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Jeong J, Oh D, Ju Y, Goh M. Energy-efficient chemical recycling of CFRP and analysis of the interfacial shear strength on recovered carbon fiber. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 187:134-144. [PMID: 39032436 DOI: 10.1016/j.wasman.2024.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 07/02/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
Here we report a novel chemical recycling of carbon fiber-reinforced plastic (CFRP) using meta-chloroperoxybenzoic acid (mCPBA) as the representative oxidizing agent. The optimal decomposition conditions for the epoxy (EP) resin in CFRP were investigated by varying mCPBA concentration and reaction time. The CFRP decomposed completely within 6 h using a 1.5 M mCPBA solution at 40 °C. Tensile strength of recovered CF (r-CF) measured 4.4 GPa, 93.6% of virgin CF (v-CF), and electrical conductivity reached 590 S/cm, 95% of v-CF. Furthermore, the interfacial shear strength (IFSS) of the recovered carbon fibers (r-CF) using EP resin and polyamide 6 (PA6) was analyzed. For EP resin, the IFSS of r-CF was 88 MPa, a 26 % increase compared to v-CF. In the case of PA6 resin, IFSS values were 80 MPa for r-CF, a 17% improvement over v-CF. The study highlights superior mechanical properties and favorable IFSS of r-CF, positioning them as promising for composite regeneration. Remarkably, this method operated at relatively low temperatures compared to existing technologies, with energy consumption recorded at 35 MJ/kg, establishing it as the most energy-efficient recycling method available.
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Affiliation(s)
- Jisu Jeong
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Dongki Oh
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; Research Infrastructure Utilization Center, FITI Testing & Research Institute, 79 Magokjungang 8-ro 3-gil, Gangseo-gu, Seoul 07791, Republic of Korea
| | - Yeonha Ju
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Munju Goh
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
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2
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Mendes TDC, Viana GM, de Abreu LCL, Anselmo CDS, Pereira HMG, da Silva AJR, Cabral LM, de Sousa VP. Identification and Characterization of Rotigotine Degradation Products by HPLC Coupled DAD and CAD Detectors and HRMS Through Q-Orbitrap and Electrospray Ionization. J Pharm Sci 2024; 113:2542-2551. [PMID: 38815860 DOI: 10.1016/j.xphs.2024.05.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/01/2024]
Abstract
Rotigotine (RTG) is a dopamine agonist used in the treatment of Parkinson's disease. As it is susceptible to oxidation, stability studies must be carefully designed for the identification and characterization of all possible degradation products. Here, RTG degradation was evaluated according to the International Conference on Harmonization guidelines under various stress conditions, including acidic and basic hydrolysis, oxidative, metallic, photolytic, and thermal conditions. Additionally, more severe stress conditions were applied to induce RTG degradation. Significant degradation was only observed under oxidative and photolytic conditions. The samples were analyzed by high performance liquid chromatography coupled to photodiode array detectors, charged aerosol, and high-resolution mass spectrometry. Chromatographic analyses revealed the presence of eight substances related to RTG, four of which were already described and were qualified impurities (impurities B, C, K and E) and four new degradation products (DP-1 - DP-4), whose structures were characterized by high-resolution mass spectrometry through Q-Orbitrap and electrospray ionization. In the stress testing of the active pharmaceutical ingredient in solid form, significant RTG degradation was observed in the presence of the oxidative matrix. The results corroborate the literature that confirm the high susceptibility of RTG to oxidation and the importance of using different detectors to detect degradation products in forced degradation studies.
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Affiliation(s)
- Thamara de Carvalho Mendes
- Department of Drugs and Pharmaceutics, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gil Mendes Viana
- Department of Drugs and Pharmaceutics, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Carina de Souza Anselmo
- Federal University of Rio de Janeiro, Institute of Chemistry, LBCD - LADETEC, Rio de Janeiro, Brazil
| | | | | | - Lucio Mendes Cabral
- Department of Drugs and Pharmaceutics, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Valeria Pereira de Sousa
- Department of Drugs and Pharmaceutics, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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3
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Irie Y, Yokoshima S. Total Synthesis of Putative Melognine. J Am Chem Soc 2024; 146:9526-9531. [PMID: 38546412 DOI: 10.1021/jacs.4c02086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Total synthesis of melognine was accomplished. A 10-membered cyclic alkyne was prepared via an intramolecular SN2 reaction of a nosylamide. Enyne metathesis of the cyclic alkyne under an atmosphere of ethylene afforded a 1,3-diene. Intramolecular cycloaddition of a nitrone and an azomethine ylide with the 1,3-diene moiety constructed the characteristic highly fused skeleton. Further transformation, including ring-closing metathesis, resulted in the synthesis of melognine, whose NMR spectra did not match the reported data. Close inspection of the spectra of melognine in the literature suggested that the structure of melognine might be identical with that of a known alkaloid, melodinine L.
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Affiliation(s)
- Yui Irie
- Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Satoshi Yokoshima
- Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
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4
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Recent Advances in the Use of Dimethyl Sulfoxide as a Synthon in Organic Chemistry. Top Curr Chem (Cham) 2022; 380:55. [DOI: 10.1007/s41061-022-00411-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 10/06/2022] [Indexed: 11/27/2022]
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5
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Norén R. Evaluation of 2-(piperidine-1-yl)-ethyl (PIP) as a protecting group for phenols: Stability to ortho-lithiation conditions and boiling concentrated hydrobromic acid, orthogonality with most common protecting group classes, and deprotection via Cope elimination or by mild Lewis acids. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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6
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Nieves-Quinones Y, Paniak TJ, Lee YE, Kim SM, Tcyrulnikov S, Kozlowski MC. Chromium-Salen Catalyzed Cross-Coupling of Phenols: Mechanism and Origin of the Selectivity. J Am Chem Soc 2019; 141:10016-10032. [PMID: 31125210 DOI: 10.1021/jacs.9b03890] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A highly chemoselective phenol cross-coupling reaction catalyzed by a Cr-salen catalyst was developed. Kinetic studies showed that the oxidation of Cr(III) to Cr(V) is the rate-determining step of the reaction. In addition, experimental stoichiometric analysis showed that a high valent Cr(V) species is the active catalyst for this process. The selectivity of the reaction was found to be determined by the cross-coupling carbon-carbon bond forming reaction, rather than any precoordination species. It appears that the lowest energy cross-coupling pathway requires a lesser degree of electronic reorganization in its transition state vs the lowest energy homocoupling pathway. This result was supported by stoichiometric Cr(V) kinetics, 13C kinetic isotope effects, and density functional theory (DFT) calculations. The understanding of the full landscape of this reaction allowed us to develop a general analysis to predict the regioselectivity of the cross-coupling reaction.
