1
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Kumar A, Iyer S, Barua S, Brean J, Besic E, Seal P, Dall’Osto M, Beddows DCS, Sarnela N, Jokinen T, Sipilä M, Harrison RM, Rissanen M. Direct Measurements of Covalently Bonded Sulfuric Anhydrides from Gas-Phase Reactions of SO 3 with Acids under Ambient Conditions. J Am Chem Soc 2024; 146:15562-15575. [PMID: 38771742 PMCID: PMC11157540 DOI: 10.1021/jacs.4c04531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/23/2024]
Abstract
Sulfur trioxide (SO3) is an important oxide of sulfur and a key intermediate in the formation of sulfuric acid (H2SO4, SA) in the Earth's atmosphere. This conversion to SA occurs rapidly due to the reaction of SO3 with a water dimer. However, gas-phase SO3 has been measured directly at concentrations that are comparable to that of SA under polluted mega-city conditions, indicating gaps in our current understanding of the sources and fates of SO3. Its reaction with atmospheric acids could be one such fate that can have significant implications for atmospheric chemistry. In the present investigation, laboratory experiments were conducted in a flow reactor to generate a range of previously uncharacterized condensable sulfur-containing reaction products by reacting SO3 with a set of atmospherically relevant inorganic and organic acids at room temperature and atmospheric pressure. Specifically, key inorganic acids known to be responsible for most ambient new particle formation events, iodic acid (HIO3, IA) and SA, are observed to react promptly with SO3 to form iodic sulfuric anhydride (IO3SO3H, ISA) and disulfuric acid (H2S2O7, DSA). Carboxylic sulfuric anhydrides (CSAs) were observed to form by the reaction of SO3 with C2 and C3 monocarboxylic (acetic and propanoic acid) and dicarboxylic (oxalic and malonic acid)-carboxylic acids. The formed products were detected by a nitrate-ion-based chemical ionization atmospheric pressure interface time-of-flight mass spectrometer (NO3--CI-APi-TOF; NO3--CIMS). Quantum chemical methods were used to compute the relevant SO3 reaction rate coefficients, probe the reaction mechanisms, and model the ionization chemistry inherent in the detection of the products by NO3--CIMS. Additionally, we use NO3--CIMS ambient data to report that significant concentrations of SO3 and its acid anhydride reaction products are present under polluted, marine and polar, and volcanic plume conditions. Considering that these regions are rich in the acid precursors studied here, the reported reactions need to be accounted for in the modeling of atmospheric new particle formation.
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Affiliation(s)
- Avinash Kumar
- Aerosol
Physics Laboratory, Physics Unit, Faculty of Engineering and Natural
Sciences, Tampere University, 33720 Tampere, Finland
| | - Siddharth Iyer
- Aerosol
Physics Laboratory, Physics Unit, Faculty of Engineering and Natural
Sciences, Tampere University, 33720 Tampere, Finland
| | - Shawon Barua
- Aerosol
Physics Laboratory, Physics Unit, Faculty of Engineering and Natural
Sciences, Tampere University, 33720 Tampere, Finland
| | - James Brean
- School
of Geography, Earth & Environmental Sciences, University of Birmingham, Birmingham B15 2TT, United
Kingdom
| | - Emin Besic
- Aerosol
Physics Laboratory, Physics Unit, Faculty of Engineering and Natural
Sciences, Tampere University, 33720 Tampere, Finland
| | - Prasenjit Seal
- Aerosol
Physics Laboratory, Physics Unit, Faculty of Engineering and Natural
Sciences, Tampere University, 33720 Tampere, Finland
| | - Manuel Dall’Osto
- Institute
of Marine Science, Consejo Superior de Investigaciones Científicas
(CSIC), Barcelona 08003, Spain
| | - David C. S. Beddows
- National
Centre for Atmospheric Science, School of Geography, Earth and Environmental
Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Nina Sarnela
- Institute
for Atmospheric and Earth System Research (INAR)/Physics, Faculty
of Science, University of Helsinki, P.O. Box 64, Helsinki 00014, Finland
| | - Tuija Jokinen
- Institute
for Atmospheric and Earth System Research (INAR)/Physics, Faculty
of Science, University of Helsinki, P.O. Box 64, Helsinki 00014, Finland
- Climate &
Atmosphere Research Centre (CARE-C), The
Cyprus Institute, P.O. Box 27456, Nicosia 1645, Cyprus
| | - Mikko Sipilä
- Institute
for Atmospheric and Earth System Research (INAR)/Physics, Faculty
of Science, University of Helsinki, P.O. Box 64, Helsinki 00014, Finland
| | - Roy M. Harrison
- School
of Geography, Earth & Environmental Sciences, University of Birmingham, Birmingham B15 2TT, United
Kingdom
| | - Matti Rissanen
- Aerosol
Physics Laboratory, Physics Unit, Faculty of Engineering and Natural
Sciences, Tampere University, 33720 Tampere, Finland
- Department
of Chemistry, University of Helsinki, P.O. Box 55, 00014 Helsinki, Finland
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2
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Lukyanova VA, Kuznetsov VV, Konstantinova NM, Dmitrenok AS, Kosaya MP, Dorofeeva OV, Druzhinina AI. Enthalpy of formation of 6-phenyl-1,5-diazabicyclo[3.1.0]hexane by combustion calorimetry and theoretical approach for efficient prediction of thermochemistry of diaziridines. Phys Chem Chem Phys 2023; 25:25289-25298. [PMID: 37701931 DOI: 10.1039/d3cp03290f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
The combustion energy and standard molar enthalpy of formation of crystalline 6-phenyl-1,5-diazabicyclo[3.1.0]hexane (PDABH) were determined using an isoperibolic calorimeter with a static bomb. PDABH is the first diaziridine for which the experimental value of the enthalpy of formation was obtained. This value was validated by the theoretical values of gas phase enthalpy of formation and enthalpy of sublimation. The gas phase enthalpy of formation was calculated using the DLPNO-CCSD(T1)/CBS method in conjunction with isodesmic-type reactions. This method was chosen in comparison to another high quality evaluative method (G4), which has been shown to provide unreliable results for cyclic nitrogen containing compounds. The descriptors of the molecular electrostatic potential (MEP) were used to estimate the enthalpy of sublimation of PDABH. The proposed MEP model is based on experimental enthalpies of sublimation for 75 compounds structurally similar to PDABH. The high-level ab initio calculations of gas phase enthalpies of formation combined with enthalpies of sublimations estimated using descriptors of MEP allow predicting the enthalpies of formation of diaziridines in the solid phase.
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Affiliation(s)
- Vera A Lukyanova
- Department of Chemistry, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Vladimir V Kuznetsov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | | | - Andrey S Dmitrenok
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Maria P Kosaya
- Department of Chemistry, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Olga V Dorofeeva
- Department of Chemistry, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Anna I Druzhinina
- Department of Chemistry, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia.
