1
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Yan X, Qu C, Li Q, Zhu L, Tong HH, Liu H, Ouyang Q, Yao X. Multiscale calculations reveal new insights into the reaction mechanism between KRAS G12C and α, β-unsaturated carbonyl of covalent inhibitors. Comput Struct Biotechnol J 2024; 23:1408-1417. [PMID: 38616962 PMCID: PMC11015740 DOI: 10.1016/j.csbj.2024.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 04/16/2024] Open
Abstract
Utilizing α,β-unsaturated carbonyl group as Michael acceptors to react with thiols represents a successful strategy for developing KRASG12C inhibitors. Despite this, the precise reaction mechanism between KRASG12C and covalent inhibitors remains a subject of debate, primarily due to the absence of an appropriate residue capable of deprotonating the cysteine thiol as a base. To uncover this reaction mechanism, we first discussed the chemical reaction mechanism in solvent conditions via density functional theory (DFT) calculation. Based on this, we then proposed and validated the enzymatic reaction mechanism by employing quantum mechanics/molecular mechanics (QM/MM) calculation. Our QM/MM analysis suggests that, in biological conditions, proton transfer and nucleophilic addition may proceed through a concerted process to form an enolate intermediate, bypassing the need for a base catalyst. This proposed mechanism differs from previous findings. Following the formation of the enolate intermediate, solvent-assisted tautomerization results in the final product. Our calculations indicate that solvent-assisted tautomerization is the rate-limiting step in the catalytic cycle under biological conditions. On the basis of this reaction mechanism, the calculated kinact/ki for two inhibitors is consistent well with the experimental results. Our findings provide new insights into the reaction mechanism between the cysteine of KRASG12C and the covalent inhibitors and may provide valuable information for designing effective covalent inhibitors targeting KRASG12C and other similar targets.
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Affiliation(s)
- Xiao Yan
- Faculty of Applied Sciences, Macao Polytechnic University, Macao Special Administrative Region of China
| | - Chuanhua Qu
- College of Pharmacy, National & Local Joint Engineering Research Center of Targeted and Innovative Therapeutics, Chongqing Key Laboratory of Kinase Modulators as Innovative Medicine, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Qin Li
- Faculty of Applied Sciences, Macao Polytechnic University, Macao Special Administrative Region of China
| | - Lei Zhu
- College of Pharmacy, Third Military Medical University, Shapingba, Chongqing 400038, China
| | - Henry H.Y. Tong
- Faculty of Applied Sciences, Macao Polytechnic University, Macao Special Administrative Region of China
| | - Huanxiang Liu
- Faculty of Applied Sciences, Macao Polytechnic University, Macao Special Administrative Region of China
| | - Qin Ouyang
- College of Pharmacy, Third Military Medical University, Shapingba, Chongqing 400038, China
| | - Xiaojun Yao
- Faculty of Applied Sciences, Macao Polytechnic University, Macao Special Administrative Region of China
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2
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Cammi R, Chen B. Activation volume and quantum tunneling in the hydrogen transfer reaction between methyl radical and methane: A first computational study. J Chem Phys 2024; 160:104103. [PMID: 38465680 DOI: 10.1063/5.0195973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/20/2024] [Indexed: 03/12/2024] Open
Abstract
We present a theory of the effect of quantum tunneling on the basic parameter that characterizes the effect of pressure on the rate constant of chemical reactions in a dense phase, the activation volume. This theory results in combining, on the one hand, the extreme pressure polarizable continuum model, a quantum chemical method to describe the effect of pressure on the reaction energy profile in a dense medium, and, on the other hand, the semiclassical version of the transition state theory, which includes the effect of quantum tunneling through a transmission coefficient. The theory has been applied to the study of the activation volume of the model reaction of hydrogen transfer between methyl radical and methane, including the primary isotope substitution of hydrogen with deuterium (H/D). The analysis of the numerical results offers, for the first time, a clear insight into the effect of quantum tunneling on the activation volume for this hydrogen transfer reaction: this effect results from the different influences that pressure has on the competing thermal and tunneling reaction mechanisms. Furthermore, the computed kinetic isotope effect (H/D) on the activation volume for this model hydrogen transfer correlates well with the experimental data for more complex hydrogen transfer reactions.
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Affiliation(s)
- Roberto Cammi
- Department of Chemistry, Life Sciences and Environmental Sustainability, Università degli Studi di Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy
| | - Bo Chen
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Spain
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3
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Du Z, Ma Y, Shen Y, Jiang X, Zhou Y, Shi T. Exploring the substrate stereoselectivity and catalytic mechanism of nonribosomal peptide macrocyclization in surugamides biosynthesis. iScience 2024; 27:108876. [PMID: 38313049 PMCID: PMC10835440 DOI: 10.1016/j.isci.2024.108876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/12/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024] Open
Abstract
SurE, the first reported penicillin-binding protein-like thioesterase (PBP-like TE), is known as a new off-loading cyclase, which catalyzes heterochiral coupling in nonribosomal peptides (NRPs). However, the structural rationale for substrate stereoselectivity and enzymatic mechanism remains mysterious. Here, computational models, integrating MD simulations and QM/MM methods, unveiled SurE's substrate recognition and catalytic process. An oxyanion hole stabilized the C-terminal D-residue during recognition. Residue R446 anchored the substrate for macrocyclization. A vital hydrogen-bonding network (Y154, K66, N156), verified by mutation results, was responsible for the recognition of N-terminal L-residue and involvement in catalytic process with a calculated 19.4 kcal/mol energy barrier. Four novel-designed peptide precursors were effectively cyclized into cyclopeptides by SurE based on computational analysis. Our results provide a comprehensive understanding of SurE's catalytic mechanism and guiding design of versatile PBP-like TEs for novel macrocyclic NRPs.
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Affiliation(s)
- Zeqian Du
- State Key Laboratory of Microbial Metabolism, Joint International Research, Laboratory of Metabolic and Developmental Sciences, School of Life Sciences, and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yinhao Ma
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Yaoyao Shen
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xuefeng Jiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Yongjun Zhou
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research, Laboratory of Metabolic and Developmental Sciences, School of Life Sciences, and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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4
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Zheng Y, Venkatesh R, Callaway CP, Viersen C, Fagbohungbe KH, Liu AL, Risko C, Reichmanis E, Silva-Acuña C. Chain Conformation and Exciton Delocalization in a Push-Pull Conjugated Polymer. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2023; 35:10258-10267. [PMID: 38107193 PMCID: PMC10720347 DOI: 10.1021/acs.chemmater.3c02665] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 12/19/2023]
Abstract
Linear and nonlinear optical line shapes reveal details of excitonic structure in polymer semiconductors. We implement absorption, photoluminescence, and transient absorption spectroscopies in DPP-DTT, an electron push-pull copolymer, to explore the relationship between their spectral line shapes and chain conformation, deduced from resonance Raman spectroscopy and from ab initio calculations. The viscosity of precursor polymer solutions before film casting displays a transition that suggests gel formation above a critical concentration. Upon crossing this viscosity deflection concentration, the line shape analysis of the absorption spectra within a photophysical aggregate model reveals a gradual increase in interchain excitonic coupling. We also observe a red-shifted and line-narrowed steady-state photoluminescence spectrum along with increasing resonance Raman intensity in the stretching and torsional modes of the dithienothiophene unit, which suggests a longer exciton coherence length along the polymer-chain backbone. Furthermore, we observe a change of line shape in the photoinduced absorption component of the transient absorption spectrum. The derivative-like line shape may originate from two possibilities: a new excited-state absorption or Stark effect, both of which are consistent with the emergence of a high-energy shoulder as seen in both photoluminescence and absorption spectra. Therefore, we conclude that the exciton is more dispersed along the polymer chain backbone with increasing concentrations, leading to the hypothesis that polymer chain order is enhanced when the push-pull polymers are processed at higher concentrations. Thus, tuning the microscopic chain conformation by concentration would be another factor of interest when considering the polymer assembly pathways for pursuing large-area and high-performance organic optoelectronic devices.
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Affiliation(s)
- Yulong Zheng
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Rahul Venkatesh
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332, United States
| | - Connor P. Callaway
- Department
of Chemistry and Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Campbell Viersen
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Kehinde H. Fagbohungbe
- Department
of Chemistry and Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Aaron L. Liu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332, United States
| | - Chad Risko
- Department
of Chemistry and Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Elsa Reichmanis
- Department
of Chemical & Biomolecular Engineering, Lehigh University, 124 East Morton Street, Bethlehem, Pennsylvania 18015, United States
| | - Carlos Silva-Acuña
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
- School
of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, Georgia 30332, United States
- School
of Materials Science and Engineering, Georgia
Institute of Technology, North Avenue, Atlanta, Georgia 30332, United States
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5
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Rastogi S, Chandra A. Free Energy Landscapes of the Tautomeric Interconversion of Pyridoxal 5'-Phosphate Aldimines at the Active Site of Ornithine Decarboxylase in Aqueous Media. J Phys Chem B 2023; 127:8139-8149. [PMID: 37721415 DOI: 10.1021/acs.jpcb.3c04142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
The pyridoxal 5'-phosphate (PLP) acts as a coenzyme for a large number of biochemical reactions. It exists in mainly two bound forms at the active site of the concerned enzyme: the internal aldimine, in which the PLP is bound with the ϵ-amino group of lysine at the active site, and the external aldimine, where the PLP is bound to the substrate amino acid. Both the internal and external aldimines have Schiff base linkage (N-H-O) and can exist in two tautomeric structures of ketoenamine and enolimine forms. In this work, we have investigated the free energy landscape for the tautomeric proton transfer in the internal and external aldimines at the active site of the ornithine decarboxylase enzyme in an aqueous medium. We performed hybrid quantum-classical metadynamics and force field-based molecular dynamics simulations, which revealed that the ketoenamine tautomer is more stable than the enolimine form. The QM/MM metadynamics calculations show that the free energy difference between the ketoenamine and enolimine forms for the internal aldimine is 3.9 kcal/mol, and it is found to be 5.8 kcal/mol for the external aldimine, with the ketoenamine form being more stable in both cases. The results are further supported by calculations of the binding free energies from classical simulations and static quantum chemical calculations in different environments. We have also analyzed the configurational structure of the microenvironment at the active site in order to have better insights into the interactions of the active site residues with the PLP in its two tautomeric forms.