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Affiliation(s)
- Yexenia Nieves-Quinones
- Department of Chemistry, Roy and Diana Vagelos Laboratories , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Thomas J Paniak
- Department of Chemistry, Roy and Diana Vagelos Laboratories , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Young Eun Lee
- Department of Chemistry, Roy and Diana Vagelos Laboratories , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Sun Min Kim
- Department of Chemistry, Roy and Diana Vagelos Laboratories , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Sergei Tcyrulnikov
- Department of Chemistry, Roy and Diana Vagelos Laboratories , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Marisa C Kozlowski
- Department of Chemistry, Roy and Diana Vagelos Laboratories , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
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7
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Ghannay S, Alminderej F, Msaddek M, Praly J, Aouadi K. Unprecedented Synthesis of 4‐Ylidene (3 S)‐3‐hydroxy‐1‐aryl (alkyl)‐pyrrolidine‐2,5‐diones Based on 1,3‐Dipolar Cycloaddition of a Sugar‐derived Nitrone toN‐Substituted Maleimides. ChemistrySelect 2019. [DOI: 10.1002/slct.201900931] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Siwar Ghannay
- University of MonastirFaculty of Sciences of MonastirLaboratory of Heterocyclic Chemistry, Natural Products and Reactivity, Avenue of the Environment 5019 Monastir Tunisia
| | - Fahad Alminderej
- Qassim University-College of ScienceDepartment of Chemistry Buraidah 51452 Saudi Arabia
| | - Moncef Msaddek
- University of MonastirFaculty of Sciences of MonastirLaboratory of Heterocyclic Chemistry, Natural Products and Reactivity, Avenue of the Environment 5019 Monastir Tunisia
| | - Jean‐Pierre Praly
- Université de Lyon, Institut de Chimie et Biochimie Moléculaires et SupramoléculairesUMR CNRS 5246Laboratoire de Chimie Organique 2-Glycochimie, Bâtiment Curien, 43 boulevard du 11 Novembre 1918, F- 69622 Villeurbanne France
| | - Kaïss Aouadi
- University of MonastirFaculty of Sciences of MonastirLaboratory of Heterocyclic Chemistry, Natural Products and Reactivity, Avenue of the Environment 5019 Monastir Tunisia
- Qassim University-College of ScienceDepartment of Chemistry Buraidah 51452 Saudi Arabia
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8
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Yang M, Yang L, Wang G, Zhou Y, Xie D, Li S. Combined Molecular Dynamics and Coordinate Driving Method for Automatic Reaction Pathway Search of Reactions in Solution. J Chem Theory Comput 2018; 14:5787-5796. [DOI: 10.1021/acs.jctc.8b00799] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manyi Yang
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Guoqiang Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Yanzi Zhou
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Daiqian Xie
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
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9
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Comparing quantitative prediction methods for the discovery of small-molecule chiral catalysts. Nat Rev Chem 2018. [DOI: 10.1038/s41570-018-0040-8] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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10
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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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11
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Nocito D, Beran GJO. Averaged Condensed Phase Model for Simulating Molecules in Complex Environments. J Chem Theory Comput 2017; 13:1117-1129. [PMID: 28170251 DOI: 10.1021/acs.jctc.6b00890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The need for configurational sampling dramatically increases the cost of combined quantum mechanics/molecular mechanics (QM/MM) simulations of chemical processes in solution. We developed an averaged condensed phase environment (ACPE) model that constructs an effective polarizable environment directly from explicitly sampled molecular dynamics configurations via the K-means++ algorithm and a mathematically rigorous translation of the molecular mechanics parameters. The model captures detailed heterogeneous features in the environment that may be difficult to describe using a conventional polarizable continuum model. Instead of performing repeated QM/MM calculations for each new configuration of the environment, the ACPE approach allows one to perform a single QM calculation on an averaged configuration. Here, we demonstrate the model by computing electronic excitation energies for several small molecules in solution. The ACPE model predicts the excitation energies in excellent agreement with conventional configurational averaging yet with orders of magnitude of reduction in the computational cost.
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Affiliation(s)
- Dominique Nocito
- Department of Chemistry, University of California , Riverside, California 92521, United States
| | - Gregory J O Beran
- Department of Chemistry, University of California , Riverside, California 92521, United States
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12
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Gunaydin H, Acevedo O, Jorgensen WL, Houk KN. Computation of Accurate Activation Barriers for Methyl-Transfer Reactions of Sulfonium and Ammonium Salts in Aqueous Solution. J Chem Theory Comput 2015; 3:1028-35. [PMID: 26627421 DOI: 10.1021/ct050318n] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The energetics of methyl-transfer reactions from dimethylammonium, tetramethylammonium, and trimethylsulfonium to dimethylamine were computed with density functional theory, MP2, CBS-QB3, and quantum mechanics/molecular mechanics (QM/MM) Monte Carlo methods. At the CBS-QB3 level, the gas-phase activation enthalpies are computed to be 9.9, 15.3, and 7.9 kcal/mol, respectively. MP2/6-31+G(d,p) activation enthalpies are in best agreement with the CBS-QB3 results. The effects of aqueous solvation on these reactions were studied with polarizable continuum model, generalized Born/surface area (GB/SA), and QM/MM Monte Carlo simulations utilizing free-energy perturbation theory in which the PDDG/PM3 semiempirical Hamiltonian for the QM and explicit TIP4P water molecules in the MM region were used. In the aqueous phase, all of these reactions proceed more slowly when compared to the gas phase, since the charged reactants are stabilized more than the transition structure geometries with delocalized positive charges. In order to obtain the aqueous-phase activation free energies, the gas-phase activation free energies were corrected with the solvation free energies obtained from single-point conductor-like polarizable continuum model and GB/SA calculations for the stationary points along the reaction coordinate.