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3
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Marques EA, De Gendt S, Pourtois G, van Setten MJ. Benchmarking First-Principles Reaction Equilibrium Composition Prediction. Molecules 2023; 28:molecules28093649. [PMID: 37175062 PMCID: PMC10179931 DOI: 10.3390/molecules28093649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
The availability of thermochemical properties allows for the prediction of the equilibrium compositions of chemical reactions. The accurate prediction of these can be crucial for the design of new chemical synthesis routes. However, for new processes, these data are generally not completely available. A solution is the use of thermochemistry calculated from first-principles methods such as Density Functional Theory (DFT). Before this can be used reliably, it needs to be systematically benchmarked. Although various studies have examined the accuracy of DFT from an energetic point of view, few studies have considered its accuracy in predicting the temperature-dependent equilibrium composition. In this work, we collected 117 molecules for which experimental thermochemical data were available. From these, we constructed 2648 reactions. These experimentally constructed reactions were then benchmarked against DFT for 6 exchange-correlation functionals and 3 quality of basis sets. We show that, in reactions that do not show temperature dependence in the equilibrium composition below 1000 K, over 90% are predicted correctly. Temperature-dependent equilibrium compositions typically demonstrate correct qualitative behavior. Lastly, we show that the errors are equally caused by errors in the vibrational spectrum and the DFT electronic ground state energy.
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Affiliation(s)
- Esteban A Marques
- Department of Chemistry, KU Leuven (University of Leuven), Celestijnenlaan 200 F, 3001 Heverlee, Belgium
- IMEC, Kapeldreef 75, 3001 Leuven, Belgium
| | - Stefan De Gendt
- Department of Chemistry, KU Leuven (University of Leuven), Celestijnenlaan 200 F, 3001 Heverlee, Belgium
- IMEC, Kapeldreef 75, 3001 Leuven, Belgium
| | | | - Michiel J van Setten
- IMEC, Kapeldreef 75, 3001 Leuven, Belgium
- ETSF European Theoretical Spectroscopy Facility, Institut de Physique, Université de Liège, Allée du 6 août 17, 4000 Liège, Belgium
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4
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Melin TRL, Harell P, Ali B, Loganathan N, Wilson AK. Thermochemistry of per- and polyfluoroalkyl substances. J Comput Chem 2023; 44:570-580. [PMID: 36334029 PMCID: PMC10098614 DOI: 10.1002/jcc.27023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 09/08/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
The determination of gas phase thermochemical properties of per- and polyfluoroalkyl substances (PFAS) is central to understanding the long-range transport behavior of PFAS in the atmosphere. Prior gas-phase studies have reported the properties of perfluorinated sulfonic acid (PFOS) and perfluorinated octanoic acid (PFOA). Here, this study reports the gas phase enthalpies of formation of short- and long-chain PFAS and their precursor molecules determined using density functional theory (DFT) and ab initio approaches. Two density functionals, two ab initio methods and an empirical method were used to compute enthalpies of formation with the total atomization approach and an isogyric reaction. The performance of the computational methods employed in this work were validated against the experimental enthalpies of linear alkanoic acids and perfluoroalkanes. The gas-phase determinations will be useful for future studies of PFAS in the atmosphere, and the methodological choices will be helpful in the study of other PFAS.
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Affiliation(s)
- Timothé R L Melin
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Preston Harell
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Betoul Ali
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | | | - Angela K Wilson
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
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5
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Dorofeeva OV, Andreychev VV. Benchmark Thermochemistry of Polycyclic Aromatic Hydrocarbons. J Phys Chem A 2022; 126:8315-8325. [DOI: 10.1021/acs.jpca.2c04956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Olga V. Dorofeeva
- Department of Chemistry, Lomonosov Moscow State University, 1-3 Leninskie Gory, Moscow119991, Russia
| | - Valeriy V. Andreychev
- Department of Chemistry, Lomonosov Moscow State University, 1-3 Leninskie Gory, Moscow119991, Russia
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6
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Otlyotov AA, Minenkov Y, Zaitsau DH, Zherikova KV, Verevkin SP. "In Vitro" and "In Vivo" Diagnostic Check for the Thermochemistry of Metal-Organic Compounds. Inorg Chem 2022; 61:10743-10755. [PMID: 35797430 DOI: 10.1021/acs.inorgchem.2c00959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Volatile metal β-diketonates are of interest from both practical and theoretical perspectives (manufacturing of film materials, catalysis, and the nature of metal-ligand bonding). Knowledge of their reliable thermochemical properties is essential for effective applications. However, there is an unacceptable scattering of the available data on the enthalpies of formation. In this work, we proposed "in vitro" and "in vivo" diagnostic tools to verify the available enthalpies of formation in both the crystalline and gaseous states for metal tris-β-diketonates. The "in vitro" procedure involved high-level quantum-chemical calculations and was applied to define a consistent data set on the enthalpies of formation for iron(III) β-diketonates. This data set has provided the basis for "in vivo" structure-property-based diagnostics to evaluate the robustness of the thermochemical data for β-diketonate tris-complexes with metals other than iron.
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Affiliation(s)
- Arseniy A Otlyotov
- N. N. Semenov Federal Research Center for Chemical Physics RAS, Moscow 119991, Russian Federation
| | - Yury Minenkov
- N. N. Semenov Federal Research Center for Chemical Physics RAS, Moscow 119991, Russian Federation.,Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow 125412, Russian Federation
| | - Dzmitry H Zaitsau
- Department of Physical Chemistry and Faculty of Interdisciplinary Research, Competence Centre CALOR, University of Rostock, 18059 Rostock, Germany
| | - Kseniya V Zherikova
- Nikolaev Institute of Inorganic Chemistry of Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Sergey P Verevkin
- Department of Physical Chemistry and Faculty of Interdisciplinary Research, Competence Centre CALOR, University of Rostock, 18059 Rostock, Germany.,Department of Physical Chemistry, Kazan Federal University, Kazan 420008, Russian Federation
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7
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Kulsha AV, Ragoyja EG, Ivashkevich OA. Strong Bases Design: Predicted Limits of Basicity. J Phys Chem A 2022; 126:3642-3652. [PMID: 35657384 DOI: 10.1021/acs.jpca.2c00521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Brønsted superbases have wide applications in organic chemistry due to their ability to activate C-H bonds. The strongest neutral bases to date are substituted aminophosphazenes developed in the late 1980s by Reinhard Schwesinger. Since then, much effort has been expended to create even stronger neutral bases. In this article, the reasons for the instability of very basic compounds are investigated by means of high-level quantum-chemical calculations. Theoretical basicity limits are suggested for solutions as well as for the gas phase. A record-breaking superbase most likely to be synthesizable and stable at ambient conditions is proposed. Hexamethylphosphoramide is considered a reliable ionizing solvent for superbases.