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Affiliation(s)
- Shreya Rastogi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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6
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Lu Y, Sen K, Yong C, Gunn DSD, Purton JA, Guan J, Desmoutier A, Abdul Nasir J, Zhang X, Zhu L, Hou Q, Jackson-Masters J, Watts S, Hanson R, Thomas HN, Jayawardena O, Logsdail AJ, Woodley SM, Senn HM, Sherwood P, Catlow CRA, Sokol AA, Keal TW. Multiscale QM/MM modelling of catalytic systems with ChemShell. Phys Chem Chem Phys 2023; 25:21816-21835. [PMID: 37097706 DOI: 10.1039/d3cp00648d] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling.
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Affiliation(s)
- You Lu
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Kakali Sen
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Chin Yong
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - David S D Gunn
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - John A Purton
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Jingcheng Guan
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Alec Desmoutier
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Jamal Abdul Nasir
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Xingfan Zhang
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Lei Zhu
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Qing Hou
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Joe Jackson-Masters
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Sam Watts
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Rowan Hanson
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Harry N Thomas
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Omal Jayawardena
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Andrew J Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Scott M Woodley
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Hans M Senn
- School of Chemistry, University of Glasgow, Joseph Black Building, Glasgow G12 8QQ, UK
| | - Paul Sherwood
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK
| | - C Richard A Catlow
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Alexey A Sokol
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Thomas W Keal
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
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7
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Pashaei B, Shahroosvand H, Douroudgari H, Abaspour S, Vahedpour M, Nazeeruddin MK. Full Solution Process of a Near-Infrared Light-Emitting Electrochemical Cell Based on Novel Emissive Ruthenium Complexes of 1,10-Phenanthroline-Derived Ligands and a Eutectic Alloy as the Top Electrode. Inorg Chem 2023; 62:7622-7635. [PMID: 37163724 DOI: 10.1021/acs.inorgchem.2c02531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Near-infrared luminescent materials have recently received considerable attention for a large number of applications, including in solid-state lighting, as bioimaging agents, as photovoltaic cells, and in the telecommunication industry. By adding diverse electron-donating or withdrawing groups on ancillary ligands based on benzenethiol-phenanthroline, we synthesized and optoelectronically characterized a series of novel ionic ruthenium complexes, namely RuS, RuSCl, RuSMe, and RuSNH2, for using in a light-emitting electrochemical cell. The synthesized complexes are intense red emitters in the range of 584-605 nm in solution, which depends on the substitutions of electron donor/acceptor moieties on the ancillary ligands. To find a suitable quantum mechanical approach, benchmark calculations based on time-dependent density functional theory were carried out on these complexes. Our benchmark revealed that the M06-L method has results close to those of the experiment. Furthermore, to gain a deeper insight into electronic transitions, several excitation processes were investigated at the TD-DFT-SMD-MN12-L/gen level. The results showed that in the designed complexes, the dominant transition is between the 4dZ2 electron of Ru (particle) and the π* orbitals of the ancillary ligand (hole). The single-layer devices, including these complexes along with a Ga/In cathode by a facile deposition method without the addition of any electron or hole transport layers, were fabricated and displayed red (678 nm) to near-infrared (701 nm) emission as well as a decrease of turn-on voltage from 3.85 to 3.10 V. In particular, adding a methyl group to the ancillary ligand in the complex RuSNH2 increases the external quantum efficiency to 0.55%, one of the highest observed values in the ruthenium phenanthroline family. This simple structure of the device lets us develop the practical applications of light-emitting electrochemical cells based on injection and screen-printing methods, which are very promising for the vacuum-free deposition of top electrodes.
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Affiliation(s)
- Babak Pashaei
- Group for Molecular Engineering of Advanced Functional Materials, Department of Chemistry, University of Zanjan, Zanjan 45371-3879, Iran
| | - Hashem Shahroosvand
- Group for Molecular Engineering of Advanced Functional Materials, Department of Chemistry, University of Zanjan, Zanjan 45371-3879, Iran
| | - Hamed Douroudgari
- Physical Chemistry, Department of Chemistry, University of Zanjan, Zanjan 45371-3879, Iran
| | - Saeid Abaspour
- Group for Molecular Engineering of Advanced Functional Materials, Department of Chemistry, University of Zanjan, Zanjan 45371-3879, Iran
| | - Morteza Vahedpour
- Physical Chemistry, Department of Chemistry, University of Zanjan, Zanjan 45371-3879, Iran
| | - Mohammad Khaja Nazeeruddin
- Group for Molecular Engineering of Functional Materials, Institute of Chemical Sciences and Engineering, Ecole Polytechnique F́ed́erale de Lausanne, Sion CH-1951, Switzerland
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8
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Du Z, Li Y, Liu Y, Shi T. Molecular Insights into Bifunctional Ambruticin DH3 for Substrate Specificity and Catalytic Mechanism. Chemistry 2023; 29:e202203420. [PMID: 36464909 DOI: 10.1002/chem.202203420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022]
Abstract
Dehydratase (DH), a domain located at polyketide synthase (PKS) modules, commonly catalyzes the dehydration of β-hydroxy to an α,β-unsaturated acyl intermediate. As a unique bifunctional dehydratase, AmbDH3 (the DH domain of module 3 of the ambruticin PKS) is verified to be responsible for both dehydration and the following pyran-forming cyclization. Besides, in vitro studies showed that its catalytic efficiency varies with different chiral substrates. However, the detailed molecular mechanism of AmbDH3 remains unclear. In this work, the structural rationale for the substrate specificity (2R/2S- and 6R/6S-substrates) in AmbDH3 was elucidated and the complete reaction pathways including dehydration and cyclization were presented. Both MD simulations and binding free energy calculations indicated AmbDH3 had a stronger preference for 2R-substrates (2R6R-2, 2R6S-3) than 2S-substrates (2S6R-1), and residue H51 and G61 around the catalytic pocket were emphasized by forming stable hydrogen bonds with 2R-substrates. In addition, AmbDH3's mild tolerance at C6 was explained by comparison of substrate conformation and hydrogen bond network in 6S- and 6R-substrate systems. The QM/MM results supported a consecutive one-base dehydration and cyclization mechanism for 2R6S-3 substrate with the energy barrier of 25.2 kcal mol-1 and 24.5 kcal mol-1 , respectively. Our computational results uncover the substrate recognition and catalytic process of the first bifunctional dehydratase-cyclase AmbDH3, which will shed light on the application of multifunctional DH domains in PKSs for diverse natural product analogs and benefit the chemoenzymatic synthesis of stereoselective pyran-containing products.
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Affiliation(s)
- Zeqian Du
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yongzhen Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yihan Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Ting Shi
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, P. R. China
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9
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Fu Y, Chen H, Fu W, Garcia-Borràs M, Yang Y, Liu P. Engineered P450 Atom-Transfer Radical Cyclases are Bifunctional Biocatalysts: Reaction Mechanism and Origin of Enantioselectivity. J Am Chem Soc 2022; 144:13344-13355. [PMID: 35830682 PMCID: PMC9339536 DOI: 10.1021/jacs.2c04937] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New-to-nature radical biocatalysis has recently emerged as a powerful strategy to tame fleeting open-shell intermediates for stereoselective transformations. In 2021, we introduced a novel metalloredox biocatalysis strategy that leverages the innate redox properties of the heme cofactor of P450 enzymes, furnishing new-to-nature atom-transfer radical cyclases (ATRCases) with excellent activity and stereoselectivity. Herein, we report a combined computational and experimental study to shed light on the mechanism and origins of enantioselectivity for this system. Molecular dynamics and quantum mechanics/molecular mechanics (QM/MM) calculations revealed an unexpected role of the key beneficial mutation I263Q. The glutamine residue serves as an essential hydrogen bond donor that engages with the carbonyl moiety of the substrate to promote bromine atom abstraction and enhance the enantioselectivity of radical cyclization. Therefore, the evolved ATRCase is a bifunctional biocatalyst, wherein the heme cofactor enables atom-transfer radical biocatalysis, while the hydrogen bond donor residue further enhances the activity and enantioselectivity. Unlike many enzymatic stereocontrol rationales based on a rigid substrate binding model, our computations demonstrate a high degree of rotational flexibility of the allyl moiety in an enzyme-substrate complex and succeeding intermediates. Therefore, the enantioselectivity is controlled by the radical cyclization transition states rather than the substrate orientation in ground-state complexes in the preceding steps. During radical cyclization, anchoring effects of the Q263 residue and steric interactions with the heme cofactor concurrently control the π-facial selectivity, allowing for highly enantioselective C-C bond formation. Our computational findings are corroborated by experiments with ATRCase mutants generated from site-directed mutagenesis.
