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Bednarska-Szczepaniak K, Hałagan K, Szwed M, Przelazły E, Leśnikowski ZJ. Quantum Chemical and Biological Insights into Redox Activity of Metallacarborane Complexes in Cancer Cells. J Chem Inf Model 2024; 64:6521-6541. [PMID: 39140958 DOI: 10.1021/acs.jcim.4c00394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
A relationship between the electronic properties of metal ions in metallacarboranes and their ability to modulate mitochondrial oxidase activity and membrane hyperpolarization in cancer cells was demonstrated. Quantum chemistry methods, including DFT and molecular dynamics simulations, were used to understand the oxidized and reduced forms of metallacarboranes and their intramolecular rotatory behavior. According to the low-spin assumption for metal ions, the intramolecular oscillations of cluster ligands in metallacarboranes are significantly influenced by the type of metal and correspond to the cellular uptake of these complexes in vitro. In particular, the low-spin iron compound may be a new xenogeneic booster of redox homeostasis in cancer cells resistant to cisplatin, which induces metabolic 'exhaustion' of cancer cells and their death.
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Affiliation(s)
- Katarzyna Bednarska-Szczepaniak
- Laboratory of Medicinal Chemistry, Polish Academy of Sciences, Institute of Medical Biology, 106 Lodowa, 92-232 Lodz, Poland
| | - Krzysztof Hałagan
- Department of Molecular Physics, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
| | - Marzena Szwed
- Department of Medical Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Institute of Biophysics, Pomorska 141/143, 90-236 Lodz, Poland
| | - Ewelina Przelazły
- Laboratory of Medicinal Chemistry, Polish Academy of Sciences, Institute of Medical Biology, 106 Lodowa, 92-232 Lodz, Poland
| | - Zbigniew J Leśnikowski
- Laboratory of Medicinal Chemistry, Polish Academy of Sciences, Institute of Medical Biology, 106 Lodowa, 92-232 Lodz, Poland
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Rangaswamy R, Sneha S, Hemavathy N, Umashankar V, Jeyakanthan J. Computational discovery of AKT serine/threonine kinase 1 inhibitors through shape screening for rheumatoid arthritis intervention. Mol Divers 2024:10.1007/s11030-024-10910-z. [PMID: 38970640 DOI: 10.1007/s11030-024-10910-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 06/02/2024] [Indexed: 07/08/2024]
Abstract
Rheumatoid Arthritis (RA) is a chronic, symmetrical inflammatory autoimmune disorder characterized by painful, swollen synovitis and joint erosions, which can cause damage to bone and cartilage and be associated with progressive disability. Despite expanded treatment options, some patients still experience inadequate response or intolerable adverse effects. Consequently, the treatment options for RA remain quite limited. The enzyme AKT1 is crucial in designing drugs for various human diseases, supporting cellular functions like proliferation, survival, metabolism, and angiogenesis in both normal and malignant cells. Therefore, AKT serine/threonine kinase 1 is considered crucial for targeting therapeutic strategies aimed at mitigating RA mechanisms. In this context, directing efforts toward AKT1 represents an innovative approach to developing new anti-arthritis medications. The primary objective of this research is to prioritize AKT1 inhibitors using computational techniques such as molecular modeling and dynamics simulation (MDS) and shape-based virtual screening (SBVS). A combined SBVS approach was employed to predict potent inhibitors against AKT1 by screening a pool of compounds sourced from the ChemDiv and IMPPAT databases. From the SBVS results, only the top three compounds, ChemDiv_7266, ChemDiv_2796, and ChemDiv_9468, were subjected to stability analysis based on their high binding affinity and favorable ADME/Tox properties. The SBVS findings have revealed that critical residues, including Glu17, Gly37, Glu85, and Arg273, significantly contribute to the successful binding of the highest-ranked lead compounds at the active site of AKT1. This insight helps to understand the specific binding mechanism of these leads in inhibiting RA, facilitating the rational design of more effective therapeutic agents.
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Affiliation(s)
- Raghu Rangaswamy
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Tamil Nadu, Karaikudi, 630 003, India
| | - Subramaniyan Sneha
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Tamil Nadu, Karaikudi, 630 003, India
| | - Nagarajan Hemavathy
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Tamil Nadu, Karaikudi, 630 003, India
| | - Vetrivel Umashankar
- Virology & Biotechnology/Bioinformatics Division, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, 600 031, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Tamil Nadu, Karaikudi, 630 003, India.
