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Pappijn CAR, Van de Vijver R, Reyniers MF, Sabbe MK, Marin GB, Van Geem KM. Modeling the thermochemistry of nitrogen-containing compounds via group additivity. Phys Chem Chem Phys 2024; 26:19021-19034. [PMID: 38953877 DOI: 10.1039/d4cp00727a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
First-principles based kinetic modeling is essential to gain insight into the governing chemistry of nitrogen-containing compounds over a wide range of technologically important processes, e.g. pyrolysis, oxidation and combustion. It also enables the development of predictive, fundamental models key to improving understanding of the influence of nitrogen-containing compounds present as impurities or process additives, considering safety, operability and quality of the product streams. A prerequisite for the generation of detailed fundamental kinetic models is the availability of accurate thermodynamic properties. To address the scarcity of thermodynamic properties for nitrogen-containing compounds, a consistent set of 91 group additive values and three non-nearest-neighbor interactions has been determined from a dataset of CBS-QB3 calculations for 300 species, including 104 radicals. This dataset contains a wide range of nitrogen-containing functionalities, i.e. imine, nitrile, nitro, nitroso, nitrite, nitrate and azo functional groups. The group additivity model enables the approximation of the standard enthalpy of formation and standard entropy at 298 K as well as the standard heat capacities over a large temperature range, i.e. 300-1500 K. For a test set of 27 nitrogen-containing compounds, the group additivity model succeeds in approximating the ab initio calculated values for the standard enthalpy of formation with a MAD of 2.3 kJ mol-1. The MAD for the standard entropy and heat capacity is lower than 4 and 2 J mol-1 K-1, respectively. For a test set of 11 nitrogen-containing compounds, the MAD between experimental and group additivity approximated values for the standard enthalpy of formation amounts to 2.8 kJ mol-1.
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Affiliation(s)
- Cato A R Pappijn
- Laboratory for Chemical Technology, Ghent University, Technologiepark 121, 9052 Zwijnaarde, Belgium.
| | - Ruben Van de Vijver
- Laboratory for Chemical Technology, Ghent University, Technologiepark 121, 9052 Zwijnaarde, Belgium.
| | - Marie-Françoise Reyniers
- Laboratory for Chemical Technology, Ghent University, Technologiepark 121, 9052 Zwijnaarde, Belgium.
| | - Maarten K Sabbe
- Laboratory for Chemical Technology, Ghent University, Technologiepark 121, 9052 Zwijnaarde, Belgium.
| | - Guy B Marin
- Laboratory for Chemical Technology, Ghent University, Technologiepark 121, 9052 Zwijnaarde, Belgium.
| | - Kevin M Van Geem
- Laboratory for Chemical Technology, Ghent University, Technologiepark 121, 9052 Zwijnaarde, Belgium.
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2
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Lemler PM, Craft CL, Pollok CH, Regan TP, Vaccaro PH. Isolated and solvated chiroptical behavior in conformationally flexible butanamines. Chirality 2023; 35:586-618. [PMID: 37550220 DOI: 10.1002/chir.23570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 08/09/2023]
Abstract
The nonresonant optical activity of two highly flexible aliphatic amines, (2R)-3-methyl-2-butanamine (R-MBA) and (2R)-(3,3)-dimethyl-2-butanamine (R-DMBA), has been probed under isolated and solvated conditions to examine the roles of conformational isomerism and to explore the influence of extrinsic perturbations. The optical rotatory dispersion (ORD) measured in six solvents presented uniformly negative rotatory powers over the 320-590 nm region, with the long-wavelength magnitude of chiroptical response growing nearly monotonically as the dielectric constant of the surroundings diminished. The intrinsic specific optical rotation,α λ T (in deg dm-1 [g/mL]-1 ), extracted for ambient vapor-phase samples of R-MBA [-11.031(98) and -2.29 (11)] and R-DMBA [-9.434 (72) and -1.350 (48)] at 355 and 633 nm were best reproduced by counterintuitive solvents of high polarity (yet low polarizability) like acetonitrile and methanol. Attempts to interpret observed spectral signatures quantitatively relied on the linear-response frameworks of density-functional theory (B3LYP, cam-B3LYP, and dispersion-corrected analogs) and coupled-cluster theory (CCSD), with variants of the polarizable continuum model (PCM) deployed to account for the effects of implicit solvation. Building on the identification of several low-lying equilibrium geometries (nine for R-MBA and three for R-DMBA), ensemble-averaged ORD profiles were calculated at T = 300 K by means of the independent-conformer ansatz, which enabled response properties predicted for the optimized structure of each isomer to be combined through Boltzmann-weighted population fractions derived from corresponding relative internal-energy or free-energy values, the latter of which stemmed from composite CBS-APNO and G4 analyses. Although reasonable accord between theory and experiment was realized for the isolated (vapor-phase) species, the solution-phase results were less satisfactory and tended to degrade progressively as the solvent polarity increased. These trends were attributed to solvent-mediated changes in structural parameters and energy metrics for the transition states that separate and putatively isolate the equilibrium conformations supported by the ground electronic potential-energy surface, with the resulting displacement of barrier locations and/or decrease of barrier heights compromising the underlying premise of the independent-conformer ansatz.
