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Koller TJ, Endraß SMJ, Rösch M, Witthaut K, Klapötke TM, Schnick W. On Tautomerism and Amphoterism: An In-Depth Structural and Physicochemical Characterization of Ammeline and Some of Its Salts. Angew Chem Int Ed Engl 2024; 63:e202404927. [PMID: 38746974 DOI: 10.1002/anie.202404927] [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: 03/12/2024] [Indexed: 06/28/2024]
Abstract
Ammeline is a simple, readily available, molecular compound, which has been known for nearly 200 years. Despite that, no proper structural characterization of ammeline has been conducted so far. For this reason, the prevalent tautomeric form of ammeline in the solid remained unknown to this date. In the course of this study, its crystal structure was finally established by single-crystal X-ray diffraction. In this structure, ammeline is exclusively found as its 4,6-diamino-1,3,5-triazin-2(1H)-one tautomer and adopts layered structure with an exceptionally high hydrogen bond density. Ammeline shows an interesting amphoteric behavior. Therefore, the synthesis and structural characterization of some of its salts were carried out to investigate the influence of the protonation degree on its molecular structure. In particular, the crystal structure of silver ammelinate monohydrate was solved as the first reported structure containing deprotonated ammeline. Moreover, the crystal structures of three different modifications of ammelinium perchlorate were elucidated and the transformation conditions between them were studied. Lastly, the crystal structure of ammelinediium diperchlorate monohydrate, containing unprecedented doubly protonated ammeline, was determined. The products' thermal behavior was studied by differential thermal analysis and thermogravimetric analysis. The perchlorate salts were additionally examined for their potential as insensitive high-energy-density materials.
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Affiliation(s)
- Thaddäus J Koller
- Department of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, 81377, Munich, Germany
| | - Simon M J Endraß
- Department of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, 81377, Munich, Germany
| | - Markus Rösch
- Department of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, 81377, Munich, Germany
| | - Kristian Witthaut
- Department of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, 81377, Munich, Germany
| | - Thomas M Klapötke
- Department of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, 81377, Munich, Germany
| | - Wolfgang Schnick
- Department of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, 81377, Munich, Germany
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2
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Kandpal SC, Otukile KP, Jindal S, Senthil S, Matthews C, Chakraborty S, Moskaleva LV, Ramakrishnan R. Stereo-electronic factors influencing the stability of hydroperoxyalkyl radicals: transferability of chemical trends across hydrocarbons and ab initio methods. Phys Chem Chem Phys 2023; 25:27302-27320. [PMID: 37791466 DOI: 10.1039/d3cp03598k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The hydroperoxyalkyl radicals (˙QOOH) are known to play a significant role in combustion and tropospheric processes, yet their direct spectroscopic detection remains challenging. In this study, we investigate molecular stereo-electronic effects influencing the kinetic and thermodynamic stability of a ˙QOOH along its formation path from the precursor, alkylperoxyl radical (ROO˙), and the depletion path resulting in the formation of cyclic ether + ˙OH. We focus on reactive intermediates encountered in the oxidation of acyclic hydrocarbon radicals: ethyl, isopropyl, isobutyl, tert-butyl, neopentyl, and their alicyclic counterparts: cyclohexyl, cyclohexenyl, and cyclohexadienyl. We report reaction energies and barriers calculated with the highly accurate method Weizmann-1 (W1) for the channels: ROO˙ ⇌ ˙QOOH, ROO˙ ⇌ alkene + ˙OOH, ˙QOOH ⇌ alkene + ˙OOH, and ˙QOOH ⇌ cyclic ether + ˙OH. Using W1 results as a reference, we have systematically benchmarked the accuracy of popular density functional theory (DFT), composite thermochemistry methods, and an explicitly correlated coupled-cluster method. We ascertain inductive, resonance, and steric effects on the overall stability of ˙QOOH and computationally investigate the possibility of forming more stable species. With new reactions as test cases, we probe the capacity of various ab initio methods to yield quantitative insights on the elementary steps of combustion.
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Affiliation(s)
| | - Kgalaletso P Otukile
- Department of Chemistry, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa.
| | - Shweta Jindal
- Tata Institute of Fundamental Research, Hyderabad 500046, India.
| | - Salini Senthil
- Tata Institute of Fundamental Research, Hyderabad 500046, India.
| | - Cameron Matthews
- Department of Chemistry, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa.
| | | | - Lyudmila V Moskaleva
- Department of Chemistry, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa.
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3
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Landeros-Rivera B, Ramírez-Palma D, Cortés-Guzmán F, Dominiak PM, Contreras-García J. How do density functionals affect the Hirshfeld atom refinement? Phys Chem Chem Phys 2023; 25:12702-12711. [PMID: 36644944 DOI: 10.1039/d2cp04098k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In this work, the effect of mixing different amounts of Hartree-Fock (HF) exchange with hybrid density functionals applied to the Hirshfeld atom refinement (HAR) of urea and oxalic acid dihydrate is explored. Together, the influence of using different basis sets, methods (including MP2 and HF) and cluster sizes (to model bulk effects) is studied. The results show that changing the amount of HF exchange, no matter the level of theory, has an impact almost exclusively on the H atom refinement parameters. Contrary to pure quantum mechanical calculations where good geometries are obtained with intermediate HF exchange mixtures, in the HAR the best match with neutron diffraction reference values is not necessarily found for these admixtures. While the non-hydrogen covalent bond lengths are insensitive to the combination of method or basis set employed, the X-H bond lengths always increase proportionally to the HF exchange for the analysed systems. This outcome is opposite to what is normally observed from geometry optimisations, i.e., shorter bonds are obtained with greater HF exchange. Additionally, the thermal ellipsoids tend to shrink with larger HF exchange, especially for the H atoms involved in strong hydrogen bonding. Thus, it may be the case that the development of density functionals or basis sets suitable for quantum crystallography should take a different path than those fitted for quantum chemistry calculations.
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Affiliation(s)
| | - David Ramírez-Palma
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV), Avenida IPN 2508, Col. San Pedro Zacatenco, Ciudad de México, 07360, Mexico
| | - Fernando Cortés-Guzmán
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Ciudad de México, 04510, Mexico
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Poland
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4
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Robinson HT, Haakansson CT, Corkish TR, Watson PD, McKinley AJ, Wild DA. Hydrogen Bonding versus Halogen Bonding: Spectroscopic Investigation of Gas-Phase Complexes Involving Bromide and Chloromethanes. Chemphyschem 2022; 24:e202200733. [PMID: 36504309 DOI: 10.1002/cphc.202200733] [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: 10/05/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/14/2022]
Abstract
Hydrogen bonding and halogen bonding are important non-covalent interactions that are known to occur in large molecular systems, such as in proteins and crystal structures. Although these interactions are important on a large scale, studying hydrogen and halogen bonding in small, gas-phase chemical species allows for the binding strengths to be determined and compared at a fundamental level. In this study, anion photoelectron spectra are presented for the gas-phase complexes involving bromide and the four chloromethanes, CH3 Cl, CH2 Cl2 , CHCl3 , and CCl4 . The stabilisation energy and electron binding energy associated with each complex are determined experimentally, and the spectra are rationalised by high-level CCSD(T) calculations to determine the non-covalent interactions binding the complexes. These calculations involve nucleophilic bromide and electrophilic bromine interactions with chloromethanes, where the binding motifs, dissociation energies and vertical detachment energies are compared in terms of hydrogen bonding and halogen bonding.
