced Textiles Materials and Manufacture Technology, Ministry of Education , Zhejiang Sci-Tech University , Hangzhou 310018 , China
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90
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Khire SS, Bartolotti LJ, Gadre SR. Harmonizing accuracy and efficiency: A pragmatic approach to fragmentation of large molecules. J Chem Phys 2018; 149:064112. [PMID: 30111143 DOI: 10.1063/1.5036595] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Fragmentation methods offer an attractive alternative for ab initio treatment of large molecules and molecular clusters. However, balancing the accuracy and efficiency of these methods is a tight-rope-act. With this in view, we present an algorithm for automatic molecular fragmentation within Molecular Tailoring Approach (MTA) achieving this delicate balance. The automated code is tested out on a variety of molecules and clusters at the Hartree-Fock (HF)- and Møller-Plesset second order perturbation theory as well as density functional theory employing augmented Dunning basis sets. The results show remarkable accuracy and efficiency vis-à-vis the respective full calculations. Thus the present work forms an important step toward the development of an MTA-based black box code for implementation of HF as well as correlated quantum chemical calculations on large molecular systems.
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Affiliation(s)
- Subodh S Khire
- Interdisciplinary School of Scientific Computing, Savitribai Phule Pune University, Pune 411007, India
| | - Libero J Bartolotti
- Department of Physical and Computational Chemistry, East Carolina University, Greenville, North Carolina 27858, USA
| | - Shridhar R Gadre
- Interdisciplinary School of Scientific Computing, Savitribai Phule Pune University, Pune 411007, India
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91
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Lomas JS. Intramolecular O-H⋯O and C-H⋯O hydrogen bond cooperativity in D-glucopyranose and D-galactopyranose-A DFT/GIAO, QTAIM/IQA, and NCI approach. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:748-766. [PMID: 29498091 DOI: 10.1002/mrc.4728] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/07/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Density functional theory calculations are used to compute proton nuclear magnetic resonance (NMR) chemical shifts, interatomic distances, atom-atom interaction energies, and atomic charges for partial structures and conformers of α-D-glucopyranose, β-D-glucopyranose, and α-D-galactopyranose built up by introducing OH groups into 2-methyltetrahydropyran stepwisely. For the counterclockwise conformers, the most marked effects on the NMR shift and the charge on the OH1 proton are produced by OH2, those of OH3 and OH4 being somewhat smaller. This argues for a diminishing cooperative effect. The effect of OH6 depends on the configuration of the hydroxymethyl group and the position, axial or equatorial, of OH4, which controls hydrogen bonding in the 1,3-diol motif. Variations in the interaction energies reveal that a "new" hydrogen bond is sometimes formed at the expense of a preexisting one, probably due to geometrical constraints. Whereas previous work showed that complexing a conformer with pyridine affects only the nearest neighbour, successive OH groups increase the interaction energy of the N⋯H1 hydrogen bond and reduce its length. Analogous results are obtained for the clockwise conformers. The interaction energies for C-H⋯OH hydrogen bonding between axial CH protons and OH groups in certain conformers are much smaller than for O-H⋯OH bonds but they are largely covalent, whereas those of the latter are predominantly coulombic. These interactions are modified by complexation with pyridine in the same way as O-H⋯OH interactions: the computed NMR shifts of the CH protons increase, the atom-atom distances are shorter, and interaction energies are enhanced.
