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Oliveira AGC, Barbosa MR, Matias PHF, Silva CAL, Machado DFS, de Lira Machado ÂH, Benedito de Oliveira HC. Deciphering Stereoselectivity in Hurd-Claisen Rearrangements: A Comprehensive Study of Electrostatic Interactions from Shubin's Energy Decomposition Analysis. Chemphyschem 2024; 25:e202400565. [PMID: 38923801 DOI: 10.1002/cphc.202400565] [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: 05/16/2024] [Revised: 06/12/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024]
Abstract
In this study, we explore the stereoselectivity of Hurd-Claisen Rearrangements, focusing on the influence of two electron-withdrawing groups and eight diverse substituents. Utilizing the Curtin-Hammett principle, we performed energy calculations for reactions, products, and transition states using the M062X/def2TZVPP compound model. Our analysis reveals that kinetic factors predominantly dictate the reaction equilibrium. A key aspect of our research is the application of Shubin's energy decomposition analysis to optimized transition states, highlighting the significant role of electrostatic interactions in determining stereoselectivity. We further dissected each transition state into four fragments: the electron-withdrawing groups (C O 2 E t ${CO_2 Et}$ ,C N ${CN}$ ), the Hurd group ( H ${H}$ ), various substituents (C H 3 ${CH_3 }$ ,E t ${Et}$ ,S P r o p ${SProp}$ ,T B u t ${TBut}$ ,I s o B u t ${IsoBut}$ ,N H 2 P h ${NH_2 Ph}$ ,N O 2 P h ${NO_2 Ph}$ ,P h ${Ph}$ ), and the central fragment. This fragmentation approach enabled an in-depth analysis of group dipole moments, providing insights into the electrostatic forces at play. Our findings shed light on the intricate mechanisms driving stereoselectivity in Hurd-Claisen Rearrangements and enhance the understanding of molecular interactions, offering valuable implications for organic synthesis.
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Affiliation(s)
- Ana Gabriela Coelho Oliveira
- Laboratório de Estrutura Eletrônica e Dinâmica Molecular (LEEDMOL), Instituto de Química, Universidade Federal de Goiás, Campus Samambaia, 74690-900 -, Goiânia, GO, Brazil
| | - Mateus Rodrigues Barbosa
- Laboratório de Estrutura Eletrônica e Dinâmica Molecular (LEEDMOL), Instituto de Química, Universidade Federal de Goiás, Campus Samambaia, 74690-900 -, Goiânia, GO, Brazil
| | | | | | | | | | - Heibbe Cristhian Benedito de Oliveira
- Laboratório de Estrutura Eletrônica e Dinâmica Molecular (LEEDMOL), Instituto de Química, Universidade Federal de Goiás, Campus Samambaia, 74690-900 -, Goiânia, GO, Brazil
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2
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Zhang J, He X, Wang B, Rong C, Zhao D, Liu S. Density-based quantification of steric effects: validation by Taft steric parameters from acid-catalyzed hydrolysis of esters. Phys Chem Chem Phys 2024; 26:23447-23456. [PMID: 39221570 DOI: 10.1039/d4cp02702g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The steric effect is one of the most widely used concepts for chemical understanding in publications and textbooks, yet a well-accepted formulation of this effect is still elusive. Experimentally, this concept was quantified by the acid-catalyzed hydrolysis of esters, yielding the so-called Taft steric parameter. Theoretically, we recently proposed a density-based scheme to quantify the effect from density functional theory. In this work, we directly compare these two schemes, one from theory and the other from experiment. To this end, we first establish the ester hydrolysis mechanism with multiple water molecules explicitly considered and then apply the energetic span model to represent the hydrolysis barrier height between the two schemes. Our results show that the barrier height of the reaction series is strongly correlated with both Taft steric parameters from experiment and steric quantification from theory. We also obtained strong correlations with steric potential, steric force, and steric charge from our theoretical scheme. Strong correlations with a few information-theoretic quantities are additionally unveiled. To the best of our knowledge, this is the first time in the literature that such a direct comparison between theoretical and experimental results is made. These results also suggest that our proposed two-water three-step mechanism for ester hydrolysis is effective, and our theoretical quantification of the steric effect is valid, robust, and experimentally comparable. In our view, this work should have satisfactorily addressed the issue of how the steric effect can be formulated and quantified, and thus it lays the groundwork for future applications.
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Affiliation(s)
- Jingwen Zhang
- College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China.
| | - Xin He
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao, Shandong 266237, China
| | - Bin Wang
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - Chunying Rong
- College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China.
| | - Dongbo Zhao
- Institute of Biomedical Research, Yunnan University, Kunming 650500, Yunnan, China
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill NC 27599-3420, USA
- Department of Chemistry, University of North Carolina, Chapel Hill NC 27599-3290, USA
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3
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Zhang W, He X, Li M, Zhang J, Zhao D, Liu S, Rong C. Simultaneous identification of strong and weak interactions with Pauli energy, Pauli potential, Pauli force, and Pauli charge. J Chem Phys 2023; 159:184104. [PMID: 37942871 DOI: 10.1063/5.0173666] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
Strong and weak interatomic interactions in chemical and biological systems are ubiquitous, yet how to identify them on a unified theoretical foundation is still not well established. Recently, we proposed employing Pauli energy-based indexes, such as strong covalent interaction and bonding and noncovalent interaction indexes, in the framework of density functional theory for the purpose. In this work, we extend our previous theoretical work by directly employing Pauli energy, Pauli potential, Pauli force, and Pauli charge to simultaneously identify both strong covalent bonding and weak noncovalent interactions. Our results from this work elucidate that using their signature isosurfaces, we can identify different types of interactions, either strong or weak, including single, double, triple, and quadruple covalent bonds, ionic bond, metallic bond, hydrogen bonding, and van der Waals interaction. We also discovered strong linear correlations between Pauli energy derived quantities and different covalent bond orders. These qualitative and quantitative results from our present study solidify the viewpoint that a unified approach to simultaneously identify both strong and weak interactions is possible. In our view, this work signifies one step forward towards the goal of establishing a density-based theory of chemical reactivity in density functional theory.