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Affiliation(s)
- Hayden T Robinson
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009
| | - Christian T Haakansson
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009
| | - Timothy R Corkish
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009
| | - Peter D Watson
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009.,Department of Chemistry, University of Oxford, South Parks Road, Oxford, United Kingdom, OX1 3QZ
| | - Allan J McKinley
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009
| | - Duncan A Wild
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009.,School of Science, Edith Cowan University, Joondalup, Western Australia, 6027
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5
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Robinson HT, Corkish TR, Haakansson CT, Watson PD, McKinley AJ, Wild DA. Spectroscopic Study of the Br - +CH 3 I→I - +CH 3 Br S N 2 Reaction. Chemphyschem 2022; 23:e202200278. [PMID: 35708114 PMCID: PMC9804238 DOI: 10.1002/cphc.202200278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/06/2022] [Indexed: 01/05/2023]
Abstract
Mass spectrometry and anion photoelectron spectroscopy have been used to study the gas-phaseS N 2 ${{{\rm S}}_{{\rm N}}2}$ reaction involvingB r - ${{{\rm B}{\rm r}}^{-}}$ andC H 3 I ${{{\rm C}{\rm H}}_{3}{\rm I}}$ . The anion photoelectron spectra associated with the reaction intermediates of thisS N 2 ${{{\rm S}}_{{\rm N}}2}$ reaction are presented. High-level CCSD(T) calculations have been utilised to investigate the reaction intermediates that may form as a result of theS N 2 ${{{\rm S}}_{{\rm N}}2}$ reaction along various different reaction pathways, including back-side attack and front-side attack. In addition, simulated vertical detachment energies of each reaction intermediate have been calculated to rationalise the photoelectron spectra.
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Affiliation(s)
- Hayden T. Robinson
- School of Molecular SciencesThe University of Western AustraliaCrawleyWestern Australia6009
| | - Timothy R. Corkish
- School of Molecular SciencesThe University of Western AustraliaCrawleyWestern Australia6009
| | | | - Peter D. Watson
- School of Molecular SciencesThe University of Western AustraliaCrawleyWestern Australia6009
- Department of ChemistryUniversity of OxfordSouth Parks RoadOxfordUnited KingdomOX1 3QZ
| | - Allan J. McKinley
- School of Molecular SciencesThe University of Western AustraliaCrawleyWestern Australia6009
| | - Duncan A. Wild
- School of Molecular SciencesThe University of Western AustraliaCrawleyWestern Australia6009
- School of ScienceEdith Cowan UniversityJoondalupWestern Australia6027
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6
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Otsuka M, Miyaguchi H. Theoretical evaluation of the hydrolysis of conventional nerve agents and novichok agents. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.139116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Sandler I, Sharma S, Chan B, Ho J. Accurate Quantum Chemical Prediction of Gas-Phase Anion Binding Affinities and Their Structure-Binding Relationships. J Phys Chem A 2021; 125:9838-9851. [PMID: 34739245 DOI: 10.1021/acs.jpca.1c06648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper systematically examines the performance of contemporary wavefunction and density functional theory methods to identify robust and cost-efficient methods for predicting gas-phase anion binding energies. This includes the local coupled cluster LNO-CCSD(T) and DLPNO-CCSD(T), as well as double-hybrid DSD-PBEP86-D3(BJ) and various hybrid functionals M06-2X, B3LYP-D3(BJ), ωB97M-V, and ωB97X-V. The focus is on dual-hydrogen-bonding anion receptors that are commonly found in supramolecular chemistry and organocatalysis, namely, (thio)ureas, deltamides, (thio)squaramides, and croconamides as well as the yet-to-be-explored rhodizonamides. Of the methods examined, M06-2X emerged as the overall best performing method as the other functionals including DSD-PBEP86-D3(BJ) and the local coupled cluster DLPNO-CCSD(T) method displayed systematic errors that increase with the degree of carbonylation of the receptors. Hybrid ONIOM models that employed semiempirical methods (PM7, GFN1-xTB, and GFN2-xTB) and "threefold"-corrected small-basis set potentials (HF-3c, B97-3c, and PBEh-3c) were explored, and the best models resulted in 50- to 500-fold reduction in CPU time compared to W1-local. These calculations provide important insight into the structure-binding relationships where there is a direct correlation between Brønsted acidity and anion binding affinity, though the strength of the correlation also depends on other factors such as hydrogen-bonding geometry and the geometrical distortion that the receptor needs to undergo to bind the anion.
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Affiliation(s)
- Isolde Sandler
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Shaleen Sharma
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Bun Chan
- Graduate School of Engineering, Nagasaki University, Bukyo-Machi 1-14, Nagasaki 852-8521, Japan
| | - Junming Ho
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
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8
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Alkorta I, Elguero J. The SN2 reaction and its relationship with the Walden inversion, the Finkelstein and Menshutkin reactions together with theoretical calculations for the Finkelstein reaction. Struct Chem 2021. [DOI: 10.1007/s11224-021-01805-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractThis communication gives an overview of the relationships between four reactions that although related were not always perceived as such: SN2, Walden, Finkelstein, and Menshutkin. Binary interactions (SN2 & Walden, SN2 & Menshutkin, SN2 & Finkelstein, Walden & Menshutkin, Walden & Finkelstein, Menshutkin & Finkelstein) were reported. Carbon, silicon, nitrogen, and phosphorus as central atoms and fluorides, chlorides, bromides, and iodides as lateral atoms were considered. Theoretical calculations provide Gibbs free energies that were analyzed with linear models to obtain the halide contributions. The M06-2x DFT computational method and the 6-311++G(d,p) basis set have been used for all atoms except for iodine where the effective core potential def2-TZVP basis set was used. Concerning the central atom pairs, carbon/silicon vs. nitrogen/phosphorus, we reported here for the first time that the effect of valence expansion was known for Si but not for P. Concerning the lateral halogen atoms, some empirical models including the interaction between F and I as entering and leaving groups explain the Gibbs free energies.
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9
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Jackson R, Zhang W, Pearson J. TSNet: predicting transition state structures with tensor field networks and transfer learning. Chem Sci 2021; 12:10022-10040. [PMID: 34377396 PMCID: PMC8317659 DOI: 10.1039/d1sc01206a] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/21/2021] [Indexed: 12/14/2022] Open
Abstract
Transition states are among the most important molecular structures in chemistry, critical to a variety of fields such as reaction kinetics, catalyst design, and the study of protein function. However, transition states are very unstable, typically only existing on the order of femtoseconds. The transient nature of these structures makes them incredibly difficult to study, thus chemists often turn to simulation. Unfortunately, computer simulation of transition states is also challenging, as they are first-order saddle points on highly dimensional mathematical surfaces. Locating these points is resource intensive and unreliable, resulting in methods which can take very long to converge. Machine learning, a relatively novel class of algorithm, has led to radical changes in several fields of computation, including computer vision and natural language processing due to its aptitude for highly accurate function approximation. While machine learning has been widely adopted throughout computational chemistry as a lightweight alternative to costly quantum mechanical calculations, little research has been pursued which utilizes machine learning for transition state structure optimization. In this paper TSNet is presented, a new end-to-end Siamese message-passing neural network based on tensor field networks shown to be capable of predicting transition state geometries. Also presented is a small dataset of SN2 reactions which includes transition state structures - the first of its kind built specifically for machine learning. Finally, transfer learning, a low data remedial technique, is explored to understand the viability of pretraining TSNet on widely available chemical data may provide better starting points during training, faster convergence, and lower loss values. Aspects of the new dataset and model shall be discussed in detail, along with motivations and general outlook on the future of machine learning-based transition state prediction.