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Affiliation(s)
- Andrey V Kulsha
- Chemical Department, Belarusian State University, 4 Nezavisimosti Avenue, 220030 Minsk, Republic of Belarus
| | - Ekaterina G Ragoyja
- Chemical Department, Belarusian State University, 4 Nezavisimosti Avenue, 220030 Minsk, Republic of Belarus
| | - Oleg A Ivashkevich
- Laboratory for Chemistry of Condensed Systems, Research Institute for Physical Chemical Problems of the Belarusian State University, 14 Leningradskaya Street, 220006 Minsk, Republic of Belarus
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8
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Minenkova I, Otlyotov AA, Cavallo L, Minenkov Y. Gas-phase thermochemistry of polycyclic aromatic hydrocarbons: an approach integrating the quantum chemistry composite scheme and reaction generator. Phys Chem Chem Phys 2022; 24:3163-3181. [PMID: 35040851 DOI: 10.1039/d1cp03702a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We introduce a protocol aimed at predicting the accurate gas-phase enthalpies of formation of polycyclic aromatic hydrocarbons (PAHs). Automatic generation of a dataset of equilibrated chemical reactions preserving the number of carbon atoms in each hybridization state on each side of equations is at the core of our scheme. The performed tests suggest the recommended enthalpy of formation to be derived via a two-step scheme. First, we consider the reactions with a minimal sum of the total number of particles involved, N, and the absolute difference between the total number of products and reactants, |ΔN|. Second, among these reactions, we identify the one with the smallest absolute reaction enthalpy change, . This approach has been applied to predict the gas-phase enthalpies of formation of 113 PAHs via the Feller-Peterson-Dixon approach. Our calculated values provide the mean absolute deviations of 1.7, 1.9, 4.2, 8.1, and 18.5 kJ mol-1 with respect to the literature group-based error corrected (GBEC) G3MP2B3, ATOMIC (HC), group equivalent M06-2X, GBEC B3LYP, and G4MP2 values. Our predicted values give the mean signed and mean absolute errors of -7.5 and 12.9 kJ mol-1 with respect to the experimental enthalpies of formation. The combination of our predicted and the experimental values provide the solid-state enthalpies of formation, , which are not available for a few species. Approaching these values as well as , producing large discrepancies from the experimental side, would be indispensable for testing and further tuning of computational chemistry approaches.
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Affiliation(s)
- Irina Minenkova
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119071, Russian Federation
| | - Arseniy A Otlyotov
- N. N. Semenov Federal Research Center for Chemical Physics RAS, Kosygina Street 4, 119991 Moscow, Russian Federation.
| | - Luigi Cavallo
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology, Thuwal-23955-6900, Saudi Arabia.
| | - Yury Minenkov
- N. N. Semenov Federal Research Center for Chemical Physics RAS, Kosygina Street 4, 119991 Moscow, Russian Federation. .,Joint Institute for High Temperatures, Russian Academy of Sciences, 13-2 Izhorskaya Street, Moscow 125412, Russian Federation
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9
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Yan L, Li S, Zhou S. On the origin of reactivity variation upon sequential ligation: the [Re(Cl) x] +/CH 4 ( x = 1-3) couples. Phys Chem Chem Phys 2021; 23:24319-24327. [PMID: 34673861 DOI: 10.1039/d1cp03468e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The potential of [ReClx]+ (x = 1-3) in activating methane has been explored by using a combination of gas-phase experiments and high-level quantum calculations. When the number of Cl ligands increases, the reactivity towards methane activation varies accordingly. While [ReClx]+ (x = 1-2) are able to dehydrogenate methane by a three-state reactivity scenario, [ReCl3]+ shows inertness towards methane at ambient conditions. Furthermore, the product ion [ClRe(H)CH]+ of the [ReCl]+/CH4 couple could continue to activate methane and liberate molecular dihydrogen but another product ion [Cl2ReCH2]+ is unreactive with methane. Obviously, the nature and the number of ligands make a difference to the reactivity towards methane activation. The associated reaction mechanism and the electron origins for the rather different reactivities are discussed in detail. Finally and more importantly, instructive information concerning the rational design of Re-catalysts for methane conversion is obtained.
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Affiliation(s)
- Linghui Yan
- College of Chemical and Biological Engineering, Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology, Zhejiang University, 310027 Hangzhou, P. R. China. .,Institute of Zhejiang University - Quzhou, 78 Jiuhua Boulevard North, 324000 Quzhou, P. R. China
| | - Shihan Li
- College of Chemical and Biological Engineering, Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology, Zhejiang University, 310027 Hangzhou, P. R. China. .,Institute of Zhejiang University - Quzhou, 78 Jiuhua Boulevard North, 324000 Quzhou, P. R. China
| | - Shaodong Zhou
- College of Chemical and Biological Engineering, Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology, Zhejiang University, 310027 Hangzhou, P. R. China. .,Institute of Zhejiang University - Quzhou, 78 Jiuhua Boulevard North, 324000 Quzhou, P. R. China
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10
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Dorofeeva OV, Druzhinina AI. Enthalpy formation of fluorene: a challenging problem for theory or experiment? Phys Chem Chem Phys 2021; 23:18777-18783. [PMID: 34612416 DOI: 10.1039/d1cp02023d] [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
The large discrepancy between the experimental enthalpy of formation of fluorene and theoretical value calculated by the G3(MP2) method was revealed more than ten years ago. Three years later, a new experimental study of this compound was undertaken to ascertain whether there is any significant error in the thermochemical data. However, after this research, the agreement between theory and experiment was improved only slightly. In this work we decided to calculate the enthalpy of formation of fluorene using the high-level DLPNO-CCSD(T1)/CBS method which shows better results compared to Gn theories. To examine the accuracy of the available experimental data, the calculations were performed not only for fluorene but also for eleven fluorene derivatives. The discrepancy of about 9 kJ mol-1 between the experimental and theoretical enthalpies of formation of fluorene was confirmed by the present calculations, whereas good agreement was observed for the fluorene derivatives. It is highly unlikely that this discrepancy may disappear when using a higher-level theory. The possible reason for such inconsistency might be the experimental difficulty associated with the glass transition discovered in the stable crystalline state of fluorene. In this case, new experiments using the latest methods, such as differential scanning calorimetry combined with X-ray powder diffraction, are needed to gain deeper insight into the solid phase transformations of fluorene.
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Affiliation(s)
- Olga V Dorofeeva
- Department of Chemistry, Lomonosov Moscow State University, 1-3 Leninskie Gory, Moscow, 119991, Russia.