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Affiliation(s)
- Paul M Lemler
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Intel Corporation, Hillsboro, Oregon, USA
| | - Clayton L Craft
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- United States Air Force Research Laboratory, Rome, New York, USA
| | - Corina H Pollok
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Organische Chemie II, Ruhr-Universität Bochum, Bochum, Germany
| | - Thomas P Regan
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Patrick H Vaccaro
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
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3
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Würmel J, Simmie JM. Abstraction and addition reactions of four γ‐lactones with H‐atoms and methyl radicals. INT J CHEM KINET 2023. [DOI: 10.1002/kin.21638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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4
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Jia MX, Wang QD, Ren XF, Kang GJ. Benchmarking Composite Methods for Thermodynamic Properties of Nitro, Nitrite, and Nitrate Species Relevant to Energetic Materials. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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5
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Simmie JM. C 2H 5NO Isomers: From Acetamide to 1,2-Oxazetidine and Beyond. J Phys Chem A 2022; 126:924-939. [PMID: 35113546 PMCID: PMC8859852 DOI: 10.1021/acs.jpca.1c09984] [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] [Indexed: 11/30/2022]
Abstract
![]()
This work documents
the properties of a number of isomers of molecular
formula C2H5NO from the most stable, acetamide,
through 1,2-oxazetidine and including even higher energy species largely
of a dipolar nature. Only two of the isomers have been detected in
emissions from the interstellar medium (ISM); possible further candidates
are identified, and the likelihood of their being detectable is considered.
In general, hardly any of these compounds have been discussed in the
existing chemical literature, so this work represents an important
contribution extending the canon of chemical bonding which can contribute
to machine learning, providing a more exacting test of AI applications.
The presence in the ISM of acetamide, CH3C(O)NH2, is the subject of current debate with no clear and obvious paths
to its formation; it is shown that a 1,3-[H]-transfer from (E,Z)-ethanimidic acid, CH3C(OH)=NH, is
feasible in spite of an energy barrier of 130 kJ mol–1. It is speculated that imidic acid can itself be formed from abundant
precursors, H2O and CH3C≡N, in an acid-induced,
water addition, autocatalytic reaction on water–ice grains.
H3CC≡NH3CC≡NH+ +
H2OH3CC(O+H2)=NHH3CC(OH)=NH
+ H3O+
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Affiliation(s)
- John M Simmie
- School of Chemistry, National University of Ireland, Galway H91 TK33, Ireland
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6
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Unknown Knowns: Case studies in uncertainties in the computation of thermochemical parameters. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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7
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Pelucchi M, Arunthanayothin S, Song Y, Herbinet O, Stagni A, Carstensen HH, Faravelli T, Battin-Leclerc F. Pyrolysis and Combustion Chemistry of Pyrrole, a Reference Component for Bio-oil Surrogates: Jet-Stirred Reactor Experiments and Kinetic Modeling. ENERGY & FUELS : AN AMERICAN CHEMICAL SOCIETY JOURNAL 2021; 35:7265-7284. [PMID: 34083872 PMCID: PMC8161689 DOI: 10.1021/acs.energyfuels.0c03874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/18/2021] [Indexed: 06/12/2023]
Abstract
Fast-pyrolysis bio-oils (FPBOs) obtained from lignocellulosic biomass are gaining attention as sustainable fuels for various applications, including the transport sector and power production. A significant fraction of bio-oils is constituted by nitrogen-containing compounds (N fuels) that should be considered when developing surrogate models for FPBOs. Moreover, the content of N fuels in FPBOs is expected to strongly contribute to the production of nitrogen oxides (NO x ) directly from fuel-bound nitrogen (fuel NO x ), in addition to the thermal NO x formation pathways typical of high-temperature combustion conditions. This work investigates the pyrolysis and combustion chemistry of pyrrole (C4H5N), a candidate reference fuel component for FPBO surrogate models. Speciation measurements in an atmospheric pressure jet-stirred reactor have been performed for both pyrolysis and oxidation conditions. Pyrolysis experiments have been performed for 1% pyrrole/helium mixtures over the temperature range T = 925-1200 K. Oxidation experiments were carried out for 1% pyrrole/oxygen/helium mixtures at three equivalence ratios (φ = 0.5, 1.0, and 2.0) over the temperature range T = 700-1200 K. These new data significantly extend the number of experimental targets for kinetic model validation available at present for pyrrole combustion. After a thorough revision of previous theoretical and kinetic modeling studies, a preliminary kinetic model is developed and validated by means of comparison to new experimental data and those previously reported in the literature. The rate of production and sensitivity analyses highlight important pathways deserving further investigations for a better understanding of pyrrole and, more in general, N fuel combustion chemistry. A critical discussion on experimental challenges to be faced when dealing with pyrrole is also reported, encouraging further experimental investigation with advanced diagnostics.