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Affiliation(s)
- Riley Jackson
- Department of Chemistry, University of Prince Edward Island Canada
| | - Wenyuan Zhang
- Department of Chemistry, University of Prince Edward Island Canada
| | - Jason Pearson
- Department of Chemistry, University of Prince Edward Island Canada
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10
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Otsuka M, Miyaguchi H. Evaluation of the possibility of binary synthesis of VX by theoretical calculation. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Messaoudi B. Quantum chemical study of the reaction of trichloroethylene with O(
3
P). INT J CHEM KINET 2020. [DOI: 10.1002/kin.21372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Boulanouar Messaoudi
- Laboratoire de Thermodynamique Appliquée et Modélisation MoléculaireDépartement de Chimie, Faculté des SciencesUniversité Abou Bekr Belkaid Tlemcen Algeria
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12
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Sweeny BC, Pan H, Kassem A, Sawyer JC, Ard SG, Shuman NS, Viggiano AA, Brickel S, Unke OT, Upadhyay M, Meuwly M. Thermal activation of methane by MgO+: temperature dependent kinetics, reactive molecular dynamics simulations and statistical modeling. Phys Chem Chem Phys 2020; 22:8913-8923. [DOI: 10.1039/d0cp00668h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The kinetics methane activation (MgO+ + CH4) was studied experimentally and computationally by running and analyzing reactive atomistic simulations.
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Affiliation(s)
- Brendan C. Sweeny
- NRC Postdoc at Air Force Research Laboratory
- Space Vehicles Directorate
- Kirtland Air Force Base
- USA
| | - Hanqing Pan
- USRA Space Scholar at Air Force Research Laboratory
- Space Vehicles Directorate
- Kirtland Air Force Base
- USA
| | - Asmaa Kassem
- USRA Space Scholar at Air Force Research Laboratory
- Space Vehicles Directorate
- Kirtland Air Force Base
- USA
| | - Jordan C. Sawyer
- NRC Postdoc at Air Force Research Laboratory
- Space Vehicles Directorate
- Kirtland Air Force Base
- USA
| | - Shaun G. Ard
- Air Force Research Laboratory
- Space Vehicles Directorate
- Kirtland Air Force Base
- USA
| | - Nicholas S. Shuman
- Air Force Research Laboratory
- Space Vehicles Directorate
- Kirtland Air Force Base
- USA
| | - Albert A. Viggiano
- Air Force Research Laboratory
- Space Vehicles Directorate
- Kirtland Air Force Base
- USA
| | | | - Oliver T. Unke
- Department of Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
| | - Meenu Upadhyay
- Department of Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
| | - Markus Meuwly
- Department of Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
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13
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Martínez González M, Xavier FGD, Li J, Montero-Cabrera LA, Garcia de la Vega JM, Varandas AJC. Role of Augmented Basis Sets and Quest for ab Initio Performance/Cost Alternative to Kohn–Sham Density Functional Theory. J Phys Chem A 2019; 124:126-134. [DOI: 10.1021/acs.jpca.9b09504] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marco Martínez González
- Department of Chemistry, and Chemistry Centre, University of Coimbra, 3004-535 Coimbra, Portugal
- Universidad de La Habana, Facultad de Química, calle San Lázaro sn., 10400 La Habana, Cuba
| | - F. George D. Xavier
- Department of Chemistry, and Chemistry Centre, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Jing Li
- School of Physics and Physical Engineering, Qufu Normal University, 273165 Qufu, China
| | - Luis A. Montero-Cabrera
- Universidad de La Habana, Facultad de Química, calle San Lázaro sn., 10400 La Habana, Cuba
- Donostia International Physics Center, Av. Tolosa 72, 20018 San Sebastián, Spain
| | - Jose M. Garcia de la Vega
- Department of Chemistry, and Chemistry Centre, University of Coimbra, 3004-535 Coimbra, Portugal
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - António J. C. Varandas
- Department of Chemistry, and Chemistry Centre, University of Coimbra, 3004-535 Coimbra, Portugal
- School of Physics and Physical Engineering, Qufu Normal University, 273165 Qufu, China
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14
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Meyer J, Carrascosa E, Michaelsen T, Bastian B, Li A, Guo H, Wester R. Unexpected Indirect Dynamics in Base-Induced Elimination. J Am Chem Soc 2019; 141:20300-20308. [DOI: 10.1021/jacs.9b10575] [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)
- Jennifer Meyer
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Eduardo Carrascosa
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Tim Michaelsen
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Björn Bastian
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Anyang Li
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, Ministry of Education, College of Chemistry and Materials Science, Northwest Universtiy, 710127 Xian, People’s Republic of China
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Roland Wester
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
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15
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Affiliation(s)
- F. Ruipérez
- POLYMAT, University of the Basque Country UPV/EHU, Donostia-San Sebastián, Spain
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16
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Galabov B, Koleva G, Schaefer HF, Allen WD. Nucleophilic Influences and Origin of the S N 2 Allylic Effect. Chemistry 2018; 24:11637-11648. [PMID: 29806167 DOI: 10.1002/chem.201801187] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/14/2018] [Indexed: 11/07/2022]
Abstract
The potential energy surfaces for the SN 2 reactions of allyl and propyl chlorides with 21 anionic and neutral nucleophiles was studied by using ωB97X-D/6-311++G(3df,2pd) computations. The "allylic effect" on SN 2 barriers was observed for all reactions, and compared with propyl substrates, the energy barriers differed by -0.2 to -4.5 kcal mol-1 in the gas phase. Strong correlations of the SN 2 net activation barriers with cation affinities, proton affinities, and electrostatic potentials at nuclei demonstrated the powerful influence of electrostatic interactions on these reactions. For the reactions of anionic (but not neutral) nucleophiles with allyl chloride, some of the incoming negative charge (0.2-18 %) migrated into the carbon chains, which would provide secondary stabilization of the SN 2 transition states. Activation strain analysis provided additional insight into the allylic effect by showing that the energy of geometric distortion for the reactants to reach the SN 2 transition state was smaller for each allylic reaction than for its propyl analogue. In many cases, the interaction energies between the substrate and nucleophile in this analysis were more favorable for propyl chloride reactions, but this compensation did not overcome the predominant strain energy effect.
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Affiliation(s)
- Boris Galabov
- Department of Chemistry and Pharmacy, University of Sofia, Sofia, 1164, Bulgaria
| | - Gergana Koleva
- Department of Chemistry and Pharmacy, University of Sofia, Sofia, 1164, Bulgaria
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA, 30602, USA
| | - Wesley D Allen
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA, 30602, USA
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17
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Lima MCP, Seabra GM. Reaction mechanism of the dengue virus serine protease: a QM/MM study. Phys Chem Chem Phys 2018; 18:30288-30296. [PMID: 27341353 DOI: 10.1039/c6cp03209e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dengue virus (DENV) is the causative agent of the viral infection dengue fever. In spite of all the efforts made to prevent the spread of the disease, once it is contracted, there is no specific treatment for dengue and the WHO guidelines are limited to rest and symptomatic treatment. In its reproductive cycle, DENV utilizes the NS2B-NS3pro, a serine protease, to cleave the viral polyprotein into its constituents. This enzyme is essential for the virus lifecycle, and presents an attractive target for the development of specific dengue treatments. Here we used a hybrid Quantum Mechanics and Molecular Mechanics (QM/MM) Molecular Dynamics approach and Umbrella Sampling to study the first step (acylation) of the reaction catalyzed by NS2B-NS3pro, using the Pairwise Distance Directed Gaussian PM3 (PDDG/PM3) semi-empirical Hamiltonian for the QM subsystem, and Amber ff99SB for the MM subsystem. Our results indicate that the nucleophilic attack on the substrate by Ser135 occurs in a stepwise manner, in which a proton transfer to His51 first activates Ser135, which only later attacks the substrate. The rate-determining step is the Ser135 activation, with a barrier of 24.1 kcal mol-1. Water molecules completing the oxyanion hole stabilize the negative charge formed on the carbonyl oxygen of the substrate. The final step in the process is a proton transfer from His51 to the substrate's nitrogen, which happens with a lower barrier of 5.1 kcal mol-1, and leads directly to the breakage of the peptide bond.
