1
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Gorantla K, Krishnan A, Waheed SO, Varghese A, DiCastri I, LaRouche C, Paik M, Fields GB, Karabencheva-Christova TG. Novel Insights into the Catalytic Mechanism of Collagenolysis by Zn(II)-Dependent Matrix Metalloproteinase-1. Biochemistry 2024; 63:1925-1940. [PMID: 38963231 PMCID: PMC11309001 DOI: 10.1021/acs.biochem.4c00076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 06/14/2024] [Accepted: 06/24/2024] [Indexed: 07/05/2024]
Abstract
Collagen hydrolysis, catalyzed by Zn(II)-dependent matrix metalloproteinases (MMPs), is a critical physiological process. Despite previous computational investigations into the catalytic mechanisms of MMP-mediated collagenolysis, a significant knowledge gap in understanding remains regarding the influence of conformational sampling and entropic contributions at physiological temperature on enzymatic collagenolysis. In our comprehensive multilevel computational study, employing quantum mechanics/molecular mechanics (QM/MM) metadynamics (MetD) simulations, we aimed to bridge this gap and provide valuable insights into the catalytic mechanism of MMP-1. Specifically, we compared the full enzyme-substrate complex in solution, clusters in solution, and gas-phase to elucidate insights into MMP-1-catalyzed collagenolysis. Our findings reveal significant differences in the catalytic mechanism when considering thermal effects and the dynamic evolution of the system, contrasting with conventional static potential energy surface QM/MM reaction path studies. Notably, we observed a significant stabilization of the critical tetrahedral intermediate, attributed to contributions from conformational flexibility and entropy. Moreover, we found that protonation of the scissile bond nitrogen occurs via proton transfer from a Zn(II)-coordinated hydroxide rather than from a solvent water molecule. Following C-N bond cleavage, the C-terminus remains coordinated to the catalytic Zn(II), while the N-terminus forms a hydrogen bond with a solvent water molecule. Subsequently, the release of the C-terminus is facilitated by the coordination of a water molecule. Our study underscores the pivotal role of protein conformational dynamics at physiological temperature in stabilizing the transition state of the rate-limiting step and key intermediates, compared to the corresponding reaction in solution. These fundamental insights into the mechanism of collagen degradation provide valuable guidance for the development of MMP-1-specific inhibitors.
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Affiliation(s)
- Koteswara
Rao Gorantla
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Anandhu Krishnan
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Sodiq O. Waheed
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Ann Varghese
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Isabella DiCastri
- Department
of Chemical Engineering, Michigan Technological
University, Houghton, Michigan 49931, United States
| | - Ciara LaRouche
- Department
of Chemical Engineering, Michigan Technological
University, Houghton, Michigan 49931, United States
| | - Meredith Paik
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Gregg B. Fields
- Department
of Chemistry and Biochemistry and I-HEALTH, Florida Atlantic University, Jupiter, Florida 33458, United States
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2
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Zhang H, Juraskova V, Duarte F. Modelling chemical processes in explicit solvents with machine learning potentials. Nat Commun 2024; 15:6114. [PMID: 39030199 PMCID: PMC11271496 DOI: 10.1038/s41467-024-50418-6] [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: 08/06/2023] [Accepted: 07/08/2024] [Indexed: 07/21/2024] Open
Abstract
Solvent effects influence all stages of the chemical processes, modulating the stability of intermediates and transition states, as well as altering reaction rates and product ratios. However, accurately modelling these effects remains challenging. Here, we present a general strategy for generating reactive machine learning potentials to model chemical processes in solution. Our approach combines active learning with descriptor-based selectors and automation, enabling the construction of data-efficient training sets that span the relevant chemical and conformational space. We apply this strategy to investigate a Diels-Alder reaction in water and methanol. The generated machine learning potentials enable us to obtain reaction rates that are in agreement with experimental data and analyse the influence of these solvents on the reaction mechanism. Our strategy offers an efficient approach to the routine modelling of chemical reactions in solution, opening up avenues for studying complex chemical processes in an efficient manner.
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Affiliation(s)
- Hanwen Zhang
- Chemistry Research Laboratory, Oxford, United Kingdom
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3
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Hao H, Ruiz Pestana L, Qian J, Liu M, Xu Q, Head‐Gordon T. Chemical transformations and transport phenomena at interfaces. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hongxia Hao
- Kenneth S. Pitzer Theory Center and Department of Chemistry University of California Berkeley California USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
| | - Luis Ruiz Pestana
- Department of Civil and Architectural Engineering University of Miami Coral Gables Florida USA
| | - Jin Qian
- Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
| | - Meili Liu
- Department of Civil and Architectural Engineering University of Miami Coral Gables Florida USA
| | - Qiang Xu
- Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
| | - Teresa Head‐Gordon
- Kenneth S. Pitzer Theory Center and Department of Chemistry University of California Berkeley California USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
- Department of Bioengineering and Chemical and Biomolecular Engineering University of California Berkeley California USA
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4
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BF3–Catalyzed Diels–Alder Reaction between Butadiene and Methyl Acrylate in Aqueous Solution—An URVA and Local Vibrational Mode Study. Catalysts 2022. [DOI: 10.3390/catal12040415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In this study we investigate the Diels–Alder reaction between methyl acrylate and butadiene, which is catalyzed by BF3 Lewis acid in explicit water solution, using URVA and Local Mode Analysis as major tools complemented with NBO, electron density and ring puckering analyses. We considered four different starting orientations of methyl acrylate and butadiene, which led to 16 DA reactions in total. In order to isolate the catalytic effects of the BF3 catalyst and those of the water environment and exploring how these effects are synchronized, we systematically compared the non-catalyzed reaction in gas phase and aqueous solution with the catalyzed reaction in gas phase and aqueous solution. Gas phase studies were performed at the B3LYP/6-311+G(2d,p) level of theory and studies in aqueous solution were performed utilizing a QM/MM approach at the B3LYP/6-311+G(2d,p)/AMBER level of theory. The URVA results revealed reaction path curvature profiles with an overall similar pattern for all 16 reactions showing the same sequence of CC single bond formation for all of them. In contrast to the parent DA reaction with symmetric substrates causing a synchronous bond formation process, here, first the new CC single bond on the CH2 side of methyl acrylate is formed followed by the CC bond at the ester side. As for the parent DA reaction, both bond formation events occur after the TS, i.e., they do not contribute to the energy barrier. What determines the barrier is the preparation process for CC bond formation, including the approach diene and dienophile, CC bond length changes and, in particular, rehybridization of the carbon atoms involved in the formation of the cyclohexene ring. This process is modified by both the BF3 catalyst and the water environment, where both work in a hand-in-hand fashion leading to the lowest energy barrier of 9.06 kcal/mol found for the catalyzed reaction R1 in aqueous solution compared to the highest energy barrier of 20.68 kcal/mol found for the non-catalyzed reaction R1 in the gas phase. The major effect of the BF3 catalyst is the increased mutual polarization and the increased charge transfer between methyl acrylate and butadiene, facilitating the approach of diene and dienophile and the pyramidalization of the CC atoms involved in the ring formation, which leads to a lowering of the activation energy. The catalytic effect of water solution is threefold. The polar environment leads also to increased polarization and charge transfer between the reacting species, similar as in the case of the BF3 catalyst, although to a smaller extend. More important is the formation of hydrogen bonds with the reaction complex, which are stronger for the TS than for the reactant, thus stabilizing the TS which leads to a further reduction of the activation energy. As shown by the ring puckering analysis, the third effect of water is space confinement of the reacting partners, conserving the boat form of the six-member ring from the entrance to the exit reaction channel. In summary, URVA combined with LMA has led to a clearer picture on how both BF3 catalyst and aqueous environment in a synchronized effort lower the reaction barrier. These new insights will serve to further fine-tune the DA reaction of methyl acrylate and butadiene and DA reactions in general.