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Affiliation(s)
- Yue Fu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Heyu Chen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Wenzhen Fu
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Marc Garcia-Borràs
- Institut de Química Computacional i Catalisi (IQCC) and Departament de Química, Universitat de Girona, Girona 17003, Spain
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Biomolecular Science and Engineering (BMSE) Program, University of California, Santa Barbara, California 93106, United States
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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10
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Yu Q, Lu W, Li D, Shi T. Insight into substrate‐assisted catalytic mechanism and stereoselectivity of bifunctional nocardicin thioesterase. Proteins 2022; 90:2035-2044. [DOI: 10.1002/prot.26395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 05/30/2022] [Accepted: 06/21/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Qian Yu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai China
| | - Wei Lu
- Department of Food Science and Engineering School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai China
| | - Daixi Li
- Institute of Biothermal Science and Technology, University of Shanghai for Science and Technology Shanghai China
- AI Research Center Peng Cheng National Laboratory Shenzhen Guangdong China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai China
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11
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Mai BK, Neris NM, Yang Y, Liu P. C-N Bond Forming Radical Rebound Is the Enantioselectivity-Determining Step in P411-Catalyzed Enantioselective C(sp 3)-H Amination: A Combined Computational and Experimental Investigation. J Am Chem Soc 2022; 144:11215-11225. [PMID: 35583461 DOI: 10.1021/jacs.2c02283] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Engineered metalloenzymes represent promising catalysts for stereoselective C-H functionalization reactions. Recently, P450 enzymes have been evolved to allow for new-to-nature intramolecular C(sp3)-H amination reactions via a nitrene transfer mechanism, giving rise to diamine derivatives with excellent enantiocontrol. To shed light on the origin of enantioselectivity, a combined computational and experimental study was carried out. Hybrid quantum mechanics/molecular mechanics calculations were performed to investigate the activation energies and enantioselectivities of both the hydrogen atom transfer (HAT) and the subsequent C-N bond forming radical rebound steps. Contrary to previously hypothesized enantioinduction mechanisms, our calculations show that the radical rebound step is enantioselectivity-determining, whereas the preceding HAT step is only moderately stereoselective. Furthermore, the selectivity in the initial HAT is ablated by rapid conformational change of the radical intermediate prior to C-N bond formation. This finding is corroborated by our experimental study using a set of enantiomerically pure, monodeuterated substrates. Furthermore, classical and ab initio molecular dynamics simulations were carried out to investigate the conformational flexibility of the carbon-centered radical intermediate. This key radical species undergoes a facile conformational change in the enzyme active site from the pro-(R) to the pro-(S) configuration, whereas the radical rebound is slower due to the spin-state change and ring strain of the cyclization process, thereby allowing stereoablative C-N bond formation. Together, these studies revealed an underappreciated enantioinduction mechanism in biocatalytic C(sp3)-H functionalizations involving radical intermediates, opening up new avenues for the development of other challenging asymmetric C(sp3)-H functionalizations.
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Affiliation(s)
- Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Natalia M Neris
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Biomolecular Science and Engineering (BMSE) Program, University of California, Santa Barbara, California 93106, United States
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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12
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Paciotti R, Chiavarino B, Coletti C, Scuderi D, Re N, Corinti D, Rotari L, Fornarini S, Crestoni ME. IRMPD Spectroscopy of Bare Monodeprotonated Genistein, an Antioxidant Flavonoid. ACS OMEGA 2022; 7:19535-19544. [PMID: 35721943 PMCID: PMC9202291 DOI: 10.1021/acsomega.2c01236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/17/2022] [Indexed: 05/11/2023]
Abstract
Genistein is a naturally occurring polyphenol belonging to the family of flavonoids with estrogenic properties and proven antioxidant, anti-inflammatory, and hormonal effects. Genistein and its derivatives are involved in radical scavenging activity by way of mechanisms based on sequential proton-loss electron transfer. In view of this role, a detailed structural characterization of its bare deprotonated form, [geni-H]-, generated by electrospray ionization, has been performed by tandem mass spectrometry and infrared multiple photon dissociation (IRMPD) spectroscopy in the 800-1800 cm-1 spectral range. Quantum chemical calculations at the B3LYP/6-311+G(d,p) level of theory were carried out to determine geometries, thermochemical data, and anharmonic vibrational properties of low-lying isomers, enabling to interpret the experimental spectrum. Evidence is gathered that the conjugate base of genistein exists as a single isomeric form, which is deprotonated at the most acidic site (7-OH) and benefits from a strong intramolecular H-bond interaction between 5-OH and the adjacent carbonyl oxygen in the most stable arrangement.
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Affiliation(s)
- Roberto Paciotti
- Dipartimento
di Farmacia, Università G. D’Annunzio
Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Barbara Chiavarino
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Cecilia Coletti
- Dipartimento
di Farmacia, Università G. D’Annunzio
Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Debora Scuderi
- Institut
de Chimie Physique (UMR8000), CNRS, Université Paris-Saclay, 91405 Orsay, France
| | - Nazzareno Re
- Dipartimento
di Farmacia, Università G. D’Annunzio
Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Davide Corinti
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Lucretia Rotari
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy
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13
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Zheng DZ, Li DH, Liu H, Shao Y, Ke Z, Liu FS. Bis(imino)acenaphthene (BIAN)-Supported N-Heterocyclic Carbene Palladium Complexes with Ancillary Ligands: Readily Activated Precatalysts for Direct C–H Arylation of Thiophenes. Organometallics 2022. [DOI: 10.1021/acs.organomet.2c00007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Di-Zhong Zheng
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Zhongshan, Guangdong 528458, China
| | - Dong-Hui Li
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Zhongshan, Guangdong 528458, China
| | - Huan Liu
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Zhongshan, Guangdong 528458, China
| | - Youxiang Shao
- School of Materials Science &Engineering, PCFM Lab, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhuofeng Ke
- School of Materials Science &Engineering, PCFM Lab, Sun Yat-sen University, Guangzhou 510006, China
| | - Feng-Shou Liu
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Zhongshan, Guangdong 528458, China
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14
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Anene UA, Alpay SP. Ab Initio Study of Hydrostable Metal-Organic Frameworks for Postsynthetic Modification and Tuning toward Practical Applications. ACS OMEGA 2022; 7:7791-7805. [PMID: 35284705 PMCID: PMC8908368 DOI: 10.1021/acsomega.1c06658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Metal-organic frameworks (MOFs), a subclass of nanoporous coordination polymers, have emerged as one of the most promising next-generation materials. The postsynthetic modification method, a strategy that provides tunability and control of these materials, plays an important role in enhancing its properties and functionalities. However, knowing adjustments which leads to a desired structure-function a priori remains a challenge. In this comprehensive study, the intermolecular interactions between 21 industrially important gases and a hydrostable STAM-17-OEt MOF were investigated using density functional theory. Substitutions on its 5-ethoxy isophthalate linker included two classes of chemical groups, electron-donating (-NH2, -OH, and -CH3) and electron-withdrawing (-CN, -COOH, and -F), as well as the effect of mono-, di-, and tri-substitutions. This resulted in 651 unique MOF-gas complexes. The adsorption energies at the ground state and room temperature, bond lengths, adsorption geometry, natural bond orbital analysis of the electric structure, HOMO-LUMO interactions, and the predicted zwitterionic properties are presented and discussed. This study provides a viable strategy for the functionalization, which leads to the strongest affinity for each gas, an insight into the role of different chemical groups in adsorbing various gas molecules, and identifies synthetic routes for moderating the gas adsorption capacity and reducing water adsorption. Recommendations for various applications are discussed. A custom Python script to assess and visualize the hypothetical separation of two equal gas mixtures of interest is provided. The methodology presented here provides new opportunities to expand the chemical space and physical properties of STAM-17-OEt and advances the development of other hydrostable MOFs.
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Affiliation(s)
- Uchenna A. Anene
- Department
of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - S. Pamir Alpay
- Department
of Materials Science and Engineering, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department
of Physics, University of Connecticut, Storrs, Connecticut 06269, United States
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15
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Ngo ST, Nguyen TH, Tung NT, Mai BK. Insights into the binding and covalent inhibition mechanism of PF-07321332 to SARS-CoV-2 M pro. RSC Adv 2022; 12:3729-3737. [PMID: 35425393 PMCID: PMC8979274 DOI: 10.1039/d1ra08752e] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/13/2022] [Indexed: 12/20/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been causing the COVID-19 pandemic, resulting in several million deaths being reported. Numerous investigations have been carried out to discover a compound that can inhibit the biological activity of the SARS-CoV-2 main protease, which is an enzyme related to the viral replication. Among these, PF-07321332 (Nirmatrelvir) is currently under clinical trials for COVID-19 therapy. Therefore, in this work, atomistic and electronic simulations were performed to unravel the binding and covalent inhibition mechanism of the compound to Mpro. Initially, 5 μs of steered-molecular dynamics simulations were carried out to evaluate the ligand-binding process to SARS-CoV-2 Mpro. The successfully generated bound state between the two molecules showed the important role of the PF-07321332 pyrrolidinyl group and the residues Glu166 and Gln189 in the ligand-binding process. Moreover, from the MD-refined structure, quantum mechanics/molecular mechanics (QM/MM) calculations were carried out to unravel the reaction mechanism for the formation of the thioimidate product from SARS-CoV-2 Mpro and the PF-07321332 inhibitor. We found that the catalytic triad Cys145-His41-Asp187 of SARS-CoV-2 Mpro plays an important role in the activation of the PF-07321332 covalent inhibitor, which renders the deprotonation of Cys145 and, thus, facilitates further reaction. Our results are definitely beneficial for a better understanding of the inhibition mechanism and designing new effective inhibitors for SARS-CoV-2 Mpro.