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Affiliation(s)
- Wenbiao Zhang
- Key Laboratory of Light Energy Conversion Materials of Hunan Province College, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
| | - Xin He
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, China
| | - Meng Li
- Key Laboratory of Light Energy Conversion Materials of Hunan Province College, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
| | - Jingwen Zhang
- Key Laboratory of Light Energy Conversion Materials of Hunan Province College, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
| | - Dongbo Zhao
- Institute of Biomedical Research, Yunnan University, Kunming 650500, People's Republic of China
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, USA
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| | - Chunying Rong
- Key Laboratory of Light Energy Conversion Materials of Hunan Province College, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
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4
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He X, Lu T, Rong C, Liu S, Ayers PW, Liu W. Topological analysis of information-theoretic quantities in density functional theory. J Chem Phys 2023; 159:054112. [PMID: 37548307 DOI: 10.1063/5.0159941] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/06/2023] [Indexed: 08/08/2023] Open
Abstract
We have witnessed considerable research interest in the recent literature about the development and applications of quantities from the information-theoretic approach (ITA) in density functional theory. These ITA quantities are explicit density functionals, whose local distributions in real space are continuous and well-behaved. In this work, we further develop ITA by systematically analyzing the topological behavior of its four representative quantities, Shannon entropy, two forms of Fisher information, and relative Shannon entropy (also called information gain or Kullback-Leibler divergence). Our results from their topological analyses for 103 molecular systems provide new insights into bonding interactions and physiochemical properties, such as electrophilicity, nucleophilicity, acidity, and aromaticity. We also compare our results with those from the electron density, electron localization function, localized orbital locator, and Laplacian functions. Our results offer a new methodological approach and practical tool for applications that are especially promising for elucidating chemical bonding and reactivity propensity.
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Affiliation(s)
- Xin He
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, China
| | - Tian Lu
- Beijing Kein Research Center for Natural Sciences, Beijing 100022, China
| | - Chunying Rong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, China
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, USA
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, China
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5
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Sinha S, Giri S, Chakraborty A. Exploring an intermolecular Ge/B frustrated Lewis pair from a multicentre Zintl Lewis base. Theor Chem Acc 2023. [DOI: 10.1007/s00214-023-02961-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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6
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Bocalandro M, González Armesto JJ, Montero-Cabrera LA, Martínez González M. 1,3 Dipolar Cycloaddition of Münchnones: Factors behind the Regioselectivity. J Phys Chem A 2023; 127:645-660. [PMID: 36629023 DOI: 10.1021/acs.jpca.2c06472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The 1,3 dipolar cycloaddition reactions of münchnones and alkenes provide an expedite synthetic way to substituted pyrroles, an exceedingly important structural motif in the pharmaceutical and material science fields of research. The factors governing their regioselectivity rationalization are not well understood. Using several approaches, we investigate a set of 14 reactions (featuring two münchnones, 12 different alkenes, and two alkynes). The Natural Bond Theory and the Non-Covalent Interaction Index analyses of the noncovalent interaction energies fail to predict the experimental major regioisomer. Employing global cDFT descriptors or local ones such as the Fukui function and dual descriptor yields similarly inaccurate predictions. Only the local softness pairing, within Pearson's Hard and Soft Acids and Bases principle, constitutes a reliable predictor for the major reaction product. By taking into account an estimator for the steric effects, the correct regioisomer is predicted. Steric effects play a major role in driving the regioselectivity, as was corroborated by energy decomposition analysis of the transition states.
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Affiliation(s)
- Meylin Bocalandro
- Laboratory of Computational and Theoretical Chemistry, Faculty of Chemistry, University of Havana, Havana10400, Cuba
| | | | - Luis A Montero-Cabrera
- Laboratory of Computational and Theoretical Chemistry, Faculty of Chemistry, University of Havana, Havana10400, Cuba
| | - Marco Martínez González
- Laboratory of Computational and Theoretical Chemistry, Faculty of Chemistry, University of Havana, Havana10400, Cuba
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7
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Wang K, He X, Rong C, Zhong A, Liu S, Zhao D. On the origin and nature of internal methyl rotation barriers: an information-theoretic approach study. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02910-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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8
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Kossaka Macedo G, Haiduke RLA. The performance of exchange-correlation functionals in describing electron density parameters of saddle point structures along chemical reactions. J Comput Chem 2022; 43:1830-1838. [PMID: 36053978 DOI: 10.1002/jcc.26985] [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: 11/10/2021] [Revised: 05/26/2022] [Accepted: 08/03/2022] [Indexed: 11/07/2022]
Abstract
This work is focused on evaluating the performance of exchange-correlation functionals from density functional theory in providing descriptor values derived from the electron density of saddle point structures (transition states) in chemical reactions. The properties investigated were obtained from the quantum theory of atoms in molecules, including atomic charges and electron density topological data at the bond critical points. In addition, parameters from the Interacting quantum atom energy partition were used as well in this comparative study. The reference values are attained in coupled cluster calculations with iterative single and double excitations (CCSD). Six elementary reactions are considered here: CO + H2 ↔ H2 CO, CO + H2 O ↔ HCOOH, HCN ↔ HNC, H + F2 ↔ HF + F, H + N2 ↔ HN2 , and H + CO ↔ HCO. In general, the BB1K functional (hybrid-meta-generalized gradient approximation) provides the best description of these properties. Our study indicates that an intermediate percentage of nonlocal exact exchange, around 40%-55% (perhaps even larger), is probably required for attaining more accurate values with actual functionals, although this condition is not able of explaining all the trends observed.
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Affiliation(s)
- Gabriel Kossaka Macedo
- Department of Chemistry and Molecular Physics, São Carlos Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Roberto Luiz Andrade Haiduke
- Department of Chemistry and Molecular Physics, São Carlos Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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9
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Miranda-Quintana RA, Heidar-Zadeh F, Fias S, Chapman AEA, Liu S, Morell C, Gómez T, Cárdenas C, Ayers PW. Molecular Interactions From the Density Functional Theory for Chemical Reactivity: The Interaction Energy Between Two-Reagents. Front Chem 2022; 10:906674. [PMID: 35769444 PMCID: PMC9234655 DOI: 10.3389/fchem.2022.906674] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/19/2022] [Indexed: 12/13/2022] Open
Abstract
Reactivity descriptors indicate where a reagent is most reactive and how it is most likely to react. However, a reaction will only occur when the reagent encounters a suitable reaction partner. Determining whether a pair of reagents is well-matched requires developing reactivity rules that depend on both reagents. This can be achieved using the expression for the minimum-interaction-energy obtained from the density functional reactivity theory. Different terms in this expression will be dominant in different circumstances; depending on which terms control the reactivity, different reactivity indicators will be preferred.