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5
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Jeyapalan V, Varadharajan R, Babu Veerakanellore G, Ramamurthy V. Water: An underappreciated reaction medium for photodimerizations. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2021.113492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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6
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Hennefarth MR, Alexandrova AN. Heterogeneous Intramolecular Electric Field as a Descriptor of Diels–Alder Reactivity. J Phys Chem A 2021; 125:1289-1298. [DOI: 10.1021/acs.jpca.1c00181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Matthew R. Hennefarth
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Anastassia N. Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
- California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, California 90095-1569, United States
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7
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Ruiz-Lopez MF, Francisco JS, Martins-Costa MTC, Anglada JM. Molecular reactions at aqueous interfaces. Nat Rev Chem 2020; 4:459-475. [PMID: 37127962 DOI: 10.1038/s41570-020-0203-2] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2020] [Indexed: 12/16/2022]
Abstract
This Review aims to critically analyse the emerging field of chemical reactivity at aqueous interfaces. The subject has evolved rapidly since the discovery of the so-called 'on-water catalysis', alluding to the dramatic acceleration of reactions at the surface of water or at its interface with hydrophobic media. We review critical experimental studies in the fields of atmospheric and synthetic organic chemistry, as well as related research exploring the origins of life, to showcase the importance of this phenomenon. The physico-chemical aspects of these processes, such as the structure, dynamics and thermodynamics of adsorption and solvation processes at aqueous interfaces, are also discussed. We also present the basic theories intended to explain interface catalysis, followed by the results of advanced ab initio molecular-dynamics simulations. Although some topics addressed here have already been the focus of previous reviews, we aim at highlighting their interconnection across diverse disciplines, providing a common perspective that would help us to identify the most fundamental issues still incompletely understood in this fast-moving field.
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8
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Kitanosono T, Kobayashi S. Reactions in Water Involving the “On‐Water” Mechanism. Chemistry 2020; 26:9408-9429. [DOI: 10.1002/chem.201905482] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/08/2020] [Indexed: 11/07/2022]
Affiliation(s)
- Taku Kitanosono
- Department of ChemistrySchool of ScienceThe University of Tokyo Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Shū Kobayashi
- Department of ChemistrySchool of ScienceThe University of Tokyo Hongo Bunkyo-ku Tokyo 113-0033 Japan
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9
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Sowlati-Hashjin S, Carbone P, Karttunen M. Insights into the Polyhexamethylene Biguanide (PHMB) Mechanism of Action on Bacterial Membrane and DNA: A Molecular Dynamics Study. J Phys Chem B 2020; 124:4487-4497. [DOI: 10.1021/acs.jpcb.0c02609] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Shahin Sowlati-Hashjin
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
- The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Paola Carbone
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
- The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
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10
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Yang Y, Zhang X, Zhong LP, Lan J, Li X, Li CC, Chung LW. Unusual KIE and dynamics effects in the Fe-catalyzed hetero-Diels-Alder reaction of unactivated aldehydes and dienes. Nat Commun 2020; 11:1850. [PMID: 32296076 PMCID: PMC7160212 DOI: 10.1038/s41467-020-15599-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/13/2020] [Indexed: 12/30/2022] Open
Abstract
Hetero-Diels-Alder (HDA) reaction is an important synthetic method for many natural products. An iron(III) catalyst was developed to catalyze the challenging HDA reaction of unactivated aldehydes and dienes with high selectivity. Here we report extensive density-functional theory (DFT) calculations and molecular dynamics simulations that show effects of iron (including its coordinate mode and/or spin state) on the dynamics of this reaction: considerably enhancing dynamically stepwise process, broadening entrance channel and narrowing exit channel from concerted asynchronous transition states. Also, our combined computational and experimental secondary KIE studies reveal unexpectedly large KIE values for the five-coordinate pathway even with considerable C-C bond forming, due to equilibrium isotope effect from the change in the metal coordination. Moreover, steric and electronic effects are computationally shown to dictate the C=O chemoselectivity for an α,β-unsaturated aldehyde, which is verified experimentally. Our mechanistic study may help design homogeneous, heterogeneous and biological catalysts for this challenging reaction.
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Affiliation(s)
- Yuhong Yang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xiaoyong Zhang
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Li-Ping Zhong
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jialing Lan
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xin Li
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chuang-Chuang Li
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Lung Wa Chung
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.