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Nguyen Thanh Tung
- Institute of Materials Science, Vietnam Academy of Science and Technology Hanoi 11307 Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology Hanoi 11307 Vietnam
| | - Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
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16
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Nauton L, Hecquet L, Théry V. QM/MM Study of Human Transketolase: Thiamine Diphosphate Activation Mechanism and Complete Catalytic Cycle. J Chem Inf Model 2021; 61:3502-3515. [PMID: 34161071 DOI: 10.1021/acs.jcim.1c00190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A computational model for human transketolase was proposed, showing that thiamine diphosphate activation was based on His110 in place of His481 reported in yeast transketolase. In addition, a complete catalytic reaction pathway was investigated using d-xylulose-5-phosphate and d-ribose-5-phosphate as substrates, showing at every step a perfect superimposition of our model with high-resolution crystallographic structures 3MOS, 4KXV, and 4KXX. This study shows that H2N4' of the active thiamine diphosphate "V form" no longer has a self-activating role but allows self-stabilization of the cofactor and of the Breslow intermediate. These advances in our knowledge of the human transketolase mechanism offer interesting prospects for the design of new drugs, this enzyme being involved in several diseases, and for a better understanding of the reactions catalyzed by transketolases from other sources.
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Affiliation(s)
- Lionel Nauton
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, ICCF, F-63000 Clermont-Ferrand, France
| | - Laurence Hecquet
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, ICCF, F-63000 Clermont-Ferrand, France
| | - Vincent Théry
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, ICCF, F-63000 Clermont-Ferrand, France
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17
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Yan Z, Li X, Chung LW. Multiscale Quantum Refinement Approaches for Metalloproteins. J Chem Theory Comput 2021; 17:3783-3796. [PMID: 34032440 DOI: 10.1021/acs.jctc.1c00148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Biomolecules with metal ion(s) (e.g., metalloproteins) play many important biological roles. However, accurate structural determination of metalloproteins, particularly those containing transition metal ion(s), is challenging due to their complicated electronic structure, complex bonding of metal ions, and high number of conformations in biomolecules. Quantum refinement, which was proposed to combine crystallographic data with computational chemistry methods by several groups, can improve the local structures of some proteins. In this study, a quantum refinement method combining several multiscale computational schemes with experimental (X-ray diffraction) information was developed for metalloproteins. Various quantum refinement approaches using different ONIOM (our own N-layered integrated molecular orbital and molecular mechanics) combinations of quantum mechanics (QM), semiempirical (SE), and molecular mechanics (MM) methods were conducted to assess the performance and reliability on the refined local structure in two metalloproteins. The structures for two (Cu- or Zn-containing) metalloproteins were refined by combining two-layer ONIOM2(QM1/QM2) and ONIOM2(QM/MM) and three-layer ONIOM3(QM1/QM2/MM) schemes with experimental data. The accuracy of the quantum-refined metal binding sites was also examined and compared in these multiscale quantum refinement calculations. ONIOM3(QM/SE/MM) schemes were found to give good results with lower computational costs and were proposed to be a good choice for the multiscale computational scheme for quantum refinement calculations of metal binding site(s) in metalloproteins with high efficiency. Additionally, a two-center ONIOM approach was employed to speed up the quantum refinement calculations for the Zn metalloprotein with two remote active sites/ligands. Moreover, a recent quantum-embedding wavefunction-in-density functional theory (WF-in-DFT) method was also adopted as the high-level method in unprecedented ONIOM2(CCSD-in-B3LYP/MM) and ONIOM3(CCSD-in-B3LYP/SE/MM) calculations, which can be regarded as novel pseudo-three- and pseudo-four-layer ONIOM methods, respectively, to refine the key Zn binding site at the coupled-cluster singles and doubles (CCSD) level. These refined results indicate that multiscale quantum refinement schemes can be used to improve the structural accuracy obtained for local metal binding site(s) in metalloproteins with high efficiency.
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Affiliation(s)
- Zeyin Yan
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xin Li
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Lung Wa Chung
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
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18
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Maeda S, Harabuchi Y. Exploring paths of chemical transformations in molecular and periodic systems: An approach utilizing force. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1538] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI‐ICReDD), Hokkaido University Sapporo Hokkaido Japan
- Department of Chemistry, Faculty of Science Hokkaido University Sapporo Hokkaido Japan
- JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project Sapporo Hokkaido Japan
- National Institute for Materials Science (NIMS) Research and Services Division of Materials Data and Integrated System (MaDIS) Tsukuba Ibaraki Japan
| | - Yu Harabuchi
- Institute for Chemical Reaction Design and Discovery (WPI‐ICReDD), Hokkaido University Sapporo Hokkaido Japan
- Department of Chemistry, Faculty of Science Hokkaido University Sapporo Hokkaido Japan
- JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project Sapporo Hokkaido Japan
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19
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Liang Z, Choi HH, Luo X, Liu T, Abtahi A, Ramasamy US, Hitron JA, Baustert KN, Hempel JL, Boehm AM, Ansary A, Strachan DR, Mei J, Risko C, Podzorov V, Graham KR. n-type charge transport in heavily p-doped polymers. NATURE MATERIALS 2021; 20:518-524. [PMID: 33398117 DOI: 10.1038/s41563-020-00859-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 10/20/2020] [Indexed: 06/12/2023]
Abstract
It is commonly assumed that charge-carrier transport in doped π-conjugated polymers is dominated by one type of charge carrier, either holes or electrons, as determined by the chemistry of the dopant. Here, through Seebeck coefficient and Hall effect measurements, we show that mobile electrons contribute substantially to charge-carrier transport in π-conjugated polymers that are heavily p-doped with strong electron acceptors. Specifically, the Seebeck coefficient of several p-doped polymers changes sign from positive to negative as the concentration of the oxidizing agents FeCl3 or NOBF4 increase, and Hall effect measurements for the same p-doped polymers reveal that electrons become the dominant delocalized charge carriers. Ultraviolet and inverse photoelectron spectroscopy measurements show that doping with oxidizing agents results in elimination of the transport gap at high doping concentrations. This approach of heavy p-type doping is demonstrated to provide a promising route to high-performance n-type organic thermoelectric materials.
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Affiliation(s)
- Zhiming Liang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Hyun Ho Choi
- Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey, USA
| | - Xuyi Luo
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Tuo Liu
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Ashkan Abtahi
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
- Department of Physics & Astronomy, University of Kentucky, Lexington, Kentucky, USA
| | - Uma Shantini Ramasamy
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
- Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky, USA
| | | | - Kyle N Baustert
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Jacob L Hempel
- Department of Physics & Astronomy, University of Kentucky, Lexington, Kentucky, USA
| | - Alex M Boehm
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Armin Ansary
- Department of Physics & Astronomy, University of Kentucky, Lexington, Kentucky, USA
| | - Douglas R Strachan
- Department of Physics & Astronomy, University of Kentucky, Lexington, Kentucky, USA
| | - Jianguo Mei
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Chad Risko
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
- Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky, USA
| | - Vitaly Podzorov
- Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey, USA
| | - Kenneth R Graham
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA.
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20
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Lu C, Tang W, Dou Z, Xie P, Xu X, Zhao S. A reaction density functional theory study of solvent effects on keto-enol tautomerism and isomerization in pyruvic acid. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Wang R, Tao W, Liu L, Li C, Bai L, Zhao YL, Shi T. Insights into specificity and catalytic mechanism of amphotericin B/nystatin thioesterase. Proteins 2021; 89:558-568. [PMID: 33389775 DOI: 10.1002/prot.26041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/22/2020] [Accepted: 12/27/2020] [Indexed: 11/12/2022]
Abstract
Polyene polyketides amphotericin B (AMB) and nystatin (NYS) are important antifungal drugs. Thioesterases (TEs), located at the last module of PKS, control the release of polyketides by cyclization or hydrolysis. Intrigued by the tiny structural difference between AMB and NYS, as well as the high sequence identity between AMB TE and NYS TE, we constructed four systems to study the structural characteristics, catalytic mechanism, and product release of AMB TE and NYS TE with combined MD simulations and quantum mechanics/molecular mechanics calculations. The results indicated that compared with AMB TE, NYS TE shows higher specificity on its natural substrate and R26 as well as D186 were proposed to a key role in substrate recognition. The energy barrier of macrocyclization in AMB-TE-Amb and AMB-TE-Nys systems were calculated to be 14.0 and 22.7 kcal/mol, while in NYS-TE-Nys and NYS-TE-Amb systems, their energy barriers were 17.5 and 25.7 kcal/mol, suggesting the cyclization with their natural substrates were more favorable than that with exchanged substrates. At last, the binding free energy obtained with the MM-PBSA.py program suggested that it was easier for natural products to leave TE enzymes after cyclization. And key residues to the departure of polyketide product from the active site were highlighted. We provided a catalytic overview of AMB TE and NYS TE including substrate recognition, catalytic mechanism and product release. These will improve the comprehension of polyene polyketide TEs and benefit for broadening the substrate flexibility of polyketide TEs.
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Affiliation(s)
- Rufan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wentao Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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22
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Liu L, Yu Q, Zhang H, Tao W, Wang R, Bai L, Zhao YL, Shi T. Theoretical study on substrate recognition and catalytic mechanisms of gephyronic acid dehydratase DH1. Catal Sci Technol 2021. [DOI: 10.1039/d0cy01776k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The bifunctional dehydratase GphF DH1 catalyzes both the dehydration of β-hydroxy and the double bond isomerization with the energy barrier of 27.0 kcal mol−1 and 17.2 kcal mol−1 respectively.
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Affiliation(s)
- Lei Liu
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Qian Yu
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Haoqing Zhang
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Wentao Tao
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Rufan Wang
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
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23
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Zhou W, Ge L, Cooper GA, Crane SW, Evans MH, Ashfold MNR, Vallance C. Coulomb explosion imaging for gas-phase molecular structure determination: An ab initio trajectory simulation study. J Chem Phys 2020; 153:184201. [PMID: 33187401 DOI: 10.1063/5.0024833] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Coulomb explosion velocity-map imaging is a new and potentially universal probe for gas-phase chemical dynamics studies, capable of yielding direct information on (time-evolving) molecular structure. The approach relies on a detailed understanding of the mapping between the initial atomic positions within the molecular structure of interest and the final velocities of the fragments formed via Coulomb explosion. Comprehensive on-the-fly ab initio trajectory studies of the Coulomb explosion dynamics are presented for two prototypical small molecules, formyl chloride and cis-1,2-dichloroethene, in order to explore conditions under which reliable structural information can be extracted from fragment velocity-map images. It is shown that for low parent ion charge states, the mapping from initial atomic positions to final fragment velocities is complex and very sensitive to the parent ion charge state as well as many other experimental and simulation parameters. For high-charge states, however, the mapping is much more straightforward and dominated by Coulombic interactions (moderated, if appropriate, by the requirements of overall spin conservation). This study proposes minimum requirements for the high-charge regime, highlights the need to work in this regime in order to obtain robust structural information from fragment velocity-map images, and suggests how quantitative structural information may be extracted from experimental data.