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11
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Yu M, Ge X, Zhou S. On the origins of the mechanistic variants in the thermal reactions of S x+ (x = 1-3) with benzene. Phys Chem Chem Phys 2021; 23:17512-17520. [PMID: 34364310 DOI: 10.1039/d1cp01959g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The S-π interaction between sulfur atom(s) and aromatic ring prevails in chemical and biochemical processes. The thermal gas-phase reactions of the Sn+ (n = 1-3) ions with benzene have been explored by using Quadrupole-Ion Trap (Q-IT) mass spectrometry complemented by quantum chemical calculations. Charge transfer was found to be the only reaction channel for S2+/C6H6, while both charge transfer and bond activation are available for the S+/C6H6 and S3+/C6H6 couples. Upon interrogating the associated electronic origins, multiple factors were found to matter for these processes. In contrast to the σ-type two-center three-electron (2c-3e) S-π hemibond as reported previously, unusual S-π hemibonds were addressed for the Sn+/C6H6 couples, i.e. the 2c-3e π(S061Eπ) and the three-center three-electron (3c-3e) σ(S2061Eπ) hemibonds. Such S-π interaction was found to be responsible for the charge transfer processes in S+/C6H6 and S2+/C6H6, but uninvolved in any transformation for S3+/C6H6.
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Affiliation(s)
- Mincheng Yu
- College of Chemical and Biological Engineering, Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology, Zhejiang University, 310027 Hangzhou, P. R. China.
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12
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Affiliation(s)
- Min Sheng
- Reactive Chemicals Group, Corteva Agriscience, Midland, Michigan 48667, United States
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13
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Dobbelaere MR, Plehiers PP, Van de Vijver R, Stevens CV, Van Geem KM. Learning Molecular Representations for Thermochemistry Prediction of Cyclic Hydrocarbons and Oxygenates. J Phys Chem A 2021; 125:5166-5179. [PMID: 34081474 DOI: 10.1021/acs.jpca.1c01956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate thermochemistry estimation of polycyclic molecules is crucial for kinetic modeling of chemical processes that use renewable and alternative feedstocks. In kinetic model generators, molecular properties are estimated rapidly with group additivity, but this method is known to have limitations for polycyclic structures. This issue has been resolved in our work by combining a geometry-based molecular representation with a deep neural network trained on ab initio data. Each molecule is transformed into a probabilistic vector from its interatomic distances, bond angles, and dihedral angles. The model is tested on a small experimental dataset (200 molecules) from the literature, a new medium-sized set (4000 molecules) with both open-shell and closed-shell species, calculated at the CBS-QB3 level with empirical corrections, and a large G4MP2-level QM9-based dataset (40 000 molecules). Heat capacities between 298.15 and 2500 K are calculated in the medium set with an average deviation of about 1.5 J mol-1 K-1 and the standard entropy at 298.15 K is predicted with an average error below 4 J mol-1 K-1. The standard enthalpy of formation at 298.15 K has an average out-of-sample error below 4 kJ mol-1 on a QM9 training set size of around 15 000 molecules. By fitting NASA polynomials, the enthalpy of formation at higher temperatures can be calculated with the same accuracy as the standard enthalpy of formation. Uncertainty quantification by means of the ensemble standard deviation is included to indicate when molecules that are on the edge or outside of the application range of the model are evaluated.
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Affiliation(s)
- Maarten R Dobbelaere
- Laboratory for Chemical Technology, Department of Materials, Textiles and Chemical Engineering, Ghent University, Technologiepark 125, 9052 Gent, Belgium
| | - Pieter P Plehiers
- Laboratory for Chemical Technology, Department of Materials, Textiles and Chemical Engineering, Ghent University, Technologiepark 125, 9052 Gent, Belgium
| | - Ruben Van de Vijver
- Laboratory for Chemical Technology, Department of Materials, Textiles and Chemical Engineering, Ghent University, Technologiepark 125, 9052 Gent, Belgium
| | - Christian V Stevens
- SynBioC Research Group, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Kevin M Van Geem
- Laboratory for Chemical Technology, Department of Materials, Textiles and Chemical Engineering, Ghent University, Technologiepark 125, 9052 Gent, Belgium
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14
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Sandler I, Chen J, Taylor M, Sharma S, Ho J. Accuracy of DLPNO-CCSD(T): Effect of Basis Set and System Size. J Phys Chem A 2021; 125:1553-1563. [PMID: 33560853 DOI: 10.1021/acs.jpca.0c11270] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The DLPNO-CCSD(T) method is designed to study large molecular systems at significantly reduced cost relative to its canonical counterpart. However, the error in this approach is also size-extensive and relies on cancellation of errors for the calculation of relative energies. This work provides a direct comparison of canonical CCSD(T) and TightPNO DLPNO-CCSD(T) calculations of reaction energies and barriers of a broad range of chemical reactions. The dataset includes acidities, anion binding affinities, enolization, Diels-Alder, nucleophilic substitution, and atom transfer reactions and complements existing theoretical datasets in terms of system size as well as new reaction types (e.g., anion binding affinities and chlorine atom transfer reactions). The performance of DLPNO-CCSD(T) was further examined with respect to systematic variation of basis set and system size and amounts of nonbonded interaction present in the system. The errors in the DLPNO-CCSD(T) were found to be relatively insensitive to the choice of basis set for small systems but increase monotonically with system size. Additionally, calculations of barriers appear to be more challenging than reaction energies with errors exceeding 5 kJ mol-1 for many Diels-Alder reactions. Further tests on three realistic organic reactions reveal the impact of the DLPNO approximation in calculating absolute and relative barriers that are important for predictions such as stereoselectivity.
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Affiliation(s)
- Isolde Sandler
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Junbo Chen
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mackenzie Taylor
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Shaleen Sharma
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Junming Ho
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
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15
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Dorofeeva OV, Ryzhova ON. Accurate estimation of enthalpies of formation for C-, H-, O-, and N-containing compounds using DLPNO-CCSD(T1)/CBS method. Struct Chem 2021. [DOI: 10.1007/s11224-020-01681-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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16
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Minenkova I, Osina EL, Cavallo L, Minenkov Y. Gas-Phase Thermochemistry of MX 3 and M 2X 6 (M = Sc, Y; X = F, Cl, Br, I) from a Composite Reaction-Based Approach: Homolytic versus Heterolytic Cleavage. Inorg Chem 2020; 59:17084-17095. [PMID: 33210914 DOI: 10.1021/acs.inorgchem.0c02292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A domain-based local-pair natural-orbital coupled-cluster approach with single, double, and improved linear-scaling perturbative triple correction via an iterative algorithm, DLPNO-CCSD(T1), was applied within the framework of the Feller-Peterson-Dixon approach to derive gas-phase heats of formation of scandium and yttrium trihalides and their dimers via a set of homolytic and heterolytic dissociation reactions. All predicted heats of formation moderately depend on the reaction type with the most and least negative values obtained for homolytic and heterolytic dissociation, respectively. The basis set size dependence, as well as the influence of static correlation effects not covered by the standard (DLPNO-)CCSD(T) approach, suggests that exploitation of the heterolytic dissociation reactions with the formation of M3+ and X- ions leads to the most robust heats of formation. The gas-phase formation enthalpies ΔHf°(0 K)/ΔHf°(298.15 K) and absolute entropies S°(298.15 K) were obtained for the first time for the Sc2F6, Sc2Br6, and Sc2I6 species. For ScBr3, ScI3, Sc2Cl6, and Y2Cl6, we suggest a reexamination of the experimental heats of formation available in the literature. For other compounds, the predicted values were found to be in good agreement with the experimental estimates. Extracted MX3 (M = Sc, Y; X = F, Cl, Br, and I) 0 K atomization enthalpies indicate weaker bonding when moving from fluorine to iodine and from yttrium to scandium. Likewise, the stability of yttrium trihalide dimers degrades when going from fluorine to iodine. Respective scandium trihalide dimers are less stable, with 0 K dimer dissociation energy decreasing in the row fluorine - chlorine - bromine ≈ iodine. Correlation of the (n - 1)s2p6 electrons on bromine and iodine, inclusion of zero-point energy, relativistic effects, and the effective-core-potential correction as well as amelioration of the DLPNO localization inaccuracy are shown to be of similar magnitude, which is critical if accurate heats of formation are a goal.