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11
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Accurate Diels-Alder Energies and Endo Selectivity in Ionic Liquids Using the OPLS-VSIL Force Field. Int J Mol Sci 2020; 21:ijms21041190. [PMID: 32054023 PMCID: PMC7072795 DOI: 10.3390/ijms21041190] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/06/2020] [Accepted: 02/08/2020] [Indexed: 01/17/2023] Open
Abstract
Our recently developed optimized potentials for liquid simulations-virtual site ionic liquid (OPLS-VSIL) force field has been shown to provide accurate bulk phase properties and local ion-ion interactions for a wide variety of imidazolium-based ionic liquids. The force field features a virtual site that offloads negative charge to inside the plane of the ring with careful attention given to hydrogen bonding interactions. In this study, the Diels-Alder reaction between cyclopentadiene and methyl acrylate was computationally investigated in the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate, [BMIM][PF6], as a basis for the validation of the OPLS-VSIL to properly reproduce a reaction medium environment. Mixed ab initio quantum mechanics and molecular mechanics (QM/MM) calculations coupled to free energy perturbation and Monte Carlo sampling (FEP/MC) that utilized M06-2X/6-31G(d) and OPLS-VSIL gave activation free energy barriers of 14.9 and 16.0 kcal/mol for the endo-cis and exo-cis Diels-Alder reaction pathways, respectively (exptl. ΔH‡ of 14.6 kcal/mol). The endo selectivity trend was correctly predicted with a calculated 73% endo preference. The rate and selectivity enhancements present in the endo conformation were found to arise from preferential hydrogen bonding with the exposed C4 ring hydrogen on the BMIM cation. Weaker electronic stabilization of the exo transition state was predicted. For comparison, our earlier ±0.8 charge-scaled OPLS-2009IL force field also yielded a ΔG‡ of 14.9 kcal/mol for the favorable endo reaction pathway but did not adequately capture the highly organized solvent interactions present between the cation and Diels-Alder transition state.
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12
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Jia W, Sun Y, Zuo M, Feng Y, Tang X, Zeng X, Lin L. One-Pot Synthesis of Renewable Phthalic Anhydride from 5-Hydroxymethfurfural by using MoO 3 /Cu(NO 3 ) 2 as Catalyst. CHEMSUSCHEM 2020; 13:640-646. [PMID: 31758660 DOI: 10.1002/cssc.201902590] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/17/2019] [Indexed: 06/10/2023]
Abstract
Herein, a synthetic pathway to renewable phthalic anhydride (PA) from 5-hydroxymethfurfural (HMF) in one pot is reported. The commonly available catalysts MoO3 and Cu(NO3 )2 play a crucial role in integrating the multiple steps of the reaction, namely decarbonylation of HMF to active furyl intermediate (AFI), oxidation of HMF to maleic anhydride (MA), Diels-Alder cycloaddition of AFI and MA, and subsequent dehydration, in one pot. Under mild reaction conditions, a 63.2 % yield of PA is obtained from HMF. Compared with the currently reported route to renewable PA based on the Diels-Alder cycloaddition of biomass-derived MA and furan, this convenient one-pot synthesis represents a great improvement in efficiency.
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Affiliation(s)
- Wenlong Jia
- Xiamen Key Laboratory of Clean and High-valued Utilization for Biomass, College of Energy, Xiamen University, Xiamen, 361102, P.R. China
| | - Yong Sun
- Xiamen Key Laboratory of Clean and High-valued Utilization for Biomass, College of Energy, Xiamen University, Xiamen, 361102, P.R. China
- Fujian Engineering and Research Center of Clean and High-valued Technologies for Biomass, Xiamen University, Xiamen, 361102, P.R. China
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Hubei Normal University, Huangshi, 435002, Hubei, P.R. China
| | - Miao Zuo
- Xiamen Key Laboratory of Clean and High-valued Utilization for Biomass, College of Energy, Xiamen University, Xiamen, 361102, P.R. China
| | - Yunchao Feng
- Xiamen Key Laboratory of Clean and High-valued Utilization for Biomass, College of Energy, Xiamen University, Xiamen, 361102, P.R. China
| | - Xing Tang
- Xiamen Key Laboratory of Clean and High-valued Utilization for Biomass, College of Energy, Xiamen University, Xiamen, 361102, P.R. China
| | - Xianhai Zeng
- Xiamen Key Laboratory of Clean and High-valued Utilization for Biomass, College of Energy, Xiamen University, Xiamen, 361102, P.R. China
| | - Lu Lin
- Xiamen Key Laboratory of Clean and High-valued Utilization for Biomass, College of Energy, Xiamen University, Xiamen, 361102, P.R. China
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13
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Pestana LR, Hao H, Head-Gordon T. Diels-Alder Reactions in Water Are Determined by Microsolvation. NANO LETTERS 2020; 20:606-611. [PMID: 31771330 DOI: 10.1021/acs.nanolett.9b04369] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nanoconfined aqueous environments and the recent advent of accelerated chemistry in microdroplets are increasingly being investigated for catalysis. The mechanisms underlying the enhanced reactivity in alternate solvent environments and whether the enhanced reactivity due to nanoconfinement is a universal phenomenon are not fully understood. Here, we use ab initio molecular dynamics simulations to characterize the free energy of a retro-Diels-Alder reaction in bulk water at very different densities and in water nanoconfined by parallel graphene sheets. We find that the broadly different global solvation environments accelerate the reactions to a similar degree with respect to the gas-phase reaction, with activation free energies that do not differ by more than kbT from each other. The reason for the same acceleration factor in the extremely different solvation environments is that it is the microsolvation of the dienophile's carbonyl group that governs the transition-state stabilization and mechanism, which is not significantly disrupted by either the lower density in bulk water or the strong nanoconfinement conditions used here. Our results also suggest that significant acceleration of Diels-Alder reactions in microdroplets or on-water conditions cannot arise from local microsolvation when water is present but instead must come from highly altered reaction environments that drastically change the reaction mechanisms.
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Affiliation(s)
- Luis Ruiz Pestana
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
- Pitzer Center for Theoretical Chemistry, Departments of Chemistry, Bioengineering, and Chemical and Biomolecular Engineering , University of California , Berkeley , California 94720 , United States
| | - Hongxia Hao
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
- Pitzer Center for Theoretical Chemistry, Departments of Chemistry, Bioengineering, and Chemical and Biomolecular Engineering , University of California , Berkeley , California 94720 , United States
| | - Teresa Head-Gordon
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
- Pitzer Center for Theoretical Chemistry, Departments of Chemistry, Bioengineering, and Chemical and Biomolecular Engineering , University of California , Berkeley , California 94720 , United States
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14
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Gallo A, Farinha ASF, Emwas AH, Santana A, Nielsen RJ, Goddard WA, Mishra H. Reply to the 'Comment on "The chemical reactions in electrosprays of water do not always correspond to those at the pristine air-water interface"' by A. J. Colussi and S. Enami, Chem. Sci., 2019, 10, DOI: 10.1039/c9sc00991d. Chem Sci 2019; 10:8256-8261. [PMID: 31859689 PMCID: PMC6837019 DOI: 10.1039/c9sc02702e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 06/30/2019] [Indexed: 12/20/2022] Open
Abstract
We explain why chemical reactions in/on electrosprays of water may not always represent those at the air–water interface. Thus, electrospray-based techniques cannot be relied upon as generalized “surface-specific” platforms for water. The air–water interface serves as a crucial site for numerous chemical and physical processes in environmental science and engineering, such as cloud chemistry, ocean-atmosphere exchange, and wastewater treatment. The development of “surface-selective” techniques for probing interfacial properties of water therefore lies at the forefront of research in chemical science. Recently, researchers have adapted electrospray ionization mass spectrometry (ESIMS) to generate microdroplets of water to investigate interfacial phenomena at thermodynamic equilibrium. In contrast, using a broad set of experimental and theoretical techniques, we found that electrosprays of water could facilitate partially hydrated (gas-phase) ions (e.g., H3O+·(H2O)2) to drive/catalyze chemical reactions that are otherwise not possible to accomplish by purely interfacial effects (e.g., enhanced water–hydrophobe surface area) (Chem. Sci., 2019, 10, 2566). Thus, techniques exploiting electrosprays of water cannot be relied upon as generalized surface-selective platforms. Here, we respond to the comments raised by Colussi & Enami (Chem. Sci., 2019, 10, DOI: ; 10.1039/c9sc00991d) on our paper.