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Affiliation(s)
- Ramón Alain Miranda-Quintana
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, United States
- *Correspondence: Ramón Alain Miranda-Quintana, ; Carlos Cárdenas, ; Paul W. Ayers, ; Tatiana Gómez,
| | | | - Stijn Fias
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Allison E. A. Chapman
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, NC, United States
| | - Christophe Morell
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques-UMR CNRS 5280, Villeurbanne, France
| | - Tatiana Gómez
- Theoretical and Computational Chemistry Center, Institute of Applied Chemical Sciences, Faculty of Engineering, Universidad Autonoma de Chile, Santiago, Chile
- *Correspondence: Ramón Alain Miranda-Quintana, ; Carlos Cárdenas, ; Paul W. Ayers, ; Tatiana Gómez,
| | - Carlos Cárdenas
- Departamento de Fisica, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro para el desarrollo de la Nanociencias y Nanotecnologia, CEDENNA, Santiago, Chile
- *Correspondence: Ramón Alain Miranda-Quintana, ; Carlos Cárdenas, ; Paul W. Ayers, ; Tatiana Gómez,
| | - Paul W. Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
- *Correspondence: Ramón Alain Miranda-Quintana, ; Carlos Cárdenas, ; Paul W. Ayers, ; Tatiana Gómez,
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10
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Rehman U, Mansha A, Zahid M, Asim S, Zahoor AF, Rehan ZA. Quantum mechanical modeling unveils the effect of substitutions on the activation barriers of the Diels–Alder reactions of an antiviral compound 7H-benzo[a]phenalene. Struct Chem 2022. [DOI: 10.1007/s11224-022-01948-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Zhong S, He X, Liu S, Wang B, Lu T, Rong C, Liu S. Toward Density-Based and Simultaneous Description of Chemical Bonding and Noncovalent Interactions with Pauli Energy. J Phys Chem A 2022; 126:2437-2444. [PMID: 35389639 DOI: 10.1021/acs.jpca.2c00224] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemical bonds and noncovalent interactions are extraordinarily important concepts in chemistry and beyond. Using density-based quantities to describe them has a long history in the literature, yet none can satisfactorily describe the entire spectrum of interactions from strong chemical bonds to weak van der Waals forces. In this work, employing Pauli energy as the theoretical foundation, we fill in that knowledge gap. Our results show that the newly established density-based index can describe single and multiple covalent bonds, ionic bonds, metallic bonds, and different kinds of noncovalent interactions, all with unique and readily identifiable signature shapes. Two new descriptors, BNI (bonding and noncovalent interaction) index and USI (ultra-strong interaction) index, have been introduced in this work. Together with NCI (noncovalent interaction) and SCI (strong covalent interaction) indexes already available in the literature, a density-based description of both chemical bonds and noncovalent interactions is accomplished.
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Affiliation(s)
- Shujing Zhong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Xin He
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Siyuan Liu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Bin Wang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P.R. China.,Eenheid Algemene Chemie, Faculteit Wetenschappen, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
| | - Tian Lu
- Beijing Kein Research Center for Natural Sciences, Beijing 100022, P. R. China
| | - Chunying Rong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3420, United States.,Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
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12
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Revisiting the trapping of noble gases (He-Kr) by the triatomic H 3+ and Li 3+ species: a density functional reactivity theory study. J Mol Model 2022; 28:122. [PMID: 35437635 DOI: 10.1007/s00894-022-05099-7] [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: 11/30/2021] [Accepted: 03/22/2022] [Indexed: 10/18/2022]
Abstract
Small atomic clusters with exotic stability, bonding, aromaticity, and reactivity properties can be made use of for various purposes. In this work, we revisit the trapping of noble gas atoms (He-Kr) by the triatomic H3+ and Li3+ species by using some analytical tools from density functional theory, conceptual density functional theory, and the information-theoretic approach. Our results showcase that though similar in geometry, H3+ and Li3+ exhibit markedly different behavior in bonding, aromaticity, and reactivity properties after the addition of noble gas atoms. Moreover, the exchange-correlation interaction and steric effect are key energy components in stabilizing the clusters. This study also finds that the origin of the molecular stability of these species is due to the spatial delocalization of the electron density distribution. Our work provides an additional arsenal towards a better understanding of small atomic clusters capturing noble gases.
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13
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Nogueira D, Oliveira RR, Rocha AB. Microsolvation effect on chlorination reaction of simple alcohols. INT J CHEM KINET 2022. [DOI: 10.1002/kin.21567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Diogo Nogueira
- Instituto de Química, Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Ricardo R. Oliveira
- Instituto de Química, Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Alexandre B. Rocha
- Instituto de Química, Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
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14
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The Synergetic and Multifaceted Nature of Carbon‐Carbon Rotation Reveals the Origin of Conformational Barrier Heights with Bulky Alkane Groups. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4352] [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]
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15
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Gallegos M, Costales A, Martín Pendás Á. A real space picture of the role of steric effects in
S
N
2
reactions. J Comput Chem 2022; 43:785-795. [PMID: 35277994 PMCID: PMC9314895 DOI: 10.1002/jcc.26834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/23/2022] [Accepted: 02/24/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Miguel Gallegos
- Department of Analytical and Physical Chemistry University of Oviedo Oviedo Spain
| | - Aurora Costales
- Department of Analytical and Physical Chemistry University of Oviedo Oviedo Spain
| | - Ángel Martín Pendás
- Department of Analytical and Physical Chemistry University of Oviedo Oviedo Spain
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16
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Abstract
There are different kinds of molecular chirality, such as zero-dimensional point chirality, one-dimensional axial chirality, 2D planar chirality, and 3D chirality. When they coexist in one system, such as in helical structures of proteins and DNA, they form a chirality hierarchy. Earlier, we showed that the chirality propensity of a lower level in a hierarchy is dictated by that of a higher level and henceforth proposed the Principle of Chirality Hierarchy. In this work, we confirm the validity of this principle in the three-blade propeller molecular system. Our results show that the preference of the 0D chirality of a functional group in the propeller system is determined by the 1D chirality, and homochirality is also a remarkable feature for this system. The establishment and confirmation of the Principle of Chirality Hierarchy from this work should find important applications in asymmetric synthesis, macromolecular assembly, and many others.
