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Rusdipoetra RA, Suwito H, Puspaningsih NNT, Haq KU. Theoretical insight of reactive oxygen species scavenging mechanism in lignin waste depolymerization products. RSC Adv 2024; 14:6310-6323. [PMID: 38380240 PMCID: PMC10877321 DOI: 10.1039/d3ra08346b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
Apart from natural products and synthesis, phenolic compounds can be produced from the depolymerization of lignin, a major waste in biofuel and paper production. This process yields a plethora of aryl propanoid phenolic derivatives with broad biological activities, especially antioxidant properties. Due to its versatility, our study focuses on investigating the antioxidant mechanisms of several phenolic compounds obtained from renewable and abundant resources, namely, syringol (Hs), 4-allylsyringol (HAs), 4-propenylsyringol (HPns), and 4-propylsyringol (HPs). Employing the density functional theory (DFT) approach in conjunction with the QM-ORSA protocol, we aim to explore the reactivity of these compounds in neutralizing hydroperoxyl radicals in physiological and non-polar media. Kinetic and thermodynamic parameter calculations on the antioxidant activity of these compounds were also included in this study. Additionally, our research utilizes the activation strain model (ASM) for the first time to explain the reactivity of the HT and RAF mechanisms in the peroxyl radical scavenging process. It is predicted that HPs has the best rate constant in both media (1.13 × 108 M-1 s-1 and 1.75 × 108 M-1 s-1, respectively). Through ASM analysis, it is observed that the increase in the interaction energy due to the formation of intermolecular hydrogen bonds during the reaction is an important feature for accelerating the hydrogen transfer process. Furthermore, by examining the physicochemical and toxicity parameters, only Hs is not suitable for further investigation as a therapeutic agent because of potential toxicity and mutagenicity. However, overall, all compounds are considered potent HOO˙ scavengers in lipid-rich environments compared to previously studied antioxidants.
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Affiliation(s)
- Rahmanto Aryabraga Rusdipoetra
- Bioinformatic Research Group, Research Centre of Bio-Molecule Engineering (BIOME), Airlangga University Jl. Ir. H. Soekarno Mulyorejo Surabaya Indonesia
- Department of Chemistry, Faculty of Science and Technology, Airlangga University Jl. Ir. H. Soekarno Mulyorejo Surabaya Indonesia
| | - Hery Suwito
- Department of Chemistry, Faculty of Science and Technology, Airlangga University Jl. Ir. H. Soekarno Mulyorejo Surabaya Indonesia
| | - Ni Nyoman Tri Puspaningsih
- Department of Chemistry, Faculty of Science and Technology, Airlangga University Jl. Ir. H. Soekarno Mulyorejo Surabaya Indonesia
- Proteomic Research Group, Research Centre of Bio-Molecule Engineering (BIOME), Airlangga University Jl. Ir. H. Soekarno Mulyorejo Surabaya Indonesia
| | - Kautsar Ul Haq
- Bioinformatic Research Group, Research Centre of Bio-Molecule Engineering (BIOME), Airlangga University Jl. Ir. H. Soekarno Mulyorejo Surabaya Indonesia
- Department of Chemistry, Faculty of Science and Technology, Airlangga University Jl. Ir. H. Soekarno Mulyorejo Surabaya Indonesia
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2
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Alcázar JJ, Misad Saide AC, Campodónico PR. Reliable and accurate prediction of basic pK[Formula: see text] values in nitrogen compounds: the pK[Formula: see text] shift in supramolecular systems as a case study. J Cheminform 2023; 15:90. [PMID: 37770903 PMCID: PMC10540475 DOI: 10.1186/s13321-023-00763-3] [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: 06/29/2023] [Accepted: 09/20/2023] [Indexed: 09/30/2023] Open
Abstract
This article presents a quantitative structure-activity relationship (QSAR) approach for predicting the acid dissociation constant (pK[Formula: see text]) of nitrogenous compounds, including those within supramolecular complexes based on cucurbiturils. The model combines low-cost quantum mechanical calculations with QSAR methodology and linear regressions to achieve accurate predictions for a broad range of nitrogen-containing compounds. The model was developed using a diverse dataset of 130 nitrogenous compounds and exhibits excellent predictive performance, with a high coefficient of determination (R[Formula: see text]) of 0.9905, low standard error (s) of 0.3066, and high Fisher statistic (F) of 2142. The model outperforms existing methods, such as Chemaxon software and previous studies, in terms of accuracy and its ability to handle heterogeneous datasets. External validation on pharmaceutical ingredients, dyes, and supramolecular complexes based on cucurbiturils confirms the reliability of the model. To enhance usability, a script-like tool has been developed, providing a streamlined process for users to access the model. This study represents a significant advancement in pK[Formula: see text] prediction, offering valuable insights for drug design and supramolecular system optimization.