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Affiliation(s)
- Irina Minenkova
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119071, Russia
| | - Evgeniya L Osina
- Joint Institute for High Temperatures, Russian Academy of Sciences, 13-2 Izhorskaya Street, Moscow 125412, Russia
| | - Luigi Cavallo
- Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Yury Minenkov
- Joint Institute for High Temperatures, Russian Academy of Sciences, 13-2 Izhorskaya Street, Moscow 125412, Russia.,N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Kosygina Street 4, Moscow 119991, Russia
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17
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Singh I, Al-Wahaibi LH, Srivastava R, Prasad O, Pathak SK, Kumar S, Parveen S, Banerjee M, El-Emam AA, Sinha L. DFT Study on the Electronic Properties, Spectroscopic Profile, and Biological Activity of 2-Amino-5-trifluoromethyl-1,3,4-thiadiazole with Anticancer Properties. ACS OMEGA 2020; 5:30073-30087. [PMID: 33251442 PMCID: PMC7689922 DOI: 10.1021/acsomega.0c04474] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 11/03/2020] [Indexed: 11/29/2022]
Abstract
Extensive investigation on the molecular and electronic structure of 2-amino-5-trifluoromethyl-1,3,4-thiadiazole in the ground state and in the first excited state has been performed. The energy barrier corresponding to the conversion between imino and amino tautomers has been calculated, which indicates the existence of amino tautomer in solid state for the title compound. The FT-Raman and FT-IR spectra were recorded and compared with theoretical vibrational wavenumbers, and a good coherence has been observed. The MESP map, dipole moment, polarizability, and hyperpolarizability have been calculated to comprehend the properties of the title molecule. High polarizability value estimation of the title compound may enhance its bioactivity. Natural bonding orbital analysis has been done on monomer and dimer to investigate the charge delocalization and strength of hydrogen bonding, respectively. Strong hydrogen bonding interaction energies of 17.09/17.49 kcal mol-1 have been calculated at the B3LYP/M06-2X functional. The UV-vis spectrum was recorded and related to the theoretical spectrum. The title compound was biologically examined for anticancer activity by studying the cytotoxic performance against two human cancer cell lines (A549 and HeLa) along with the molecular docking simulation. Both molecular docking and cytotoxic performance against cancer cell lines show positive outcomes, and the title compound appears to be a promising anticancer agent.
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Affiliation(s)
- Isha Singh
- Department of Physics, University of Lucknow, Lucknow 226007, India
| | - Lamya H. Al-Wahaibi
- Department of Chemistry, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Ruchi Srivastava
- Department of Physics, University of Lucknow, Lucknow 226007, India
| | - Onkar Prasad
- Department of Physics, University of Lucknow, Lucknow 226007, India
| | - Shilendra K. Pathak
- Department of Physics, M. M. M. P. G. College, Bhatpar Rani, Deoria 274702, India
| | - Saurabh Kumar
- Molecular & Human Genetics Lab, Department of Zoology, University of Lucknow, Lucknow 226007, India
| | - Shama Parveen
- Molecular & Human Genetics Lab, Department of Zoology, University of Lucknow, Lucknow 226007, India
| | - Monisha Banerjee
- Molecular & Human Genetics Lab, Department of Zoology, University of Lucknow, Lucknow 226007, India
| | - Ali A. El-Emam
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Mansoura, Mansoura 35516, Egypt
| | - Leena Sinha
- Department of Physics, University of Lucknow, Lucknow 226007, India
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18
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Dorofeeva OV. Accurate prediction of norbornadiene cycle enthalpies by DLPNO-CCSD(T 1 )/CBS method. J Comput Chem 2020; 41:2352-2364. [PMID: 32798279 DOI: 10.1002/jcc.26394] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/04/2020] [Accepted: 07/15/2020] [Indexed: 11/06/2022]
Abstract
The DLPNO-CCSD(T1 )/CBS method combined with simple reactions containing small reference species leads to an improvement in the accuracy of theoretically evaluated enthalpies of formation of medium-sized polyalicyclic hydrocarbons when compared with the widely used composite approach. The efficiency of the DLPNO-CCSD(T1 )/CBS method is most vividly demonstrated by comparing with the results of G4 calculations for adamantane. The most important factor in choosing appropriate working reaction is the same number of species on both sides of the equation. Among these reactions, the reactions with small enthalpy change usually provide a better cancellation of errors. The DLPNO-CCSD(T1 )/CBS method was used to calculate the enthalpies of formation of compounds belonging to the norbornadiene cycle (norbornadiene, quadricyclane, norbornene, nortricyclane, and norbornane). The most reliable experimental enthalpies of formation are recommended for these compounds by comparing calculated values with conflicting experimental data.
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Affiliation(s)
- Olga V Dorofeeva
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
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19
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Lawer A, Epton RG, Stephens TC, Palate KY, Lodi M, Marotte E, Lamb KJ, Sangha JK, Lynam JM, Unsworth WP. Evaluating the Viability of Successive Ring-Expansions Based on Amino Acid and Hydroxyacid Side-Chain Insertion. Chemistry 2020; 26:12674-12683. [PMID: 32432817 PMCID: PMC7589337 DOI: 10.1002/chem.202002164] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Indexed: 01/20/2023]
Abstract
The outcome of ring-expansion reactions based on amino/hydroxyacid side-chain insertion is strongly dependent on ring size. This manuscript, which builds upon our previous work on Successive Ring Expansion (SuRE) methods, details efforts to better define the scope and limitations of these reactions on lactam and β-ketoester ring systems with respect to ring size and additional functionality. The synthetic results provide clear guidelines as to which substrate classes are more likely to be successful and are supported by computational results, using a density functional theory (DFT) approach. Calculating the relative Gibbs free energies of the three isomeric species that are formed reversibly during ring expansion enables the viability of new synthetic reactions to be correctly predicted in most cases. The new synthetic and computational results are expected to support the design of new lactam- and β-ketoester-based ring-expansion reactions.