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Chen JY, Li M, Liao RZ. Mechanistic Insights into Photochemical CO 2 Reduction to CH 4 by a Molecular Iron-Porphyrin Catalyst. Inorg Chem 2023. [PMID: 37279181 DOI: 10.1021/acs.inorgchem.3c00402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Iron tetraphenylporphyrin complex modified with four trimethylammonium groups (Fe-p-TMA) is found to be capable of catalyzing the eight-electron eight-proton reduction of CO2 to CH4 photochemically in acetonitrile. In the present work, density functional theory (DFT) calculations have been performed to investigate the reaction mechanism and to rationalize the product selectivity. Our results revealed that the initial catalyst Fe-p-TMA ([Cl-Fe(III)-LR4]4+, where L = tetraphenylporphyrin ligand with a total charge of -2, and R4 = four trimethylammonium groups with a total charge of +4) undergoes three reduction steps, accompanied by the dissociation of the chloride ion to form [Fe(II)-L••2-R4]2+. [Fe(II)-L••2-R4]2+, bearing a Fe(II) center ferromagnetically coupled with a tetraphenylporphyrin diradical, performs a nucleophilic attack on CO2 to produce the 1η-CO2 adduct [CO2•--Fe(II)-L•-R4]2+. Two intermolecular proton transfer steps then take place at the CO2 moiety of [CO2•--Fe(II)-L•-R4]2+, resulting in the cleavage of the C-O bond and the formation of the critical intermediate [Fe(II)-CO]4+ after releasing a water molecule. Subsequently, [Fe(II)-CO]4+ accepts three electrons and one proton to generate [CHO-Fe(II)-L•-R4]2+, which finally undergoes a successive four-electron-five-proton reduction to produce methane without forming formaldehyde, methanol, or formate. Notably, the redox non-innocent tetraphenylporphyrin ligand was found to play an important role in CO2 reduction since it could accept and transfer electron(s) during catalysis, thus keeping the ferrous ion at a relatively high oxidation state. Hydrogen evolution reaction via the formation of Fe-hydride ([Fe(II)-H]3+) turns out to endure a higher total barrier than the CO2 reduction reaction, therefore providing a reasonable explanation for the origin of the product selectivity.
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Affiliation(s)
- Jia-Yi Chen
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Man Li
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
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Rezaei M, Kalhor HR. Amyloid fibril reduction through covalently modified lysine in HEWL and insulin. Arch Biochem Biophys 2022; 727:109350. [PMID: 35830943 DOI: 10.1016/j.abb.2022.109350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022]
Abstract
Proteins possess a variety of nucleophiles, which can carry out different reactions in the functioning cells. Proteins endogenously and synthetically can be modified through their nucleophilic sites. The roles of these chemical modifications have not been completely revealed. These modifications can alter the protein folding process. Protein folding directly affects the function of proteins. If an error in protein folding occurs, it may cause protein malfunction leading to several neurodegenerative disorders such as Alzheimer's and Parkinson's. In this study, Hen Egg White Lysozyme (HEWL) and bovine insulin, as model proteins for studying the amyloid formation, were covalently attached with 5(6)-thiophenolfluorescein. The amyloid formation of the covalently labeled lysozyme and insulin were compared with the native proteins. Interestingly, the results indicated that the covalent attachment of fluorescein slowed down the amyloid formation of HEWL and insulin significantly. The amyloid formation was examined using Thioflavin T (ThT) fluorescence assay, circular dichroism, FTIR, and gel electrophoresis. Tandem mass spectrometry was employed to identify the sites of covalent modifications in HEWL. It turned out that two surface lysine residues (K97 and K 116) in HEWL were modified. Computational studies, including docking and molecular simulations, revealed that 5(6)-thiophenolfluorescein makes several non-covalent interactions with HEWL residues, including Lys 97, leading to the reduction of the β-sheet in the protein. Additionally, AFM analysis confirmed the amyloid fibril reduction of lysine-modified bovine insulin and HEWL. Altogether, our results expand mechanistic insights into preventing amyloid formation by providing an approach for reducing amyloid formation by modifying specific lysine residues in the proteins.
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Affiliation(s)
- Mohsen Rezaei
- Biochemistry and Chemical Biology Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran
| | - Hamid Reza Kalhor
- Biochemistry and Chemical Biology Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran.