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Affiliation(s)
- Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
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17
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Li R, Du T, Liu J, Aquino AJA, Zhang J. Theoretical Study of O-CH 3 Bond Dissociation Enthalpy in Anisole Systems. ACS OMEGA 2021; 6:21952-21959. [PMID: 34497890 PMCID: PMC8412933 DOI: 10.1021/acsomega.1c02310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Understanding ubiquitous methyl transfer reactions requires a systematic study of thermodynamical parameters that could reveal valuable information about the nature of the chemical bond and the feasibility of those processes. In the present study, the O-CH3 bond dissociation enthalpies (BDEs) of 67 compounds belonging to phenol/anisole systems were calculated employing the Gaussian-4 (G4) method. Those compounds contain different substituents including alkyl groups, electron-donating groups (EDGs), and electron-withdrawing groups (EWGs). The results show that the bigger branched alkyl groups and EDGs will destabilize the O-CH3 bond, while EWGs have the opposite effect. A combination of different effects including steric effects, hydrogen bonds, and substituents and their position can achieve around 20 kcal/mol difference compared to the basic phenyl frame. Also, the linear correlation between σp + and O-CH3 BDE can provide a reference for the O-CH3 BDE prediction. The present study represents a step forward to establish a comprehensive O-CH3 BDE database to understand the substituent effect and make its contribution to the rational design of inhibitors and drugs.
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Affiliation(s)
- Rui Li
- School
of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Naikai District, Tianjin 300072, P. R. China
| | - Tianshu Du
- School
of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Naikai District, Tianjin 300072, P. R. China
| | - Jingxing Liu
- School
of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Naikai District, Tianjin 300072, P. R. China
| | - Adelia J. A. Aquino
- School
of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Naikai District, Tianjin 300072, P. R. China
- Department
of Mechanical Engineering, Texas Tech University, Lubbock, Texas 79409, United States
- Institute
for Soil Research, University of Natural
Resources and Life Sciences, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Jianyu Zhang
- School
of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Naikai District, Tianjin 300072, P. R. China
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18
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Parida R, Inostroza Rivera R, Sinha S, Giri S. Can Superhalogen Ligand Make More Reactive Frustrated Lewis Pairs? ChemistrySelect 2021. [DOI: 10.1002/slct.202102189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Rakesh Parida
- School of Applied Science and Humanities Haldia Institute of Technology Haldia 721657 India
- Department of Chemistry National Institute of Technology Rourkela Odisha 769008 India
| | - Ricardo Inostroza Rivera
- Departmento de Quimica Organica Facultad de Química y de Farmacia Pontificia Universidad Católica de Chile Macul 7820436 Santiago Chile
| | - Swapan Sinha
- School of Applied Science and Humanities Haldia Institute of Technology Haldia 721657 India
| | - Santanab Giri
- School of Applied Science and Humanities Haldia Institute of Technology Haldia 721657 India
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19
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He X, Li M, Yu D, Wang B, Zhao D, Rong C, Liu S. Conformational changes for porphyrinoid derivatives: an information-theoretic approach study. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02824-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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20
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Wang B, Zhao D, Lu T, Liu S, Rong C. Quantifications and Applications of Relative Fisher Information in Density Functional Theory. J Phys Chem A 2021; 125:3802-3811. [PMID: 33891419 DOI: 10.1021/acs.jpca.1c02099] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Though density functional theory is widely accepted as one of the most successful developments in theoretical chemistry in the past few decades, the knowledge of how to apply this new electronic structure theory, to help us better understand chemical processes and transformations, is still an unaccomplished task. The information-theoretic approach is emerging as a viable option for that purpose in the recent literature, providing new insights about steric effect, cooperativity, electrophilicity, nucleophilicity, stereoselectivity, homochirality, etc. In this work, based on the result from a recent paper by one of us [ J. Chem. Phys, 2019, 151, 141103], we present two quantifications of the relative Fisher information and discuss their physiochemical properties and possible applications. To that end, their analytical properties have been elucidated. They have also been applied to six categories of systems to illustrate their applicability. A better descriptor to quantify the single bond rotation barrier has been obtained. The relative Fisher information can also simultaneously determine electrophilicity and nucleophilicity, and effectively describe helical structures with different homochiral and heterochiral propensities. As integral parts of the information-theoretic approach, these newly introduced quantities will provide us with more analytical tools toward the long-term goal of crafting a chemical reactivity theory in the density-based language.
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Affiliation(s)
- Bin Wang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Dongbo Zhao
- Institute of Biomedical Research, Yunnan University, Chenggong District, Kunming 650500, Yunnan P.R. China
| | - Tian Lu
- Beijing Kein Research Center for Natural Sciences, Beijing 100022, P.R. China
| | - Shubin Liu
- Research Computing Center, University of North Carolina Chapel Hill, North Carolina 27599-3420, United States
| | - Chunying Rong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P.R. China
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21
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Gallegos M, Costales A, Pendás ÁM. Energetic Descriptors of Steric Hindrance in Real Space: An Improved IQA Picture*. Chemphyschem 2021; 22:775-787. [PMID: 33497008 DOI: 10.1002/cphc.202000975] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/05/2021] [Indexed: 11/11/2022]
Abstract
Steric hindrance (SH) plays a central role in the modern chemical narrative, lying at the core of chemical intuition. As it however happens with many successful chemical concepts, SH lacks an underlying physically sound root, and multiple mutually inconsistent approximations have been devised to relate this fuzzy concept to computationally derivable descriptors. We here argue that being SH related to spatial as well as energetic features of interacting systems, SH can be properly handled if we chose a real space energetic stance like the Interacting Quantum Atoms (IQA) approach. Drawing on previous work by Popelier and coworkers (ChemistryOpen 8, 560, 2019) we build an energetic estimator of SH, referred to as EST . We show that the rise in the self-energy of a fragment that accompanies steric congestion is a faithful proxy for the chemist's SH concept if we remove the effect of charge transfer. This can be done rigorously, and the EST here defined provides correct sterics even for hydrogen atoms, where the plain use of deformation energies leads to non-chemical results. The applicability of EST is validated in several chemical scenarios, going from atomic compressions to archetypal SN2 reactions. EST is shown to be a robust steric hindrance descriptor.