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Affiliation(s)
- M C P Lima
- Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Av. Jornalista Anibal Fernandes, s/no, Cidade Universitária - Recife, PE - CEP 50.740-560, Brazil.
| | - G M Seabra
- Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Av. Jornalista Anibal Fernandes, s/no, Cidade Universitária - Recife, PE - CEP 50.740-560, Brazil.
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18
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Price C, Winfough M, Park H, Meloni G. Computational investigation of LiF containing hypersalts. Dalton Trans 2018; 47:13204-13213. [DOI: 10.1039/c8dt02530d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This study explores the design of possible hypersalts starting from the hyperhalogen Li3F4 plus a Li atom and the hyperalkali Li4F3 plus a F atom.
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Affiliation(s)
- Chelsea Price
- Department of Chemistry
- University of San Francisco
- San Francisco
- USA
| | - Matthew Winfough
- Department of Chemistry
- University of San Francisco
- San Francisco
- USA
| | - Heejune Park
- Department of Chemistry
- University of San Francisco
- San Francisco
- USA
| | - Giovanni Meloni
- Department of Physical and Chemical Sciences
- Universitá degli Studi de L'Aquila
- L'Aquila 67100
- Italy
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19
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Winfough M, Meloni G. Ab initio analysis on potential superbases of several hyperlithiated species: Li3F2O and Li3F2OHn (n = 1, 2). Dalton Trans 2018; 47:159-168. [DOI: 10.1039/c7dt03579a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A systematic investigation on the potential basicity of the novel hyperlithiated species Li3F2O and Li3F2(OH)n (n = 1, 2) based upon the superalkali cluster Li3F2 was conducted using high-level ab initio techniques.
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Affiliation(s)
- Matthew Winfough
- University of San Francisco
- Department of Chemistry
- San Francisco
- USA
| | - Giovanni Meloni
- University of San Francisco
- Department of Chemistry
- San Francisco
- USA
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20
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Kosar N, Mahmood T, Ayub K. Role of dispersion corrected hybrid GGA class in accurately calculating the bond dissociation energy of carbon halogen bond: A benchmark study. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.08.104] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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21
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Szabó I, Czakó G. Dynamics and Novel Mechanisms of S N2 Reactions on ab Initio Analytical Potential Energy Surfaces. J Phys Chem A 2017; 121:9005-9019. [PMID: 28985079 DOI: 10.1021/acs.jpca.7b08140] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a novel theoretical approach to the bimolecular nucleophilic substitution (SN2) reactions that is based on analytical potential energy surfaces (PESs) obtained by fitting a few tens of thousands high-level ab initio energy points. These PESs allow computing millions of quasi-classical trajectories thereby providing unprecedented statistical accuracy for SN2 reactions, as well as performing high-dimensional quantum dynamics computations. We developed full-dimensional ab initio PESs for the F- + CH3Y [Y = F, Cl, I] systems, which describe the direct and indirect, complex-forming Walden-inversion, the frontside attack, and the new double-inversion pathways as well as the proton-transfer channels. Reaction dynamics simulations on the new PESs revealed (a) a novel double-inversion SN2 mechanism, (b) frontside complex formation,
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Affiliation(s)
- István Szabó
- Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged , Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Gábor Czakó
- Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged , Rerrich Béla tér 1, Szeged H-6720, Hungary
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22
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Szabó I, Czakó G. Benchmark ab Initio Characterization of the Complex Potential Energy Surface of the Cl– + CH3I Reaction. J Phys Chem A 2017; 121:5748-5757. [DOI: 10.1021/acs.jpca.7b05503] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- István Szabó
- Department of Physical Chemistry
and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Gábor Czakó
- Department of Physical Chemistry
and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
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23
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Varandas AJC, Martínez González M, Montero-Cabrera LA, Garcia de la Vega JM. Assessing How Correlated Molecular Orbital Calculations Can Perform versus Kohn-Sham DFT: Barrier Heights/Isomerizations. Chemistry 2017; 23:9122-9129. [PMID: 28380281 DOI: 10.1002/chem.201700928] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Indexed: 11/06/2022]
Abstract
To assess the title issue, 38 hydrogen transfer barrier heights and 38 non-hydrogen transfer barrier heights/isomerizations extracted from extensive databases have been considered, in addition to 4 2 p-isomerization reactions and 6 others for large organic molecules. All Kohn-Sham DFT calculations have employed the popular M06-2X functional, whereas the correlated molecular orbital (MO)-based ones are from single-reference MP2 and CCSD(T) methods. They have all utilized the same basis sets, with raw MO energies subsequently extrapolated to the complete basis set limit without additional cost. MP2 calculations are found to be as cost-effective as DFT ones and often slightly more, while showing a satisfactory accuracy when compared with the reference data. Although the focus is on barrier heights, the results may bear broader implications, in that one may see successes and difficulties of DFT when compared with traditional MO theories for the same data.
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Affiliation(s)
- António J C Varandas
- Departamento de Química, and Centro de Química, Universidade de Coimbra, 3004-535, Coimbra, Portugal
| | - Marco Martínez González
- Departamento de Química, and Centro de Química, Universidade de Coimbra, 3004-535, Coimbra, Portugal.,Universidad de La Habana, Facultad de Química, calle San Lázaro sn., 10400, La Habana, Cuba
| | - Luis A Montero-Cabrera
- Universidad de La Habana, Facultad de Química, calle San Lázaro sn., 10400, La Habana, Cuba
| | - José M Garcia de la Vega
- Departamento de Química, and Centro de Química, Universidade de Coimbra, 3004-535, Coimbra, Portugal.,Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain
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24
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Pedraza-González L, Galindo JF, González R, Reyes A. Revisiting the Dielectric Constant Effect on the Nucleophile and Leaving Group of Prototypical Backside S N2 Reactions: A Reaction Force and Atomic Contribution Analysis. J Phys Chem A 2016; 120:8360-8368. [PMID: 27718576 DOI: 10.1021/acs.jpca.6b06517] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solvent effect on the nucleophile and leaving group atoms of the prototypical F- + CH3Cl → CH3F + Cl- backside bimolecular nucleophilic substitution reaction (SN2) is analyzed employing the reaction force and the atomic contributions methods on the intrinsic reaction coordinate (IRC). Solvent effects were accounted for using the polarizable continuum solvent model. Calculations were performed employing 11 dielectric constants, ε, ranging from 1.0 to 78.5, to cover a wide spectrum of solvents. The reaction force data reveal that the solvent mainly influences the region of the IRC preceding the energy barrier, where the structural rearrangement to reach the transition state occurs. A detailed analysis of the atomic role in the reaction as a function of ε reveals that the nucleophile and the carbon atom are the ones that contribute the most to the energy barrier. In addition, we investigated the effect of the choice of nucleophile and leaving group on the ΔE0 and ΔE‡ of Y- + CH3X → YCH3 + X- (X, Y = F, Cl, Br, I) in aqueous solution. Our analysis allowed us to find relationships between the atomic contributions to the activation energy and leaving group ability and nucleophilicity.