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Affiliation(s)
- Weiwei Zhou
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd., Oxford OX1 3TA, United Kingdom
| | - Lingfeng Ge
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Graham A Cooper
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Stuart W Crane
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Michael H Evans
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Michael N R Ashfold
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Claire Vallance
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd., Oxford OX1 3TA, United Kingdom
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24
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Midoro Y, Kodaya Y, Oki T, Mukai A, Yamakado H, Ohno K. Conformation Search of Glycine by Applying the Scaled Hypersphere Search Method to Discrete Atoms in the Molecule. CHEM LETT 2020. [DOI: 10.1246/cl.200239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yuuki Midoro
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Yoshitomo Kodaya
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Takuto Oki
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Akira Mukai
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Hideo Yamakado
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Koichi Ohno
- Institute for Quantum Chemical Exploration, 1-9-36 Konan, Minato-ku, Tokyo 108-0075, Japan
- Graduate School of Science, Tohoku University, 6-3 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
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25
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Pirillo J, Hijikata Y. Trans Influence across a Metal-Metal Bond of a Paddle-Wheel Unit on Interaction with Gases in a Metal-Organic Framework. Inorg Chem 2020; 59:1193-1203. [PMID: 31825598 DOI: 10.1021/acs.inorgchem.9b02911] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Metal-organic frameworks (MOFs) are known as promising adsorbent materials that can recognize gases specifically. In the frameworks, gases favor interacting with specific binding sites such as open metal sites (OMSs), which can consist of various metals and show characteristic adsorption properties. A recently reported framework possessing OMSs of rhodium paddle-wheel (Rh-PW) showed distinct adsorption properties between NO and CO. We investigated theoretically the reasons for stronger NO binding to the Rh-PW and different adsorption amounts between NO and CO using Rh-PW cluster models, as well as the frequently reported Cu-PW for comparison. We also analyzed the cases of CO2 and N2, which are often used to probe functions of MOFs. We observed an increase in binding energy of NO at the second adduction of NO. On the basis of energy decomposition analysis, we found that Rh-NO bond formation inducing a trans influence is important for the stronger binding than with CO. Furthermore, we proposed a reason for twice the adsorption amount of NO than CO. The results are consistent with experimental observations, giving us insight into design functions of MOFs by selecting metal species.
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Affiliation(s)
- Jenny Pirillo
- Institute for chemical reaction discovery and design (WPI-ICReDD) , Hokkaido University , Kita 21 Nishi 10, Kita-ku , Sapporo , Hokkaido 001-0021 , Japan
| | - Yuh Hijikata
- Institute for chemical reaction discovery and design (WPI-ICReDD) , Hokkaido University , Kita 21 Nishi 10, Kita-ku , Sapporo , Hokkaido 001-0021 , Japan
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26
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Cheema H, Baumann A, Loya EK, Brogdon P, McNamara LE, Carpenter CA, Hammer NI, Mathew S, Risko C, Delcamp JH. Near-Infrared-Absorbing Indolizine-Porphyrin Push-Pull Dye for Dye-Sensitized Solar Cells. ACS APPLIED MATERIALS & INTERFACES 2019; 11:16474-16489. [PMID: 30964274 DOI: 10.1021/acsami.8b21414] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Porphyrins are attractive chromophores for application in dye-sensitized solar cells (DSCs), as judicious tuning of donor-acceptor properties can enable excellent near-infrared (NIR) absorption and exceptional device performance. Here, we report a porphyrin-based dye (SM85) conjugated to the planar strong electron donor, indolizine, designed to extend absorption further into the NIR region by inducing π-π interactions such as head-to-tail dye aggregation. The optoelectronic consequences of indolizine incorporation in SM85 include raising the ground-state oxidation potential and broadening and red-shifting ultraviolet-visible-NIR absorptions, along with increased molar absorptivity when compared to the dye SM315. Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations confirm the push-pull character of SM85, which features an overlap of frontier occupied and unoccupied orbitals. Steady-state spectrophotometric analyses reveal the presence of solution aggregates via absorption and emission spectroscopies. Aggregate modes were probed by DFT and TD-DFT analyses, and plausible models are presented. SM85-based DSC devices demonstrate a 5.7% power conversion efficiency (PCE) at full sun (7.4% PCE at 10% sun) with an exceptional improvement to the incident photon-to-current conversion onset at ∼850 nm. Current dynamics measurements, time-correlated single photon counting, and computational analyses are used to better understand device performances. This study puts forward a novel intramolecular charge-transfer porphyrin system with a dramatic shift into the NIR region, as is needed for nonprecious metal-based sensitizers, and provides an example of controlled, donor-acceptor-mediated aggregation as a complementary strategy to traditional donor-acceptor modifications to single-molecule π-systems in accessing enhancements in long wavelength light harvesting in molecular-based optoelectronic devices.
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Affiliation(s)
- Hammad Cheema
- Chemistry Department , University of Mississippi , University , Mississippi 38677 , United States
| | - Alexandra Baumann
- Chemistry Department , University of Mississippi , University , Mississippi 38677 , United States
| | - E Kirkbride Loya
- Department of Chemistry & Center for Applied Energy Research (CAER) , University of Kentucky , Lexington , Kentucky 40506 , United States
| | - Phillip Brogdon
- Chemistry Department , University of Mississippi , University , Mississippi 38677 , United States
| | - Louis E McNamara
- Chemistry Department , University of Mississippi , University , Mississippi 38677 , United States
| | - Casey A Carpenter
- Chemistry Department , University of Mississippi , University , Mississippi 38677 , United States
| | - Nathan I Hammer
- Chemistry Department , University of Mississippi , University , Mississippi 38677 , United States
| | - Simon Mathew
- van't Hoff Institute for Molecular Sciences , Universiteit van Amsterdam , Science Park 904 , 1098 XH Amsterdam , Netherlands
| | - Chad Risko
- Department of Chemistry & Center for Applied Energy Research (CAER) , University of Kentucky , Lexington , Kentucky 40506 , United States
| | - Jared H Delcamp
- Chemistry Department , University of Mississippi , University , Mississippi 38677 , United States
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27
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Aboelnga MM, Wetmore SD. Unveiling a Single-Metal-Mediated Phosphodiester Bond Cleavage Mechanism for Nucleic Acids: A Multiscale Computational Investigation of a Human DNA Repair Enzyme. J Am Chem Soc 2019; 141:8646-8656. [PMID: 31046259 DOI: 10.1021/jacs.9b03986] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Mohamed M. Aboelnga
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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28
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Can multiscale simulations unravel the function of metallo-enzymes to improve knowledge-based drug discovery? Future Med Chem 2019; 11:771-791. [DOI: 10.4155/fmc-2018-0495] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Metallo-enzymes are a large class of biomolecules promoting specialized chemical reactions. Quantum-classical quantum mechanics/molecular mechanics molecular dynamics, describing the metal site at quantum mechanics level, while accounting for the rest of system at molecular mechanics level, has an accessible time-scale limited by its computational cost. Hence, it must be integrated with classical molecular dynamics and enhanced sampling simulations to disentangle the functions of metallo-enzymes. In this review, we provide an overview of these computational methods and their capabilities. In particular, we will focus on some systems such as CYP19A1 a Fe-dependent enzyme involved in estrogen biosynthesis, and on Mg2+-dependent DNA/RNA processing enzymes/ribozymes and the spliceosome, a protein-directed ribozyme. This information may guide the discovery of drug-like molecules and genetic manipulation tools.
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29
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Mutation Spectrum in TPO Gene of Bangladeshi Patients with Thyroid Dyshormonogenesis and Analysis of the Effects of Different Mutations on the Structural Features and Functions of TPO Protein through In Silico Approach. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9218903. [PMID: 30915365 PMCID: PMC6409061 DOI: 10.1155/2019/9218903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 01/03/2019] [Accepted: 01/10/2019] [Indexed: 11/17/2022]
Abstract
Although thyroid dyshormonogenesis (TDH) accounts for 10-20% of congenital hypothyroidism (CH), the molecular etiology of TDH is unknown in Bangladesh. Thyroid peroxidase (TPO) is most frequently associated with TDH and the present study investigated the spectrum of TPO mutations in Bangladeshi patients and analyzed the effects of mutations on TPO protein structure through in silico approach. Sequencing-based analysis of TPO gene revealed four mutations in 36 diagnosed patients with TDH including three nonsynonymous mutations, namely, p.Ala373Ser, p.Ser398Thr, and p.Thr725Pro, and one synonymous mutation p.Pro715Pro. Homology modelling-based analysis of predicted structures of MPO-like domain (TPO142-738) and the full-length TPO protein (TPO1-933) revealed differences between mutant and wild type structures. Molecular docking studies were performed between predicted structures and heme. TPO1-933 predicted structure showed more reliable results in terms of interactions with the heme prosthetic group as the binding energies were -11.5 kcal/mol, -3.2 kcal/mol, -11.5 kcal/mol, and -7.9 kcal/mol for WT, p.Ala373Ser, p.Ser398Thr, and p.Thr725Pro, respectively, implying that p.Ala373Ser and p.Thr725Pro mutations were more damaging than p.Ser398Thr. However, for the TPO142-738 predicted structures, the binding energies were -11.9 kcal/mol, -10.8 kcal/mol, -2.5 kcal/mol, and -5.3 kcal/mol for the wild type protein, mutant proteins with p.Ala373Ser, p.Ser398Thr, and p.Thr725Pro substitutions, respectively. However, when the interactions between the crucial residues including residues His239, Arg396, Glu399, and His494 of TPO protein and heme were taken into consideration using both TPO1-933 and TPO142-738 predicted structures, it appeared that p.Ala373Ser and p.Thr725Pro could affect the interactions more severely than the p.Ser398Thr. Validation of the molecular docking results was performed by computer simulation in terms of quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulation. In conclusion, the substitutions mutations, namely, p.Ala373Ser, p.Ser398Thr, and p.Thr725Pro, had been involved in Bangladeshi patients with TDH and molecular docking-based study revealed that these mutations had damaging effect on the TPO protein activity.