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Jaramillo DE, Jaffe A, Snyder BER, Smith A, Taw E, Rohde RC, Dods MN, DeSnoo W, Meihaus KR, Harris TD, Neaton JB, Long JR. Metal-organic frameworks as O 2-selective adsorbents for air separations. Chem Sci 2022; 13:10216-10237. [PMID: 36277628 PMCID: PMC9473493 DOI: 10.1039/d2sc03577d] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/21/2022] [Indexed: 02/05/2023] Open
Abstract
Oxygen is a critical gas in numerous industries and is produced globally on a gigatonne scale, primarily through energy-intensive cryogenic distillation of air. The realization of large-scale adsorption-based air separations could enable a significant reduction in associated worldwide energy consumption and would constitute an important component of broader efforts to combat climate change. Certain small-scale air separations are carried out using N2-selective adsorbents, although the low capacities, poor selectivities, and high regeneration energies associated with these materials limit the extent of their usage. In contrast, the realization of O2-selective adsorbents may facilitate more widespread adoption of adsorptive air separations, which could enable the decentralization of O2 production and utilization and advance new uses for O2. Here, we present a detailed evaluation of the potential of metal-organic frameworks (MOFs) to serve as O2-selective adsorbents for air separations. Drawing insights from biological and molecular systems that selectively bind O2, we survey the field of O2-selective MOFs, highlighting progress and identifying promising areas for future exploration. As a guide for further research, the importance of moving beyond the traditional evaluation of O2 adsorption enthalpy, ΔH, is emphasized, and the free energy of O2 adsorption, ΔG, is discussed as the key metric for understanding and predicting MOF performance under practical conditions. Based on a proof-of-concept assessment of O2 binding carried out for eight different MOFs using experimentally derived capacities and thermodynamic parameters, we identify two existing materials and one proposed framework with nearly optimal ΔG values for operation under user-defined conditions. While enhancements are still needed in other material properties, the insights from the assessments herein serve as a guide for future materials design and evaluation. Computational approaches based on density functional theory with periodic boundary conditions are also discussed as complementary to experimental efforts, and new predictions enable identification of additional promising MOF systems for investigation.
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Affiliation(s)
- David E Jaramillo
- Department of Chemistry, University of California Berkeley Berkeley California 94720 USA
| | - Adam Jaffe
- Department of Chemistry, University of California Berkeley Berkeley California 94720 USA
| | - Benjamin E R Snyder
- Department of Chemistry, University of California Berkeley Berkeley California 94720 USA
| | - Alex Smith
- Department of Physics, University of California Berkeley Berkeley California 94720 USA
| | - Eric Taw
- Department of Chemical and Biomolecular Engineering, University of California Berkeley Berkeley California 94720 USA
- Materials Science Division, Lawrence Berkeley National Laboratory Berkeley California 94720 USA
| | - Rachel C Rohde
- Department of Chemistry, University of California Berkeley Berkeley California 94720 USA
| | - Matthew N Dods
- Department of Chemistry, University of California Berkeley Berkeley California 94720 USA
| | - William DeSnoo
- Department of Physics, University of California Berkeley Berkeley California 94720 USA
| | - Katie R Meihaus
- Department of Chemistry, University of California Berkeley Berkeley California 94720 USA
| | - T David Harris
- Department of Chemistry, University of California Berkeley Berkeley California 94720 USA
| | - Jeffrey B Neaton
- Department of Physics, University of California Berkeley Berkeley California 94720 USA
- Molecular Foundry, Lawrence Berkeley National Laboratory Berkeley California 94720 USA
- Kavli Nanosciences Institute at Berkeley Berkeley California 94720 USA
| | - Jeffrey R Long
- Department of Chemistry, University of California Berkeley Berkeley California 94720 USA
- Department of Chemical and Biomolecular Engineering, University of California Berkeley Berkeley California 94720 USA
- Materials Science Division, Lawrence Berkeley National Laboratory Berkeley California 94720 USA
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6
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Polivanovskaia DA, Abdulaeva IA, Birin KP, Gorbunova YG, Tsivadze AY. Diaryl-pyrazinoporphyrins – Prospective photocatalysts for efficient sulfoxidation. J Catal 2022. [DOI: 10.1016/j.jcat.2022.06.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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de Souza JR, de Moraes MMF, Aoto YA, Homem-de-Mello P. Can one use the electronic absorption spectra of metalloporphyrins to benchmark electronic structure methods? A case study on the cobalt porphyrin. Phys Chem Chem Phys 2020; 22:23886-23898. [PMID: 33073830 DOI: 10.1039/d0cp04699j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this article, we describe calculations on the absorption spectrum of cobalt(ii) porphyrin, using density functional (DFT) and multireference n-electron valence perturbation (NEVPT) theories. With these calculations, we describe the lowest-energy states of doublet and quartet spin multiplicities, the excited states that originate the Q and B bands of porphyrins, some higher-energy π-π* excitations and charge-transfer states, HOMO-LUMO gaps, and ionisation potentials. Results undoubtedly show that the position of B band is essentially independent on the DFT functional, while the Q band is better described by pure functionals, and these bands do not depend on the initial state of the transition (whether doublet or quartet) as well. However, other excitation energies, orbital energies, and ionisation potentials strongly depend on the functional, in some cases varying more than 2 eV. Based on these results we conclude that one should not use the UV-Vis spectrum of metalloporphyrins to benchmark density functionals, mainly those properties related to coordination with the metallic ion. Furthermore, the results show that functionals that yield correct spectra may be based on an incorrect ground state description. Moreover, we reinforce that one must be skeptical about the reference chosen to benchmark electronic structure calculations, such as DFT functionals and active spaces for multireference calculations.