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Affiliation(s)
- Adair Gallo
- King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia . .,Water Desalination and Reuse Center (WDRC) , Thuwal 23955-6900 , Saudi Arabia.,Division of Biological and Environmental Sciences (BESE) , Thuwal 23955-6900 , Saudi Arabia
| | - Andreia S F Farinha
- King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia . .,Water Desalination and Reuse Center (WDRC) , Thuwal 23955-6900 , Saudi Arabia.,Division of Biological and Environmental Sciences (BESE) , Thuwal 23955-6900 , Saudi Arabia
| | - Abdul-Hamid Emwas
- King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia . .,Core Labs , Thuwal 23955-6900 , Saudi Arabia
| | - Adriano Santana
- King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia . .,Water Desalination and Reuse Center (WDRC) , Thuwal 23955-6900 , Saudi Arabia.,Division of Biological and Environmental Sciences (BESE) , Thuwal 23955-6900 , Saudi Arabia
| | - Robert J Nielsen
- Materials and Process Simulation Center , California Institute of Technology , Pasadena , CA 91125 , USA
| | - William A Goddard
- Materials and Process Simulation Center , California Institute of Technology , Pasadena , CA 91125 , USA
| | - Himanshu Mishra
- King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia . .,Water Desalination and Reuse Center (WDRC) , Thuwal 23955-6900 , Saudi Arabia.,Division of Biological and Environmental Sciences (BESE) , Thuwal 23955-6900 , Saudi Arabia
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15
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Li P, Liu F, Shao Y, Mei Y. Computational Insights into Endo/Exo Selectivity of the Diels–Alder Reaction in Explicit Solvent at Ab Initio Quantum Mechanical/Molecular Mechanical Level. J Phys Chem B 2019; 123:5131-5138. [DOI: 10.1021/acs.jpcb.9b01989] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pengfei Li
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
| | - Fengjiao Liu
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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16
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Zhang Y, Luo L, Ge J, Yan SQ, Peng YX, Liu YR, Liu JX, Liu C, Ma T, Luo HQ. "On Water" Direct Organocatalytic Cyanoarylmethylation of Isatins for the Diastereoselective Synthesis of 3-Hydroxy-3-cyanomethyl Oxindoles. J Org Chem 2019; 84:4000-4008. [PMID: 30864430 DOI: 10.1021/acs.joc.8b03194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An "on water" organocatalytic cyanoarylmethylation of aryl acetonitrile to isatins is developed, giving products in high yields and up to excellent diastereoselectivities. A remarkable enhancement of reaction rates and diastereoselectivities by water was observed under mild conditions. Moreover, this approach provides a highly efficient and environmentally benign access to thermodynamic 3-hydroxy-3-cyanomethyl oxindoles.
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Affiliation(s)
- Yong Zhang
- Key Laboratory of Organo-pharmaceutical Chemistry , Gannan Normal University , Ganzhou 341000 , China
| | - Liang Luo
- Key Laboratory of Organo-pharmaceutical Chemistry , Gannan Normal University , Ganzhou 341000 , China
| | - Jin Ge
- Key Laboratory of Organo-pharmaceutical Chemistry , Gannan Normal University , Ganzhou 341000 , China
| | - Su-Qiong Yan
- Key Laboratory of Organo-pharmaceutical Chemistry , Gannan Normal University , Ganzhou 341000 , China
| | - Yan-Xin Peng
- Key Laboratory of Organo-pharmaceutical Chemistry , Gannan Normal University , Ganzhou 341000 , China
| | - Ya-Ru Liu
- Key Laboratory of Organo-pharmaceutical Chemistry , Gannan Normal University , Ganzhou 341000 , China
| | - Jin-Xiang Liu
- Key Laboratory of Organo-pharmaceutical Chemistry , Gannan Normal University , Ganzhou 341000 , China
| | - Chong Liu
- Inorganic Systems Engineering group, Chemical Engineering Department , Delft University of Technology , Van der Maasweg 9 , 2629 HZ Delft , The Netherlands
| | - Tianqiong Ma
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering , Lanzhou University , Lanzhou , Gansu 730000 , China
| | - Hai-Qing Luo
- Key Laboratory of Organo-pharmaceutical Chemistry , Gannan Normal University , Ganzhou 341000 , China
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17
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Chang YL, Sasaki T, Ribas-Ariño J, Machida M, Shiga M. Understanding Competition of Polyalcohol Dehydration Reactions in Hot Water. J Phys Chem B 2019; 123:1662-1671. [DOI: 10.1021/acs.jpcb.8b11615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yong Lik Chang
- Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa 277-8561, Japan
| | - Takehiko Sasaki
- Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa 277-8561, Japan
| | - Jordi Ribas-Ariño
- Departament de Química-Física i CERQT, Universitat de Barcelona, Diagonal, 645, 08028 Barcelona, Spain
| | - Masahiko Machida
- Center for Computational Science and e-Systems, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
| | - Motoyuki Shiga
- Center for Computational Science and e-Systems, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
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18
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Gallo A, Farinha ASF, Dinis M, Emwas AH, Santana A, Nielsen RJ, Goddard WA, Mishra H. The chemical reactions in electrosprays of water do not always correspond to those at the pristine air-water interface. Chem Sci 2018; 10:2566-2577. [PMID: 30996971 PMCID: PMC6422012 DOI: 10.1039/c8sc05538f] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 12/21/2018] [Indexed: 12/11/2022] Open
Abstract
The recent application of electrosprays to characterize the air-water interface, along with the reports on dramatically accelerated chemical reactions in aqueous electrosprays, have sparked a broad interest. Herein, we report on complementary laboratory and in silico experiments tracking the oligomerization of isoprene, an important biogenic gas, in electrosprays and isoprene-water emulsions to differentiate the contributions of interfacial effects from those of high voltages leading to charge-separation and concentration of reactants in the electrosprays. To this end, we employed electrospray ionization mass spectrometry, proton nuclear magnetic resonance, ab initio calculations and molecular dynamics simulations. We found that the oligomerization of isoprene in aqueous electrosprays involved minimally hydrated and highly reactive hydronium ions. Those conditions, however, are non-existent at pristine air-water interfaces and oil-water emulsions under normal temperature and pressure. Thus, electrosprays should be complemented with surface-specific platforms and theoretical methods to reliably investigate chemistries at the pristine air-water interface.