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Affiliation(s)
- Hakan Gunaydin
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, and Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107
| | - Orlando Acevedo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, and Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107
| | - William L Jorgensen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, and Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, and Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107
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13
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Cheng GJ, Zhang X, Chung LW, Xu L, Wu YD. Computational organic chemistry: bridging theory and experiment in establishing the mechanisms of chemical reactions. J Am Chem Soc 2015; 137:1706-25. [PMID: 25568962 DOI: 10.1021/ja5112749] [Citation(s) in RCA: 234] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the mechanisms of chemical reactions, especially catalysis, has been an important and active area of computational organic chemistry, and close collaborations between experimentalists and theorists represent a growing trend. This Perspective provides examples of such productive collaborations. The understanding of various reaction mechanisms and the insight gained from these studies are emphasized. The applications of various experimental techniques in elucidation of reaction details as well as the development of various computational techniques to meet the demand of emerging synthetic methods, e.g., C-H activation, organocatalysis, and single electron transfer, are presented along with some conventional developments of mechanistic aspects. Examples of applications are selected to demonstrate the advantages and limitations of these techniques. Some challenges in the mechanistic studies and predictions of reactions are also analyzed.
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Affiliation(s)
- Gui-Juan Cheng
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School , Shenzhen 518055, China
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14
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Qiao Y, Han K, Zhan CG. Reaction pathways and free energy profiles for cholinesterase-catalyzed hydrolysis of 6-monoacetylmorphine. Org Biomol Chem 2014; 12:2214-27. [PMID: 24595354 DOI: 10.1039/c3ob42464b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As the most active metabolite of heroin, 6-monoacetylmorphine (6-MAM) can penetrate into the brain for the rapid onset of heroin effects. The primary enzymes responsible for the metabolism of 6-MAM to the less potent morphine in humans are acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). The detailed reaction pathways for AChE- and BChE-catalyzed hydrolysis of 6-MAM to morphine have been explored, for the first time, in the present study by performing first-principles quantum mechanical/molecular mechanical free energy calculations. It has been demonstrated that the two enzymatic reaction processes follow similar catalytic reaction mechanisms, and the whole catalytic reaction pathway for each enzyme consists of four reaction steps. According to the calculated results, the second reaction step associated with the transition state TS2(a)/TS2(b) should be rate-determining for the AChE/BChE-catalyzed hydrolysis, and the free energy barrier calculated for the AChE-catalyzed hydrolysis (18.3 kcal mol(-1)) is 2.5 kcal mol(-1) lower than that for the BChE-catalyzed hydrolysis (20.8 kcal mol(-1)). The free energy barriers calculated for the AChE- and BChE-catalyzed reactions are in good agreement with the experimentally derived activation free energies (17.5 and 20.7 kcal mol(-1) for the AChE- and BChE-catalyzed reactions, respectively). Further structural analysis reveals that the aromatic residues Phe295 and Phe297 in the acyl pocket of AChE (corresponding to Leu286 and Val288 in BChE) contribute to the lower energy of TS2(a) relative to TS2(b). The obtained structural and mechanistic insights could be valuable for use in future rational design of a novel therapeutic treatment of heroin abuse.
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Affiliation(s)
- Yan Qiao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, P. R. China
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15
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Kitamura Y, Takenaka N, Koyano Y, Nagaoka M. Dual Approach to Vibrational Spectra in Solution: Microscopic Influence of Hydrogen Bonding to the State of Motion of Glycine in Water. J Chem Theory Comput 2014; 10:3369-79. [PMID: 26588305 DOI: 10.1021/ct500235a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have proposed a new theoretical methodology to clarify the microscopic nature of the vibrational properties in solution, which consists of a combination of the vibrational frequency analyses (VFAs) with two kinds of Hessian matrices, that is, the effective Hessian on the free energy surface (free energy Hessian: "FE-Hessian") and the instantaneous one (instantaneous normal mode Hessian: "INM-Hessian") within QM/MM framework. In these VFAs, the Hessians were obtained by the analytical approach, having the advantages from the aspect of both the computational efficiency and accuracy in comparison to those obtained by the numerical one. In the present study, we have applied them to the glycine aqueous solution. First, by using the VFA with the FE-Hessian (VFA-FEH), we estimated the vibrational frequency shifts induced by solvent water molecules. The calculated values were quantitatively in agreement with experimental ones. It was clearly demonstrated that such vibrational shifts are attributed to not only the structural relaxation but also the explicit solute-solvent interactions (i.e., interatomic interactions). Second, by using the VFA with the INM-Hessian (VFA-INMH), the vibrational spectra in solution were investigated through the vibrational INM densities of states (DOS). By the comparison between the spectroscopic features and the microscopic solvation structure around glycine molecule, it was found that the frequency shifts and bandwidths in IR spectra are closely correlated with the hydrogen bonding (HB) network formations. In particular, the instantaneous changes of vibrational states of the hydroxyl group and carbonyl one, showing apparently inverse tendency on the strength of the HB interaction, can be explained very well on the basis of two different mechanisms, that is, the direct change of electron density in the bonding orbitals and the indirect one due to hyperconjugation between the lone electron pair and the antibonding orbitals, respectively. In conclusion, the present dual VFA approach is a quite useful strategy to interpret the microscopic origin of the experimental vibrational spectra.
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Affiliation(s)
- Yukichi Kitamura
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Japan Society for the Promotion of Science (JSPS), Tokyo 102-0083, Japan
| | - Norio Takenaka
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University Katsura , Kyoto 615-8520, Japan
| | - Yoshiyuki Koyano
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Masataka Nagaoka
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University Katsura , Kyoto 615-8520, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency , Honmachi, Kawaguchi 332-0012, Japan
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16
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Zeng Q, Liu J, Liang W. Molecular properties of excited electronic state: formalism, implementation, and applications of analytical second energy derivatives within the framework of the time-dependent density functional theory/molecular mechanics. J Chem Phys 2014; 140:18A506. [PMID: 24832314 DOI: 10.1063/1.4863563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
This work extends our previous works [J. Liu and W. Z. Liang, J. Chem. Phys. 135, 014113 (2011); J. Liu and W. Z. Liang, J. Chem. Phys. 135, 184111 (2011)] on analytical excited-state energy Hessian within the framework of time-dependent density functional theory (TDDFT) to couple with molecular mechanics (MM). The formalism, implementation, and applications of analytical first and second energy derivatives of TDDFT/MM excited state with respect to the nuclear and electric perturbations are presented. Their performances are demonstrated by the calculations of adiabatic excitation energies, and excited-state geometries, harmonic vibrational frequencies, and infrared intensities for a number of benchmark systems. The consistent results with the full quantum mechanical method and other hybrid theoretical methods indicate the reliability of the current numerical implementation of developed algorithms. The computational accuracy and efficiency of the current analytical approach are also checked and the computational efficient strategies are suggested to speed up the calculations of complex systems with many MM degrees of freedom. Finally, we apply the current analytical approach in TDDFT/MM to a realistic system, a red fluorescent protein chromophore together with part of its nearby protein matrix. The calculated results indicate that the rearrangement of the hydrogen bond interactions between the chromophore and the protein matrix is responsible for the large Stokes shift.