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Affiliation(s)
- Jhonathan Rosa de Souza
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Av. dos Estados, 5001, Santo André, SP 09210-580, Brazil.
| | - Matheus Morato F de Moraes
- Centro de Matemática, Computação e Cognição (CMCC), Universidade Federal do ABC (UFABC), Av. dos Estados, 5001, Santo André, SP 09210-580, Brazil.
| | - Yuri Alexandre Aoto
- Centro de Matemática, Computação e Cognição (CMCC), Universidade Federal do ABC (UFABC), Av. dos Estados, 5001, Santo André, SP 09210-580, Brazil.
| | - Paula Homem-de-Mello
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Av. dos Estados, 5001, Santo André, SP 09210-580, Brazil.
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Bioengineering of Cytochrome P450 OleT JE: How Does Substrate Positioning Affect the Product Distributions? Molecules 2020; 25:molecules25112675. [PMID: 32526971 PMCID: PMC7321372 DOI: 10.3390/molecules25112675] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/29/2020] [Accepted: 06/04/2020] [Indexed: 02/04/2023] Open
Abstract
The cytochromes P450 are versatile enzymes found in all forms of life. Most P450s use dioxygen on a heme center to activate substrates, but one class of P450s utilizes hydrogen peroxide instead. Within the class of P450 peroxygenases, the P450 OleTJE isozyme binds fatty acid substrates and converts them into a range of products through the α-hydroxylation, β-hydroxylation and decarboxylation of the substrate. The latter produces hydrocarbon products and hence can be used as biofuels. The origin of these product distributions is unclear, and, as such, we decided to investigate substrate positioning in the active site and find out what the effect is on the chemoselectivity of the reaction. In this work we present a detailed computational study on the wild-type and engineered structures of P450 OleTJE using a combination of density functional theory and quantum mechanics/molecular mechanics methods. We initially explore the wild-type structure with a variety of methods and models and show that various substrate activation transition states are close in energy and hence small perturbations as through the protein may affect product distributions. We then engineered the protein by generating an in silico model of the double mutant Asn242Arg/Arg245Asn that moves the position of an active site Arg residue in the substrate-binding pocket that is known to form a salt-bridge with the substrate. The substrate activation by the iron(IV)-oxo heme cation radical species (Compound I) was again studied using quantum mechanics/molecular mechanics (QM/MM) methods. Dramatic differences in reactivity patterns, barrier heights and structure are seen, which shows the importance of correct substrate positioning in the protein and the effect of the second-coordination sphere on the selectivity and activity of enzymes.
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Structure, Properties, and Reactivity of Porphyrins on Surfaces and Nanostructures with Periodic DFT Calculations. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10030740] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Porphyrins are fascinating molecules with applications spanning various scientific fields. In this review we present the use of periodic density functional theory (PDFT) calculations to study the structure, electronic properties, and reactivity of porphyrins on ordered two dimensional surfaces and in the formation of nanostructures. The focus of the review is to describe the application of PDFT calculations for bridging the gaps in experimental studies on porphyrin nanostructures and self-assembly on 2D surfaces. A survey of different DFT functionals used to study the porphyrin-based system as well as their advantages and disadvantages in studying these systems is presented.
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Rathi P, Butcher R, Sankar M. Unsymmetrical nonplanar 'push-pull' β-octasubstituted porphyrins: facile synthesis, structural, photophysical and electrochemical redox properties. Dalton Trans 2019; 48:15002-15011. [PMID: 31556414 DOI: 10.1039/c9dt02792k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mixed substitution at the β-position of porphyrins influences their photophysical and electrochemical redox properties. Two new series of asymmetrically mixed β-octasubstituted porphyrins viz. MTPP(Ph)2Br5X (X = NO2 or Br and M = 2H, Co(ii), Ni(ii), Cu(ii), and Zn(ii)) have been synthesized and characterized by various spectroscopic techniques. The single crystal X-ray structure of H2TPP(NO2)(Ph)2Br5 showed a nonplanar saddle shape conformation of the macrocyclic core. Furthermore, the fully optimized geometries confirmed the saddle shape conformation of H2TPP(Ph)2Br5X (X = NO2 or Br). Electronic spectra revealed a significant bathochromic shift by appending both electron donor and acceptor substituents at the β-position of the meso-tetraphenylporphyrin skeleton, which reflects the following order H2TPP < H2TPP(NO2) < H2TPP(NO2)(Ph)2 < H2TPP(Ph)2Br6 < H2TPP(NO2)(Ph)2Br5. H2TPP(Ph)2Br5X (X = NO2 or Br) exhibited a significant bathochromic shift (Δλmax = 53-61 nm) in the Soret band and (Δλmax = 90-95 nm) in the longest wavelength Qx(0,0) band as compared to H2TPP. Nonplanar conformations and electron withdrawing β-substituents induce higher protonation and deprotonation constants for H2TPP(NO2)(Ph)2Br5 and H2TPP(Ph)2Br6 as compared to precursor porphyrins viz. H2TPP, H2TPP(NO2) and H2TPP(NO2)(Ph)2. The electronic spectral properties and redox potentials of MTPP(Ph)2Br5X (X = NO2 or Br and M = 2H, Co, Ni, Cu and Zn) are affected by β-substituents at the periphery of the porphyrin core. Redox tunability was achieved by appending push-pull substituents at the β-position of the MTPP (M = 2H, CoII, NiII, CuII, and ZnII) skeleton of the macrocycle. CuTPP(Ph)2Br6 and CuTPP(NO2)(Ph)2Br5 exhibited a dramatically reduced HOMO-LUMO gap with a difference of 0.55 V and 0.62 V, respectively as compared to CuTPP due to the push-pull effect of β-substituents and nonplanarity of the porphyrin core.