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Affiliation(s)
- Jackson J. Alcázar
- Centro de Química Médica, Universidad del Desarrollo, Av.Plaza 680, 7780272 Santiago, RM Chile
| | | | - Paola R. Campodónico
- Centro de Química Médica, Universidad del Desarrollo, Av.Plaza 680, 7780272 Santiago, RM Chile
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3
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Li F, Wang KY, Liu Z, Han Z, Kuai D, Fan W, Feng L, Wang Y, Wang X, Li Y, Yang Z, Wang R, Sun D, Zhou HC. Ortho Effects of Tricarboxylate Linkers in Regulating Topologies of Rare-Earth Metal-Organic Frameworks. JACS AU 2023; 3:1337-1347. [PMID: 37234108 PMCID: PMC10207104 DOI: 10.1021/jacsau.2c00635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 05/27/2023]
Abstract
A linker design strategy is developed to attain novel polynuclear rare-earth (RE) metal-organic frameworks (MOFs) with unprecedented topologies. We uncover the critical role of ortho-functionalized tricarboxylate ligands in directing the construction of highly connected RE MOFs. The acidity and conformation of the tricarboxylate linkers were altered by substituting with diverse functional groups at the ortho position of the carboxyl groups. For instance, the acidity difference between carboxylate moieties resulted in forming three hexanuclear RE MOFs with novel (3,3,3,10,10)-c wxl, (3,12)-c gmx, and (3,3,3,12)-c joe topologies, respectively. In addition, when a bulky methyl group was introduced, the incompatibility between the net topology and ligand conformation guided the co-appearance of hexanuclear and tetranuclear clusters, generating a novel 3-periodic MOF with a (3,3,8,10)-c kyw net. Interestingly, a fluoro-functionalized linker prompted the formation of two unusual trinuclear clusters and produced a MOF with a fascinating (3,8,10)-c lfg topology, which could be gradually replaced by a more stable tetranuclear MOF with a new (3,12)-c lee topology with extended reaction time. This work enriches the polynuclear clusters library of RE MOFs and unveils new opportunities to construct MOFs with unprecedented structural complexity and vast application potential.
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Affiliation(s)
- Fugang Li
- School
of Materials Science and Engineering, College of Chemistry and Chemical
Engineering, China University of Petroleum
(East China), Qingdao, Shandong 266580, China
| | - Kun-Yu Wang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United
States
| | - Zhengyang Liu
- School
of Materials Science and Engineering, College of Chemistry and Chemical
Engineering, China University of Petroleum
(East China), Qingdao, Shandong 266580, China
| | - Zongsu Han
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United
States
| | - Dacheng Kuai
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United
States
| | - Weidong Fan
- School
of Materials Science and Engineering, College of Chemistry and Chemical
Engineering, China University of Petroleum
(East China), Qingdao, Shandong 266580, China
| | - Liang Feng
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United
States
| | - Yutong Wang
- School
of Materials Science and Engineering, College of Chemistry and Chemical
Engineering, China University of Petroleum
(East China), Qingdao, Shandong 266580, China
| | - Xiaokang Wang
- School
of Materials Science and Engineering, College of Chemistry and Chemical
Engineering, China University of Petroleum
(East China), Qingdao, Shandong 266580, China
| | - Yue Li
- School
of Materials Science and Engineering, College of Chemistry and Chemical
Engineering, China University of Petroleum
(East China), Qingdao, Shandong 266580, China
| | - Zhentao Yang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United
States
| | - Rongming Wang
- School
of Materials Science and Engineering, College of Chemistry and Chemical
Engineering, China University of Petroleum
(East China), Qingdao, Shandong 266580, China
| | - Daofeng Sun
- School
of Materials Science and Engineering, College of Chemistry and Chemical
Engineering, China University of Petroleum
(East China), Qingdao, Shandong 266580, China
| | - Hong-Cai Zhou
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United
States
- Department
of Materials Science and Engineering, Texas
A&M University, College Station, Texas 77843-3255, United States
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4