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Affiliation(s)
- Aggie Lawer
- Department of ChemistryUniversity of YorkYorkYO10 5DDUK
| | - Ryan G. Epton
- Department of ChemistryUniversity of YorkYorkYO10 5DDUK
| | | | | | - Mahendar Lodi
- Department of ChemistryUniversity of YorkYorkYO10 5DDUK
| | - Emilie Marotte
- ENSICAEN6 Boulevard Maréchal Juin, CS 4505314050Caen Cedex 04France
| | - Katie J. Lamb
- Department of ChemistryUniversity of YorkYorkYO10 5DDUK
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20
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Yalamanchi KK, Monge-Palacios M, van Oudenhoven VCO, Gao X, Sarathy SM. Data Science Approach to Estimate Enthalpy of Formation of Cyclic Hydrocarbons. J Phys Chem A 2020; 124:6270-6276. [PMID: 32648745 PMCID: PMC7458419 DOI: 10.1021/acs.jpca.0c02785] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In
spite of increasing importance of cyclic hydrocarbons in various
chemical systems, studies on the fundamental properties of these compounds,
such as enthalpy of formation, are still scarce. One of the reasons
for this is the fact that the estimation of the thermodynamic properties
of cyclic hydrocarbon species via cost-effective computational approaches,
such as group additivity (GA), has several limitations and challenges.
In this study, a machine learning (ML) approach is proposed using
a support vector regression (SVR) algorithm to predict the standard
enthalpy of formation of cyclic hydrocarbon species. The model is
developed based on a thoroughly selected dataset of accurate experimental
values of 192 species collected from the literature. The molecular
descriptors used as input to the SVR are calculated via alvaDesc software,
which computes in total 5255 features classified into 30 categories.
The developed SVR model has an average error of approximately 10 kJ/mol.
In comparison, the SVR model outperforms the GA approach for complex
molecules and can be therefore proposed as a novel data-driven approach
to estimate enthalpy values for complex cyclic species. A sensitivity
analysis is also conducted to examine the relevant features that play
a role in affecting the standard enthalpy of formation of cyclic species.
Our species dataset is expected to be updated and expanded as new
data are available to develop a more accurate SVR model with broader
applicability.
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Affiliation(s)
- Kiran K Yalamanchi
- Physical Sciences and Engineering Division, Clean Combustion Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - M Monge-Palacios
- Physical Sciences and Engineering Division, Clean Combustion Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Vincent C O van Oudenhoven
- Physical Sciences and Engineering Division, Clean Combustion Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - S Mani Sarathy
- Physical Sciences and Engineering Division, Clean Combustion Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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21
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Zhao Q, Savoie BM. Self-Consistent Component Increment Theory for Predicting Enthalpy of Formation. J Chem Inf Model 2020; 60:2199-2207. [PMID: 32159955 DOI: 10.1021/acs.jcim.0c00092] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Qiyuan Zhao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47906, United States
| | - Brett M. Savoie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47906, United States
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22
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Patel P, Wilson AK. Domain-based local pair natural orbital methods within the correlation consistent composite approach. J Comput Chem 2019; 41:800-813. [PMID: 31891196 DOI: 10.1002/jcc.26129] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/29/2019] [Accepted: 12/01/2019] [Indexed: 01/15/2023]
Abstract
Ab initio composite approaches have been utilized to model and predict main group thermochemistry within 1 kcal mol-1 , on average, from well-established reliable experiments, primarily for molecules with less than 30 atoms. For molecules of increasing size and complexity, such as biomolecular complexes, composite methodologies have been limited in their application. Therefore, the domain-based local pair natural orbital (DLPNO) methods have been implemented within the correlation consistent composite approach (ccCA) framework, namely DLPNO-ccCA, to reduce the computational cost (disk space, CPU (central processing unit) time, memory) and predict energetic properties such as enthalpies of formation, noncovalent interactions, and conformation energies for organic biomolecular complexes including one of the largest molecules examined via composite strategies, within 1 kcal mol-1 , after calibration with 119 molecules and a set of linear alkanes. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Prajay Patel
- Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824
| | - Angela K Wilson
- Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824
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23
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Kiselev VG, Goldsmith CF. Accurate Thermochemistry of Novel Energetic Fused Tricyclic 1,2,3,4-Tetrazine Nitro Derivatives from Local Coupled Cluster Methods. J Phys Chem A 2019; 123:9818-9827. [DOI: 10.1021/acs.jpca.9b08356] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vitaly G. Kiselev
- School of Engineering, Brown University, 184 Hope Str., Providence, Rhode Island 02912, United States
- Semenov Institute of Chemical Physics RAS, 4 Kosygina Str., 119991 Moscow, Russia
- Institute of Chemical Kinetics and Combustion SB RAS, 3 Institutskaya Str., 630090 Novosibirsk, Russia
- Novosibirsk State University, 2 Pirogova Str., 630090 Novosibirsk, Russia
| | - C. Franklin Goldsmith
- School of Engineering, Brown University, 184 Hope Str., Providence, Rhode Island 02912, United States
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24
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Kulsha AV, Sharapa DI. Superhalogen and Superacid. J Comput Chem 2019; 40:2293-2300. [PMID: 31254480 DOI: 10.1002/jcc.26007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/25/2019] [Accepted: 05/30/2019] [Indexed: 11/10/2022]
Abstract
A superhalogen F@C20 (CN)20 and a corresponding Brønsted superacid were designed and investigated on DFT and DLPNO-CCSD(T) levels of theory. Calculated compounds have outstanding electron affinity and deprotonation energy, respectively. We consider superacid H[F@C20 (CN)20 ] to be able to protonate molecular nitrogen. The stability of these structures is discussed, while some of the previous predictions concerning neutral Brønsted superacids of record strength are doubted. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Andrey V Kulsha
- Lyceum of Belarusian State University, 8 Ulijanauskaja Str., Minsk, 220030, Belarus
| | - Dmitry I Sharapa
- Chair of Theoretical Chemistry and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander-Universitat Erlangen-Nürnberg, Egerlandstraße 3, 91058, Erlangen, Germany.,Institute of Catalysis Research and Technology (IKFT), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, D-76344, Germany
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25
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Rahrt R, Auth T, Demireva M, Armentrout PB, Koszinowski K. Benzhydrylpyridinium Ions: A New Class of Thermometer Ions for the Characterization of Electrospray-Ionization Mass Spectrometers. Anal Chem 2019; 91:11703-11711. [DOI: 10.1021/acs.analchem.9b02257] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Rene Rahrt
- Institut für Organische und Biomolekulare Chemie, Universität Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
| | - Thomas Auth
- Institut für Organische und Biomolekulare Chemie, Universität Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
| | - Maria Demireva
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, Utah 84112, United States
| | - P. B. Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, Utah 84112, United States
| | - Konrad Koszinowski