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Affiliation(s)
- Pinki Rathi
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee - 247667, India.
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11
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Reyes YIA, Franco FC. DFT study on the effect of proximal residues on the Mycobacterium tuberculosis catalase-peroxidase (katG) heme compound I intermediate and its bonding interaction with isoniazid. Phys Chem Chem Phys 2019; 21:16515-16525. [PMID: 31298238 DOI: 10.1039/c9cp01465a] [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
Isoniazid (INH) is converted into isonicotinyl radical through its interaction with the catalase-peroxidase (katG) enzyme present in the cells of Mycobacterium tuberculosis (M. tb.), the bacteria that causes the tuberculosis disease. This process is important because resistance of M. tb. cells to INH treatment has been associated with the failure of completion of this process. However, this process is poorly understood and there are a variety of conflicting theories about the details of the mechanism of this process. One theory suggests that INH binds to katG and transfers a single electron to the heme while the heme is in its two electron oxidized state, compound I [Fe(iv)Por˙+] (CpdI). In this study, DFT calculations at the UB3LYP/6-31g(d)-LANL2DZ level of theory are used to study the M. tb. katG CpdI molecule. Different models of the M. tb. CpdI molecule were prepared and the calculations revealed the impact of Trp321 on the electronic properties of the heme. Without Trp321 the heme assumed a triradical state with single electrons on the πxy and πyz orbitals of Fe and another on the a2u orbital of the porphyrin ring that can either be coupled with the first two, to assume a quartet state, or decoupled to form a doublet state. With Trp321, however, a transfer of an electron from the πTrp orbital to a2u porphyrin orbital leads to loss of radical character of the porphyrin and leaves the Trp321 group with a radical character. INH was observed to have strong interaction with CpdI and the absence of Trp321 significantly decreased the binding energy by 2 kcal mol-1 explaining the importance of Trp321 in the binding of INH. The results in this study show the importance of Trp321 in the binding of INH and its effect on its electronic properties, which is consistent with previous experimental findings that mutation of Trp321 results in an increase in drug resistance.
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Affiliation(s)
- Yves Ira A Reyes
- Chemistry Department, De La Salle University, 2401 Taft Avenue, 0922 Manila, Philippines.
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12
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Qi Q, Taniguchi M, Lindsey JS. Heuristics from Modeling of Spectral Overlap in Förster Resonance Energy Transfer (FRET). J Chem Inf Model 2019; 59:652-667. [PMID: 30715870 DOI: 10.1021/acs.jcim.8b00753] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Among the photophysical parameters that underpin Förster resonance energy transfer (FRET), perhaps the least explored is the spectral overlap term ( J). While by definition J increases linearly with acceptor molar absorption coefficient (ε(A) in M-1 cm-1), is proportional to wavelength (λ4), and depends on the degree of overlap of the donor fluorescence and acceptor absorption spectra, the question arose as to the value of J for the case of perfect spectral overlap versus that for representative fluorophores with incomplete spectral overlap. Here, Gaussian distributions of absorption and fluorescent spectra have been modeled that encompass varying degrees of overlap, full-width-at-half-maximum (fwhm), and Stokes shift. For ε(A) = 105 M-1 cm-1 and perfect overlap, the J value (in M-1 cm-1 nm4) ranges from 1.15 × 1014 (200 nm) to 7.07 × 1016 (1000 nm), is almost linear with λ4 (average of λabs and λflu), and is nearly independent of fwhm. For visible-region fluorophores with perfectly overlapped Gaussian spectra, the resulting value of J ( JG-0) is ∼0.71 ε(A)λ4 (M-1 cm-1 nm4). The experimental J values for homotransfer, as occurs in light-harvesting antennas, were calculated with spectra from a static database of 60 representative compounds (12 groups, 5 compounds each) and found to range from 4.2 × 1010 ( o-xylene) to 5.3 × 1016 M-1 cm-1 nm4 (a naphthalocyanine). The degree of overlap, defined by the ratio of the experimental J to the model JG-0 for perfectly overlapped spectra, ranges from ∼0.5% (coumarin 151) to 77% (bacteriochlorophyll a). The results provide insights into how a variety of factors affect the resulting J values. The high degree of spectral overlap for (bacterio)chlorophylls prompts brief conjecture concerning the relevance of energy transfer to the question "why chlorophyll".