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Affiliation(s)
- Miguel Gallegos
- Department of Analytical and Physical Chemistry, University of Oviedo, E-33006, Oviedo, Spain
| | - Aurora Costales
- Department of Analytical and Physical Chemistry, University of Oviedo, E-33006, Oviedo, Spain
| | - Ángel Martín Pendás
- Department of Analytical and Physical Chemistry, University of Oviedo, E-33006, Oviedo, Spain
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22
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Li M, He X, Chen J, Wang B, Liu S, Rong C. Density Functional Theory and Information-Theoretic Approach Study on the Origin of Homochirality in Helical Structures. J Phys Chem A 2021; 125:1269-1278. [PMID: 33527833 DOI: 10.1021/acs.jpca.0c10310] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Homochirality of macromolecules such as proteins and DNA is one of the most striking features in nature; yet, there is still no convincing theory to explain its origin. In a recent work by one of the present authors (J. Phys. Chem. Lett. 2020, 11, 8690-8696), a general proposal from the viewpoint of thermodynamics has been put forward. It proposes that it is the handedness of helices ubiquitous in biological macromolecules that plays the decisive role. It also unveiled that there exist strong cooperativity effects dominated by favorable electrostatic interactions in the homochiral conformer. In this work, making use of analytical tools, we recently developed a density functional theory and an information-theoretic approach and through four sets of helical structures we designed for the present study, we examine these systems to provide new insights about these properties. We found that the 310-helix and the α-helix are markedly different in cooperativity from the viewpoint of both the total energy and its three components. The electrostatic dominance of homochiral species is manifested by both the electron charge distribution and information gain. At the atomic level, different elements behave significantly differently because they play different roles in the systems. Our results from this work validate that these analytical tools can be applied to homochiral systems, which can be further extended to others with potential interest in asymmetric synthesis and macromolecular assembly where the Principle of Homochirality Hierarchy comes into play.
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Affiliation(s)
- Meng Li
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Xin He
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Jie Chen
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Bin Wang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States
| | - Chunying Rong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P.R. China
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23
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von Rudorff GF, Heinen SN, Bragato M, von Lilienfeld OA. Thousands of reactants and transition states for competing E2 and S$_\mathrm{N}$2 reactions. MACHINE LEARNING-SCIENCE AND TECHNOLOGY 2020. [DOI: 10.1088/2632-2153/aba822] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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24
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Abstract
Homochirality is a common feature of amino acids and carbohydrates, and its origin is still unknown. Meanwhile, right-handed helices are ubiquitous in nature. Are these two phenomena intrinsically correlated? Here, we propose that homochirality of amino acids and nucleotide sugars originated from the handedness of helices. We show that right-handed 310-helix and α-helix favor the l-chiral form for amino acids, but for deoxyribose sugars, right-handed helices prefer the d-chiral form instead. Our analyses unveil strong cooperativity effects dominated by electrostatic interactions. This work not only resolves the mystery of homochirality by providing a unified explanation for the origin of homochirality in proteins and DNA using helical secondary structures as the root cause but also ratifies the Principle of Chirality Hierarchy, in which the chirality of a higher hierarchy dictates that of lower ones. Possible applications of this work to asymmetric synthesis and macromolecular assembly are discussed.
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Affiliation(s)
- Shubin Liu
- Research Computing Center, The University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States
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25
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Rong C, Wang B, Zhao D, Liu S. Information‐theoretic approach in density functional theory and its recent applications to chemical problems. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1461] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Chunying Rong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China) Hunan Normal University Changsha P.R. China
- Department of Chemistry, College of Chemistry and Chemical Engineering Hunan Normal University Changsha P.R. China
| | - Bin Wang
- Department of Chemistry, College of Chemistry and Chemical Engineering Hunan Normal University Changsha P.R. China
| | - Dongbo Zhao
- Department of Chemistry, School of Chemistry and Chemical Engineering Nanjing University Nanjing P.R. China
| | - Shubin Liu
- Research Computing Centre University of North Carolina Chapel Hill North Carolina
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26
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Wang B, Yu D, Zhao D, Rong C, Liu S. Nature and origin of γ-gauche effect in sulfoxides: A density functional theory and information-theoretic approach study. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.06.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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Wu J, Yu D, Liu S, Rong C, Zhong A, Chattaraj PK, Liu S. Is It Possible To Determine Oxidation States for Atoms in Molecules Using Density-Based Quantities? An Information-Theoretic Approach and Conceptual Density Functional Theory Study. J Phys Chem A 2019; 123:6751-6760. [PMID: 31305075 DOI: 10.1021/acs.jpca.9b05054] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxidation state, also called oxidation number, of atoms in molecules is a fundamental chemical concept. It is defined as the charge of an atom in a molecule after the ionic approximation of its heteronuclear bonds is applied. Even though for simple molecules the assignment of oxidation states is straightforward, redundancy and ambiguity do exist for others. In this work, we present a density-based framework to determine the oxidation state using the quantities from the information-theoretic approach. As a proof of concept, we examined six elements for a total of 49 molecules. Strong linear correlations were obtained with Shannon entropy, Ghosh-Berkowitz-Parr entropy, information gain, relative Rényi entropy of orders 2 and 3, and Hirshfeld charge. We also discovered that the crystal radius of elements plays the key role in rationalizing the system dependent nature of these strong linear correlations. The validity and effectiveness of our results were demonstrated by the examples of molecules containing elements with two or more oxidation states. Our results should be applicable to more complicated systems in assigning different oxidation states.