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Affiliation(s)
- Qiao Zeng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Province Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jie Liu
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - WanZhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Province Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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17
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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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18
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Beauchemin AM. Recent developments in Cope-type hydroamination reactions of hydroxylamine and hydrazine derivatives. Org Biomol Chem 2014; 11:7039-50. [PMID: 24056974 DOI: 10.1039/c3ob41172a] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cope-type hydroaminations are versatile for the direct amination of alkenes, alkynes and allenes using hydroxylamines and hydrazine derivatives. These reactions occur via a concerted, 5-membered cyclic transition state that is the microscopic reverse of the Cope elimination. This article focuses on recent developments, including intermolecular variants, directed reactions, and asymmetric variants using aldehydes as tethering catalysts, and their applications in target-oriented synthesis.
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Affiliation(s)
- André M Beauchemin
- Centre for Catalysis Research and Innovation, Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada. andre.beauchemin@uottawa
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19
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Xie HB, He N, Song Z, Chen J, Li X. Theoretical Investigation on the Different Reaction Mechanisms of Aqueous 2-Amino-2-methyl-1-propanol and Monoethanolamine with CO2. Ind Eng Chem Res 2014. [DOI: 10.1021/ie403280h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Hong-Bin Xie
- Key
Laboratory of Industrial Ecology and Environmental Engineering (MOE),
School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ning He
- State
Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, China
| | - Zhiquan Song
- Key
Laboratory of Industrial Ecology and Environmental Engineering (MOE),
School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jingwen Chen
- Key
Laboratory of Industrial Ecology and Environmental Engineering (MOE),
School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xuehua Li
- Key
Laboratory of Industrial Ecology and Environmental Engineering (MOE),
School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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20
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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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21
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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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22
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Wei D, Fang L, Tang M, Zhan CG. Fundamental reaction pathway for peptide metabolism by proteasome: insights from first-principles quantum mechanical/molecular mechanical free energy calculations. J Phys Chem B 2013; 117:13418-34. [PMID: 24111489 DOI: 10.1021/jp405337v] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Proteasome is the major component of the crucial non-lysosomal protein degradation pathway in the cells, but the detailed reaction pathway is unclear. In this study, first-principles quantum mechanical/molecular mechanical free energy calculations have been performed to explore, for the first time, possible reaction pathways for proteasomal proteolysis/hydrolysis of a representative peptide, succinyl-leucyl-leucyl-valyl-tyrosyl-7-amino-4-methylcoumarin (Suc-LLVY-AMC). The computational results reveal that the most favorable reaction pathway consists of six steps. The first is a water-assisted proton transfer within proteasome, activating Thr1-O(γ). The second is a nucleophilic attack on the carbonyl carbon of a Tyr residue of substrate by the negatively charged Thr1-O(γ), followed by the dissociation of the amine AMC (third step). The fourth step is a nucleophilic attack on the carbonyl carbon of the Tyr residue of substrate by a water molecule, accompanied by a proton transfer from the water molecule to Thr1-N(z). Then, Suc-LLVY is dissociated (fifth step), and Thr1 is regenerated via a direct proton transfer from Thr1-N(z) to Thr1-O(γ). According to the calculated energetic results, the overall reaction energy barrier of the proteasomal hydrolysis is associated with the transition state (TS3(b)) for the third step involving a water-assisted proton transfer. The determined most favorable reaction pathway and the rate-determining step have provided a reasonable interpretation of the reported experimental observations concerning the substituent and isotopic effects on the kinetics. The calculated overall free energy barrier of 18.2 kcal/mol is close to the experimentally derived activation free energy of ∼18.3-19.4 kcal/mol, suggesting that the computational results are reasonable.
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Affiliation(s)
- Donghui Wei
- Department of Chemistry, Zhengzhou University , 75 Daxue Road, Zhengzhou, Henan 450052, China
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23
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Qiao Y, Han K, Zhan CG. Fundamental reaction pathway and free energy profile for butyrylcholinesterase-catalyzed hydrolysis of heroin. Biochemistry 2013; 52:6467-79. [PMID: 23992153 DOI: 10.1021/bi400709v] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The pharmacological function of heroin requires an activation process that transforms heroin into 6-monoacetylmorphine (6-MAM), which is the most active form. The primary enzyme responsible for this activation process in human plasma is butyrylcholinesterase (BChE). The detailed reaction pathway of the activation process via BChE-catalyzed hydrolysis has been explored computationally, for the first time, in this study via molecular dynamics simulation and first-principles quantum mechanical/molecular mechanical free energy calculations. It has been demonstrated that the whole reaction process includes acylation and deacylation stages. The acylation consists of two reaction steps, i.e., the nucleophilic attack on the carbonyl carbon of the 3-acetyl group of heroin by the hydroxyl oxygen of the Ser198 side chain and the dissociation of 6-MAM. The deacylation also consists of two reaction steps, i.e., the nucleophilic attack on the carbonyl carbon of the acyl-enzyme intermediate by a water molecule and the dissociation of the acetic acid from Ser198. The calculated free energy profile reveals that the second transition state (TS2) should be rate-determining. The structural analysis reveals that the oxyanion hole of BChE plays an important role in the stabilization of rate-determining TS2. The free energy barrier (15.9 ± 0.2 or 16.1 ± 0.2 kcal/mol) calculated for the rate-determining step is in good agreement with the experimentally derived activation free energy (~16.2 kcal/mol), suggesting that the mechanistic insights obtained from this computational study are reliable. The obtained structural and mechanistic insights could be valuable for use in the future rational design of a novel therapeutic treatment of heroin abuse.
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Affiliation(s)
- Yan Qiao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science , Zhongshan Road 457, Dalian 116023, P. R. China
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24
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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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25
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Brown AR, Uyeda C, Brotherton CA, Jacobsen EN. Enantioselective thiourea-catalyzed intramolecular cope-type hydroamination. J Am Chem Soc 2013; 135:6747-9. [PMID: 23597402 PMCID: PMC3689223 DOI: 10.1021/ja402893z] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Catalysis of Cope-type rearrangements of bis-homoallylic hydroxylamines is demonstrated using chiral thiourea derivatives. This formal intramolecular hydroamination reaction provides access to highly enantioenriched α-substituted pyrrolidine products and represents a complementary approach to metal-catalyzed methods.