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Affiliation(s)
- John S Lomas
- ITODYS (CNRS UMR-7086), Paris Diderot University, Sorbonne Paris Cité, F-75205, Paris, France
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92
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Malloum A, Fifen JJ, Conradie J. Structures and spectroscopy of the ammonia eicosamer, (NH3)n=20. J Chem Phys 2018; 149:024304. [DOI: 10.1063/1.5031790] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Alhadji Malloum
- Faculty of Science, Department of Physics, University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon
| | - Jean Jules Fifen
- Faculty of Science, Department of Physics, University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
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93
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Hashim R, Sugimura A, Nguan HS, Rahman M, Zimmermann H. Anhydrous octyl-glucoside phase transition from lamellar to isotropic induced by electric and magnetic fields. J Chem Phys 2018; 146:084702. [PMID: 28249421 DOI: 10.1063/1.4976979] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A static deuterium nuclear magnetic resonance (2HNMR) technique (magnetic field, B = 7.05 T) was employed to monitor the thermotropic lamellar phase of the anhydrous 1:1 mixture sample of octyl-b-D-glucoside (βOG) and that of partially deuterium labelled at the alpha position on the chain, i.e.,βOG-d2 In the absence of an electric field, the 2H NMR spectrum of the mixture gives a typical quadrupolar doublet representing the aligned lamellar phase. Upon heating to beyond the clearing temperature at 112 °C, this splitting converts to a single line expected for an isotropic phase. Simultaneous application of magnetic and electric fields (E = 0.4 MV/m) at 85 °C in the lamellar phase, whose direction was set to be parallel or perpendicular to the magnetic field, resulted in the change of the doublet into a single line and this recovers to the initial doublet with time for both experimental geometries. This implies E- and B-field-induced phase transitions from the lamellar to an isotropic phase and a recovery to the lamellar phase again with time. Moreover, these phase transformations are accompanied by a transient current. A similar observation was made in a computational study when an electric field was applied to a water cluster system. Increasing the field strength distorts the water cluster and weakens its hydrogen bonds leading to a structural breakdown beyond a threshold field-strength. Therefore, we suggest the observed field-induced transition is likely due to a structure change of the βOG lamellar assembly caused by the field effect and not due to Joule heating.
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Affiliation(s)
- Rauzah Hashim
- Centre of Fundamental and Frontier Science of Self-Assembly, Department of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Akihiko Sugimura
- School of Information Systems Engineering, Osaka Sangyo University, 3-1-1 Nakagaito, Daito-Shi, Osaka 574-8530, Japan
| | - Hock-Seng Nguan
- Centre of Fundamental and Frontier Science of Self-Assembly, Department of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Matiur Rahman
- Centre of Fundamental and Frontier Science of Self-Assembly, Department of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Herbert Zimmermann
- Department of Biophysics, Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, D-69120 Heidelberg, Germany
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94
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Barclay AJ, Pietropolli Charmet A, Michaelian KH, Moazzen-Ahmadi N. Characterization of OCS–HCCCCH and N2O–HCCCCH Dimers: Theory and Experiment. J Phys Chem A 2018; 122:5383-5390. [DOI: 10.1021/acs.jpca.8b03645] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- A. J. Barclay
- Department of Physics and Astronomy, University of Calgary, 2500 University Drive North West, Calgary, Alberta T2N 1N4, Canada
| | - A. Pietropolli Charmet
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Via Torino 155, I-30172 Mestre, Venezia, Italy
| | - K. H. Michaelian
- CanmetENERGY, Natural Resources Canada, One Oil Patch Drive, Devon, Alberta T9G 1A8, Canada
| | - N. Moazzen-Ahmadi
- Department of Physics and Astronomy, University of Calgary, 2500 University Drive North West, Calgary, Alberta T2N 1N4, Canada
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95
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Yang J, Kong X, Jiang L. On the solvation of hydronium by carbon dioxide: Structural and infrared spectroscopic study of (H3O+)(CO2). Chem Phys 2018. [DOI: 10.1016/j.chemphys.2017.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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96
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Li Y, Yuan D, Wang Q, Li W, Li S. Accurate prediction of the structure and vibrational spectra of ionic liquid clusters with the generalized energy-based fragmentation approach: critical role of ion-pair-based fragmentation. Phys Chem Chem Phys 2018; 20:13547-13557. [DOI: 10.1039/c8cp00513c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The GEBF method with the ion-pair-based fragmentation has been developed to facilitate ab initio calculations of general ionic liquid clusters.
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Affiliation(s)
- Yunzhi Li
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Dandan Yuan
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Qingchun Wang
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Wei Li
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Shuhua Li
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
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97
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Florez E, Acelas N, Ramírez F, Hadad C, Restrepo A. Microsolvation of F−. Phys Chem Chem Phys 2018; 20:8909-8916. [DOI: 10.1039/c8cp00819a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The effective charge in F− is strong enough to induce water dissociation even for small molecularities in the gas phase.