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Affiliation(s)
- Laura Pedraza-González
- Departamento de Quı́mica, Universidad Nacional de Colombia , Av. Cra 30 # 45-03, Bogotá, Colombia
| | - Johan F Galindo
- Departamento de Quı́mica, Universidad Nacional de Colombia , Av. Cra 30 # 45-03, Bogotá, Colombia
| | - Ronald González
- Departamento de Quı́mica, Universidad Nacional de Colombia , Av. Cra 30 # 45-03, Bogotá, Colombia
| | - Andrés Reyes
- Departamento de Quı́mica, Universidad Nacional de Colombia , Av. Cra 30 # 45-03, Bogotá, Colombia
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25
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Chauvin JPR, Haidasz EA, Griesser M, Pratt DA. Polysulfide-1-oxides react with peroxyl radicals as quickly as hindered phenolic antioxidants and do so by a surprising concerted homolytic substitution. Chem Sci 2016; 7:6347-6356. [PMID: 28567247 PMCID: PMC5450444 DOI: 10.1039/c6sc01434h] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/22/2016] [Indexed: 11/21/2022] Open
Abstract
Polysulfides are important additives to a wide variety of industrial and consumer products and figure prominently in the chemistry and biology of garlic and related medicinal plants. Although their antioxidant activity in biological contexts has received only recent attention, they have long been ascribed 'secondary antioxidant' activity in the chemical industry, where they are believed to react with the hydroperoxide products of autoxidation to slow the auto-initiation of new autoxidative chain reactions. Herein we demonstrate that the initial products of trisulfide oxidation, trisulfide-1-oxides, are surprisingly reactive 'primary antioxidants', which slow autoxidation by trapping chain-carrying peroxyl radicals. In fact, they do so with rate constants (k = 1-2 × 104 M-1 s-1 at 37 °C) that are indistinguishable from those of the most common primary antioxidants, i.e. hindered phenols, such as BHT. Experimental and computational studies demonstrate that the reaction occurs by a concerted bimolecular homolytic substitution (SH2), liberating a perthiyl radical - which is ca. 16 kcal mol-1 more stable than a peroxyl radical. Interestingly, the (electrophilic) peroxyl radical nominally reacts as a nucleophile - attacking the of the trisulfide-1-oxide - a role hitherto suspected only for its reactions at metal atoms. The analogous reactions of trisulfides are readily reversible and not kinetically competent to inhibit hydrocarbon autoxidation, consistent with the longstanding view that organosulfur compounds must be oxidized to afford significant antioxidant activity. The reactivity of trisulfides and their oxides are contrasted with what is known of their shorter cousins and predictions are made and tested with regards to the reactivity of higher polysulfides and their 1-oxides - the insights from which may be exploited in the design of future antioxidants.
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Affiliation(s)
- Jean-Philippe R Chauvin
- Department of Chemistry and Biomolecular Sciences , University of Ottawa , 10 Marie Curie Pvt. , Ottawa , Ontario , Canada . ; ; Tel: +1-613-562-5800 ext. 2119
| | - Evan A Haidasz
- Department of Chemistry and Biomolecular Sciences , University of Ottawa , 10 Marie Curie Pvt. , Ottawa , Ontario , Canada . ; ; Tel: +1-613-562-5800 ext. 2119
| | - Markus Griesser
- Department of Chemistry and Biomolecular Sciences , University of Ottawa , 10 Marie Curie Pvt. , Ottawa , Ontario , Canada . ; ; Tel: +1-613-562-5800 ext. 2119
| | - Derek A Pratt
- Department of Chemistry and Biomolecular Sciences , University of Ottawa , 10 Marie Curie Pvt. , Ottawa , Ontario , Canada . ; ; Tel: +1-613-562-5800 ext. 2119
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26
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Lv J, Zhang J, Wang D. A multi-level quantum mechanics and molecular mechanics study of SN2 reaction at nitrogen: NH2Cl + OH(-) in aqueous solution. Phys Chem Chem Phys 2016; 18:6146-52. [PMID: 26847380 DOI: 10.1039/c5cp07370g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We employed a multi-level quantum mechanics and molecular mechanics approach to study the reaction NH2Cl + OH(-) in aqueous solution. The multi-level quantum method (including the DFT method with both the B3LYP and M06-2X exchange-correlation functionals and the CCSD(T) method, and both methods with the aug-cc-pVDZ basis set) was used to treat the quantum reaction region in different stages of the calculation in order to obtain an accurate potential of mean force. The obtained free energy activation barriers at the DFT/MM level of theory yielded a big difference of 21.8 kcal mol(-1) with the B3LYP functional and 27.4 kcal mol(-1) with the M06-2X functional respectively. Nonetheless, the barrier heights become very close when shifted from DFT to CCSD(T): 22.4 kcal mol(-1) and 22.9 kcal mol(-1) at CCSD(T)(B3LYP)/MM and CCSD(T)(M06-2X)/MM levels of theory, respectively. The free reaction energy obtained using CCSD(T)(M06-2X)/MM shows an excellent agreement with the one calculated using the available gas-phase data. Aqueous solution plays a significant role in shaping the reaction profile. In total, the water solution contributes 13.3 kcal mol(-1) and 14.6 kcal mol(-1) to the free energy barrier heights at CCSD(T)(B3LYP)/MM and CCSD(T)(M06-2X)/MM respectively. The title reaction at nitrogen is a faster reaction than the corresponding reaction at carbon, CH3Cl + OH(-).
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Affiliation(s)
- Jing Lv
- College of Physics and Electronics, Shandong Normal University, Jinan 250014, Shandong, China.
| | - Jingxue Zhang
- School of Physics, Nankai University, Tianjin 300071, China
| | - Dunyou Wang
- College of Physics and Electronics, Shandong Normal University, Jinan 250014, Shandong, China.
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27
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Karton A. A computational chemist's guide to accurate thermochemistry for organic molecules. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1249] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Amir Karton
- School of Chemistry and Biochemistry; The University of Western Australia; Perth WA Australia
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28
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Nishimoto Y. DFTB/PCM Applied to Ground and Excited State Potential Energy Surfaces. J Phys Chem A 2016; 120:771-84. [DOI: 10.1021/acs.jpca.5b10732] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yoshio Nishimoto
- Fukui Institute
for Fundamental
Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan
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29
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Zhao Y, Truhlar DG. Benchmark Databases for Nonbonded Interactions and Their Use To Test Density Functional Theory. J Chem Theory Comput 2015; 1:415-32. [PMID: 26641508 DOI: 10.1021/ct049851d] [Citation(s) in RCA: 800] [Impact Index Per Article: 88.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We present four benchmark databases of binding energies for nonbonded complexes. Four types of nonbonded interactions are considered: hydrogen bonding, charge transfer, dipole interactions, and weak interactions. We tested 44 DFT methods and 1 WFT method against the new databases; one of the DFT methods (PBE1KCIS) is new, and all of the other methods are from the literature. Among the tested methods, the PBE, PBE1PBE, B3P86, MPW1K, B97-1, and BHandHLYP functionals give the best performance for hydrogen bonding. MPWB1K, MP2, MPW1B95, MPW1K, and BHandHLYP give the best performances for charge-transfer interactions, and MPW3LYP, B97-1, PBE1KCIS, B98, and PBE1PBE give the best performance for dipole interactions. Finally, MP2, B97-1, MPWB1K, PBE1KCIS, and MPW1B95 give the best performance for weak interactions. Overall, MPWB1K is the best of all the tested DFT methods, with a relative error (highly averaged) of only 11%, and MPW1K, PBE1PBE, and B98 are the best of the tested DFT methods that do not contain kinetic energy density. Moving up the rungs of Jacob's ladder for nonempirical DFT, PBE improves significantly over the LSDA, and TPSS improve slightly over PBE (on average) for nonbonded interactions.
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Affiliation(s)
- Yan Zhao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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30
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Casanova D, Gusarov S, Kovalenko A, Ziegler T. Evaluation of the SCF Combination of KS-DFT and 3D-RISM-KH; Solvation Effect on Conformational Equilibria, Tautomerization Energies, and Activation Barriers. J Chem Theory Comput 2015; 3:458-76. [PMID: 26637028 DOI: 10.1021/ct6001785] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The effect of solvation on conformational equilibria, tautomerization energies, and activation barriers in simple SN2 reactions is reproduced by using the self-consistent field coupling of the Kohn-Sham density functional theory (KS-DFT) for electronic structure and the three-dimensional reference interaction site model with the closure approximation of Kovalenko and Hirata (3D-RISM-KH) for molecular solvation structure. These examples are used in order to validate the implementation of the 3D-RISM-KH method in the Amsterdam Density Functional package. The computations of the free energy difference in the trans/gauche conformational equilibrium for 1,2-dichloroethane in different solvents; the relative tautomerization free energy for cytosine, isocytosine, and guanine; and the free energy activation barrier for a CH3X-type (X = F, Cl, Br) SN2 reaction exhibit agreement with the experimental data. The method is also applied to the electronic and hydration structure of carbon single-wall nanotubes of different diameters, including the effect of water located in the inner space of the nanotubes. A comparison with continuum models of solvation (including COSMO) as well as with other more precise and computationally more expensive calculations is made to demonstrate the accuracy and predictive capability of the new KS-DFT/3D-RISM-KH method.