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Affiliation(s)
- Adam R. Brown
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Christopher Uyeda
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Carolyn A. Brotherton
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Eric N. Jacobsen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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26
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Kaweetirawatt T, Yamaguchi T, Higashiyama T, Sumimoto M, Hori K. Theoretical study of keto-enol tautomerism by quantum mechanical calculations (the QM/MC/FEP method). J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.2944] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Thanayuth Kaweetirawatt
- Ube Technical Center (Asia) Co., Ltd; 140/8 Moo4, Tambol Tapong Muang Rayong Rayong 21000 Thailand
- Graduate School of Science and Engineering; Yamaguchi University; 2-16-1 Tokiwadai Ube Yamaguchi 755-8611 Japan
| | - Toru Yamaguchi
- Graduate School of Science and Engineering; Yamaguchi University; 2-16-1 Tokiwadai Ube Yamaguchi 755-8611 Japan
| | - Tsutomu Higashiyama
- Nissan Chemical Industries Ltd; 722-1 Tsuboi Cho Funabashi Shi Chiba 274-8507 Japan
| | - Michinori Sumimoto
- Graduate School of Science and Engineering; Yamaguchi University; 2-16-1 Tokiwadai Ube Yamaguchi 755-8611 Japan
| | - Kenji Hori
- Graduate School of Science and Engineering; Yamaguchi University; 2-16-1 Tokiwadai Ube Yamaguchi 755-8611 Japan
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27
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Theoretical study of the hydrolysis of ethyl benzoate in acidic aqueous solution using the QM/MC/FEP method. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.06.001] [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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28
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Krenske EH, Agopcan S, Aviyente V, Houk KN, Johnson BA, Holmes AB. Causation in a cascade: the origins of selectivities in intramolecular nitrone cycloadditions. J Am Chem Soc 2012; 134:12010-5. [PMID: 22788115 DOI: 10.1021/ja300002k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The factors controlling chemo-, regio-, and stereoselectivity in a cascade of reactions starting from a bis(cyanoalkenyl)oxime and proceeding via nitrone cycloadditions have been unraveled through a series of density functional theory calculations with several different functionals. Both kinetic and thermodynamic control of the reaction cascade are important, depending upon the conditions. Kinetic control was analyzed by the distortion/interaction model and found to be dictated by differences in distortions of the cycloaddends in the transition states. A new mechanism competing with that originally proposed in the application of these reactions to the histrionicotoxin synthesis was discovered in these studies.
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29
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Wei D, Lei B, Tang M, Zhan CG. Fundamental reaction pathway and free energy profile for inhibition of proteasome by Epoxomicin. J Am Chem Soc 2012; 134:10436-50. [PMID: 22697787 DOI: 10.1021/ja3006463] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
First-principles quantum mechanical/molecular mechanical free energy calculations have been performed to provide the first detailed computational study on the possible mechanisms for reaction of proteasome with a representative peptide inhibitor, Epoxomicin (EPX). The calculated results reveal that the most favorable reaction pathway consists of five steps. The first is a proton transfer process, activating Thr1-O(γ) directly by Thr1-N(z) to form a zwitterionic intermediate. The next step is nucleophilic attack on the carbonyl carbon of EPX by the negatively charged Thr1-O(γ) atom, followed by a proton transfer from Thr1-N(z) to the carbonyl oxygen of EPX (third step). Then, Thr1-N(z) attacks on the carbon of the epoxide group of EPX, accompanied by the epoxide ring-opening (S(N)2 nucleophilic substitution) such that a zwitterionic morpholino ring is formed between residue Thr1 and EPX. Finally, the product of morpholino ring is generated via another proton transfer. Noteworthy, Thr1-O(γ) can be activated directly by Thr1-N(z) to form the zwitterionic intermediate (with a free energy barrier of only 9.9 kcal/mol), and water cannot assist the rate-determining step, which is remarkably different from the previous perception that a water molecule should mediate the activation process. The fourth reaction step has the highest free energy barrier (23.6 kcal/mol) which is reasonably close to the activation free energy (∼21-22 kcal/mol) derived from experimental kinetic data. The obtained novel mechanistic insights should be valuable for not only future rational design of more efficient proteasome inhibitors but also understanding the general reaction mechanism of proteasome with a peptide or protein.
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Affiliation(s)
- Donghui Wei
- Department of Chemistry, Zhengzhou University, Daxue Road, Zhengzhou, Henan 450052, China
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30
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Wu Q, Deng C, Peng Q, Niu Y, Shuai Z. Quantum chemical insights into the aggregation induced emission phenomena: a QM/MM study for pyrazine derivatives. J Comput Chem 2012; 33:1862-9. [PMID: 22622704 DOI: 10.1002/jcc.23019] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 04/09/2012] [Accepted: 04/22/2012] [Indexed: 11/10/2022]
Abstract
There have been intensive studies on the newly discovered phenomena called aggregation induced emission (AIE), in contrast to the conventional aggregation quenching. Through combined quantum mechanics and molecular mechanics computations, we have investigated the aggregation effects on the excited state decays, both via radiative and nonradiative routes, for pyrazine derivatives 2,3-dicyano-5,6-diphenylpyrazine (DCDPP) and 2,3-dicyanopyrazino phenanthrene (DCPP) in condensed phase. We show that for DCDPP there appear AIE for all the temperature, because the phenyl ring torsional motions in gas phase can efficiently dissipate the electronic excited state energy, and get hindered in aggregate; while for its "locked"-phenyl counterpart, DCPP, theoretical calculation can only give the normal aggregation quenching. These first-principles based findings are consistent with recent experiment. The primary origin of the exotic AIE phenomena is due to the nonradiative decay effects. This is the first time that AIE is understood based on theoretical chemistry calculations for aggregates, which helps to resolve the present disputes over the mechanism.