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Affiliation(s)
- Elizabeth Florez
- Grupo de Materiales con Impacto
- Mat&mpac. Facultad de Ciencias Básicas
- Universidad de Medellín
- Medellín
- Colombia
| | - Nancy Acelas
- Grupo de Materiales con Impacto
- Mat&mpac. Facultad de Ciencias Básicas
- Universidad de Medellín
- Medellín
- Colombia
| | - Frank Ramírez
- Instituto de Química
- Universidad de Antioquia UdeA
- Medellín
- Colombia
| | - Cacier Hadad
- Instituto de Química
- Universidad de Antioquia UdeA
- Medellín
- Colombia
| | - Albeiro Restrepo
- Instituto de Química
- Universidad de Antioquia UdeA
- Medellín
- Colombia
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98
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Vishnoi P, Kaleeswaran D, Murugavel R. Rare Supramolecular Assemblies of a Dicopper(II)-tetracarboxylate Stabilized by (Methanol)6
, Dimethyl Sulfoxide and 4,4′-Azobipyridyl Bridges. ChemistrySelect 2017. [DOI: 10.1002/slct.201702862] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Pratap Vishnoi
- Department of Chemistry; Indian Institute of Technology Bombay; Mumbai 400 076 India
| | | | - Ramaswamy Murugavel
- Department of Chemistry; Indian Institute of Technology Bombay; Mumbai 400 076 India
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99
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Sode O, Cherry JN. Development of a Flexible-Monomer Two-Body Carbon Dioxide Potential and Its Application to Clusters up to (CO 2 ) 13. J Comput Chem 2017; 38:2763-2774. [PMID: 29067701 DOI: 10.1002/jcc.25053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 07/28/2017] [Accepted: 08/03/2017] [Indexed: 12/20/2022]
Abstract
A flexible-monomer two-body potential energy function was developed that approaches the high level CCSD(T)/CBS potential energy surface (PES) of carbon dioxide (CO2 ) systems. This function was generated by fitting the electronic energies of unique CO2 monomers and dimers to permutationally invariant polynomials. More than 200,000 CO2 configurations were used to train the potential function. Comparisons of the PESs of six orientations of flexible CO2 dimers were evaluated to demonstrate the accuracy of the potential. Furthermore, the potential function was used to determine the minimum energy structures of CO2 clusters containing as many as 13 molecules. For isomers of (CO2 )3 , the potential demonstrated energetic agreement with the M06-2X functional and structural agreement of the B2PLYP-D functional at substantially reduced computational costs. A separate function, fit to MP2/aug-cc-pVDZ reference energies, was developed to directly compare the two-body potential to the ab initio MP2 level of theory. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Olaseni Sode
- Department of Chemistry, Biochemistry and Physics, The University of Tampa, Tampa, Florida, 33606
| | - Jasmine N Cherry
- Department of Chemistry, Biochemistry and Physics, The University of Tampa, Tampa, Florida, 33606
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100
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Bai SQ, Young DJ, Hor TSA. Hydrogen-Bonding Interactions in Luminescent Quinoline-Triazoles with Dominant 1D Crystals. Molecules 2017; 22:E1600. [PMID: 28937630 PMCID: PMC6151808 DOI: 10.3390/molecules22101600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 11/16/2022] Open
Abstract
Quinoline-triazoles 2-((4-(diethoxymethyl)-1H-1,2,3-triazol-1-yl)methyl)quinoline (1), 2-((4-(m-tolyl)-1H-1,2,3-triazol-1-yl)methyl)quinoline (2) and 2-((4-(p-tolyl)-1H-1,2,3-triazol-1-yl)methyl)quinoline (3) have been prepared with CuAAC click reactions and used as a model series to probe the relationship between lattice H-bonding interaction and crystal direction of growth. Crystals of 1-3 are 1D tape and prism shapes that correlate with their intermolecular and solvent 1D lattice H-bonding interactions. All compounds were thermally stable up to about 200 C and blue-green emissive in solution.
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Affiliation(s)
- Shi-Qiang Bai
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore.
| | - David James Young
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore.
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia.
| | - T S Andy Hor
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China.
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