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30
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Fan S, Wang R, Li C, Bai L, Zhao YL, Shi T. Insight into Structural Characteristics of Protein-Substrate Interaction in Pimaricin Thioesterase. Int J Mol Sci 2019; 20:ijms20040877. [PMID: 30781619 PMCID: PMC6412417 DOI: 10.3390/ijms20040877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 01/23/2023] Open
Abstract
As a polyene antibiotic of great pharmaceutical significance, pimaricin has been extensively studied to enhance its productivity and effectiveness. In our previous studies, pre-reaction state (PRS) has been validated as one of the significant conformational categories before macrocyclization, and is critical to mutual recognition and catalytic preparation in thioesterase (TE)-catalyzed systems. In our study, molecular dynamics (MD) simulations were conducted on pimaricin TE-polyketide complex and PRS, as well as pre-organization state (POS), a molecular conformation possessing a pivotal intra-molecular hydrogen bond, were detected. Conformational transition between POS and PRS was observed in one of the simulations, and POS was calculated to be energetically more stable than PRS by 4.58 kcal/mol. The structural characteristics of PRS and POS-based hydrogen-bonding, and hydrophobic interactions were uncovered, and additional simulations were carried out to rationalize the functions of several key residues (Q29, M210, and R186). Binding energies, obtained from MM/PBSA calculations, were further decomposed to residues, in order to reveal their roles in product release. Our study advanced a comprehensive understanding of pimaricin TE-catalyzed macrocyclization from the perspectives of conformational change, protein-polyketide recognition, and product release, and provided potential residues for rational modification of pimaricin TE.
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Affiliation(s)
- Shuobing Fan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Rufan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Chen Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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31
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Effect of substituents on 3(S)-amino-1-hydroxy-3,4-dihydroquinolin-2(1H)-one: a DFT study. Theor Chem Acc 2019. [DOI: 10.1007/s00214-018-2403-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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32
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Liu L, Shi T, Houk KN, Zhao YL. Understanding the R882H mutation effects of DNA methyltransferase DNMT3A: a combination of molecular dynamics simulations and QM/MM calculations. RSC Adv 2019; 9:31425-31434. [PMID: 35527972 PMCID: PMC9072302 DOI: 10.1039/c9ra06791d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 09/17/2019] [Indexed: 01/15/2023] Open
Abstract
The AML-related high-frequent R882H mutation of DNA (cytosine-5)-methyltransferase 3A (DNMT3A), a key enzyme forde novoepigenetic methylation in human beings, was characterized by a disturbing conformation ofS-adenosylmethionine (SAM).
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Affiliation(s)
- Lanxuan Liu
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry
- University of California
- Los Angeles
- USA
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
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33
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Liu L, Tao W, Bai L, Kim ES, Zhao YL, Shi T. Why does tautomycetin thioesterase prefer hydrolysis to macrocyclization? Theoretical study on its catalytic mechanism. Catal Sci Technol 2019. [DOI: 10.1039/c9cy01355e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we attempted to uncover the reasons why Tautomycetin thioesterase (TMC TE) prefers hydrolysis rather than macrocyclization, and reveal the molecular basis of TE-catalyzed hydrolysis and macrocyclization.
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Affiliation(s)
- Lei Liu
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Wentao Tao
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Eung-Soo Kim
- Department of Biological Engineering
- Inha University
- Incheon
- Korea
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
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34
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Uzunova EL. Cation pair formation in copper and palladium exchanged MFI zeolite frameworks – a theoretical study. Phys Chem Chem Phys 2019; 21:14786-14798. [DOI: 10.1039/c9cp02088h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
[Pd–O–Pd]2+ as a mediator in proton transfer from Brønsted acid sites to reactants; [Cu–OH–Cu]2+ stabilized by hydrogen bonds to framework oxygen.
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Affiliation(s)
- Ellie L. Uzunova
- Institute of General and Inorganic Chemistry
- Bulgarian Academy of Sciences
- Sofia 1113
- Bulgaria
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35
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Jouve R, Thery V, Ducki S, Helfenbein J, Thiery JC, Job A, Picard E, Mallet C, Ripoche I, Bennis K. Optimization of the synthesis of a key intermediate for the preparation of glucocorticoids. Steroids 2018; 137:14-21. [PMID: 30017852 DOI: 10.1016/j.steroids.2018.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/15/2018] [Accepted: 06/19/2018] [Indexed: 11/30/2022]
Abstract
A short and efficient synthesis, based on a one-step double elimination, of a key intermediate in the synthesis of various glucocorticosteroids has been developed. This method can be carried out on large scale for further industrial applications. The synthesis allowed us to identify a novel prednisolone derivative 10 and its anti-inflammatory activity was determined in an in vivo model of inflammation. In order to understand the regioselectivity of the double elimination under various conditions, mechanistic studies were undertaken and confirmed the experimental results. We also propose a mechanism for the formation of the new steroid 10 studied by molecular modeling.
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Affiliation(s)
- Romain Jouve
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, 63000 Clermont-Ferrand, France
| | - Vincent Thery
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, 63000 Clermont-Ferrand, France
| | - Sylvie Ducki
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, 63000 Clermont-Ferrand, France
| | | | | | - Aurélie Job
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, 63000 Clermont-Ferrand, France
| | - Elodie Picard
- Université Clermont Auvergne, Inserm, Neuro-Dol, 63000 Clermont-Ferrand, France
| | - Christophe Mallet
- Université Clermont Auvergne, Inserm, Neuro-Dol, 63000 Clermont-Ferrand, France
| | - Isabelle Ripoche
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, 63000 Clermont-Ferrand, France.
| | - Khalil Bennis
- Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, 63000 Clermont-Ferrand, France
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36
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Yousif M, Wannipurage D, Huizenga CD, Washnock-Schmid E, Peraino NJ, Ozarowski A, Stoian SA, Lord RL, Groysman S. Catalytic Nitrene Homocoupling by an Iron(II) Bis(alkoxide) Complex: Bulking Up the Alkoxide Enables a Wider Range of Substrates and Provides Insight into the Reaction Mechanism. Inorg Chem 2018; 57:9425-9438. [PMID: 30015481 DOI: 10.1021/acs.inorgchem.8b01418] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction of HOR' (OR' = di-t-butyl-(3,5-diphenylphenyl)methoxide) with an iron(II) amide precursor forms the iron(II) bis(alkoxide) complex Fe(OR')2(THF)2 (2). 2 (5-10 mol %) serves as a catalyst for the conversion of aryl azides into the corresponding azoarenes. The highest yields are observed for aryl azides featuring two ortho substituents; other substitution patterns in the aryl azide precursor lead to moderate or low yields. The reaction of 2 with stoichiometric amounts (2 equiv) of the corresponding aryl azide shows the formation of azoarenes as the only organic products for the bulkier aryl azides (Ar = mesityl, 2,6-diethylphenyl). In contrast, formation of tetrazene complexes Fe(OR')2(ArNNNNAr) (3-6) is observed for the less bulky aryl azides (Ar = phenyl, 4-methylphenyl, 4-methoxyphenyl, 3,5-dimethylphenyl). The electronic structure of selected tetrazene complexes was probed by spectroscopy (field-dependent 57Fe Mössbauer and high-frequency EPR) and density functional theory calculations. These studies revealed that Fe(OR')2(ArNNNNAr) complexes contain high-spin ( S = 5/2) iron(III) centers exchange-coupled to tetrazene radical anions. Tetrazene complexes Fe(OR')2(ArNNNNAr) produce the corresponding azoarenes (ArNNAr) upon heating. Treatment of a tetrazene complex Fe(OR')2(ArNNNNAr) with a different azide (N3Ar') produces all three possible products ArNNAr, ArNNAr', and Ar'NNAr'. These experiments and quantum mechanics/molecular mechanics calculations exploring the reaction mechanism suggest that the tetrazene functionality serves as a masked form of the reactive iron mono(imido) species.