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Affiliation(s)
- Adair Gallo
- King Abdullah University of Science and Technology (KAUST) , Saudi Arabia . .,Water Desalination and Reuse Center (WDRC) , Saudi Arabia.,Division of Biological and Environmental Sciences (BESE) , Saudi Arabia
| | - Andreia S F Farinha
- King Abdullah University of Science and Technology (KAUST) , Saudi Arabia . .,Water Desalination and Reuse Center (WDRC) , Saudi Arabia.,Division of Biological and Environmental Sciences (BESE) , Saudi Arabia
| | - Miguel Dinis
- King Abdullah University of Science and Technology (KAUST) , Saudi Arabia . .,KAUST Catalysis Center (KCC) , Saudi Arabia
| | - Abdul-Hamid Emwas
- King Abdullah University of Science and Technology (KAUST) , Saudi Arabia . .,Imaging and Characterization Core Laboratory , Thuwal 23955-6900 , Saudi Arabia
| | - Adriano Santana
- King Abdullah University of Science and Technology (KAUST) , Saudi Arabia . .,Water Desalination and Reuse Center (WDRC) , Saudi Arabia.,Division of Biological and Environmental Sciences (BESE) , Saudi Arabia
| | - Robert J Nielsen
- Materials and Process Simulation Center , California Institute of Technology , Pasadena , CA 91125 , USA
| | - William A Goddard
- Materials and Process Simulation Center , California Institute of Technology , Pasadena , CA 91125 , USA
| | - Himanshu Mishra
- King Abdullah University of Science and Technology (KAUST) , Saudi Arabia . .,Water Desalination and Reuse Center (WDRC) , Saudi Arabia.,Division of Biological and Environmental Sciences (BESE) , Saudi Arabia
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19
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Efficient Computation of Free Energy Surfaces of Diels⁻Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level. Molecules 2018; 23:molecules23102487. [PMID: 30274188 PMCID: PMC6222833 DOI: 10.3390/molecules23102487] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 11/17/2022] Open
Abstract
For Diels–Alder (DA) reactions in solution, an accurate and converged free energy (FE) surface at ab initio (ai) quantum mechanical/molecular mechanical (QM/MM) level is imperative for the understanding of reaction mechanism. However, this computation is still far too expensive. In a previous work, we proposed a new method termed MBAR+wTP, with which the computation of the ai FE profile can be accelerated by several orders of magnitude via a three-step procedure: (I) an umbrella sampling (US) using a semi-empirical (SE) QM/MM Hamiltonian is performed; (II) the FE profile is generated using the Multistate Bennett Acceptance Ratio (MBAR) analysis; and (III) a weighted Thermodynamic Perturbation (wTP) from the SE Hamiltonian to the ai Hamiltonian is performed to obtain the ai QM/MM FE profile using weight factors from the MBAR analysis. In this work, this method is extended to the calculations of two-dimensional FE surfaces of two Diels–Alder reactions of cyclopentadiene with either acrylonitrile or 1-4-naphthoquinone at ai QM/MM level. The accurate activation free energies at the ai QM/MM level, which are much closer to the experimental measurements than those calculated by other methods, indicate that this MBAR+wTP method can be applied in the studies of complex reactions in condensed phase with much-enhanced efficiency.
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20
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Study of the Deformation/Interaction Model: How Interactions Increase the Reaction Barrier. J CHEM-NY 2018. [DOI: 10.1155/2018/3106297] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The interactions (including weak interactions) between dienophiles and dienes play an important role in the Diels-Alder reaction. To elucidate the influence of these interactions on the reactivity, a popular DFT functional and a variational DFT functional corrected with dispersion terms are used to investigate different substituent groups incorporated on the dienophiles and dienes. The bond order is used to track the trajectory of the cycloaddition reaction. The deformation/interaction model is used to obtain the interaction energy from the reactant complex to the inflection point until reaching the saddle point. The interaction energy initially increases with a decrease in the interatomic distance, reaching a maximum value, but then decreases when the dienophiles and dienes come closer. Reduced density gradient and chemical energy component analysis are used to analyse the interaction. Traditional transition state theory and variational transition state theory are used to obtain the reaction rates. The influence of tunneling on the reaction rate is also discussed.
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21
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Bain RM, Sathyamoorthi S, Zare RN. “On‐Droplet” Chemistry: The Cycloaddition of Diethyl Azodicarboxylate and Quadricyclane. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Ryan M. Bain
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | | | - Richard N. Zare
- Department of Chemistry Stanford University Stanford CA 94305 USA
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22
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Bain RM, Sathyamoorthi S, Zare RN. “On‐Droplet” Chemistry: The Cycloaddition of Diethyl Azodicarboxylate and Quadricyclane. Angew Chem Int Ed Engl 2017; 56:15083-15087. [DOI: 10.1002/anie.201708413] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 08/19/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Ryan M. Bain
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | | | - Richard N. Zare
- Department of Chemistry Stanford University Stanford CA 94305 USA
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23
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Comparison of DFT, MP2/CBS, and CCSD(T)/CBS methods for a dual-level QM/MM Monte Carlo simulation approach calculating the free energy of activation of reactions in solution and “on water”: a case study. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2103-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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24
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Jezorek RL, Enayati M, Smail RB, Lejnieks J, Grama S, Monteiro MJ, Percec V. The stirring rate provides a dramatic acceleration of the ultrafast interfacial SET-LRP in biphasic acetonitrile–water mixtures. Polym Chem 2017. [DOI: 10.1039/c7py00659d] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The rate of interfacial SET-LRP in biphasic acetonitrile–water mixtures is stirring rate dependent.