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Affiliation(s)
- Jingyi Wu
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha , Hunan 410081 , P.R. China
| | - Donghai Yu
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha , Hunan 410081 , P.R. China
| | - Siyuan Liu
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha , Hunan 410081 , P.R. China
| | - Chunying Rong
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha , Hunan 410081 , P.R. China
| | - Aiguo Zhong
- School of Pharmaceutical and Chemical Engineering , Taizhou University , 1139 Shifu Road , Linhai , Zhejiang 318000 , P.R. China
| | - Pratim K Chattaraj
- Department of Chemistry and Center for Theoretical Studies , Indian Institute of Technology , Kharagpur 721302 , India
| | - Shubin Liu
- Research Computing Center , University of North Carolina , Chapel Hill , North Carolina 27599-3420 , United States
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28
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Theoretical study of metal ion impact on geometric and electronic properties of terbutaline compounds. MONATSHEFTE FUR CHEMIE 2019. [DOI: 10.1007/s00706-019-02419-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Unke OT, Meuwly M. PhysNet: A Neural Network for Predicting Energies, Forces, Dipole Moments, and Partial Charges. J Chem Theory Comput 2019; 15:3678-3693. [DOI: 10.1021/acs.jctc.9b00181] [Citation(s) in RCA: 285] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Oliver T. Unke
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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30
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Rong C, Zhao D, Zhou T, Liu S, Yu D, Liu S. Homogeneous Molecular Systems are Positively Cooperative, but Charged Molecular Systems are Negatively Cooperative. J Phys Chem Lett 2019; 10:1716-1721. [PMID: 30916572 DOI: 10.1021/acs.jpclett.9b00639] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Molecular systems bound together through noncovalent interactions are ubiquitous in nature, many of which are involved in essential life processes, yet little is known about the principles governing their structure, stability, and function. Cooperativity as one of the intrinsic properties in these systems plays a key role. In this work, on the basis of our recent quantification scheme of the cooperativity effect, we present a general pattern to identify which systems are positively cooperative and which are negatively cooperative. We show that cooperativity in homogeneous molecular systems is positive, but cooperativity in charged molecular systems is negative. We also employ analytical tools from energetics and information perspectives to appreciate the origin of the cooperativity effect. We find that positive cooperativity is dominated by the exchange-correlation interaction and steric effect, whereas negative cooperativity is governed by the electrostatic interaction. Our results should have strong implications for better understanding molecular recognition, protein folding, signal transduction, allosteric regulation, and other processes.
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Affiliation(s)
- Chunying Rong
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha Hunan 410081 , People's Republic of China
| | - Dongbo Zhao
- School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210093 , People's Republic of China
| | - Tianjing Zhou
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha Hunan 410081 , People's Republic of China
| | - Siyuan Liu
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha Hunan 410081 , People's Republic of China
| | - Donghai Yu
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha Hunan 410081 , People's Republic of China
| | - Shubin Liu
- Research Computing Center , University of North Carolina , Chapel Hill , North Carolina 27599-3420 , United States
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31
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Effect of solvent polarity on the potential energy surface in the SN2 reaction of F− + CH3Cl. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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32
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Zhao D, Liu S, Rong C, Zhong A, Liu S. Toward Understanding the Isomeric Stability of Fullerenes with Density Functional Theory and the Information-Theoretic Approach. ACS OMEGA 2018; 3:17986-17990. [PMID: 31458389 PMCID: PMC6643390 DOI: 10.1021/acsomega.8b02702] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
For a given size of one fullerene molecule, there could exist many different isomers and their energy landscape is remarkably complex. To have a better understanding of the nature and origin of their isomeric stability, as a continuation of our previous endeavors, we systematically dissect the molecular stability of four fullerene systems, C44, C48, C52, and C60, with a total of 2547 structures, using density functional theory and the information-theoretic approach. The total energy decomposition analysis is beneficial to understand the origin and nature of isomeric stability. Our results showcase that the electrostatic potential is the dominant factor contributing to the isomeric stability of these fullerenes, and other contributions such as steric and quantum effects play minor but indispensable roles. This study also finds that the origin of the isomeric stability of these species is due to the spatial delocalization of the electron density. Our work should provide novel insights into the isomeric stability of fullerene molecules, which have found tremendous applications in solar-energy studies and nanomaterial sciences.
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Affiliation(s)
- Dongbo Zhao
- School
of Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, People’s Republic
of China
| | - Siyuan Liu
- College
of Chemistry and Chemical Engineering, Hunan
Normal University, Changsha 410081, People’s Republic
of China
| | - Chunying Rong
- College
of Chemistry and Chemical Engineering, Hunan
Normal University, Changsha 410081, People’s Republic
of China
| | - Aiguo Zhong
- School
of Pharmaceutical and Chemical Engineering, Taizhou University, Linhai 318000, Zhejiang, People’s Republic of China
| | - Shubin Liu
- Research
Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States
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33
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Bazargan G, Sohlberg K. Investigation of net unidirectional ring shuttling in a chemically fueled [2]catenane. J Mol Model 2018; 24:291. [PMID: 30242486 DOI: 10.1007/s00894-018-3830-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/12/2018] [Indexed: 11/25/2022]
Abstract
Switchable rotaxanes and catenanes are environmentally responsive mechanically interlocked molecular architectures (MIMAs). Because of their ability to exhibit reversible and controllable motion in response to environmental stimuli, switchable rotaxanes and catenanes show promise for the advancement of nanoscale devices. Herein we present a study of the first 'autonomous' catenane-based motor (Wilson et al. in Nature 534(7606):235-240, 2016) through a domestically developed simulation tool designed to capture the basic physics/chemistry of the ring shuttling process. The results of the simulation are consistent with the experimentally inferred unidirectional motion in the catenane motor. The factors that affect ring shuttling are explored, and the features of the system that could potentially be modified to influence the rate and directional preference of ring shuttling are reported.
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Affiliation(s)
- Gloria Bazargan
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA.
| | - Karl Sohlberg
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA
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34
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SCI: a robust and reliable density-based descriptor to determine multiple covalent bond orders. J Mol Model 2018; 24:213. [PMID: 30032451 DOI: 10.1007/s00894-018-3721-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/15/2018] [Indexed: 12/13/2022]
Abstract
Very recently [J. Phys. Chem. A 2018, 122 (11), 3087-3095], we proposed to employ the Pauli energy to identify and determine strong covalent interactions (SCI), whose bond order are equal to or larger than two. This is done through the signature isosurface shape between the two bonding atoms. We discovered that the signature shape for a double, triple, and quadruple covalent bond is like a dumbbell, donut (torus), and four-beats, respectively. Systems with even higher bond orders were examined and confirmed. This work is a follow-up study of our previous work. The dependence of the signature isosurface shape on the choice of methodologies and basis sets is systematically investigated. Its effectiveness and robustness in determining bond orders are highlighted again with more examples. In addition, using the molybdenum dimer in different environments, e.g., in vacuum, sandwiched between molecules, and encapsulated in the C80 cage, as illustrative examples, we show that, generally speaking, bond strength and bond order are two different chemical concepts. For systems containing transition metals, it is not always true that a short metal-metal bond length corresponds to a larger bond order. Put together, these results should provide additional pieces of convincing evidence showing that the SCI index is a robust and reliable density-based descriptor to accurately determine multiple covalent bond orders.