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Affiliation(s)
- David Casanova
- Departament de Química Inorgànica and Centre de Recerca en Química Teòrica, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain, National Institute for Nanotechnology, National Research Council of Canada, 421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada, Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, T6G 2G8, Canada, and Department of Chemistry, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Sergey Gusarov
- Departament de Química Inorgànica and Centre de Recerca en Química Teòrica, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain, National Institute for Nanotechnology, National Research Council of Canada, 421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada, Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, T6G 2G8, Canada, and Department of Chemistry, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Andriy Kovalenko
- Departament de Química Inorgànica and Centre de Recerca en Química Teòrica, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain, National Institute for Nanotechnology, National Research Council of Canada, 421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada, Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, T6G 2G8, Canada, and Department of Chemistry, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Tom Ziegler
- Departament de Química Inorgànica and Centre de Recerca en Química Teòrica, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain, National Institute for Nanotechnology, National Research Council of Canada, 421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada, Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta, T6G 2G8, Canada, and Department of Chemistry, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
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31
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González-García N, Pu J, González-Lafont À, Lluch JM, Truhlar DG. Searching for Saddle Points by Using the Nudged Elastic Band Method: An Implementation for Gas-Phase Systems. J Chem Theory Comput 2015; 2:895-904. [PMID: 26633048 DOI: 10.1021/ct060032y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A new implementation of the Nudged Elastic Band (NEB) optimization method is presented. This approach uses a global procedure that yields the whole reaction path, and thus it provides an alternative to the sequential optimization of the transition state and consequent calculation of the minimum energy path. Furthermore the algorithm is very useful when one is not sure if a saddle point exists, because it can be used to eliminate the possibility of a saddle point when one does not exist. Three different versions of the NEB algorithm have been implemented. The influences of various parameters and methodological choices on the performance of the method have been studied, and the quality of the results is assessed by comparison with the saddle point and minimum energy path calculations sequential method. Recommendations are made for algorithmic choices and default parameters.
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Affiliation(s)
- Núria González-García
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431
| | - Jingzhi Pu
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431
| | - Àngels González-Lafont
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431
| | - José M Lluch
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431
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32
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Tishchenko O, Zheng J, Truhlar DG. Multireference Model Chemistries for Thermochemical Kinetics. J Chem Theory Comput 2015; 4:1208-19. [PMID: 26631697 DOI: 10.1021/ct800077r] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
By combining the generalized valence bond ansatz of correlated participating orbitals (CPO) with the complete-active-space prescription for selecting configurations and with the use of multireference second order perturbation theory (MRMP2) for including dynamical correlation, we define three levels of multireference (MR) theoretical model chemistries for electronic structure calculations of chemical reaction energies and barrier heights. The three levels differ in their choice of which orbitals are considered to be participating; the choices are called nominal (nom-CPO), moderate (mod-CPO), and extended (ext-CPO). Combining any of these three choices with a method for treatment of dynamical correlation energy and a one-electron basis set yields a theoretical model chemistry. Unlike the full-valence choice of active orbitals, the CPO choices lead to active spaces that contain the orbitals needed to include important static correlation effects on chemical reactions but do not increase with the size of the nonparticipating portion of the system, and hence they remain viable computational options even for many large and complex reacting systems. The accuracies of the new levels, combined with the MG3S basis set (a partially augmented, multiply polarized valence triple-ζ basis with appropriately tight d functions for 3p-block elements) and with the fully augmented correlation-consistent aug-cc-pVTZ basis set, are assessed against a previously presented database of barrier heights for diverse reaction types. We find that nom-CPO level captures the bulk of the static correlation energy, and MRMP2/nom-CPO calculations have an average error of only 1.4 kcal/mol in barrier heights, which may be compared to 5.0 kcal/mol for single-reference MP2 theory, 2.5 kcal/mol for CCSD, and 4.1 and 1.0 kcal/mol for the B3LYP and M06-2X density functionals, respectively. The accuracy of MRMP2/CPO for transition structure bond lengths and donor-acceptor distances is excellent, with a mean unsigned error of only 0.007 Å as compared to 0.018 Å for CCSD, 0.019 Å for M06-2X, and 0.039 Å for MP2 and B3LYP. We also introduce a new multireference diagnostic, called the M diagnostic, that allows one to measure the importance of static correlation in a given reagent or transition state.
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Affiliation(s)
- Oksana Tishchenko
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Jingjing Zheng
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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33
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Gunaydin H, Acevedo O, Jorgensen WL, Houk KN. Computation of Accurate Activation Barriers for Methyl-Transfer Reactions of Sulfonium and Ammonium Salts in Aqueous Solution. J Chem Theory Comput 2015; 3:1028-35. [PMID: 26627421 DOI: 10.1021/ct050318n] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The energetics of methyl-transfer reactions from dimethylammonium, tetramethylammonium, and trimethylsulfonium to dimethylamine were computed with density functional theory, MP2, CBS-QB3, and quantum mechanics/molecular mechanics (QM/MM) Monte Carlo methods. At the CBS-QB3 level, the gas-phase activation enthalpies are computed to be 9.9, 15.3, and 7.9 kcal/mol, respectively. MP2/6-31+G(d,p) activation enthalpies are in best agreement with the CBS-QB3 results. The effects of aqueous solvation on these reactions were studied with polarizable continuum model, generalized Born/surface area (GB/SA), and QM/MM Monte Carlo simulations utilizing free-energy perturbation theory in which the PDDG/PM3 semiempirical Hamiltonian for the QM and explicit TIP4P water molecules in the MM region were used. In the aqueous phase, all of these reactions proceed more slowly when compared to the gas phase, since the charged reactants are stabilized more than the transition structure geometries with delocalized positive charges. In order to obtain the aqueous-phase activation free energies, the gas-phase activation free energies were corrected with the solvation free energies obtained from single-point conductor-like polarizable continuum model and GB/SA calculations for the stationary points along the reaction coordinate.
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Affiliation(s)
- Hakan Gunaydin
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, and Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107
| | - Orlando Acevedo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, and Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107
| | - William L Jorgensen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, and Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, and Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107
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Ahmadi AA, Fattahi A. Influence of a β-OH substituent on SN2 reactions of fluoroethane: Intramolecular hydrogen bonding catalysis or inhibition? A theoretical study. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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35
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Proenza YG, de Souza MAF, Ventura E, do Monte SA, Longo RL. Assessment of density-functionals for describing the X(-) + CH3ONO2 gas-phase reactions with X = F, OH, CH2CN. Phys Chem Chem Phys 2015; 16:26769-78. [PMID: 25372179 DOI: 10.1039/c4cp03674c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The energetics of the ECO2, SN2@C and SN2@N channels of X(-) + CH3ONO2 (X = F, OH, CH2CN) gas-phase reactions were computed using the CCSD(T)/CBS method. This benchmark extends a previous study with X = OH [M. A. F. de Souza et al., J. Am. Chem. Soc., 2012, 134, 19004] and was used to ascertain the accuracy and robustness of nineteen density-functionals for describing these potential energy profiles (PEP) as well as the kinetic product distributions obtained from RRKM calculations. Assessments were based on the mean unsigned error (MUE), the mean signed error (MSE), the #best : #worst (BW) criterion and the statistical confidence interval (CI) for the MSE. In general, double-hybrid (DH) functionals perform better than the range-separated ones, and both are better than the global-hybrid functionals. Based on the MUE and CI criteria the B2GPPLYP, B2PLYP, M08-SO, BMK, ωB97X-D, CAM-B3LYP, M06, M08-HX, ωB97X and B97-K functionals show the best performance in the description of these PEPs. Within this set, the B2GPPLYP functional is the most accurate and robust. The RRKM results indicate that the DHs are the best for describing the selectivities of these reactions. Compared to CCSD(T), the B2PLYP method has a relative error of only ca. 1% for the selectivity and the accuracy to provide the correct conclusion concerning the nonstatistical behavior of these reactions.