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Affiliation(s)
- Maryam Yousif
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Duleeka Wannipurage
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Caleb D Huizenga
- Department of Chemistry , Grand Valley State University , Allendale , Michigan 49401 , United States
| | - Elizabeth Washnock-Schmid
- Department of Chemistry , Grand Valley State University , Allendale , Michigan 49401 , United States
| | - Nicholas J Peraino
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
| | - Andrew Ozarowski
- National High Magnetic Field Laboratory , Florida State University , Tallahassee , Florida 32310 , United States
| | - Sebastian A Stoian
- Department of Chemistry , University of Idaho , Moscow , Idaho 83844 , United States
| | - Richard L Lord
- Department of Chemistry , Grand Valley State University , Allendale , Michigan 49401 , United States
| | - Stanislav Groysman
- Department of Chemistry , Wayne State University , 5101 Cass Avenue , Detroit , Michigan 48202 , United States
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37
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Assessment of Ab Initio and Density Functional Theory Methods for the Excitations of Donor-Acceptor Complexes: The Case of the Benzene-Tetracyanoethylene Model. Int J Mol Sci 2018; 19:ijms19041134. [PMID: 29642604 PMCID: PMC5979477 DOI: 10.3390/ijms19041134] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/16/2018] [Accepted: 03/20/2018] [Indexed: 12/27/2022] Open
Abstract
The understanding of the excited-state properties of electron donors, acceptors and their interfaces in organic optoelectronic devices is a fundamental issue for their performance optimization. In order to obtain a balanced description of the different excitation types for electron-donor-acceptor systems, including the singlet charge transfer (CT), local excitations, and triplet excited states, several ab initio and density functional theory (DFT) methods for excited-state calculations were evaluated based upon the selected model system of benzene-tetracyanoethylene (B-TCNE) complexes. On the basis of benchmark calculations of the equation-of-motion coupled-cluster with single and double excitations method, the arithmetic mean of the absolute errors and standard errors of the electronic excitation energies for the different computational methods suggest that the M11 functional in DFT is superior to the other tested DFT functionals, and time-dependent DFT (TDDFT) with the Tamm–Dancoff approximation improves the accuracy of the calculated excitation energies relative to that of the full TDDFT. The performance of the M11 functional underlines the importance of kinetic energy density, spin-density gradient, and range separation in the development of novel DFT functionals. According to the TDDFT results, the performances of the different TDDFT methods on the CT properties of the B-TCNE complexes were also analyzed.
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38
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Uzunova EL. Theoretical study of nitrogen dioxide and nitric oxide co-adsorption and DeNO x reaction on Cu-SAPO−34 and Cu-SSZ−13 in presence of Brønsted acid sites. MOLECULAR CATALYSIS 2018. [DOI: 10.1016/j.mcat.2018.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Maeda S, Harabuchi Y, Takagi M, Saita K, Suzuki K, Ichino T, Sumiya Y, Sugiyama K, Ono Y. Implementation and performance of the artificial force induced reaction method in the GRRM17 program. J Comput Chem 2017; 39:233-251. [PMID: 29135034 PMCID: PMC5765425 DOI: 10.1002/jcc.25106] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 12/20/2022]
Abstract
This article reports implementation and performance of the artificial force induced reaction (AFIR) method in the upcoming 2017 version of GRRM program (GRRM17). The AFIR method, which is one of automated reaction path search methods, induces geometrical deformations in a system by pushing or pulling fragments defined in the system by an artificial force. In GRRM17, three different algorithms, that is, multicomponent algorithm (MC-AFIR), single-component algorithm (SC-AFIR), and double-sphere algorithm (DS-AFIR), are available, where the MC-AFIR was the only algorithm which has been available in the previous 2014 version. The MC-AFIR does automated sampling of reaction pathways between two or more reactant molecules. The SC-AFIR performs automated generation of global or semiglobal reaction path network. The DS-AFIR finds a single path between given two structures. Exploration of minimum energy structures within the hypersurface in which two different electronic states degenerate, and an interface with the quantum mechanics/molecular mechanics method, are also described. A code termed SAFIRE will also be available, as a visualization software for complicated reaction path networks. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yu Harabuchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan
| | - Makito Takagi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
| | - Kenichiro Saita
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kimichi Suzuki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto, 606-8103, Japan
| | - Tomoya Ichino
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yosuke Sumiya
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
| | - Kanami Sugiyama
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
| | - Yuriko Ono
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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40
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Reina M, Martinez A, Cammarano C, Leroi C, Hulea V, Mineva T. Conversion of Methyl Mercaptan to Hydrocarbons over H-ZSM-5 Zeolite: DFT/BOMD Study. ACS OMEGA 2017; 2:4647-4656. [PMID: 30023728 PMCID: PMC6044670 DOI: 10.1021/acsomega.7b00756] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/03/2017] [Indexed: 06/08/2023]
Abstract
Methyl mercaptan-a harmful impurity in natural gas-may be selectively converted into H2S and hydrocarbons [methyl mercaptan to hydrocarbon (M2TH) process], using zeolite catalysts. When M2TH is compared with the well-known MTH (methanol to hydrocarbons) process, significant differences emerge, essentially regarding the formation and distribution of products. Density functional theory (DFT) and Born-Oppenheimer molecular dynamics (BOMD) were employed to reveal possible origins for the experimentally observed differences. We established a close similarity between DFT intrinsic (electronic) reaction profiles in the stepwise mechanism of methanol and mercaptan dehydration, although no variance in reactivity was revealed. BOMD simulations at the experimental temperature of 823 K reveal rapid hydrogen abstraction from the methyl group in mercaptan, adsorbed in the zeolite cavity in the presence of the methoxy intermediate. The formation of •CH2SH radical is 10 times faster than that of •CH2OH at the same temperature. The varied reactivity of methanol and mercaptan in MTH and M2TH processes, respectively, can therefore first be attributed to very rapid hydrogen abstraction in mercaptan, which occurs in the zeolite cavity, following the formation of surface methoxy.
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Affiliation(s)
- Miguel Reina
- Institut
Charles Gerhardt Montpellier, UMR 5253 CNRS/ENSCM/UM2/UM1, 8, rue de l’Ecole Normale, 34296 Montpellier Cedex 5, France
- Departamento
de Materiales de Baja Dimensionalidad, Instituto de Investigaciones
en Materiales, Universidad Nacional Autónoma
de México, Circuito
Exterior s/n, CU, P.O. Box 70-360, Coyoacán 04510, Ciudad de México, México
| | - Ana Martinez
- Departamento
de Materiales de Baja Dimensionalidad, Instituto de Investigaciones
en Materiales, Universidad Nacional Autónoma
de México, Circuito
Exterior s/n, CU, P.O. Box 70-360, Coyoacán 04510, Ciudad de México, México
| | - Claudia Cammarano
- Institut
Charles Gerhardt Montpellier, UMR 5253 CNRS/ENSCM/UM2/UM1, 8, rue de l’Ecole Normale, 34296 Montpellier Cedex 5, France
| | - Cathérine Leroi
- TOTAL
SA, Exploration & Production, 126, Avenue Larribau, 64018 Pau Cedex, France
| | - Vasile Hulea
- Institut
Charles Gerhardt Montpellier, UMR 5253 CNRS/ENSCM/UM2/UM1, 8, rue de l’Ecole Normale, 34296 Montpellier Cedex 5, France
| | - Tzonka Mineva
- Institut
Charles Gerhardt Montpellier, UMR 5253 CNRS/ENSCM/UM2/UM1, 8, rue de l’Ecole Normale, 34296 Montpellier Cedex 5, France
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41
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Atkins AJ, Talotta F, Freitag L, Boggio-Pasqua M, González L. Assessing Excited State Energy Gaps with Time-Dependent Density Functional Theory on Ru(II) Complexes. J Chem Theory Comput 2017; 13:4123-4145. [DOI: 10.1021/acs.jctc.7b00379] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Andrew J. Atkins
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Francesco Talotta
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
- Laboratoire de
Chimie et Physique Quantiques (UMR5626), CNRS et Université
de Toulouse 3, 31062 Toulouse, France
| | - Leon Freitag
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Martial Boggio-Pasqua
- Laboratoire de
Chimie et Physique Quantiques (UMR5626), CNRS et Université
de Toulouse 3, 31062 Toulouse, France
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
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42
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Suzuki K, Morokuma K, Maeda S. Multistructural microiteration technique for geometry optimization and reaction path calculation in large systems. J Comput Chem 2017. [PMID: 28643353 DOI: 10.1002/jcc.24857] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We propose a multistructural microiteration (MSM) method for geometry optimization and reaction path calculation in large systems. MSM is a simple extension of the geometrical microiteration technique. In conventional microiteration, the structure of the non-reaction-center (surrounding) part is optimized by fixing atoms in the reaction-center part before displacements of the reaction-center atoms. In this method, the surrounding part is described as the weighted sum of multiple surrounding structures that are independently optimized. Then, geometric displacements of the reaction-center atoms are performed in the mean field generated by the weighted sum of the surrounding parts. MSM was combined with the QM/MM-ONIOM method and applied to chemical reactions in aqueous solution or enzyme. In all three cases, MSM gave lower reaction energy profiles than the QM/MM-ONIOM-microiteration method over the entire reaction paths with comparable computational costs. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Kimichi Suzuki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto, 606-8103, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto, 606-8103, Japan
| | - Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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43
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Biancardi A, Barnes J, Caricato M. Point charge embedding for ONIOM excited states calculations. J Chem Phys 2017; 145:224109. [PMID: 27984901 DOI: 10.1063/1.4972000] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hybrid quantum mechanical methods can assist in the interpretation and prediction of the electronic spectra of large molecular structures. In this work, we study the performance of the ONIOM (Our own N-layered Integrated molecular Orbital molecular Mechanics) hybrid method for the calculation of transition energies and oscillator strengths by embedding the core region in a field of fixed point charges. These charges introduce polarization effects from the substituent groups to the core region. We test various charge definitions, with particular attention to the issue of overpolarization near the boundary between layers. To minimize this issue, we fit the charges on the electrostatic potential of the entire structure in the presence of the link atoms used to cap dangling bonds. We propose two constrained fitting strategies: one that produces an average set of charges common to both model system calculations, EE(L1), and one that produces two separate sets of embedding charges, EE(L2). The results from our tests show that indeed electronic embedding with constrained-fitted charges tends to improve the performance of ONIOM compared to non-embedded calculations. However, the EE(L2) charges work best for transition energies, and the EE(L1) charges work best for oscillator strengths. This may be an indication that fixed point charges do not have enough flexibility to adapt to each system, and other effects (e.g., polarization of the embedding field) may be necessary.