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Affiliation(s)
- Qunyan Wu
- Department of Chemistry, MOE Key Laboratory of Organic OptoElectronics and Molecular Engineering, Tsinghua University, Beijing, People's Republic of China
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31
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Wu Q, Peng Q, Niu Y, Gao X, Shuai Z. Theoretical Insights into the Aggregation-Induced Emission by Hydrogen Bonding: A QM/MM Study. J Phys Chem A 2012; 116:3881-8. [DOI: 10.1021/jp3002367] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Qunyan Wu
- MOE Key Laboratory
of Organic
OptoElectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, People’s
Republic of China
| | - Qian Peng
- Key Laboratory
of Organic Solids,
Beijing National Laboratory for Molecular Science (BNLMS), Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Yingli Niu
- Key Laboratory
of Organic Solids,
Beijing National Laboratory for Molecular Science (BNLMS), Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Xing Gao
- MOE Key Laboratory
of Organic
OptoElectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, People’s
Republic of China
| | - Zhigang Shuai
- MOE Key Laboratory
of Organic
OptoElectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, People’s
Republic of China
- Key Laboratory
of Organic Solids,
Beijing National Laboratory for Molecular Science (BNLMS), Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
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32
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Krenske EH, Davison EC, Forbes IT, Warner JA, Smith AL, Holmes AB, Houk KN. Reverse cope elimination of hydroxylamines and alkenes or alkynes: theoretical investigation of tether length and substituent effects. J Am Chem Soc 2012; 134:2434-41. [PMID: 22280245 DOI: 10.1021/ja211568k] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantum mechanical calculations have been used to study the intramolecular additions of hydroxylamines to alkenes and alkynes ("reverse Cope eliminations"). In intermolecular reverse Cope eliminations, alkynes are more reactive than alkenes. However, competition experiments have shown that tethering the hydroxylamine to the alkene or alkyne can reverse the reactivity order from that normally observed. The exact outcome depends on the length of the tether. In agreement with experiment, a range of density functional theory methods and CBS-QB3 calculations predict that the activation energies for intramolecular reverse Cope eliminations follow the order 6-exo-dig < 5-exo-trig < 5-exo-dig ≈ 7-exo-dig. The order of the barriers for the 5-, 6-, and 7-exo-dig reactions of alkynes arises mainly from differences in tether strain in the transition states (TSs), but is also influenced by the TS interaction between the hydroxylamine and alkyne. Cyclization onto an alkene in the 5-exo-trig fashion incurs slightly less tether strain than a 6-exo-dig alkyne cyclization, but its activation energy is higher because the hydroxylamine fragment must distort more before the TS is reached. If the alkene terminus is substituted with two methyl groups, the barrier becomes so much higher that it is also disfavored compared to the 5- and 7-exo-dig cyclizations.
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33
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Alexandrova AN, Jorgensen WL. On the mechanism and rate of spontaneous decomposition of amino acids. J Phys Chem B 2011; 115:13624-32. [PMID: 21995727 PMCID: PMC3241013 DOI: 10.1021/jp2081808] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spontaneous decarboxylation of amino acids is among the slowest known reactions; it is much less facile than the cleavage of amide bonds in polypeptides. Establishment of the kinetics and mechanisms for this fundamental reaction is important for gauging the proficiency of enzymes. In the present study, multiple mechanisms for glycine decomposition in water are explored using QM/MM Monte Carlo simulations and free energy perturbation theory. Simple CO(2) detachment emerges as the preferred pathway for decarboxylation; it is followed by water-assisted proton transfer to yield the products: CO(2) and methylamine. The computed free energy of activation of 45 kcal/mol, and the resulting rate-constant of 1 × 10(-21) s(-1), can be compared with an extrapolated experimental rate constant of ~2 × 10(-17) s(-1) at 25 °C. The half-life for the reaction is more than 1 billion years. Furthermore, examination of deamination finds simple NH(3)-detachment yielding α-lactone to be the favored route, though it is less facile than decarboxylation by 6 kcal/mol. Ab initio and DFT calculations with the CPCM hydration model were also carried out for the reactions; the computed free energies of activation for glycine decarboxylation agree with the QM/MM result, whereas deamination is predicted to be more favorable. QM/MM calculations were also performed for decarboxylation of alanine; the computed barrier is 2 kcal/mol higher than for glycine in qualitative accord with experiment.
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Affiliation(s)
- Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA.
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34
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On the smoothing of free energy landscape of solute molecules in solution: A demonstration of the stability of glycine conformers via ab initio QM/MM free energy calculation. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.08.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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35
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Menikarachchi LC, Gascón JA. An extrapolation method for computing protein solvation energies based on density fragmentation of a graphical surface tessellation. J Mol Graph Model 2011; 30:38-45. [PMID: 21715202 DOI: 10.1016/j.jmgm.2011.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 05/26/2011] [Accepted: 06/02/2011] [Indexed: 11/28/2022]
Abstract
Modeling chemical events inside proteins often require the incorporation of solvent effects via continuum polarizable models. One of these approaches is based on the assumption that the interface between solute and solvent acts as a conductor. Image charges are added on the molecular surface to satisfy the appropriate conductor boundary conditions in the presence of solute charges. As in the case of other polarizable continuum models that are based on surface tessellation, the simplest implementation of this approach is often limited to several hundred atoms due to a matrix inversion, which scales as the cube of the number or tesserae. For larger systems, approaches that use iterative matrix solvers coupled to fast summation methods must be used. In the present work, we develop a self-consistent approach to obtain conductor-like screening charges suitable for applications in proteins. The approach is based on a density fragmentation of a graphical surface tessellation. This method, although approximate, provides a straightforward scheme of parallelization, which can in principle be added to existing linear scaling implementations of conductor-like models. We implement this method in conjunction with a fixed charge model for the protein, as well as with a moving domain QM/MM description of the protein. In the latter case, the overall result leads to a charge distribution within the protein determined by self-polarization and polarization due to solvent.
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Affiliation(s)
- Lochana C Menikarachchi
- Department of Chemistry, University of Connecticut, 55 North Eagleville Rd., Unit 3060, Storrs, CT 06269, USA
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36
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Hori K, Yamaguchi T, Uezu K, Sumimoto M. A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): Application to highly solvent-dependent reactions. J Comput Chem 2010; 32:778-86. [DOI: 10.1002/jcc.21653] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 07/28/2010] [Accepted: 07/30/2010] [Indexed: 11/09/2022]
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37
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Kostal J, Jorgensen WL. Thorpe-Ingold acceleration of oxirane formation is mostly a solvent effect. J Am Chem Soc 2010; 132:8766-73. [PMID: 20524660 PMCID: PMC2892976 DOI: 10.1021/ja1023755] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Thorpe-Ingold hypothesis for the gem-dimethyl effect in the cyclization reactions of 2-chloroethoxide derivatives has been investigated computationally in the gas phase and in aqueous solution. Ab initio MP2/6-311+G(d,p) and CBS-Q calculations reveal little intrinsic difference in reactivity with increasing alpha-methylation for the series of reactants 1-3. However, inclusion of continuum hydration or of explicit hydration through mixed quantum and statistical mechanics (MC/FEP) simulations does reproduce the substantial, experimentally observed rate increases with increasing alpha-methylation. Analysis of the MC/FEP results provides clear evidence that the rate increases stem primarily from increased steric hindrance to hydration of the nucleophilic oxygen atom with increasing alpha-methylation. Thus, the gem-dimethyl acceleration of oxirane formation for 1-3 is found to be predominantly a solvent effect.