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Affiliation(s)
- Yaicel G Proenza
- Departamento de Química Fundamental, CCEN, Universidade Federal de Pernambuco, Cidade Universitária, Recife, PE 50.740-560, Brazil.
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36
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Szabó I, Czakó G. Double-inversion mechanisms of the X⁻ + CH₃Y [X,Y = F, Cl, Br, I] SN2 reactions. J Phys Chem A 2015; 119:3134-40. [PMID: 25746441 DOI: 10.1021/acs.jpca.5b00988] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The double-inversion and front-side attack transition states as well as the proton-abstraction channels of the X(-) + CH3Y [X,Y = F, Cl, Br, I] reactions are characterized by the explicitly correlated CCSD(T)-F12b/aug-cc-pVTZ(-PP) level of theory using small-core relativistic effective core potentials and the corresponding aug-cc-pVTZ-PP bases for Br and I. In the X = F case the double-inversion classical(adiabatic) barrier heights are 28.7(25.6), 15.8(13.4), 13.2(11.0), and 8.6(6.6) kcal mol(-1) for Y = F, Cl, Br, and I, respectively, whereas the barrier heights are in the 40-90 kcal mol(-1) range for the other 12 reactions. The abstraction channels are always above the double-inversion saddle points. For X = F, the front-side attack classical(adiabatic) barrier heights, 45.8(44.8), 31.0(30.3), 24.7(24.2), and 19.5(19.3) kcal mol(-1) for Y = F, Cl, Br, and I, respectively, are higher than the corresponding double-inversion ones, whereas for the other systems the front-side attack saddle points are in the 35-70 kcal mol(-1) range. The double-inversion transition states have XH···CH2Y(-) structures with Cs point-group symmetry, and the front-side attack saddle points have either Cs (X = F or X = Y) or C1 symmetry with XCY angles in the 78-88° range. On the basis of the previous reaction dynamics simulations and the minimum energy path computations along the inversion coordinate of selected XH···CH2Y(-) systems, we suggest that the double inversion may be a general mechanism for SN2 reactions.
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Affiliation(s)
- István Szabó
- Laboratory of Molecular Structure and Dynamics, Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518 Budapest 112, Hungary
| | - Gábor Czakó
- Laboratory of Molecular Structure and Dynamics, Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518 Budapest 112, Hungary
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37
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Darensbourg DJ, Chung WC, Yeung AD, Luna M. Dramatic Behavioral Differences of the Copolymerization Reactions of 1,4-Cyclohexadiene and 1,3-Cyclohexadiene Oxides with Carbon Dioxide. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b00172] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Donald J. Darensbourg
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Wan-Chun Chung
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Andrew D. Yeung
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Mireya Luna
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
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38
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Liang J, Su Q, Zheng S, Yu J, Geng Z. Computational comparison of reactions of CS2 with CHX•- (X = F, Cl, and Br): Do F, Cl, and Br substitutions effect differently? JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1142/s0219633615500091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Calculations based on density functional theory (DFT) have been carried out for the gas-phase ion-molecule reactions of CS 2 with CHX •- ( X = F , Cl , and Br ) to investigate the effect of the halogen-substituent on the reaction mechanism. The doublet potential energy surfaces (PESs), involving two striking reaction patterns named by the middle-C attack and the end-S attack in terms of anion attack on the C and S atoms of CS 2, have been explored and characterized in detail. Compared with the results of the end-S attack, reaction with the middle-C attack pattern displays more efficiency on PES. For a given reaction pattern, the reactions of CHCl •- and CHBr •- occur with similar efficiencies and reactivity trends. The CHF •- anion displays remarkably different reactivity, which is traced to its lower electron binding energy and the effect of the electronegative fluorine substituent. This is in good agreement with the experimental observation. According to the property of the product branching ratios in experiment, dynamical effect is used to evaluate the reason that the end-S attack with less energetically favorable obtained in our theoretical studies is comparable to the middle-C attack.
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Affiliation(s)
- Junxi Liang
- Gansu Key Laboratory of Environmental Friendly, Composites and Biomass Utilization, College of Chemical Engineering, Northwest University for Nationalities, Lanzhou, Gansu 730030, P. R. China
| | - Qiong Su
- Gansu Key Laboratory of Environmental Friendly, Composites and Biomass Utilization, College of Chemical Engineering, Northwest University for Nationalities, Lanzhou, Gansu 730030, P. R. China
| | - Shijie Zheng
- Gansu Key Laboratory of Environmental Friendly, Composites and Biomass Utilization, College of Chemical Engineering, Northwest University for Nationalities, Lanzhou, Gansu 730030, P. R. China
| | - Jing Yu
- Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, P. R. China
| | - Zhiyuan Geng
- Gansu Key Laboratory of Polymer Materials, College of Chemistry and Chemical Engineering, Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education, Northwest Normal University, Lanzhou, Gansu 730070, P. R. China
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Karton A, Goerigk L. Accurate reaction barrier heights of pericyclic reactions: Surprisingly large deviations for the CBS-QB3 composite method and their consequences in DFT benchmark studies. J Comput Chem 2015; 36:622-32. [DOI: 10.1002/jcc.23837] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/17/2014] [Accepted: 12/21/2014] [Indexed: 01/18/2023]
Affiliation(s)
- Amir Karton
- School of Chemistry and Biochemistry; The University of Western Australia; Perth WA 6009 Australia
| | - Lars Goerigk
- School of Chemistry; The University of Melbourne; Parkville VIC 3010 Australia
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40
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Simmie JM, Somers KP. Benchmarking Compound Methods (CBS-QB3, CBS-APNO, G3, G4, W1BD) against the Active Thermochemical Tables: A Litmus Test for Cost-Effective Molecular Formation Enthalpies. J Phys Chem A 2015; 119:7235-46. [PMID: 25580800 DOI: 10.1021/jp511403a] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The theoretical atomization energies of some 45 CxHyOz molecules present in the Active Thermochemical Tables compilation and of particular interest to the combustion chemistry community have been computed using five composite model chemistries as titled. The species contain between 1-8 "heavy" atoms, and a few are conformationally diverse with up to nine conformers. The enthalpies of formation at 0 and 298.15 K are then derived via the atomization method and compared against the recommended values. In general, there is very good agreement between our averaged computed values and those in the ATcT; those for 1,3-cyclopentadiene exceptionally differ considerably, and we show from isodesmic reactions that the true value for 1,3-cyclopentadiene is closer to 134 kJ mol(-1) than the reported 101 kJ mol(-1). If one is restricted to using a single method, statistical measures indicate that the best methods are in the rank order G3 ≈ G4 > W1BD > CBS-APNO > CBS-QB3. The CBS-x methods do on average predict ΔfH(⊖)(298.15 K) within ≈5 kJ mol(-1) but are prone to occasional lapses. There are statistical advantages to be gained from using a number of methods in tandem, and all possible combinations have been tested. We find that the average formation enthalpy coming from using CBS-APNO/G4, CBS-APNO/G3, and G3/G4 show lower mean signed and mean unsigned errors, and lower standard and root-mean-squared deviations, than any of these methods in isolation. Combining these methods also leads to the added benefit of providing an uncertainty rooted in the chemical species under investigation. In general, CBS-APNO and W1BD tend to underestimate the formation enthalpies of target species, whereas CBS-QB3, G3, and G4 have a tendency to overestimate the same. Thus, combining CBS-APNO with a G3/G4 combination leads to an improvement in all statistical measures of accuracy and precision, predicting the ATcT values to within 0.14 ± 4.21 kJ mol(-1), thus rivalling "chemical accuracy" (±4.184 kJ mol(-1)) without the excessive cost associated with higher-level methods such as W1BD.