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Affiliation(s)
- Ryan L. Jezorek
- Roy & Diana Vagelos Laboratories
- Department of Chemistry
- University of Pennsylvania
- Philadelphia
- USA
| | - Mojtaba Enayati
- Roy & Diana Vagelos Laboratories
- Department of Chemistry
- University of Pennsylvania
- Philadelphia
- USA
| | - Rauan B. Smail
- Roy & Diana Vagelos Laboratories
- Department of Chemistry
- University of Pennsylvania
- Philadelphia
- USA
| | - Jānis Lejnieks
- Roy & Diana Vagelos Laboratories
- Department of Chemistry
- University of Pennsylvania
- Philadelphia
- USA
| | - Silvia Grama
- Roy & Diana Vagelos Laboratories
- Department of Chemistry
- University of Pennsylvania
- Philadelphia
- USA
| | - Michael J. Monteiro
- Australian Institute for Bioengineering and Nanotechnology
- The University of Queensland
- St. Lucia
- Australia
| | - Virgil Percec
- Roy & Diana Vagelos Laboratories
- Department of Chemistry
- University of Pennsylvania
- Philadelphia
- USA
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25
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Zhang Y, Wei BW, Zou LN, Kang ML, Luo HQ, Fan XL. ‘On water’ direct vinylogous Henry (nitroaldol) reactions of 3,5-dimethyl-4-nitroisoxazole with aldehydes and trifluoromethyl ketones. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.03.072] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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26
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Butler RN, Coyne AG. Organic synthesis reactions on-water at the organic–liquid water interface. Org Biomol Chem 2016; 14:9945-9960. [DOI: 10.1039/c6ob01724j] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Organic synthesis on-water has shown surprising successful synthetic methods. This review discusses the array of chemistry, which has been adapted with this methodology.
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Affiliation(s)
| | - Anthony G. Coyne
- Department of Chemistry
- University of Cambridge
- Cambridge CB2 1EW
- UK
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27
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Ruiz-Barragan S, Ribas Ariño J, Shiga M. The reaction mechanism of polyalcohol dehydration in hot pressurized water. Phys Chem Chem Phys 2016; 18:32438-32447. [DOI: 10.1039/c6cp05695d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The use of high-temperature liquid water (HTW) as a reaction medium is a very promising technology in the field of green chemistry.
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Affiliation(s)
- Sergi Ruiz-Barragan
- CCSE
- Japan Atomic Energy Agency
- Kashiwa
- Japan
- Department of Theoretical and Computational Molecular Science
| | - Jordi Ribas Ariño
- Departament de Química-Física i CERQT
- Universitat de Barcelona
- 08028-Barcelona
- Spain
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28
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Guo D, Zhu D, Zhou X, Zheng B. Accelerating the "On Water" Reaction: By Organic-Water Interface or By Hydrodynamic Effects? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:13759-63. [PMID: 26624935 DOI: 10.1021/acs.langmuir.5b04031] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
A series of organic reactions proceed dramatically faster in a heterogeneous mixture of the reactants and water than in a homogeneous mixture. Currently it is unclear whether the rate acceleration is due to the free OH groups at the organic-water interface, or due to the hydrodynamic effects caused by vigorous stirring, vortexing, or ultrasonication. Herein we produced static droplets in microfluidic devices to answer this question. In the work, a series of organic droplets containing diethyl azodicarboxylate (DEAD) and quadricyclane surrounded by water were produced, which were transferred to and confined in glass capillaries to minimize the hydrodynamic effects. The cycloaddition process of DEAD with quadricyclane was recorded by a CCD camera. The results showed the reaction proceeded in three steps, and the organic-water interface alone was catalytically efficient enough to enhance the reaction rate to the same level as in the bulk emulsion reaction, indicating that the hydrodynamic effects were negligible.
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Affiliation(s)
- Dameng Guo
- Department of Chemistry, The Chinese University of Hong Kong , Hong Kong, The People's Republic of China
| | - Deyong Zhu
- Department of Chemistry, The Chinese University of Hong Kong , Hong Kong, The People's Republic of China
| | - Xiaohu Zhou
- Department of Chemistry, The Chinese University of Hong Kong , Hong Kong, The People's Republic of China
| | - Bo Zheng
- Department of Chemistry, The Chinese University of Hong Kong , Hong Kong, The People's Republic of China
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29
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Titantah JT, Karttunen M. Hydrophobicity: effect of density and order on water's rotational slowing down. SOFT MATTER 2015; 11:7977-7985. [PMID: 26327528 DOI: 10.1039/c5sm00930h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Ab initio molecular dynamics (AIMD) simulations of over 4.5 ns were performed in the temperature range of T = 260-350 K with van der Waals corrections to investigate the relationship between local water density and tetrahedral order in bulk water and in the presence of a hydrophobe, tetramethylurea (TMU). We demonstrate that in bulk water, defects consisting of 5- and higher coordinated water are a major contributor to dynamics. Close to a hydrophobe, 3-coordinated defects take over. The co-existence of these defects gives rise to very different local densities. We propose that the slowing down of rotational motion close to a hydrophobe is induced by an interplay between density and order with the slowing down decreasing in the following order: (i) low-density ordered-water, (ii) normal-density ordered-water, (iii) high-density ordered-water and (iv) disordered-water. The proportions of these water environments vary with temperature. These local environments also support the idea of water's polymorphism, i.e., the existence of the high- and low-density states in supercooled water.
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Affiliation(s)
- John Tatini Titantah
- Department of Applied Mathematics, University of Western Ontario, 1151 Richmond Street North, London, Ontario, Canada N6A 5B7
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30
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Vilseck JZ, Kostal J, Tirado-Rives J, Jorgensen WL. Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions. J Comput Chem 2015; 36:2064-74. [PMID: 26311531 PMCID: PMC4575649 DOI: 10.1002/jcc.24045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/17/2015] [Accepted: 07/20/2015] [Indexed: 01/06/2023]
Abstract
Hybrid quantum mechanics and molecular mechanics (QM/MM) computer simulations have become an indispensable tool for studying chemical and biological phenomena for systems too large to treat with QM alone. For several decades, semiempirical QM methods have been used in QM/MM simulations. However, with increased computational resources, the introduction of ab initio and density function methods into on-the-fly QM/MM simulations is being increasingly preferred. This adaptation can be accomplished with a program interface that tethers independent QM and MM software packages. This report introduces such an interface for the BOSS and Gaussian programs, featuring modification of BOSS to request QM energies and partial atomic charges from Gaussian. A customizable C-shell linker script facilitates the interprogram communication. The BOSS-Gaussian interface also provides convenient access to Charge Model 5 (CM5) partial atomic charges for multiple purposes including QM/MM studies of reactions. In this report, the BOSS-Gaussian interface is applied to a nitroaldol (Henry) reaction and two methyl transfer reactions in aqueous solution. Improved agreement with experiment is found by determining free-energy surfaces with MP2/CM5 QM/MM simulations than previously reported investigations using semiempirical methods.