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Affiliation(s)
- Matteo Pelucchi
- CRECK
Modeling Lab, Department of Chemistry Materials and Chemical Engineering, Politecnico di Milano, 20133 Milano, Italy
| | - Suphaporn Arunthanayothin
- Laboratoire
Réactions et Génie des Procédés, CNRS,
Université de Lorraine, ENSIC, 54001 Nancy Cedex, France
| | - Yu Song
- Laboratoire
Réactions et Génie des Procédés, CNRS,
Université de Lorraine, ENSIC, 54001 Nancy Cedex, France
- University
Orléans, INSA-CVL, PRISME, EA 4229, 45072 Orléans, France
| | - Olivier Herbinet
- Laboratoire
Réactions et Génie des Procédés, CNRS,
Université de Lorraine, ENSIC, 54001 Nancy Cedex, France
| | - Alessandro Stagni
- CRECK
Modeling Lab, Department of Chemistry Materials and Chemical Engineering, Politecnico di Milano, 20133 Milano, Italy
| | - Hans-Heinrich Carstensen
- Fundación
Agencia Aragonesa para la Investigación y Desarrollo (ARAID), 50018 Zaragoza, Spain
- Department
of Chemical and Environmental Engineering, Engineering and Architecture
School, University of Saragoza, 50018 Zaragoza, Spain
| | - Tiziano Faravelli
- CRECK
Modeling Lab, Department of Chemistry Materials and Chemical Engineering, Politecnico di Milano, 20133 Milano, Italy
| | - Frédérique Battin-Leclerc
- Laboratoire
Réactions et Génie des Procédés, CNRS,
Université de Lorraine, ENSIC, 54001 Nancy Cedex, France
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8
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Density functional theory for the thermodynamic gas-phase investigation of butanol biofuel and its isomers mixed with gasoline and ethanol. J Mol Model 2021; 27:80. [PMID: 33575832 DOI: 10.1007/s00894-021-04681-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/17/2021] [Indexed: 10/22/2022]
Abstract
Herein, we present the results of our study on the thermodynamic properties of the isomers of butanol (n-butanol, 2-butanol, i-butanol, and t-butanol) to evaluate their thermodynamic potential as a complementary biofuel and/or substitute for ethanol and gasoline. The Gaussian09W software was used to perform molecular geometry optimization calculations using density functional theory with the B3lyp hybrid function using the base set 6-311++g(d,p) and the compound methods G3, G4, and CBS-QB3. Calculations of the fundamental frequency of the molecules were performed to obtain the molecular vibration modes for the respective frequencies. These calculations provided thermodynamic parameters such as the entropy, enthalpy, and specific molar heat at constant pressure, all as a function of the temperature. The parameter values obtained by each method were compared to the experimental values available in the literature. The results showed good accuracy, especially those obtained at the B3lyp/6-311++g(d,p) level for n-butanol. The error between the theoretical and experimental values for the combustion enthalpy of n-butanol was less than 4% at 298.15 K; due to the good prediction of its thermodynamic properties, we used n-butanol as a model for the prediction of other thermodynamic properties. We started a molecular docking study of four ligands, namely, n-butanol, ethanol, propanol, heptane, isooctane, and methanol interacting with butanol isomers. The highest values of affinity energy found were for N-butanol. The possible formation of hydrogen bonds, associations by means of London forces, hydrogen, and alkyl interactions were analyzed. n-Butanol was added to ethanol-gasoline mixtures in the temperature range of 298.15 to 600 K and the results suggest that n-butanol has a higher calorific value than gasoline-ethanol mixtures in G30E, G40E, G50E, G60E, G70E, G80E, G90E, and E100 blends. As such, n-butanol releases greater amounts of heat during combustion and is thus a viable alternative to biofuels.