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35
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Rong C, Zhao D, Yu D, Liu S. Quantification and origin of cooperativity: insights from density functional reactivity theory. Phys Chem Chem Phys 2018; 20:17990-17998. [PMID: 29927447 DOI: 10.1039/c8cp03092h] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cooperativity is a widely used chemical concept whose existence is ubiquitous in chemical and biological systems but whose quantification is still controversial and origin much less appreciated. In this work, using the interaction energy of a molecular system, which is composed of multiple copies of a building block, we propose a quantitative measurement to evaluate the cooperativity effect. This quantification approach is then applied to six molecular systems, i.e., water cluster, argon cluster, protonated water cluster, zinc atom cluster, water cluster on top of a graphene sheet, and alpha helix of glycine amino acids, each with up to 20 copies of the building block. Cooperativity is seen in all these systems. Both positive and negative cooperativity effects are observed. Employing the two energy partition schemes in density functional theory and the information-theoretic quantities such as Shannon entropy, Fisher information, information gain, etc., we then examine the origin of the cooperativity effect for these systems. Strong linear correlations between the cooperativity measure and some of these theoretical quantities have been unveiled. With these correlations, we are able to quantitatively account for their origin of cooperativity. Our results show that the interactions governing the existence and validity of the cooperativity effect are complicated. An opposite mechanism in enthalpy-entropy compensation for positive and negative cooperativity has been unveiled. These results should provide new insights and understandings from a different viewpoint about the nature and origin of cooperativity to appreciate this vastly important chemical concept.
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Affiliation(s)
- Chunying Rong
- College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha Hunan 410081, P. R. China
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36
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Stei M, Carrascosa E, Dörfler A, Meyer J, Olasz B, Czakó G, Li A, Guo H, Wester R. Stretching vibration is a spectator in nucleophilic substitution. SCIENCE ADVANCES 2018; 4:eaas9544. [PMID: 29984305 PMCID: PMC6035035 DOI: 10.1126/sciadv.aas9544] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/22/2018] [Indexed: 06/08/2023]
Abstract
How chemical reactions are influenced by reactant vibrational excitation is a long-standing question at the core of chemical reaction dynamics. In reactions of polyatomic molecules, where the Polanyi rules are not directly applicable, certain vibrational modes can act as spectators. In nucleophilic substitution reactions, CH stretching vibrations have been considered to be such spectators. While this picture has been challenged by some theoretical studies, experimental insight has been lacking. We show that the nucleophilic substitution reaction of F- with CH3I is minimally influenced by an excitation of the symmetric CH stretching vibration. This contrasts with the strong vibrational enhancement of the proton transfer reaction measured in parallel. The spectator behavior of the stretching mode is supported by both quasi-classical trajectory simulations and the Sudden Vector Projection model.
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Affiliation(s)
- Martin Stei
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstraße 25/3, 6020 Innsbruck, Austria
| | - Eduardo Carrascosa
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstraße 25/3, 6020 Innsbruck, Austria
| | - Alexander Dörfler
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstraße 25/3, 6020 Innsbruck, Austria
| | - Jennifer Meyer
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstraße 25/3, 6020 Innsbruck, Austria
| | - Balázs Olasz
- Department of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Gábor Czakó
- Department of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Anyang Li
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry, Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710127 Xian, P. R. China
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Roland Wester
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstraße 25/3, 6020 Innsbruck, Austria
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37
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Hamlin TA, Swart M, Bickelhaupt FM. Nucleophilic Substitution (S N 2): Dependence on Nucleophile, Leaving Group, Central Atom, Substituents, and Solvent. Chemphyschem 2018; 19:1315-1330. [PMID: 29542853 PMCID: PMC6001448 DOI: 10.1002/cphc.201701363] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Indexed: 11/12/2022]
Abstract
The reaction potential energy surface (PES), and thus the mechanism of bimolecular nucleophilic substitution (SN 2), depends profoundly on the nature of the nucleophile and leaving group, but also on the central, electrophilic atom, its substituents, as well as on the medium in which the reaction takes place. Here, we provide an overview of recent studies and demonstrate how changes in any one of the aforementioned factors affect the SN 2 mechanism. One of the most striking effects is the transition from a double-well to a single-well PES when the central atom is changed from a second-period (e. g. carbon) to a higher-period element (e.g, silicon, germanium). Variations in nucleophilicity, leaving group ability, and bulky substituents around a second-row element central atom can then be exploited to change the single-well PES back into a double-well. Reversely, these variations can also be used to produce a single-well PES for second-period elements, for example, a stable pentavalent carbon species.
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Affiliation(s)
- Trevor A. Hamlin
- Department of Theoretical Chemistry andAmsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Marcel Swart
- Department of Theoretical Chemistry andAmsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Institut de Química Computacional I Catàlisi and Department de QuímicaUniversitat de Girona17003GironaSpain
- ICREAPg. Lluís Companys 2308010BarcelonaSpain
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry andAmsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Institute of Molecules and Materials (IMM)Radboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
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38
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Alkorta I, Thacker JCR, Popelier PLA. An interacting quantum atom study of model S N 2 reactions (X - ···CH 3 X, X = F, Cl, Br, and I). J Comput Chem 2018; 39:546-556. [PMID: 29125196 PMCID: PMC5836863 DOI: 10.1002/jcc.25098] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/25/2017] [Accepted: 10/17/2017] [Indexed: 12/30/2022]
Abstract
The quantum chemical topology method has been used to analyze the energetic profiles in the X- + CH3 X → XCH3 + X- SN 2 reactions, with X = F, Cl, Br, and I. The evolution of the electron density properties at the BCPs along the reaction coordinate has been analysed. The interacting quantum atoms (IQA) method has been used to evaluate the intra-atomic and interatomic energy variations along the reaction path. The different energetic terms have been examined by the relative energy gradient method and the ANANKE program, which enables automatic and unbiased IQA analysis. Four of the six most important IQA energy contributions were needed to reproduce the reaction barrier common to all reactions. The four reactions considered share many common characteristics but when X = F a number of particularities occur. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3Madrid28006Spain
| | - Joseph C. R. Thacker
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, M1 7DN, Great Britain, and School of Chemistry, University of Manchester, Oxford RoadManchesterM13 9PLGreat Britain
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, M1 7DN, Great Britain, and School of Chemistry, University of Manchester, Oxford RoadManchesterM13 9PLGreat Britain
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39
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Liu S, Rong C, Lu T. Electronic forces as descriptors of nucleophilic and electrophilic regioselectivity and stereoselectivity. Phys Chem Chem Phys 2018; 19:1496-1503. [PMID: 27982154 DOI: 10.1039/c6cp06376d] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One of the main tasks of theoretical chemistry is to rationalize computational results with chemical insights. Key concepts of such nature include nucleophilicity, electrophilicity, regioselectivity, and stereoselectivity. While computational tools are available to predict barrier heights and other reactivity properties with acceptable accuracy, a conceptual framework to appreciate above quantities is still lacking. In this work, we introduce the electronic force as the fundamental driving force of chemical processes to understand and predict molecular reactivity. It has three components but only two are independent. These forces, electrostatic and steric, can be employed as reliable descriptors for nucleophilic and electrophilic regioselectivity and stereoselectivity. The advantages of using these forces to evaluate molecular reactivity are that electrophilic and nucleophilic attacks are featured by distinct characteristics in the electrostatic force and no knowledge of quantum effects included in the kinetic and exchange-correlation energies is required. Examples are provided to highlight the validity and general applicability of these reactivity descriptors. Possible applications in ambident reactivity, σ and π holes, frustrated Lewis pairs, and stereoselective reactions are also included in this work.