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Affiliation(s)
- Jonah Z. Vilseck
- Department of Chemistry, Yale University, New Haven, CT 06520-8107USA
| | - Jakub Kostal
- Department of Chemistry, Yale University, New Haven, CT 06520-8107USA
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31
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Butler RN, Coyne AG. Understanding “On-Water” Catalysis of Organic Reactions. Effects of H+ and Li+ Ions in the Aqueous Phase and Nonreacting Competitor H-Bond Acceptors in the Organic Phase: On H2O versus on D2O for Huisgen Cycloadditions. J Org Chem 2015; 80:1809-17. [DOI: 10.1021/jo502732y] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Richard N. Butler
- School
of Chemistry, National University of Ireland, Galway, Ireland
| | - Anthony G. Coyne
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
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32
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Karhan K, Khaliullin RZ, Kühne TD. On the role of interfacial hydrogen bonds in “on-water” catalysis. J Chem Phys 2014; 141:22D528. [DOI: 10.1063/1.4902537] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Kristof Karhan
- Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
- Institute of Physical Chemistry, Johannes Gutenberg University Mainz, Staudinger Weg 7, D-55128 Mainz, Germany
| | - Rustam Z. Khaliullin
- Institute of Physical Chemistry, Johannes Gutenberg University Mainz, Staudinger Weg 7, D-55128 Mainz, Germany
| | - Thomas D. Kühne
- Department of Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn, Germany
- Institute of Physical Chemistry, Johannes Gutenberg University Mainz, Staudinger Weg 7, D-55128 Mainz, Germany
- Center for Computational Sciences, Johannes Gutenberg University Mainz, D-55128 Mainz, Germany
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33
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Richert S, Mosquera Vazquez S, Grzybowski M, Gryko DT, Kyrychenko A, Vauthey E. Excited-State Dynamics of an Environment-Sensitive Push–Pull Diketopyrrolopyrrole: Major Differences between the Bulk Solution Phase and the Dodecane/Water Interface. J Phys Chem B 2014; 118:9952-63. [DOI: 10.1021/jp506062j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sabine Richert
- Department
of Physical Chemistry, University of Geneva, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Sandra Mosquera Vazquez
- Department
of Physical Chemistry, University of Geneva, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Marek Grzybowski
- Institute of Organic Chemistry of the Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Daniel T. Gryko
- Institute of Organic Chemistry of the Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Alexander Kyrychenko
- V. N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61022, Ukraine
| | - Eric Vauthey
- Department
of Physical Chemistry, University of Geneva, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
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34
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Manna A, Kumar A. Invoking Pairwise Interactions in Water-Promoted Diels-Alder Reactions by using Ionic Liquids as Cosolvents. Chemphyschem 2014; 15:3067-77. [DOI: 10.1002/cphc.201402338] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Indexed: 11/09/2022]
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35
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Zuo YJ, Qu J. How does aqueous solubility of organic reactant affect a water-promoted reaction? J Org Chem 2014; 79:6832-9. [PMID: 25000435 DOI: 10.1021/jo500733v] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
It was widely reported that under the "on water" condition, various water-promoted organic reactions can proceed with very high speed. Thus, it is considered that the aqueous solubility of reactant is not an important issue in these reactions. Three types of water-promoted organic reactions were investigated in the current study to distinguish whether the reaction rate of an aqueous reaction was affected by the aqueous solubilities of the reactants. The results showed that, for a Diels-Alder reaction which was fast under the neat conditions, the aqueous solubilities of reactants had little influence on the reaction. However, for the reactions which proceeded slowly under the neat conditions, such as [2σ+2σ+2π] cycloaddition reactions and epoxide aminolysis reactions, the reactants with good aqueous solubilities proceeded fast in water. Poorly aqueous soluble reactants reacted slowly or did not react under the "on water" condition, and an appropriate amount of organic cosolvent was needed to make the reaction become efficient. This evidence suggested that for these two types of reactions, the dissolution of the reactants in water was required.
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Affiliation(s)
- Yi-Jie Zuo
- State Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University , Tianjin 300071, China
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36
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Yang X, Xue Y. Medium Effects on the 1,3-Dipolar Cycloaddition of Pyridazinium Dicyanomethanide with Ethyl Vinyl Ketone in Pure and Mixed Solvents from QM/MM Simulations. J Org Chem 2014; 79:4863-70. [DOI: 10.1021/jo500184f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xin Yang
- College of Chemistry, Key
Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Ying Xue
- College of Chemistry, Key
Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People’s Republic of China
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37
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Acevedo O, Jorgensen WL. Quantum and Molecular Mechanical (QM/MM) Monte Carlo Techniques for Modeling Condensed-Phase Reactions. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2014; 4:422-435. [PMID: 25431625 DOI: 10.1002/wcms.1180] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A recent review (Acc. Chem. Res. 2010, 43:142-151) examined our use and development of a combined quantum and molecular mechanical (QM/MM) technique for modelling organic and enzymatic reactions. Advances included the PDDG/PM3 semiempirical QM (SQM) method, computation of multi-dimensional potentials of mean force (PMF), incorporation of on-the-fly QM in Monte Carlo simulations, and a polynomial quadrature method for rapidly treating proton-transfer reactions. The current article serves as a follow up on our progress. Highlights include new reactions, alternative SQM methods, a polarizable OPLS force field, and novel solvent environments, e.g., "on water" and room temperature ionic liquids. The methodology is strikingly accurate across a wide range of condensed-phase and antibody-catalyzed reactions including substitution, decarboxylation, elimination, isomerization, and pericyclic classes. Comparisons are made to systems treated with continuum-based solvents and ab initio or density functional theory (DFT) methods. Overall, the QM/MM methodology provides detailed characterization of reaction paths, proper configurational sampling, several advantages over implicit solvent models, and a reasonable computational cost.
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Affiliation(s)
- Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
| | - Wiliiam L Jorgensen
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107
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Schmidt TC, Paasche A, Grebner C, Ansorg K, Becker J, Lee W, Engels B. QM/MM investigations of organic chemistry oriented questions. Top Curr Chem (Cham) 2014; 351:25-101. [PMID: 22392477 DOI: 10.1007/128_2011_309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.