- Institut für Organische und Biomolekulare Chemie, Universität Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
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26
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Maity B, Minenkov Y, Cavallo L. Evaluation of experimental alkali metal ion–ligand noncovalent bond strengths with DLPNO-CCSD(T) method. J Chem Phys 2019; 151:014301. [DOI: 10.1063/1.5099580] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Bholanath Maity
- King Abdullah University of Science and Technology (KAUST), Physical Science and Engineering Division (PSE), KAUST Catalysis Center (KCC), 23955-6900 Thuwal, Saudi Arabia
| | - Yury Minenkov
- Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, Dolgoprudny, Moscow Region 141700, Russian Federation
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Science and Engineering Division (PSE), KAUST Catalysis Center (KCC), 23955-6900 Thuwal, Saudi Arabia
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27
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Minenkova I, Sliznev VV, Cavallo L, Minenkov Y. Gas Phase Silver Thermochemistry from First Principles. Inorg Chem 2019; 58:7873-7885. [PMID: 31185536 DOI: 10.1021/acs.inorgchem.9b00556] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Domain-based local pair natural orbital coupled cluster approach with single, double, and perturbative triple excitations, DLPNO-CCSD(T), has been applied within a framework of a reduced version of the reaction-based Feller-Peterson-Dixon (FPD) scheme to predict gas phase heats of formation and absolute entropies of silver inorganic and organometallic compounds. First, we evaluated all existing experimental data currently limited by thermodynamic functions of 10 silver substances (AgH, AgF, AgBr, AgI, Ag2, Ag2S, Ag2Se, Ag2Te, AgCN, AgPO2). The mean average deviation between computed and experimental heats of formation was found to be 1.9 kcal/mol. Notably, all predicted heats of formation turned out to be within the error bounds of their experimental counterparts. Second, we predicted heats of formation and entropies for additional 90 silver species with no experimental data available, substantially enriching silver thermochemistry. Combination of gas phase heats of formation Δ Hf and entropies S° of AgNO2, AgSCN, Ag2SO4, and Ag2SeO4 obtained in this work, with respective solid-state information, resulted in accurate sublimation thermochemistry of these compounds. Complementation of predicted Δ Hf with heats of formation of some neutrals and positive ions produced 33 silver bond strengths of high reliability. Obtained thermochemical data are promising for developing the concepts of silver chemistry. In addition, derived heats of formation and bond dissociation enthalpies, due to their high diversity, are found to be relevant for testing and training of computational chemistry methods.
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Affiliation(s)
- Irina Minenkova
- Moscow Institute of Physics and Technology , Institutskiy Pereulok 9 , Dolgoprudny , Moscow Region 141700 , Russian Federation.,A.N. Frumkin Institute of Physical Chemistry and Electrochemistry , Russian Academy of Sciences , 31 Leninsky Prospect , Moscow , GSP-1, 119071 , Russian Federation
| | - Valery V Sliznev
- Research Institute for Thermodynamics and Kinetics of Chemical Processes , Ivanovo State University of Chemistry and Technology , 153460 Ivanovo , Russian Federation
| | - Luigi Cavallo
- KAUST Catalysis Center (KCC) , King Abdullah University of Science and Technology , Thuwal 23955-6900 , Saudi Arabia
| | - Yury Minenkov
- Moscow Institute of Physics and Technology , Institutskiy Pereulok 9 , Dolgoprudny , Moscow Region 141700 , Russian Federation
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28
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Deraet X, Woller T, Van Lommel R, De Proft F, Verniest G, Alonso M. A Benchmark of Density Functional Approximations For Thermochemistry and Kinetics of Hydride Reductions of Cyclohexanones. ChemistryOpen 2019; 8:788-806. [PMID: 31293871 PMCID: PMC6594353 DOI: 10.1002/open.201900085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/10/2019] [Indexed: 11/21/2022] Open
Abstract
The performance of density functionals and wavefunction methods for describing the thermodynamics and kinetics of hydride reductions of 2-substituted cyclohexanones has been evaluated for the first time. A variety of exchange correlation functionals ranging from generalized gradient approximations to double hybrids have been tested and their performance to describe the facial selectivity of hydride reductions of cyclohexanones has been carefully assessed relative to the CCSD(T) method. Among the tested methods, an approach in which single-point energy calculations using the double hybrid B2PLYP-D3 functional on ωB97X-D optimized geometries provides the most accurate transition state energies for these kinetically-controlled reactions. Moreover, the role of torsional strain, temperature, solvation, noncovalent interactions on the stereoselectivity of these reductions was elucidated. Our results indicate a prominent role of the substituent on the cis/trans ratios driven by the delicate interplay between torsional strain and dispersion interactions.
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Affiliation(s)
- Xavier Deraet
- Department of General Chemistry (ALGC)Vrije Universiteit Brussel (VUB)Pleinlaan 21050 ElseneBrusselsBelgium
| | - Tatiana Woller
- Department of General Chemistry (ALGC)Vrije Universiteit Brussel (VUB)Pleinlaan 21050 ElseneBrusselsBelgium
| | - Ruben Van Lommel
- Department of General Chemistry (ALGC)Vrije Universiteit Brussel (VUB)Pleinlaan 21050 ElseneBrusselsBelgium
- Molecular Design and SynthesisDepartment of Chemistry, KU Leuven, Celestijnenlaan 200F Leuven Chem&Tech, box 24043001LeuvenBelgium
| | - Frank De Proft
- Department of General Chemistry (ALGC)Vrije Universiteit Brussel (VUB)Pleinlaan 21050 ElseneBrusselsBelgium
| | - Guido Verniest
- Research group of Organic Chemistry (ORGC), Departments of Bio-engineering Sciences and ChemistryVrije Universiteit Brussel (VUB)Pleinlaan 21050 ElseneBrusselsBelgium
| | - Mercedes Alonso
- Department of General Chemistry (ALGC)Vrije Universiteit Brussel (VUB)Pleinlaan 21050 ElseneBrusselsBelgium
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29
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Titanocene Selenide Sulfides Revisited: Formation, Stabilities, and NMR Spectroscopic Properties. Molecules 2019; 24:molecules24020319. [PMID: 30654590 PMCID: PMC6358803 DOI: 10.3390/molecules24020319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/10/2019] [Accepted: 01/11/2019] [Indexed: 11/27/2022] Open
Abstract
[TiCp2S5] (phase A), [TiCp2Se5] (phase F), and five solid solutions of mixed titanocene selenide sulfides [TiCp2SexS5−x] (Cp = C5H5−) with the initial Se:S ranging from 1:4 to 4:1 (phases B–E) were prepared by reduction of elemental sulfur or selenium or their mixtures by lithium triethylhydridoborate in thf followed by the treatment with titanocene dichloride [TiCp2Cl2]. Their 77Se and 13C NMR spectra were recorded from the CS2 solution. The definite assignment of the 77Se NMR spectra was based on the PBE0/def2-TZVPP calculations of the 77Se chemical shifts and is supported by 13C NMR spectra of the samples. The following complexes in varying ratios were identified in the CS2 solutions of the phases B–E: [TiCp2Se5] (51), [TiCp2Se4S] (41), [TiCp2Se3S2] (31), [TiCp2SSe3S] (36), [TiCp2SSe2S2] (25), [TiCp2SSeS3] (12), and [TiCp2S5] (01). The disorder scheme in the chalcogen atom positions of the phases B–E observed upon crystal structure determinations is consistent with the spectral assignment. The enthalpies of formation calculated for all twenty [TiCp2SexS5−x] (x = 0–5) at DLPNO-CCSD(T)/CBS level including corrections for core-valence correlation and scalar relativistic, as well as spin-orbit coupling contributions indicated that within a given chemical composition, the isomers of most favourable enthalpy of formation were those, which were observed by 77Se and 13C NMR spectroscopy.