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Pappijn CA, Vermeire FH, Van de Vijver R, Reyniers M, Marin GB, Van Geem KM. Bond additivity corrections for CBS‐QB3 calculated standard enthalpies of formation of H, C, O, N, and S containing species. INT J CHEM KINET 2020. [DOI: 10.1002/kin.21447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Cato A.R. Pappijn
- Laboratory for Chemical Technology Ghent University Zwijnaarde Belgium
| | | | | | | | - Guy B. Marin
- Laboratory for Chemical Technology Ghent University Zwijnaarde Belgium
| | - Kevin M. Van Geem
- Laboratory for Chemical Technology Ghent University Zwijnaarde Belgium
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10
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11
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12
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Moharreri E, Pardakhti M, Srivastava R, Suib SL. Energy-Geometry Dependency of Molecular Structures: A Multistep Machine Learning Approach. ACS COMBINATORIAL SCIENCE 2019; 21:614-621. [PMID: 31390176 DOI: 10.1021/acscombsci.9b00028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There is growing interest in estimating quantum observables while circumventing expensive computational overhead for facile in silico materials screening. Machine learning (ML) methods are implemented to perform such calculations in shorter times. Here, we introduce a multistep method based on machine learning algorithms to estimate total energy on the basis of spatial coordinates and charges for various chemical structures, including organic molecules, inorganic molecules, and ions. This method quickly calculates total energy with 0.76 au in root-mean-square error (RMSE) and 1.5% in mean absolute percent error (MAPE) when tested on a database of optimized and unoptimized structures. Using similar molecular representations, experimental thermochemical properties were estimated, with MAPE as low as 6% and RMSE of 8 cal/mol·K for heat capacity in a 10-fold cross-validation.
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Affiliation(s)
- Ehsan Moharreri
- Institute of Material Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Maryam Pardakhti
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Ranjan Srivastava
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Steven L. Suib
- Institute of Material Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
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13
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Krdzavac N, Mosbach S, Nurkowski D, Buerger P, Akroyd J, Martin J, Menon A, Kraft M. An Ontology and Semantic Web Service for Quantum Chemistry Calculations. J Chem Inf Model 2019; 59:3154-3165. [DOI: 10.1021/acs.jcim.9b00227] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nenad Krdzavac
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, West Site, Cambridge, Cambridgeshire CB3 0AS, U.K
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, Singapore 138602
| | - Sebastian Mosbach
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, West Site, Cambridge, Cambridgeshire CB3 0AS, U.K
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, Singapore 138602
- CMCL Innovations, Sheraton House, Castle Park, Castle Street, Cambridge, Cambridgeshire CB3 0AX, U.K
| | - Daniel Nurkowski
- CMCL Innovations, Sheraton House, Castle Park, Castle Street, Cambridge, Cambridgeshire CB3 0AX, U.K
| | - Philipp Buerger
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, West Site, Cambridge, Cambridgeshire CB3 0AS, U.K
| | - Jethro Akroyd
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, West Site, Cambridge, Cambridgeshire CB3 0AS, U.K
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, Singapore 138602
- CMCL Innovations, Sheraton House, Castle Park, Castle Street, Cambridge, Cambridgeshire CB3 0AX, U.K
| | - Jacob Martin
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, West Site, Cambridge, Cambridgeshire CB3 0AS, U.K
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, Singapore 138602
| | - Angiras Menon
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, West Site, Cambridge, Cambridgeshire CB3 0AS, U.K
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, Singapore 138602
| | - Markus Kraft
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, West Site, Cambridge, Cambridgeshire CB3 0AS, U.K
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, Singapore 138602
- CMCL Innovations, Sheraton House, Castle Park, Castle Street, Cambridge, Cambridgeshire CB3 0AX, U.K
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459
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14
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Nguyen HT, Mai TVT, Huynh LK. mHDFS-HoF: A generalized multilevel homodesmotic fragment-separation reaction based program for heat-of-formation calculation for acyclic hydrocarbons. J Comput Chem 2019; 40:1360-1373. [PMID: 30786057 DOI: 10.1002/jcc.25790] [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: 08/31/2018] [Revised: 11/06/2018] [Accepted: 11/23/2018] [Indexed: 11/06/2022]
Abstract
Based on our modified classification of elemental species, a framework for automatic generation of multilevel Homodesmotic fragment-separation (mHDFS) reactions for chemical species was proposed. Combined the mHDFS framework with a database of heat of formation (HoF) and the calculated electronic structure data for the elemental mHD species, the mHDFS-HoF program was constructed in C/C++ language to calculate heat of formation for a species of interest on-the-fly. Using the electronic structure data calculated at CBS-QB3 level of theory for the elemental mHD species, applications and robustness of the code were discussed with several acyclic hydrocarbon systems including neutral and radical species. On-going work and extension to other systems were also discussed. The program and the supporting files can be freely downloaded at https://sites.google.com/view/mhdfs/. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Hieu Thanh Nguyen
- Molecular Science and Nano-Materials Laboratory, Institute for Computational Science and Technology, Ho Chi Minh city, Vietnam
| | - Tam Van-Thanh Mai
- Molecular Science and Nano-Materials Laboratory, Institute for Computational Science and Technology, Ho Chi Minh city, Vietnam.,Department of Theoretical and Physical Chemistry, University of Science, VNU-HCM, Ho Chi Minh city, Vietnam
| | - Lam Kim Huynh