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Affiliation(s)
- Qi Qi
- Department of Chemistry , North Carolina State University , Raleigh , North Carolina 27695-8204 , United States
| | - Masahiko Taniguchi
- Department of Chemistry , North Carolina State University , Raleigh , North Carolina 27695-8204 , United States
| | - Jonathan S Lindsey
- Department of Chemistry , North Carolina State University , Raleigh , North Carolina 27695-8204 , United States
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Lischka H, Nachtigallová D, Aquino AJA, Szalay PG, Plasser F, Machado FBC, Barbatti M. Multireference Approaches for Excited States of Molecules. Chem Rev 2018; 118:7293-7361. [DOI: 10.1021/acs.chemrev.8b00244] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, 78371 Olomouc, Czech Republic
| | - Adélia J. A. Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Péter G. Szalay
- ELTE Eötvös Loránd University, Laboratory of Theoretical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Felix Plasser
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- Department of Chemistry, Loughborough University, Leicestershire LE11 3TU, United Kingdom
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil
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14
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Casarin M, Carlotto S. “Pigments of Life”, Molecules Well Suited to Investigate Metal-Ligand Symmetry-Restricted Covalency. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800480] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Maurizio Casarin
- Department of Chemical Sciences; University of Padova; Via F. Marzolo 1 35131 Padova Italy
- ICMATE CNR of Padova; via F. Marzolo 1 35131 Padova Italy
| | - Silvia Carlotto
- Department of Chemical Sciences; University of Padova; Via F. Marzolo 1 35131 Padova Italy
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15
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de Visser SP. Mechanistic Insight on the Activity and Substrate Selectivity of Nonheme Iron Dioxygenases. CHEM REC 2018; 18:1501-1516. [PMID: 29878456 DOI: 10.1002/tcr.201800033] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/18/2018] [Indexed: 01/05/2023]
Abstract
Nonheme iron dioxygenases catalyze vital reactions for human health particularly related to aging processes. They are involved in the biosynthesis of amino acids, but also the biodegradation of toxic compounds. Typically they react with their substrate(s) through oxygen atom transfer, although often with the assistance of a co-substrate like α-ketoglutarate that is converted to succinate and CO2 . Many reaction processes catalyzed by the nonheme iron dioxygenases are stereoselective or regiospecific and hence understanding the mechanism and protein involvement in the selectivity is important for the design of biotechnological applications of these enzymes. To this end, I will review recent work of our group on nonheme iron dioxygenases and include background information on their general structure and catalytic cycle. Examples of stereoselective and regiospecific reaction mechanisms we elucidated are for the AlkB repair enzyme, prolyl-4-hydroxylase and the ergothioneine biosynthesis enzyme. Finally, I cover an example where we bioengineered S-p-hydroxymandelate synthase into the R-p-hydroxymandelate synthase.
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Affiliation(s)
- Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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16
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Kepp KP. Heme isomers substantially affect heme's electronic structure and function. Phys Chem Chem Phys 2018; 19:22355-22362. [PMID: 28805222 DOI: 10.1039/c7cp03285d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Inspection of heme protein structures in the protein data bank reveals four isomers of heme characterized by different relative orientations of the vinyl side chains; remarkably, all these have been reported in multiple protein structures. Density functional theory computations explain this as due to similar energy of the isomers but with a sizable (25 kJ mol-1) barrier to interconversion arising from restricted rotation around the conjugated bonds. The four isomers, EE, EZ, ZE, and ZZ, were then investigated as 4-coordinate hemes, as 5-coordinate deoxyhemes, in 6-coordinate O2-adducts of globins and as compound I intermediates typical of heme peroxidases. Substantial differences were observed in electronic properties relevant to heme function: notably, the spin state energy gap of O2-heme adducts, important for fast reversible binding of O2, depends on the isomer state, and O2-binding enthalpies change by up to 16 kJ mol-1; redox potentials change by up to 0.2 V depending on the isomer, and the doublet-quartet energy splitting of compound I, central to "two-state" reactivity, is affected by up to ∼15 kJ mol-1. These effects are consistently seen with three distinct density functionals, i.e. the effects are not method-dependent. Thus, the nature of the isomer state is an important but overlooked feature of heme chemistry and function, and previous and future studies of hemes may be reconsidered in this new context.
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Affiliation(s)
- Kasper P Kepp
- Technical University of Denmark, DTU Chemistry, Building 206, 2800 Kgs. Lyngby, DK, Denmark.
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17
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Patwari J, Chatterjee A, Sardar S, Lemmens P, Pal SK. Ultrafast dynamics in co-sensitized photocatalysts under visible and NIR light irradiation. Phys Chem Chem Phys 2018; 20:10418-10429. [DOI: 10.1039/c7cp08431e] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Activity modulation of co-sensitized light harvesting nanohybrids by tuning the ultrafast carrier dynamics under visible and NIR light irradiation.