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Affiliation(s)
- Shubin Liu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Synergetic Innovation Center for Quantum Effects and Applications (SICQEA), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China and Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, USA.
| | - Chunying Rong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Synergetic Innovation Center for Quantum Effects and Applications (SICQEA), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
| | - Tian Lu
- Beijing Kein Research Center for Natural Sciences, Beijing 100022, P. R. China and Beijing Quanton Technology Co. Ltd., Beijing 100024, P. R. China
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40
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Abstract
Steric charge is an informative descriptor providing novel insights to appreciate the steric effect and stereoselectivity for chemical processes and transformations.
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Affiliation(s)
- Shubin Liu
- Research Computing Center, University of North Carolina
- Chapel Hill
- USA
| | - Lianghong Liu
- Department of Pharmacy, Hunan University of Medicine
- P. R. China
| | - Donghai Yu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University
- P. R. China
| | - Chunying Rong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University
- P. R. China
| | - Tian Lu
- Beijing Kein Research Center for Natural Sciences
- Beijing 100022
- P. R. China
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41
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Cao X, Liu S, Rong C, Lu T, Liu S. Is there a generalized anomeric effect? Analyses from energy components and information-theoretic quantities from density functional reactivity theory. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.09.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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42
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Cao X, Rong C, Zhong A, Lu T, Liu S. Molecular acidity: An accurate description with information-theoretic approach in density functional reactivity theory. J Comput Chem 2017; 39:117-129. [PMID: 29076175 DOI: 10.1002/jcc.25090] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/14/2017] [Accepted: 10/06/2017] [Indexed: 11/10/2022]
Abstract
Molecular acidity is one of the important physiochemical properties of a molecular system, yet its accurate calculation and prediction are still an unresolved problem in the literature. In this work, we propose to make use of the quantities from the information-theoretic (IT) approach in density functional reactivity theory and provide an accurate description of molecular acidity from a completely new perspective. To illustrate our point, five different categories of acidic series, singly and doubly substituted benzoic acids, singly substituted benzenesulfinic acids, benzeneseleninic acids, phenols, and alkyl carboxylic acids, have been thoroughly examined. We show that using IT quantities such as Shannon entropy, Fisher information, Ghosh-Berkowitz-Parr entropy, information gain, Onicescu information energy, and relative Rényi entropy, one is able to simultaneously predict experimental pKa values of these different categories of compounds. Because of the universality of the quantities employed in this work, which are all density dependent, our approach should be general and be applicable to other systems as well. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Xiaofang Cao
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China
| | - Chunying Rong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China
| | - Aiguo Zhong
- School of Pharmaceutical and Chemical Engineering, Taizhou University, 1139 Shifu Road, Linhai, Zhejiang, 318000, People's Republic of China
| | - Tian Lu
- Beijing Kein Research Center for Natural Sciences, Beijing, 100022, People's Republic of China
| | - Shubin Liu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Research Computing Center, University of North Carolina, Chapel Hill, North Carolina, 27599-3420
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43
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Anomeric effect revisited: Perspective from information-theoretic approach in density functional reactivity theory. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.06.048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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44
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Affiliation(s)
- Jennifer Meyer
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, 6020 Innsbruck, Austria
| | - Roland Wester
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, 6020 Innsbruck, Austria
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45
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Uggerud E. The Factors Determining Reactivity in Nucleophilic Substitution. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2017. [DOI: 10.1016/bs.apoc.2017.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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46
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Huang Y, Rong C, Zhang R, Liu S. Evaluating frontier orbital energy and HOMO/LUMO gap with descriptors from density functional reactivity theory. J Mol Model 2016; 23:3. [DOI: 10.1007/s00894-016-3175-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 11/22/2016] [Indexed: 12/19/2022]
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47
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de Paul N. Nziko V, Scheiner S. Effects of Angular Deformation on the Energetics of the S N2 Reaction. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | - Steve Scheiner
- Department of Chemistry and Biochemistry; Utah State University; 84322-0300 Logan UT USA
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48
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Anderson JSM, Melin J, Ayers PW. Using the general-purpose reactivity indicator: challenging examples. J Mol Model 2016; 22:57. [DOI: 10.1007/s00894-016-2910-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 01/07/2016] [Indexed: 11/29/2022]
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49
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Alipour M, Safari Z. From information theory to quantitative description of steric effects. Phys Chem Chem Phys 2016; 18:17917-29. [DOI: 10.1039/c6cp02750d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, further evidences of the efficiency of informational theory for a quantitative description of steric effects are showcased.
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Affiliation(s)
- Mojtaba Alipour
- Department of Chemistry
- College of Sciences
- Shiraz University
- Shiraz
- Iran
| | - Zahra Safari
- Department of Chemistry
- College of Sciences
- Shiraz University
- Shiraz
- Iran
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50
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Influence of the leaving group on the dynamics of a gas-phase SN2 reaction. Nat Chem 2015; 8:151-6. [DOI: 10.1038/nchem.2400] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 10/16/2015] [Indexed: 12/20/2022]
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