- Chemical Engineering Department, International University, VNU-HCM, Vietnam
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15
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Grinberg Dana A, Moore KB, Jasper AW, Green WH. Large Intermediates in Hydrazine Decomposition: A Theoretical Study of the N3H5 and N4H6 Potential Energy Surfaces. J Phys Chem A 2019; 123:4679-4692. [DOI: 10.1021/acs.jpca.9b02217] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alon Grinberg Dana
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kevin B. Moore
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Ahren W. Jasper
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - William H. Green
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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16
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Feller D, Bross DH, Ruscic B. Enthalpy of Formation of C2H2O4 (Oxalic Acid) from High-Level Calculations and the Active Thermochemical Tables Approach. J Phys Chem A 2019; 123:3481-3496. [DOI: 10.1021/acs.jpca.8b12329] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David Feller
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, United States
| | - David H. Bross
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Branko Ruscic
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
- Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois 60637, United States
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17
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Mai TVT, Nguyen HT, Huynh LK. Ab initio dynamics of hydrogen abstraction from N2H4 by OH radicals: an RRKM-based master equation study. Phys Chem Chem Phys 2019; 21:23733-23741. [DOI: 10.1039/c9cp04585f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The detailed kinetic mechanism of the N2H4 + OH reaction is comprehensively reported for a wide condition range of conditions (i.e., 200–3000 K & 1–7600 Torr) using the CCSD(T)/CBS//M06-2X/6-311++G(3df,2p) level and the RRKM-based master equation rate model.
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Affiliation(s)
- Tam V.-T. Mai
- Molecular Science and Nano-Materials Lab
- Institute for Computational Science and Technology
- Ho Chi Minh City
- Vietnam
- University of Science
| | - Hieu T. Nguyen
- Molecular Science and Nano-Materials Lab
- Institute for Computational Science and Technology
- Ho Chi Minh City
- Vietnam
| | - Lam K. Huynh
- International University
- Vietnam National University – HCMC
- Ho Chi Minh City
- Vietnam
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18
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Bodi A, Hemberger P. Low-Energy Photoelectron Spectrum and Dissociative Photoionization of the Smallest Amides: Formamide and Acetamide. J Phys Chem A 2018; 123:272-283. [DOI: 10.1021/acs.jpca.8b10373] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andras Bodi
- Laboratory for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Patrick Hemberger
- Laboratory for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
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19
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Estimation of heats of formation for nitrogen-rich cations using G3, G4, and G4 (MP2) theoretical methods. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2300-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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20
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Vereecken L, Aumont B, Barnes I, Bozzelli J, Goldman M, Green W, Madronich S, Mcgillen M, Mellouki A, Orlando J, Picquet-Varrault B, Rickard A, Stockwell W, Wallington T, Carter W. Perspective on Mechanism Development and Structure-Activity Relationships for Gas-Phase Atmospheric Chemistry. INT J CHEM KINET 2018. [DOI: 10.1002/kin.21172] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- L. Vereecken
- Institute for Energy and Climate Research: IEK-8 Troposphere; Forschungszentrum Jülich GmbH; Jülich Germany
| | - B. Aumont
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA); UMR 7583 CNRS; Universités Paris-Est Créteil et Paris Diderot; Institut Pierre-Simon Laplace; Créteil Cedex France
| | - I. Barnes
- School of Mathematics and Natural Sciences; Physical & Theoretical Chemistry; University of Wuppertal; Wuppertal Germany
| | - J.W. Bozzelli
- Department of Chemistry and Environmental Science; New Jersey Institute of Technology; Newark NJ 07102
| | - M.J. Goldman
- Department of Chemical Engineering; Massachusetts Institute of Technology; Cambridge MA 02139
| | - W.H. Green
- Department of Chemical Engineering; Massachusetts Institute of Technology; Cambridge MA 02139
| | - S. Madronich
- Atmospheric Chemistry Observations and Modeling Laboratory; National Center for Atmospheric Research; Boulder CO 80307
| | - M.R. Mcgillen
- School of Chemistry; University of Bristol; Cantock's Close; Bristol BS8 1TS UK
| | - A. Mellouki
- Institut de Combustion; Aérothermique, Réactivité et Environnement (ICARE); CNRS/OSUC; 45071 Orléans Cedex 2 France
| | - J.J. Orlando
- Atmospheric Chemistry Observations and Modeling Laboratory; National Center for Atmospheric Research; Boulder CO 80307
| | - B. Picquet-Varrault
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA); UMR 7583 CNRS; Universités Paris-Est Créteil et Paris Diderot; Institut Pierre-Simon Laplace; Créteil Cedex France
| | - A.R. Rickard
- Wolfson Atmospheric Chemistry Laboratories; Department of Chemistry; University of York; York YO10 5DD UK
- National Centre for Atmospheric Science; University of York; York YO10 5DD UK
| | - W.R. Stockwell
- Department of Physics; University of Texas at El Paso; El Paso TX 79968 USA
| | - T.J. Wallington
- Research & Advanced Engineering; Ford Motor Company; Dearborn MI 48121-2053
| | - W.P.L. Carter
- College of Engineering; Center for Environmental Research and Technology (CE-CERT); University of California; Riverside CA 92521
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21
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Ghahremanpour MM, van Maaren PJ, van der Spoel D. The Alexandria library, a quantum-chemical database of molecular properties for force field development. Sci Data 2018; 5:180062. [PMID: 29633987 PMCID: PMC5892371 DOI: 10.1038/sdata.2018.62] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/19/2018] [Indexed: 12/03/2022] Open
Abstract
Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.