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Affiliation(s)
- Jayita Patwari
- Department of Chemical
- Biological and Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700 106
- India
| | - Arka Chatterjee
- Department of Chemical
- Biological and Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700 106
- India
| | - Samim Sardar
- Department of Chemical
- Biological and Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700 106
- India
| | - Peter Lemmens
- Institute for Condensed Matter Physics
- TU Braunschweig
- 38106 Braunschweig
- Germany
- Laboratory for Emerging Nanometrology
| | - Samir Kumar Pal
- Department of Chemical
- Biological and Macromolecular Sciences
- S. N. Bose National Centre for Basic Sciences
- Kolkata 700 106
- India
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18
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Tewari D, Mocan A, Parvanov ED, Sah AN, Nabavi SM, Huminiecki L, Ma ZF, Lee YY, Horbańczuk JO, Atanasov AG. Ethnopharmacological Approaches for Therapy of Jaundice: Part I. Front Pharmacol 2017; 8:518. [PMID: 28860989 PMCID: PMC5559545 DOI: 10.3389/fphar.2017.00518 10.3389/2ffphar.2017.00518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 07/24/2017] [Indexed: 09/02/2023] Open
Abstract
Jaundice is a very common symptom especially in the developing countries. It is associated with several hepatic diseases which are still major causes of death. There are many different approaches to jaundice treatment and the growing number of ethnomedicinal studies shows the plant pharmacology as very promising direction. Many medicinal plants are used for the treatment of jaundice, however a comprehensive review on this subject has not been published. The use of medicinal plants in drug discovery is highly emphasized (based on their traditional and safe uses in different folk medicine systems from ancient times). Many sophisticated analytical techniques are emerging in the pharmaceutical field to validate and discover new biologically active chemical entities derived from plants. Here, we aim to classify and categorize medicinal plants relevant for the treatment of jaundice according to their origin, geographical location, and usage. Our search included various databases like Pubmed, ScienceDirect, Google Scholar. Keywords and phrases used for these searches included: "jaundice," "hyperbilirubinemia," "serum glutamate," "bilirubin," "Ayurveda." The first part of the review focuses on the variety of medicinal plant used for the treatment of jaundice (a total of 207 medicinal plants). In the second part, possible mechanisms of action of biologically active secondary metabolites of plants from five families for jaundice treatment are discussed.
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Affiliation(s)
- Devesh Tewari
- Department of Pharmaceutical Sciences, Faculty of Technology, Kumaun UniversityNainital, India
| | - Andrei Mocan
- Department of Pharmaceutical Botany, “Iuliu Hatieganu” University of Medicine and PharmacyCluj-Napoca, Romania
- ICHAT and Institute for Life Sciences, University of Agricultural Sciences and Veterinary Medicine of Cluj-NapocaCluj-Napoca, Romania
| | - Emil D. Parvanov
- Division BIOCEV, Institute of Molecular Genetics, Academy of Sciences of the Czech RepublicPrague, Czechia
| | - Archana N. Sah
- Department of Pharmaceutical Sciences, Faculty of Technology, Kumaun UniversityNainital, India
| | - Seyed M. Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical SciencesTehran, Iran
| | - Lukasz Huminiecki
- Institute of Genetics and Animal Breeding of the Polish Academy of SciencesJastrzebiec, Poland
| | - Zheng Feei Ma
- School of Medical Sciences, Universiti Sains MalaysiaKota Bharu, Malaysia
- Department of Public Health, Xi'an Jiaotong-Liverpool UniversitySuzhou, China
| | - Yeong Yeh Lee
- School of Medical Sciences, Universiti Sains MalaysiaKota Bharu, Malaysia
| | - Jarosław O. Horbańczuk
- Institute of Genetics and Animal Breeding of the Polish Academy of SciencesJastrzebiec, Poland
| | - Atanas G. Atanasov
- Institute of Genetics and Animal Breeding of the Polish Academy of SciencesJastrzebiec, Poland
- Department of Pharmacognosy, University of ViennaVienna, Austria
- Department of Vascular Biology and Thrombosis Research, Centre for Physiology and Pharmacology, Medical University of ViennaVienna, Austria
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19
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Tewari D, Mocan A, Parvanov ED, Sah AN, Nabavi SM, Huminiecki L, Ma ZF, Lee YY, Horbańczuk JO, Atanasov AG. Ethnopharmacological Approaches for Therapy of Jaundice: Part I. Front Pharmacol 2017; 8:518. [PMID: 28860989 PMCID: PMC5559545 DOI: 10.3389/fphar.2017.00518] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 07/24/2017] [Indexed: 12/14/2022] Open
Abstract
Jaundice is a very common symptom especially in the developing countries. It is associated with several hepatic diseases which are still major causes of death. There are many different approaches to jaundice treatment and the growing number of ethnomedicinal studies shows the plant pharmacology as very promising direction. Many medicinal plants are used for the treatment of jaundice, however a comprehensive review on this subject has not been published. The use of medicinal plants in drug discovery is highly emphasized (based on their traditional and safe uses in different folk medicine systems from ancient times). Many sophisticated analytical techniques are emerging in the pharmaceutical field to validate and discover new biologically active chemical entities derived from plants. Here, we aim to classify and categorize medicinal plants relevant for the treatment of jaundice according to their origin, geographical location, and usage. Our search included various databases like Pubmed, ScienceDirect, Google Scholar. Keywords and phrases used for these searches included: “jaundice,” “hyperbilirubinemia,” “serum glutamate,” “bilirubin,” “Ayurveda.” The first part of the review focuses on the variety of medicinal plant used for the treatment of jaundice (a total of 207 medicinal plants). In the second part, possible mechanisms of action of biologically active secondary metabolites of plants from five families for jaundice treatment are discussed.