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Affiliation(s)
- Alessandro Biancardi
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
| | - Jeremy Barnes
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
| | - Marco Caricato
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, Kansas 66045, USA
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44
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Rokob TA. Pathways for Arene Oxidation in Non-Heme Diiron Enzymes: Lessons from Computational Studies on Benzoyl Coenzyme A Epoxidase. J Am Chem Soc 2016; 138:14623-14638. [PMID: 27682344 DOI: 10.1021/jacs.6b06987] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oxygenation of aromatic rings using O2 is catalyzed by several non-heme carboxylate-bridged diiron enzymes. In order to provide a general mechanistic description for these reactions, computational studies were carried out at the ONIOM(B3LYP/BP86/Amber) level on the non-heme diiron enzyme benzoyl coenzyme A epoxidase, BoxB. The calculations revealed four possible pathways for attacking the aromatic ring: (a) electrophilic (2e-) attack by a bis(μ-oxo)-diiron(IV) species (Q pathway); (b) electrophilic (2e-) attack via the σ* orbital of a μ-η2:η2-peroxo-diiron(III) intermediate (Pσ* pathway); (c) radical (1e-) attack via the π*-orbital of a superoxo-diiron(II,III) species (Pπ* pathway); (d) radical (1e-) attack of a partially quenched bis(μ-oxo)-diiron(IV) intermediate (Q' pathway). The results allowed earlier work of de Visser on olefin epoxidation by diiron complexes and QM-cluster studies of Liao and Siegbahn on BoxB to be put into a broader perspective. Parallels with epoxidation using organic peracids were also examined. Specifically for the BoxB enzyme, the Q pathway was found to be the most preferred, but the corresponding bis(μ-oxo)-diiron(IV) species is significantly destabilized and not expected to be directly observable. Epoxidation via the Pσ* pathway represents an energetically somewhat higher lying alternative; possible strategies for experimental discrimination are discussed. The selectivity toward epoxidation is shown to stem from a combination of inherent electronic properties of the thioacyl substituent and enzymatic constraints. Possible implications of the results for toluene monooxygenases are considered as well.
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Affiliation(s)
- Tibor András Rokob
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar Tudósok körútja 2, 1117 Budapest, Hungary
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45
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Protein effects in non-heme iron enzyme catalysis: insights from multiscale models. J Biol Inorg Chem 2016; 21:645-57. [DOI: 10.1007/s00775-016-1374-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/20/2016] [Indexed: 01/09/2023]
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46
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Chen XP, Shi T, Wang XL, Wang J, Chen Q, Bai L, Zhao YL. Theoretical Studies on the Mechanism of Thioesterase-Catalyzed Macrocyclization in Erythromycin Biosynthesis. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01154] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Xiong-Ping Chen
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Ting Shi
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiao-Lei Wang
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jitao Wang
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Qihua Chen
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Linquan Bai
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yi-Lei Zhao
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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47
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Uzunova EL, Mikosch H. A theoretical study of nitric oxide adsorption and dissociation on copper-exchanged zeolites SSZ-13 and SAPO-34: the impact of framework acid-base properties. Phys Chem Chem Phys 2016; 18:11233-42. [PMID: 27053488 DOI: 10.1039/c6cp01146b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The adsorption of nitric oxide as dinitrosyls and the deNOx proton-mediated reaction mechanism are assessed using electronic structure methods and transition state theory. Dinitrosyls bind to copper cations either via a N-atom or via an O-atom, with N-binding being more stable. In their ground states, dinitrosyls reach a planar configuration with the metal cation. The two nitric oxide molecules are kept together in O-bonded dinitrosyls by the N-N bond and the adsorption complex obtains a cyclic planar structure, while N-bonded dinitrosyls have out-of-plane conformations with low energy barriers. An asymmetric structure ZCu(ON)(NO) with one N-bonded nitrosyl and the other O-bonded is of the lowest stability. The cyclic hyponitrite ZCu(ON)2 adsorption complex undergoes O-N bond breaking upon protonation of one oxygen atom and this lowers the energy barrier of the first reaction step of nitric oxide dissociation to yield N2O and a hydroxylated copper site ZCu(OH) by 45 kJ mol(-1) for Cu-SAPO-34 and by 46 kJ mol(-1) for Cu-SSZ-13. The more stable N-bonded dinitrosyl ZCu(NO)2 provides less favorable reaction which passes through the asymmetric ZCu(ON)(NO) intermediate structure. Brønsted acid sites facilitate the reversal of one nitrosyl group. The role of proton transfer from a Brønsted acid site to dinitrosyls is not limited to the initial step of facilitating the N-O bond cleavage, but it also contributes to the stabilization of intermediate oxygen species formed at the copper site as hydroxide ZCu(OH) and hydroperoxide, ZCuOOH. Without protonation, the unstable ZCuO intermediate causes structural deformation with strongly lengthened T-O bonds in the framework. The rate determining step is N2O decomposition to N2 and O2, whether starting with a ZCu(NO)2 or a ZCu(ON)2 adsorption complex, and Cu-SSZ-13 has a clear advantage with an energy barrier of 195 kJ mol(-1)vs. 265 kJ mol(-1) for Cu-SAPO-34. In the final step the Brønsted acid site is restored by proton transfer from the hydroperoxide ZCuOOH to the framework and molecular oxygen is released. The overall energy barrier for the proton-assisted reaction of ZCu(ON)2 decomposition for Cu-SSZ-13 is by 48 kJ mol(-1) lower than the barrier of the proton-free pathway.
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Affiliation(s)
- Ellie L Uzunova
- Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria.
| | - Hans Mikosch
- Faculty of Physics, University of Havana, Havana 10400, Cuba and Faculty of Informatics, Vienna University of Technology, 1040 Vienna, Austria
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48
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Nauton L, Hélaine V, Théry V, Hecquet L. Insights into the Thiamine Diphosphate Enzyme Activation Mechanism: Computational Model for Transketolase Using a Quantum Mechanical/Molecular Mechanical Method. Biochemistry 2016; 55:2144-52. [PMID: 26998737 DOI: 10.1021/acs.biochem.5b00787] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose the first computational model for transketolase (TK), a thiamine diphosphate (ThDP)-dependent enzyme, using a quantum mechanical/molecular mechanical method on the basis of crystallographic TK structures from yeast and Escherichia coli, together with experimental kinetic data reported in the literature with wild-type and mutant TK. This model allowed us to define a new route for ThDP activation in the enzyme environment. We evidenced a strong interaction between ThDP and Glu418B of the TK active site, itself stabilized by Glu162A. The crucial point highlighted here is that deprotonation of ThDP C2 is not performed by ThDP N4' as reported in the literature, but by His481B, involving a HOH688A molecule bridge. Thus, ThDP N4' is converted from an amino form to an iminium form, ensuring the stabilization of the C2 carbanion or carbene. Finally, ThDP activation proceeds via an intermolecular process and not by an intramolecular one as reported in the literature. More generally, this proposed ThDP activation mechanism can be applied to some other ThDP-dependent enzymes and used to define the entire TK mechanism with donor and acceptor substrates more accurately.
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Affiliation(s)
- Lionel Nauton
- Université Clermont Auvergne, Université Blaise-Pascal , Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand, France.,CNRS , UMR 6296, ICCF, F-63178 Aubiere, France
| | - Virgil Hélaine
- Université Clermont Auvergne, Université Blaise-Pascal , Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand, France.,CNRS , UMR 6296, ICCF, F-63178 Aubiere, France
| | - Vincent Théry
- Université Clermont Auvergne, Université Blaise-Pascal , Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand, France.,CNRS , UMR 6296, ICCF, F-63178 Aubiere, France
| | - Laurence Hecquet
- Université Clermont Auvergne, Université Blaise-Pascal , Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand, France.,CNRS , UMR 6296, ICCF, F-63178 Aubiere, France
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49
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Vreven T, Byun KS, Komáromi I, Dapprich S, Montgomery JA, Morokuma K, Frisch MJ. Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM. J Chem Theory Comput 2015; 2:815-26. [PMID: 26626688 DOI: 10.1021/ct050289g] [Citation(s) in RCA: 716] [Impact Index Per Article: 79.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The purpose of this paper is 2-fold. First, we present several extensions to the ONIOM(QM:MM) scheme. In its original formulation, the electrostatic interaction between the regions is included at the classical level. Here we present the extension to electronic embedding. We show how the behavior of ONIOM with electronic embedding can be more stable than QM/MM with electronic embedding. We also investigate the link atom correction, which is implicit in ONIOM but not in QM/MM. Second, we demonstrate some of the practical aspects of ONIOM(QM:MM) calculations. Specifically, we show that the potential surface can be discontinuous when there is bond breaking and forming closer than three bonds from the MM region.
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Affiliation(s)
- Thom Vreven
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, and Cherry Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322
| | - K Suzie Byun
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, and Cherry Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322
| | - István Komáromi
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, and Cherry Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322
| | - Stefan Dapprich
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, and Cherry Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322
| | - John A Montgomery
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, and Cherry Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322
| | - Keiji Morokuma
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, and Cherry Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322
| | - Michael J Frisch
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, and Cherry Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322
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50
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Sun G, Zhao Y, Liang W. Aggregation-Induced Emission Mechanism of Dimethoxy-Tetraphenylethylene in Water Solution: Molecular Dynamics and QM/MM Investigations. J Chem Theory Comput 2015; 11:2257-67. [DOI: 10.1021/ct5009312] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Guangxu Sun
- Department of Chemical
Physics, University of Science and Technology of China, Hefei, 230026 Anhui, China
| | - Yi Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative
Innovation Center of Chemistry for Energy Materials, and Department
of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 Fujian, China
| | - WanZhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative
Innovation Center of Chemistry for Energy Materials, and Department
of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 Fujian, China
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