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Affiliation(s)
- Mohammad M. Ghahremanpour
- Uppsala Centre for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
| | - Paul J. van Maaren
- Uppsala Centre for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
| | - David van der Spoel
- Uppsala Centre for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
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22
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Gamez-Garcia VG, Galano A. Systematic Search for Chemical Reactions in Gas Phase Contributing to Methanol Formation in Interstellar Space. J Phys Chem A 2017; 121:7393-7400. [PMID: 28885025 DOI: 10.1021/acs.jpca.7b05797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A massive search for chemical routes leading to methanol formation in gas phase has been conducted using computational chemistry, at the CBS-QB3 level of theory. The calculations were performed at five different temperatures (100, 80, 50, 20, and 10 K) and at three pressures (0.1, 0.01, and 0.001 atm) for each temperature. The search was focused on identifying reactions with the necessary features to be viable in the interstellar medium (ISM). A searching strategy was applied to that purpose, which allowed to reduce an initial set of 678 possible reactions to a subset of 11 chemical routes that are recommended, for the first time, as potential candidates for contributing to methanol formation in the gas phase of the ISM. They are all barrier-less, and thus they are expected to take place at collision rates. Hopefully, including these reactions in the currently available models, for the gas-phase methanol formation in the ISM, would help improving the predicted fractional abundance of this molecule in dark clouds. Further investigations, especially those dealing with grain chemistry and electronic excited states, would be crucial to get a complete picture of the methanol formation in the ISM.
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Affiliation(s)
- Victoria G Gamez-Garcia
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa , San Rafael Atlixco 186, Col. Vicentina. Iztapalapa, C. P. 09340, México D. F. México
| | - Annia Galano
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa , San Rafael Atlixco 186, Col. Vicentina. Iztapalapa, C. P. 09340, México D. F. México
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23
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Klippenstein SJ, Harding LB, Ruscic B. Ab Initio Computations and Active Thermochemical Tables Hand in Hand: Heats of Formation of Core Combustion Species. J Phys Chem A 2017; 121:6580-6602. [DOI: 10.1021/acs.jpca.7b05945] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stephen J. Klippenstein
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Lawrence B. Harding
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Branko Ruscic
- Chemical Sciences and Engineering
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
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24
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Feller D, Bross DH, Ruscic B. Enthalpy of Formation of N2H4 (Hydrazine) Revisited. J Phys Chem A 2017; 121:6187-6198. [DOI: 10.1021/acs.jpca.7b06017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David Feller
- Department
of Chemistry Washington State University, Pullman, Washington 99164-4630, United States
| | - David H. Bross
- Chemical
Sciences and Engineering Division Argonne National Laboratory Argonne, Illinois 60439, United States
| | - Branko Ruscic
- Chemical
Sciences and Engineering Division Argonne National Laboratory Argonne, Illinois 60439, United States
- Computation
Institute, The University of Chicago, Chicago, Illinois 60637, United States
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25
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Neto AFG, Huda MN, Marques FC, Borges RS, Neto AMJC. Thermodynamic DFT analysis of natural gas. J Mol Model 2017; 23:224. [PMID: 28710571 DOI: 10.1007/s00894-017-3401-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 06/26/2017] [Indexed: 11/29/2022]
Abstract
Density functional theory was performed for thermodynamic predictions on natural gas, whose B3LYP/6-311++G(d,p), B3LYP/6-31+G(d), CBS-QB3, G3, and G4 methods were applied. Additionally, we carried out thermodynamic predictions using G3/G4 averaged. The calculations were performed for each major component of seven kinds of natural gas and to their respective air + natural gas mixtures at a thermal equilibrium between room temperature and the initial temperature of a combustion chamber during the injection stage. The following thermodynamic properties were obtained: internal energy, enthalpy, Gibbs free energy and entropy, which enabled us to investigate the thermal resistance of fuels. Also, we estimated an important parameter, namely, the specific heat ratio of each natural gas; this allowed us to compare the results with the empirical functions of these parameters, where the B3LYP/6-311++G(d,p) and G3/G4 methods showed better agreements. In addition, relevant information on the thermal and mechanic resistance of natural gases were investigated, as well as the standard thermodynamic properties for the combustion of natural gas. Thus, we show that density functional theory can be useful for predicting the thermodynamic properties of natural gas, enabling the production of more efficient compositions for the investigated fuels. Graphical abstract Investigation of the thermodynamic properties of natural gas through the canonical ensemble model and the density functional theory.