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41
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Liang J, Su Q, Wang Y, Geng Z. SN2 Reaction of IO− + CH3Cl: An Ab Initio and DFT Benchmark Study. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20140194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Junxi Liang
- Gansu Key Laboratory of Environmental Friendly Composites and Biomass Utilization, College of Chemical Engineering, Northwest University for Nationalities
| | - Qiong Su
- Gansu Key Laboratory of Environmental Friendly Composites and Biomass Utilization, College of Chemical Engineering, Northwest University for Nationalities
| | - Yanbin Wang
- Gansu Key Laboratory of Environmental Friendly Composites and Biomass Utilization, College of Chemical Engineering, Northwest University for Nationalities
| | - Zhiyuan Geng
- Gansu Key Laboratory of Polymer Materials, College of Chemistry and Chemical Engineering, Key Laboratory of Eco-environment-related Polymer Materials, Ministry of Education, Northwest Normal University
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42
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Junxi L, Yu L, Qiang Z, Zhiyuan G. Understanding halogen-substituent assistance in H-atom abstraction-based reactions of CHCl •−with CH 4 − nX n(X = H, F, Cl; n= 0-3). J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Liang Junxi
- College of Chemical Engineering; Northwest University for Nationalities; Lanzhou Gansu 730030 China
| | - Li Yu
- College of Chemical Engineering; Northwest University for Nationalities; Lanzhou Gansu 730030 China
| | - Zhang Qiang
- Institute of Arid Meteorology; CMA; Key laboratory of Arid Climatic Change and Reducing Disaster of Gansu Province; Key Open Laboratory of Arid Climatic Change and Disaster Reduction of CMA; Lanzhou 730020 China
| | - Geng Zhiyuan
- Gansu Key Laboratory of Polymer Materials, College of Chemistry and Chemical Engineering, Key Laboratory of Eco-environment-related Polymer Materials; Ministry of Education; Northwest Normal University; Lanzhou Gansu 730070 China
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43
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Kuechler ER, York DM. Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl. J Chem Phys 2014; 140:054109. [PMID: 24511924 PMCID: PMC3977776 DOI: 10.1063/1.4863344] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/13/2014] [Indexed: 11/15/2022] Open
Abstract
The nucleophilic attack of a chloride ion on methyl chloride is an important prototype SN2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resulting free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.
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Affiliation(s)
- Erich R Kuechler
- BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, USA
| | - Darrin M York
- BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, USA
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44
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Darensbourg DJ, Yeung AD. A concise review of computational studies of the carbon dioxide–epoxide copolymerization reactions. Polym Chem 2014. [DOI: 10.1039/c4py00299g] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The production of polycarbonates from carbon dioxide and epoxides is an important route by which waste CO2 is converted into useful products. This review surveys the use of computational chemistry toward understanding this reaction.
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45
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Minyaev RM, Quapp W, Schmidt B, Getmanskii IV, Koval VV. Unusual reaction paths of SN2 nucleophile substitution reactions CH4+H−→CH4+H− and CH4+F−→CH3F+H−: Quantum chemical calculations. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.08.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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46
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Concurrent Phenomena at the Reaction Path of the SN2 Reaction CH3Cl + F−. Information Planes and Statistical Complexity Analysis. ENTROPY 2013. [DOI: 10.3390/e15104084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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47
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Swart M, Bickelhaupt FM. Benchmark study on the smallest bimolecular nucleophilic substitution reaction: H⁻+CH₄-->CH₄+H⁻. Molecules 2013; 18:7726-38. [PMID: 23823873 PMCID: PMC6270058 DOI: 10.3390/molecules18077726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 06/03/2013] [Accepted: 06/28/2013] [Indexed: 11/16/2022] Open
Abstract
We report here a benchmark study on the bimolecular nucleophilic substitution (S(N)2) reaction between hydride and methane, for which we have obtained reference energies at the coupled cluster toward full configuration-interaction limit (CC-cf/CBS). Several wavefunction (HF, MP2, coupled cluster) and density functional methods are compared for their reliability regarding these reference data.
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Affiliation(s)
- Marcel Swart
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry & Amsterdam Center for Multiscale Modeling, VU University, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands; E-Mail:
- Institute of Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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48
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Váňa J, Sedlák M, Kammel R, Roithová J, Škríba A, Jašík J, Hanusek J. Inverse neighboring group participation: explanation of an unusual S→N alkyl migration of isothiuronium salts containing a lactone group. J Org Chem 2013; 78:4456-62. [PMID: 23560796 DOI: 10.1021/jo400460x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A detailed experimental and DFT study of the S to N alkyl migration of substituted S-(1(3H)-isobenzofuranon-3-yl)isothiuronium bromide to N,N'-dimethyl-N-(3-oxo-1,3-dihydro-2-benzofuran-1-yl)thiourea provided evidence for the existence of an unusual double displacement mechanism involving two consecutive back-side S(N)2 reactions where a carboxylate anion has a crucial role both as a leaving group as well as an internal nucleophile. The thiazetidine zwitterionic species that is involved in this mechanism as an intermediate was characterized by infrared multiphoton dissociation spectroscopy and was trapped with methyl iodide. It was found that the intermediate has a structure of a free ion pair. The double-displacement mechanism can be considered as a new type of inverse lactone neighboring group participation.
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Affiliation(s)
- Jiří Váňa
- Faculty of Chemical Technology, Institute of Organic Chemistry and Technology, University of Pardubice, Studentská 573, CZ-532 10 Pardubice, The Czech Republic
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Liang J, Wang Y, Hasi Q, Geng Z. CCl 4Activation Mechanisms by Gas-Phase CHBr •–and CBr 2•–: A Comparative Study. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.2.426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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50
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Junxi L, Yanbin W, Qiang Z, Yu L, Zhiyuan G, Xiuhong W. DFT study on the reactions of ClO⁻/BrO⁻ with RCl (R = CH₃, C₂H₅, and C₃H₇) in gas phase. J Mol Model 2013; 19:1739-50. [PMID: 23296567 DOI: 10.1007/s00894-012-1736-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 12/13/2012] [Indexed: 11/28/2022]
Abstract
Gas-phase reactions of ClO(-)/BrO(-) with RCl (R = CH₃, C₂H₅, and C₃H₇) have been investigated in detail using the popular DFT functional BHandHLYP/aug-cc-pVDZ level of theory. As a result, our findings strongly suggest that the type of reaction is firstly initiated by a typical SN2 fashion. Subsequently, two competitive substitution steps, named as SN2-induced substitution and SN2-induced elimination, respectively, would proceed before the initial SN2 product ion-dipole complex separates, in which the former exhibits less reactivity than the latter. Those are consistent with relevant experimental results. Moreover, we have also explored reactivity difference for the title reactions in term of some factors derived from methyl group, p-π electronic conjugation, ionization energy (IE), as well as molecular orbital (MO) analysis.
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Affiliation(s)
- Liang Junxi
- College of Chemical Engineering, Northwest University for Nationalities, Lanzhou, Gansu 730030, China.
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