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Affiliation(s)
- Jakub Kostal
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520-8107
| | - William L. Jorgensen
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520-8107
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Um JM, Kaka NS, Hodgson DM, Houk KN. Transition states and origins of 1,4-asymmetric induction in alkylations of 2,2,6-trialkylpiperidine enamines. Chemistry 2010; 16:6310-6. [PMID: 20411546 PMCID: PMC3049728 DOI: 10.1002/chem.201000046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The asymmetric C-alkylation of chiral enamines derived from terminal epoxides and lithium 2,2,6-trialkylpiperidides has previously been shown to provide alpha-alkylated aldehydes by intermolecular nucleophilic substitution in good levels of asymmetric induction. We now report a computational study of the origins of asymmetric induction in these reactions. Computational modeling with density functional theory (B3LYP/6-31G(d)) agrees closely with the experimental observations. This stereoselectivity is attributed to a preferential conformation of the enamine and the piperidine ring that places the C-6 alkyl substituent in an axial position due to A(1, 3) strain. Preferential attack occurs away from the axial group, for steric reasons. The effects of changing the C-6 substituent from methyl to isopropyl were studied, and twist transition states were found to contribute significantly in the latter alkylations.
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Affiliation(s)
- Joann M. Um
- Department of Chemistry and Biochemistry, UCLA Los Angeles, CA 90095-1569 (USA)
| | - Naeem S. Kaka
- Department of Chemistry, Chemistry Research Laboratory University of Oxford, Mansfield Road, Oxford, OX1 3TA (UK)
| | - David M. Hodgson
- Department of Chemistry, Chemistry Research Laboratory University of Oxford, Mansfield Road, Oxford, OX1 3TA (UK)
| | - K. N. Houk
- Department of Chemistry and Biochemistry, UCLA Los Angeles, CA 90095-1569 (USA)
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Acevedo O. Role of water in the multifaceted catalytic antibody 4B2 for allylic isomerization and Kemp elimination reactions. J Phys Chem B 2010; 113:15372-81. [PMID: 19860435 DOI: 10.1021/jp9069114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Specificity toward a single reaction is a well-known characteristic of catalytic antibodies. However, contrary to convention, catalytic antibody 4B2 possesses the ability to efficiently catalyze two unrelated reactions: a Kemp elimination and an allylic isomerization of a beta,gamma-unsaturated ketone. To elucidate how this multifaceted antibody operates, mixed quantum and molecular mechanics calculations coupled to Monte Carlo simulations were carried out. The antibody was determined to derive its adaptability for the mechanistically different reactions through the rearrangement of water molecules in the active site into advantageous geometric orientations for enhanced electrostatic stabilization. In the case of the Kemp elimination, a general base, Glu L34, carried out the proton abstraction from the isoxazole ring of 5-nitro-benzisoxazole while water molecules delivered specific stabilization at the transition state. The role of water was found to be more pronounced in the allylic isomerization because the solvent actively participated in the stepwise mechanism. A rate-limiting abstraction of the alpha-proton from the beta,gamma-unsaturated ketone via Glu L34 led to the formation of a neutral dienol intermediate, which was rapidly reprotonated at the gamma-position via a solvent hydronium ion. Preferential channeling of H(3)O(+) in the active site ensured a stereoselective proton exchange from the alpha- to the gamma-position, in good agreement with deuterium exchange NMR and HPLC experiments. Ideas for improved water-mediated catalytic antibody designs are presented. In a technical advancement, improvements to a recent polynomial fitting and integration technique utilizing free energy perturbation theory delivered greater accuracy and speed gains.
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Affiliation(s)
- Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA.
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40
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Deora N, Carlier PR. Computational Studies of Ion-Pair Separation of Benzylic Organolithium Compounds in THF: Importance of Explicit and Implicit Solvation. J Org Chem 2010; 75:1061-9. [DOI: 10.1021/jo9016452] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Nipa Deora
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24060
| | - Paul R. Carlier
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24060
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41
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Seabra GDM, Walker RC, Roitberg AE. Are current semiempirical methods better than force fields? A study from the thermodynamics perspective. J Phys Chem A 2010; 113:11938-48. [PMID: 19848431 DOI: 10.1021/jp903474v] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The semiempirical Hamiltonians MNDO, AM1, PM3, RM1, PDDG/MNDO, PDDG/PM3, and SCC-DFTB, when used as part of a hybrid QM/MM scheme for the simulation of biological molecules, were compared on their abilities to reproduce experimental ensemble averages at or near room temperatures for the model system alanine dipeptide in water. Free energy surfaces in the (phi, psi) dihedral angle space, (3)J(H(N),H(alpha)) NMR dipolar coupling constants, basin populations, and peptide-water radial distribution functions (RDF) were calculated from replica exchange simulations and compared to both experiment and fully classical force field calculations using the Amber ff99SB force field. In contrast with the computational chemist's intuitive idea that the more expensive a method the better its accuracy, the ff99SB force field results were more accurate than most of the semiempirical methods, with the exception of RM1. None of the methods, however, was able to accurately reproduce the experimental data. Analysis of the results indicate that the specific QM/MM interactions have little influence on the sampling of free energy surfaces, and the differences are well explained simply by the intrinsic properties of the various QM methods.