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Affiliation(s)
- Abel F G Neto
- Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C.P. 479, Belém, PA, 66075-110, Brazil.
- Post-graduation Program of Natural Resources Engineering of Amazon - PRODERNA; ITEC, State University of Pará, 2626, Belém, PA, 66.050-540, Brazil.
| | - Muhammad N Huda
- Department of Physics, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Francisco C Marques
- Gleb Wataghin Institute of Physics, State University of Campinas, São Paulo, C.P. 13083-859, Brazil
| | - Rosivaldo S Borges
- Postgraduate Program in Pharmacy, ICB, Federal University of Pará, C.P. 479, Belém, PA, 66075-900, Brazil
| | - Antonio M J C Neto
- Laboratory of Preparation and Computation of Nanomaterials (LPCN), Federal University of Pará, C.P. 479, Belém, PA, 66075-110, Brazil
- Post-graduation Program of Natural Resources Engineering of Amazon - PRODERNA; ITEC, State University of Pará, 2626, Belém, PA, 66.050-540, Brazil
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26
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Minenkov Y, Wang H, Wang Z, Sarathy SM, Cavallo L. Heats of Formation of Medium-Sized Organic Compounds from Contemporary Electronic Structure Methods. J Chem Theory Comput 2017. [DOI: 10.1021/acs.jctc.7b00335] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yury Minenkov
- King Abdullah University of Science and Technology (KAUST), Physical Science and Engineering Division (PSE), KAUST
Catalysis Center (KCC), 23955-6900 Thuwal, Saudi Arabia
| | - Heng Wang
- King Abdullah University of Science and Technology (KAUST), Physical Science and Engineering Division (PSE), Clean
Combustion Research Center (CCRC), 23955-6900 Thuwal, Saudi Arabia
| | - Zhandong Wang
- King Abdullah University of Science and Technology (KAUST), Physical Science and Engineering Division (PSE), Clean
Combustion Research Center (CCRC), 23955-6900 Thuwal, Saudi Arabia
| | - S. Mani Sarathy
- King Abdullah University of Science and Technology (KAUST), Physical Science and Engineering Division (PSE), Clean
Combustion Research Center (CCRC), 23955-6900 Thuwal, Saudi Arabia
| | - 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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Dorofeeva OV, Ryzhova ON, Suchkova TA. Enthalpies of Formation of Hydrazine and Its Derivatives. J Phys Chem A 2017. [DOI: 10.1021/acs.jpca.7b04914] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Olga V. Dorofeeva
- Faculty of Chemistry, Lomonosov Moscow State University, 1-3 Leninskie Gory, Moscow 119991, Russia
| | - Oxana N. Ryzhova
- Faculty of Chemistry, Lomonosov Moscow State University, 1-3 Leninskie Gory, Moscow 119991, Russia
| | - Taisiya A. Suchkova
- Faculty of Chemistry, Lomonosov Moscow State University, 1-3 Leninskie Gory, Moscow 119991, Russia
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28
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Paulechka E, Kazakov A. Efficient DLPNO–CCSD(T)-Based Estimation of Formation Enthalpies for C-, H-, O-, and N-Containing Closed-Shell Compounds Validated Against Critically Evaluated Experimental Data. J Phys Chem A 2017; 121:4379-4387. [PMID: 28514153 PMCID: PMC10402538 DOI: 10.1021/acs.jpca.7b03195] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
An accurate and cost-efficient methodology for the estimation of the enthalpies of formation for closed-shell compounds composed of C, H, O, and N atoms is presented and validated against critically evaluated experimental data. The computational efficiency is achieved through the use of the resolution-of-identity (RI) and domain-based local pair-natural orbital coupled cluster (DLPNO-CCSD(T)) approximations, which results in a drastic reduction in both the computational cost and the number of necessary steps for a composite quantum chemical method. The expanded uncertainty for the proposed methodology evaluated using a data set of 45 thoroughly vetted experimental values for molecules containing up to 12 heavy atoms is about 3 kJ·mol-1, competitive with those of typical calorimetric measurements. For the compounds within the stated scope, the methodology is shown to be superior to a representative, more general, and widely used composite quantum chemical method, G4.