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30
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Sharapa DI, Genaev A, Cavallo L, Minenkov Y. A Robust and Cost‐Efficient Scheme for Accurate Conformational Energies of Organic Molecules. Chemphyschem 2018; 20:92-102. [DOI: 10.1002/cphc.201801063] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Dmitry I. Sharapa
- Institute of Catalysis Research and TechnologyKarlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz Platz 1 Eggenstein-Leopoldshafen D-76344 Germany
| | - Alexander Genaev
- Vorozhtsov Novosibirsk Institute of Organic Chemistry Academician Lavrent'ev Ave., 9 Novosibirsk 630090 Russian Federation
| | - Luigi Cavallo
- KAUST Catalysis Center (KCC)King Abdullah University of Science and Technology Thuwal- 23955-6900 Saudi Arabia
| | - Yury Minenkov
- Moscow Institute of Physics and Technology Institutskiy Pereulok 9, Dolgoprudny Moscow Region 141700 Russia
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Iyer S, Reiman H, Møller KH, Rissanen MP, Kjaergaard HG, Kurtén T. Computational Investigation of RO 2 + HO 2 and RO 2 + RO 2 Reactions of Monoterpene Derived First-Generation Peroxy Radicals Leading to Radical Recycling. J Phys Chem A 2018; 122:9542-9552. [PMID: 30449100 DOI: 10.1021/acs.jpca.8b09241] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The oxidation of biogenically emitted volatile organic compounds (BVOC) plays an important role in the formation of secondary organic aerosols (SOA) in the atmosphere. Peroxy radicals (RO2) are central intermediates in the BVOC oxidation process. Under clean (low-NO x) conditions, the main bimolecular sink reactions for RO2 are with the hydroperoxy radical (HO2) and with other RO2 radicals. Especially for small RO2, the RO2 + HO2 reaction mainly leads to closed-shell hydroperoxide products. However, there exist other known RO2 + HO2 and RO2 + RO2 reaction channels that can recycle radicals and oxidants in the atmosphere, potentially leading to lower-volatility products and enhancing SOA formation. In this work, we present a thermodynamic overview of two such reactions: (a) RO2 + HO2 → RO + OH + O2 and (b) R'O2 + RO2 → R'O + RO + O2 for selected monoterpene + oxidant derived peroxy radicals. The monoterpenes considered are α-pinene, β-pinene, limonene, trans-β-ocimene, and Δ3-carene. The oxidants considered are the hydroxyl radical (OH), the nitrate radical (NO3), and ozone (O3). The reaction Gibbs energies were calculated at the DLPNO-CCSD(T)/def2-QZVPP//ωB97X-D/aug-cc-pVTZ level of theory. All reactions studied here were found to be exergonic in terms of Gibbs energy. On the basis of a comparison with previous mechanistic studies, we predict that reaction a and reaction b are likely to be most important for first-generation peroxy radicals from O3 oxidation (especially for β-pinene), while being less so for most first-generation peroxy radicals from OH and NO3 oxidation. This is because both reactions are comparatively more exergonic for the O3 oxidized systems than their OH and NO3 oxidized counterparts. Our results indicate that bimolecular reactions of certain complex RO2 may contribute to an increase in radical and oxidant recycling under high HO2 conditions in the atmosphere, which can potentially enhance SOA formation.
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Affiliation(s)
- Siddharth Iyer
- Department of Chemistry and Institute for Atmospheric and Earth System Research (INAR) , University of Helsinki , P.O. Box 55, FI-00014 , Helsinki , Finland
| | - Heidi Reiman
- Department of Chemistry , University of Helsinki , P.O. Box 55, FI-00014 , Helsinki , Finland
| | - Kristian H Møller
- Department of Chemistry , University of Copenhagen , DK-2100 Copenhagen Ø , Denmark
| | - Matti P Rissanen
- Department of Physics and Institute for Atmospheric and Earth System Research (INAR) , University of Helsinki , P.O. Box 64, FI-00014 , Helsinki , Finland
| | - Henrik G Kjaergaard
- Department of Chemistry , University of Copenhagen , DK-2100 Copenhagen Ø , Denmark
| | - Theo Kurtén
- Department of Chemistry and Institute for Atmospheric and Earth System Research (INAR) , University of Helsinki , P.O. Box 55, FI-00014 , Helsinki , Finland
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32
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Della Monica F, Maity B, Pehl T, Buonerba A, De Nisi A, Monari M, Grassi A, Rieger B, Cavallo L, Capacchione C. [OSSO]-Type Iron(III) Complexes for the Low-Pressure Reaction of Carbon Dioxide with Epoxides: Catalytic Activity, Reaction Kinetics, and Computational Study. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01695] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Francesco Della Monica
- Dipartimento di Chimica e Biologia “Adolfo Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II, 84084 Fisciano, SA, Italy
| | - Bholanath Maity
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Thomas Pehl
- WACKER-Lehrstuhl für Makromolekulare Chemie, Zentralinstitut für Katalyseforschung (CRC), Technische Universitat München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Antonio Buonerba
- Dipartimento di Chimica e Biologia “Adolfo Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II, 84084 Fisciano, SA, Italy
| | - Assunta De Nisi
- Dipartimento di Chimica G. Ciamician, Alma Mater Studiorum, Università di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Magda Monari
- Dipartimento di Chimica G. Ciamician, Alma Mater Studiorum, Università di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Alfonso Grassi
- Dipartimento di Chimica e Biologia “Adolfo Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II, 84084 Fisciano, SA, Italy
| | - Bernhard Rieger
- WACKER-Lehrstuhl für Makromolekulare Chemie, Zentralinstitut für Katalyseforschung (CRC), Technische Universitat München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Luigi Cavallo
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Carmine Capacchione
- Dipartimento di Chimica e Biologia “Adolfo Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II, 84084 Fisciano, SA, Italy
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33
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Pollice R, Bot M, Kobylianskii IJ, Shenderovich I, Chen P. Attenuation of London Dispersion in Dichloromethane Solutions. J Am Chem Soc 2017; 139:13126-13140. [DOI: 10.1021/jacs.7b06997] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Robert Pollice
- Laboratorium für Organische
Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Marek Bot
- Laboratorium für Organische
Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Ilia J. Kobylianskii
- Laboratorium für Organische
Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Ilya Shenderovich
- Laboratorium für Organische
Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Peter Chen
- Laboratorium für Organische
Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
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