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Affiliation(s)
- Thomas C Schmidt
- Institut für Phys. und Theor. Chemie, Emil-Fischer-Strasse 42, Campus Hubland Nord, 97074, Würzburg, Germany
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Cruz‐Acosta F, de Armas P, García‐Tellado F. Water‐Compatible Hydrogen‐Bond Activation: A Scalable and Organocatalytic Model for the Stereoselective Multicomponent Aza‐Henry Reaction. Chemistry 2013; 19:16550-4. [DOI: 10.1002/chem.201303448] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Fabio Cruz‐Acosta
- Departamento de Química Biológica y Biotecnología, Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones, Científicas Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife (Spain), Fax: (+34) 922260135 https://www.ipna.csic.es/dept/qbb/qob/
| | - Pedro de Armas
- Departamento de Química Biológica y Biotecnología, Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones, Científicas Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife (Spain), Fax: (+34) 922260135 https://www.ipna.csic.es/dept/qbb/qob/
| | - Fernando García‐Tellado
- Departamento de Química Biológica y Biotecnología, Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones, Científicas Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife (Spain), Fax: (+34) 922260135 https://www.ipna.csic.es/dept/qbb/qob/
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Yang X, Xue Y. QM/MM investigation on 1,3-dipolar cycloadditions of the phthalazinium dicyanomethanide with three different dipolarophiles on water and in solution. Phys Chem Chem Phys 2013; 15:11846-55. [PMID: 23760163 DOI: 10.1039/c3cp51048d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
An "on water" environment, describing the reactions with insoluble reactants in water, has been reported to give high yields of products compared to organic solvents. The 1,3-dipolar cycloadditions of phthalazinium dicyanomethanide 1 with three different dipolarophiles, methyl vinyl ketone (MVK), methyl acrylate (MAC), and styrene (STY), have been investigated using QM/MM calculations in water, acetonitrile, and acetonitrile-water solvent mixtures, as well as at the vacuum-water interface. Monte Carlo statistical mechanics simulations utilizing the free-energy perturbation theory and PDDG/PM3 for the QM method have been used. The transition structures for all three reactions do not show large variations among different solvents. However, the calculated free energies of activation at the interface are found to be higher than those calculated in bulk water. Computed energy pair distributions and radial distribution functions reveal a uniform loss of hydrogen bonds for the reactants and transitions states in progressing from bulk water to the vacuum-water interface. The hydrophobic effects in the reactions of 1 with MVK and MAC are similar for both, and weaker than the effect in the reaction with STY. According to the results in water-acetonitrile mixtures at different molar ratios, it is clear that the special hydrogen bonding effects are the main reason which leads to the rapid rate enhancement in progressing from a water-acetonitrile molar ratio of 0.9 : 0.1 to pure water. New insights into solvent effects for 1,3-dipolar cycloadditions are presented herein.
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Affiliation(s)
- Xin Yang
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People's Republic of China
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Manna A, Kumar A. Why Does Water Accelerate Organic Reactions under Heterogeneous Condition? J Phys Chem A 2013; 117:2446-54. [DOI: 10.1021/jp4002934] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Arpan Manna
- Physical and Materials Chemistry Division, National
Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Anil Kumar
- Physical and Materials Chemistry Division, National
Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
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Zhang B, Song J, Liu H, Han B, Jiang T, Fan H, Zhang Z, Wu T. Acceleration of disproportionation of aromatic alcohols through self-emulsification of reactants in water. CHEMSUSCHEM 2012; 5:2469-2473. [PMID: 23090937 DOI: 10.1002/cssc.201200562] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Indexed: 06/01/2023]
Abstract
Exploration of new and effective routes to conduct organic reactions in water using the special properties of water/organics is of great importance. In this work, we performed the disproportionation of various aromatic alcohols in water and in different organic solvents. It was demonstrated that the disproportionation reactions of the alcohols were accelerated more effectively in water than organic-solvent-based or solvent-free reactions. A series of control experiments were conducted to study the mechanism of the accelerated reaction rate in water. It was shown that the reactants could emulsify the reactant/water systems at the reaction conditions owing to their amphiphilic nature. The regularly orientated reactant molecules at the water/reactant droplet interface improved the contact probability of the reactive groups and the Pd nanocatalysts, which is one of the main reasons for the enhanced reaction rate in water. Controlling the self-emulsification of amphiphilic reactant/water systems has great application potential for optimizing the rate and/or selectivity of many organic reactions.
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Affiliation(s)
- Binbin Zhang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid and Interface and Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, PR China
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Sunoj RB, Anand M. Microsolvated transition state models for improved insight into chemical properties and reaction mechanisms. Phys Chem Chem Phys 2012; 14:12715-36. [PMID: 22893252 DOI: 10.1039/c2cp41719g] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over the years, several methods have been developed to effectively represent the chemical behavior of solutes in solvents. The environmental effects arising due to solvation can generally be achieved either through inclusion of discrete solvent molecules or by inscribing into a cavity in a homogeneous and continuum dielectric medium. In both these approaches of computational origin, the perturbations on the solute induced by the surrounding solvent are at the focus of the problem. While the rigor and method of inclusion of solvent effects vary, such solvation models have found widespread applications, as evident from modern chemical literature. A hybrid method, commonly referred to as cluster-continuum model (CCM), brings together the key advantages of discrete and continuum models. In this perspective, we intend to highlight the latent potential of CCM toward obtaining accurate estimates on a number of properties as well as reactions of contemporary significance. The objective has generally been achieved by choosing illustrative examples from the literature, besides expending efforts to bring out the complementary advantages of CCM as compared to continuum or discrete solvation models. The majority of examples emanate from the prevalent applications of CCM to organic reactions, although a handful of interesting organometallic reactions have also been discussed. In addition, increasingly accurate computations of properties like pK(a) and solvation of ions obtained using the CCM protocol are also presented.
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Affiliation(s)
- Raghavan B Sunoj
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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Hub JS, Caleman C, van der Spoel D. Organic molecules on the surface of water droplets – an energetic perspective. Phys Chem Chem Phys 2012; 14:9537-45. [DOI: 10.1039/c2cp40483d] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Kammath VB, Šebej P, Slanina T, Kříž Z, Klán P. Photoremovable chiral auxiliary. Photochem Photobiol Sci 2012; 11:500-7. [DOI: 10.1039/c1pp05096f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Affiliation(s)
- James K Beattie
- School of Chemistry, The University of Sydney, NSW, 2006 Australia.
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Butler RN, Coyne AG. Water: Nature’s Reaction Enforcer—Comparative Effects for Organic Synthesis “In-Water” and “On-Water”. Chem Rev 2010; 110:6302-37. [DOI: 10.1021/cr100162c] [Citation(s) in RCA: 897] [Impact Index Per Article: 64.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Richard N. Butler
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland, and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Anthony G. Coyne
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland, and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
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