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Affiliation(s)
- Devesh Tewari
- Department of Pharmaceutical Sciences, Faculty of Technology, Kumaun UniversityNainital, India
| | - Andrei Mocan
- Department of Pharmaceutical Botany, "Iuliu Hatieganu" University of Medicine and PharmacyCluj-Napoca, Romania.,ICHAT and Institute for Life Sciences, University of Agricultural Sciences and Veterinary Medicine of Cluj-NapocaCluj-Napoca, Romania
| | - Emil D Parvanov
- Division BIOCEV, Institute of Molecular Genetics, Academy of Sciences of the Czech RepublicPrague, Czechia
| | - Archana N Sah
- Department of Pharmaceutical Sciences, Faculty of Technology, Kumaun UniversityNainital, India
| | - Seyed M Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical SciencesTehran, Iran
| | - Lukasz Huminiecki
- Institute of Genetics and Animal Breeding of the Polish Academy of SciencesJastrzebiec, Poland
| | - Zheng Feei Ma
- School of Medical Sciences, Universiti Sains MalaysiaKota Bharu, Malaysia.,Department of Public Health, Xi'an Jiaotong-Liverpool UniversitySuzhou, China
| | - Yeong Yeh Lee
- School of Medical Sciences, Universiti Sains MalaysiaKota Bharu, Malaysia
| | - Jarosław O Horbańczuk
- Institute of Genetics and Animal Breeding of the Polish Academy of SciencesJastrzebiec, Poland
| | - Atanas G Atanasov
- Institute of Genetics and Animal Breeding of the Polish Academy of SciencesJastrzebiec, Poland.,Department of Pharmacognosy, University of ViennaVienna, Austria.,Department of Vascular Biology and Thrombosis Research, Centre for Physiology and Pharmacology, Medical University of ViennaVienna, Austria
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20
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Strengths, Weaknesses, Opportunities and Threats: Computational Studies of Mn- and Fe-Catalyzed Epoxidations. Catalysts 2016. [DOI: 10.3390/catal7010002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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21
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Yang T, Quesne MG, Neu HM, Cantú Reinhard FG, Goldberg DP, de Visser SP. Singlet versus Triplet Reactivity in an Mn(V)-Oxo Species: Testing Theoretical Predictions Against Experimental Evidence. J Am Chem Soc 2016; 138:12375-86. [PMID: 27545752 PMCID: PMC5228574 DOI: 10.1021/jacs.6b05027] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Discerning the factors that control the reactivity of high-valent metal-oxo species is critical to both an understanding of metalloenzyme reactivity and related transition metal catalysts. Computational studies have suggested that an excited higher spin state in a number of metal-oxo species can provide a lower energy barrier for oxidation reactions, leading to the conclusion that this unobserved higher spin state complex should be considered as the active oxidant. However, testing these computational predictions by experiment is difficult and has rarely been accomplished. Herein, we describe a detailed computational study on the role of spin state in the reactivity of a high-valent manganese(V)-oxo complex with para-Z-substituted thioanisoles and utilize experimental evidence to distinguish between the theoretical results. The calculations show an unusual change in mechanism occurs for the dominant singlet spin state that correlates with the electron-donating property of the para-Z substituent, while this change is not observed on the triplet spin state. Minimum energy crossing point calculations predict small spin-orbit coupling constants making the spin state change from low spin to high spin unlikely. The trends in reactivity for the para-Z-substituted thioanisole derivatives provide an experimental measure for the spin state reactivity in manganese-oxo corrolazine complexes. Hence, the calculations show that the V-shaped Hammett plot is reproduced by the singlet surface but not by the triplet state trend. The substituent effect is explained with valence bond models, which confirm a change from an electrophilic to a nucleophilic mechanism through a change of substituent.
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Affiliation(s)
- Tzuhsiung Yang
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Matthew G. Quesne
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Heather M. Neu
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Fabián G. Cantú Reinhard
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - David P. Goldberg
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Sam P. de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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