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Affiliation(s)
- Eugene Paulechka
- Thermodynamics
Research Center,
Applied Chemicals and Materials Division, National Institute of Standards and Technology, 325 Broadway, Boulder, Colorado 80305-3337, United States
| | - Andrei Kazakov
- Thermodynamics
Research Center,
Applied Chemicals and Materials Division, National Institute of Standards and Technology, 325 Broadway, Boulder, Colorado 80305-3337, United States
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29
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Dorofeeva OV, Osina EL. Performance of DFT, MP2, and composite ab initio methods for the prediction of enthalpies of formations of CHON compounds using isodesmic reactions. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.03.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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30
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Emel’yanenko VN, Zaitseva KV, Nagrimanov RN, Solomonov BN, Verevkin SP. Benchmark Thermodynamic Properties of Methyl- and Methoxybenzamides: Comprehensive Experimental and Theoretical Study. J Phys Chem A 2016; 120:8419-8429. [DOI: 10.1021/acs.jpca.6b08027] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vladimir N. Emel’yanenko
- Department
of Physical Chemistry and Department “Science and Technology
of Life, Light and Matter”, University of Rostock, Dr-Lorenz-Weg
1, D-18059, Rostock, Germany
| | - Ksenia V. Zaitseva
- Department
of Physical Chemistry and Department “Science and Technology
of Life, Light and Matter”, University of Rostock, Dr-Lorenz-Weg
1, D-18059, Rostock, Germany
| | - Ruslan N. Nagrimanov
- Department
of Physical Chemistry, Kazan Federal University, Kremlevskaya str. 18, 420008 Kazan, Russia
| | - Boris N. Solomonov
- Department
of Physical Chemistry, Kazan Federal University, Kremlevskaya str. 18, 420008 Kazan, Russia
| | - Sergey P. Verevkin
- Department
of Physical Chemistry and Department “Science and Technology
of Life, Light and Matter”, University of Rostock, Dr-Lorenz-Weg
1, D-18059, Rostock, Germany
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31
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Bugler J, Somers KP, Simmie JM, Güthe F, Curran HJ. Modeling Nitrogen Species as Pollutants: Thermochemical Influences. J Phys Chem A 2016; 120:7192-7. [PMID: 27547977 DOI: 10.1021/acs.jpca.6b05723] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To simulate emissions of nitrogen-containing compounds in practical combustion environments, it is necessary to have accurate values for their thermochemical parameters, as well as accurate kinetic values to describe the rates of their formation and decomposition. Significant disparity is observed in the literature for the former, and we therefore present herein high-accuracy ab initio gas-phase thermochemistry for 60 nitrogenous compounds, many of which are important in the formation and consumption chemistry of NOx species. Several quantum-chemical composite methods (CBS-APNO, G3, and G4) were utilized to derive enthalpies of formation via the atomization method. Entropies and heat capacities were calculated from traditional statistical thermodynamics, with oscillators treated as anharmonic based on ro-vibrational property analyses carried out at the B3LYP/cc-pVTZ level of theory. The use of quantum chemical methods, along with the treatments of anharmonicities and hindered rotors, ensures accurate enthalpy of formation, entropy, and heat capacity values across the temperature range 298.15-3000 K. The implications of these results for atmospheric and combustion modeling are discussed.
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Affiliation(s)
- John Bugler
- Combustion Chemistry Centre, National University of Ireland , Galway H91 TK33, Ireland
| | - Kieran P Somers
- Combustion Chemistry Centre, National University of Ireland , Galway H91 TK33, Ireland
| | - John M Simmie
- Combustion Chemistry Centre, National University of Ireland , Galway H91 TK33, Ireland
| | - Felix Güthe
- GE Power - GSTRB , Brown Boveri Strasse 7, 5401 Baden, Switzerland
| | - Henry J Curran
- Combustion Chemistry Centre, National University of Ireland , Galway H91 TK33, Ireland
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32
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Simmie JM, Sheahan JN. Validation of a Database of Formation Enthalpies and of Mid-Level Model Chemistries. J Phys Chem A 2016; 120:7370-84. [DOI: 10.1021/acs.jpca.6b07503] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. M. Simmie
- Combustion Chemistry Centre & School of Chemistry, National University of Ireland, Galway H91 TK33, Ireland
| | - J. N. Sheahan
- School of Mathematics & Statistics, National University of Ireland, Galway H91 TK33, Ireland
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