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Affiliation(s)
- Gustavo de M Seabra
- Quantum Theory Project and Department of Chemistry, University of Florida, 2234 New Physics Building #92, P.O. Box 118435, Gainesville, Florida 32611-8435, USA
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42
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Acevedo O, Armacost K. Claisen Rearrangements: Insight into Solvent Effects and “on Water” Reactivity from QM/MM Simulations. J Am Chem Soc 2010; 132:1966-75. [DOI: 10.1021/ja908680c] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
| | - Kira Armacost
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
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43
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Acevedo O, Jorgensen WL. Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions. Acc Chem Res 2010; 43:142-51. [PMID: 19728702 DOI: 10.1021/ar900171c] [Citation(s) in RCA: 176] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Application of combined quantum and molecular mechanical (QM/MM) methods focuses on predicting activation barriers and the structures of stationary points for organic and enzymatic reactions. Characterization of the factors that stabilize transition structures in solution and in enzyme active sites provides a basis for design and optimization of catalysts. Continued technological advances allowed for expansion from prototypical cases to mechanistic studies featuring detailed enzyme and condensed-phase environments with full integration of the QM calculations and configurational sampling. This required improved algorithms featuring fast QM methods, advances in computing changes in free energies including free-energy perturbation (FEP) calculations, and enhanced configurational sampling. In particular, the present Account highlights development of the PDDG/PM3 semi-empirical QM method, computation of multi-dimensional potentials of mean force (PMF), incorporation of on-the-fly QM in Monte Carlo (MC) simulations, and a polynomial quadrature method for efficient modeling of proton-transfer reactions. The utility of this QM/MM/MC/FEP methodology is illustrated for a variety of organic reactions including substitution, decarboxylation, elimination, and pericyclic reactions. A comparison to experimental kinetic results on medium effects has verified the accuracy of the QM/MM approach in the full range of solvents from hydrocarbons to water to ionic liquids. Corresponding results from ab initio and density functional theory (DFT) methods with continuum-based treatments of solvation reveal deficiencies, particularly for protic solvents. Also summarized in this Account are three specific QM/MM applications to biomolecular systems: (1) a recent study that clarified the mechanism for the reaction of 2-pyrone derivatives catalyzed by macrophomate synthase as a tandem Michael-aldol sequence rather than a Diels-Alder reaction, (2) elucidation of the mechanism of action of fatty acid amide hydrolase (FAAH), an unusual Ser-Ser-Lys proteolytic enzyme, and (3) the construction of enzymes for Kemp elimination of 5-nitrobenzisoxazole that highlights the utility of QM/MM in the design of artificial enzymes.
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Affiliation(s)
- Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
| | - William L. Jorgensen
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107
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Alexandrova AN, Röthlisberger D, Baker D, Jorgensen WL. Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination. J Am Chem Soc 2009; 130:15907-15. [PMID: 18975945 DOI: 10.1021/ja804040s] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of enzymes for Kemp elimination of 5-nitrobenzisoxazole has been recently designed and tested. In conjunction with the design process, extensive computational analyses were carried out to evaluate the potential performance of four of the designs, as presented here. The enzyme-catalyzed reactions were modeled using mixed quantum and molecular mechanics (QM/MM) calculations in the context of Monte Carlo (MC) statistical mechanics simulations. Free-energy perturbation (FEP) calculations were used to characterize the free-energy surfaces for the catalyzed reactions as well as for reference processes in water. The simulations yielded detailed information about the catalytic mechanisms, activation barriers, and structural evolution of the active sites over the course of the reactions. The catalytic mechanism for the designed enzymes KE07, KE10(V131N), and KE15 was found to be concerted with proton transfer, generally more advanced in the transition state than breaking of the isoxazolyl N-O bond. On the basis of the free-energy results, all three enzymes were anticipated to be active. Ideas for further improvement of the enzyme designs also emerged. On the technical side, the synergy of parallel QM/MM and experimental efforts in the design of artificial enzymes is well illustrated.
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Affiliation(s)
- Anastassia N Alexandrova
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
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Moran J, Pfeiffer JY, Gorelsky SI, Beauchemin AM. Ketonitrones via Cope-Type Hydroamination of Allenes. Org Lett 2009; 11:1895-8. [DOI: 10.1021/ol900292r] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joseph Moran
- Centre for Catalysis Research and Innovation, Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario, Canada K1N 6N5
| | - Jennifer Y. Pfeiffer
- Centre for Catalysis Research and Innovation, Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario, Canada K1N 6N5
| | - Serge I. Gorelsky
- Centre for Catalysis Research and Innovation, Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario, Canada K1N 6N5
| | - André M. Beauchemin
- Centre for Catalysis Research and Innovation, Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario, Canada K1N 6N5
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Abstract
Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.
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Affiliation(s)
- Hans Martin Senn
- Department of Chemistry, WestCHEM and University of Glasgow, Glasgow G12 8QQ, UK.
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47
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Alexandrova AN, Jorgensen WL. Origin of the activity drop with the E50D variant of catalytic antibody 34E4 for Kemp elimination. J Phys Chem B 2009; 113:497-504. [PMID: 19132861 DOI: 10.1021/jp8076084] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In enzymes, multiple structural effects cooperatively lead to the high catalytic activity, while individually these effects can be small. The design of artificial enzymes requires the understanding and ability to manipulate such subtle effects. The 34E4 catalytic antibody, catalyzing Kemp elimination of 5-nitrobenzisoxazole, and its Glu50Asp (E50D) variant are the subject of the present investigation. This removal of only a methylene group yields an approximately 30-fold reduction in the rate for the catalyzed Kemp elimination. Here, the aim is to understand this difference in the catalytic performance. The mechanism of Kemp elimination catalyzed by 34E4 and the E50D mutant is elucidated using QM/MM Monte Carlo simulations and free energy perturbation theory. In both proteins, the reaction is shown to follow a single-step, concerted mechanism. In the mutant, the activation barrier rises by 2.4 kcal/mol, which corresponds to a 62-fold rate deceleration, which is in good agreement with the experimental data. The positions and functionality of the residues in the active site are monitored throughout the reaction. It is concluded that the looser contact with the base, shorter base-Asn58 contact, less favorable pi-stacking with Trp91 in the transition state of the reaction, and different solvation pattern all contribute to the reduction of the reaction rate in the E50D variant of 34E4.
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Affiliation(s)
- Anastassia N Alexandrova
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.
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48
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Sheppard AN, Acevedo O. Multidimensional Exploration of Valley−Ridge Inflection Points on Potential-Energy Surfaces. J Am Chem Soc 2009; 131:2530-40. [DOI: 10.1021/ja803879k] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- April N. Sheppard
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
| | - Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
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49
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50
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Brancato G, Rega N, Barone V. A hybrid explicit/implicit solvation method for first-principle molecular dynamics simulations. J Chem Phys 2008; 128:144501. [DOI: 10.1063/1.2897759] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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