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Fowles DJ, Palmer DS. Solvation entropy, enthalpy and free energy prediction using a multi-task deep learning functional in 1D-RISM. Phys Chem Chem Phys 2023; 25:6944-6954. [PMID: 36806875 DOI: 10.1039/d3cp00199g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Simultaneous calculation of entropies, enthalpies and free energies has been a long-standing challenge in computational chemistry, partly because of the difficulty in obtaining estimates of all three properties from a single consistent simulation methodology. This has been particularly true for methods from the Integral Equation Theory of Molecular Liquids such as the Reference Interaction Site Model which have traditionally given large errors in solvation thermodynamics. Recently, we presented pyRISM-CNN, a combination of the 1 Dimensional Reference Interaction Site Model (1D-RISM) solver, pyRISM, with a deep learning based free energy functional, as a method of predicting solvation free energy (SFE). With this approach, a 40-fold improvement in prediction accuracy was delivered for a multi-solvent, multi-temperature dataset when compared to the standard 1D-RISM theory [Fowles et al., Digital Discovery, 2023, 2, 177-188]. Here, we report three further developments to the pyRISM-CNN methodology. Firstly, solvation free energies have been introduced for organic molecular ions in methanol or water solvent systems at 298 K, with errors below 4 kcal mol-1 obtained without the need for corrections or additional descriptors. Secondly, the number of solvents in the training data has been expanded from carbon tetrachloride, water and chloroform to now also include methanol. For neutral solutes, prediction errors nearing or below 1 kcal mol-1 are obtained for each organic solvent system at 298 K and water solvent systems at 273-373 K. Lastly, pyRISM-CNN was successfully applied to the simultaneous prediction of solvation enthalpy, entropy and free energy through a multi-task learning approach, with errors of 1.04, 0.98 and 0.47 kcal mol-1, respectively, for water solvent systems at 298 K.
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Affiliation(s)
- Daniel J Fowles
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, UK.
| | - David S Palmer
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, UK.
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5
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Zhang CZ, Jin RH, Shen QQ, Liu LL. Synthesis of graphene oxide grafted by diazanyl groups and its application in recovery of lead from lead-acid wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:29844-29858. [PMID: 36418827 DOI: 10.1007/s11356-022-24319-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Heavy metal ion (HMI) in wastewater is a kind of resource that is wrongly placed. Recovery of heavy metal from lead-acid wastewater desires efficient and reusable functional materials. In this paper, graphene oxide-like with diazanyl groups (GOLA) was synthesized by a nucleophilic substitution reaction of graphene oxide-like with hydroxyl groups (GOLH) with diazane. GOLA exhibited good stability and recyclability in wastewater. The maximal adsorption capacity (qmax) values of GOLA for Pb(II), Cd(II), Cu(II), Ni(II), and Cr(III) ions were 505.80, 401.99, 83.48, 82.29, and 147.77 mg/g, respectively. The equilibrium time of GOLA adsorbing HMIs was 20 min. GOLA was employed to recover lead ions from lead-acid wastewater to give Pb(OH)2 and reusable water. Therefore, this paper provides a useful method of recycling lead from lead-acid wastewater.
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Affiliation(s)
- Chao-Zhi Zhang
- School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, People's Republic of China.
- School of Chemistry and Materials Science, Nanjing University of Information Science & Technology, Nanjing, 210044, People's Republic of China.
| | - Rui-Hua Jin
- School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, People's Republic of China
| | - Qian-Qian Shen
- School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, People's Republic of China
| | - Ling-Ling Liu
- School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, People's Republic of China
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6
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Fossat M, Zeng X, Pappu RV. Uncovering Differences in Hydration Free Energies and Structures for Model Compound Mimics of Charged Side Chains of Amino Acids. J Phys Chem B 2021; 125:4148-4161. [PMID: 33877835 PMCID: PMC8154595 DOI: 10.1021/acs.jpcb.1c01073] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/07/2021] [Indexed: 02/07/2023]
Abstract
Free energies of hydration are of fundamental interest for modeling and understanding conformational and phase equilibria of macromolecular solutes in aqueous phases. Of particular relevance to systems such as intrinsically disordered proteins are the free energies of hydration and hydration structures of model compounds that mimic charged side chains of Arg, Lys, Asp, and Glu. Here, we deploy a Thermodynamic Cycle-based Proton Dissociation (TCPD) approach in conjunction with data from direct measurements to obtain estimates for the free energies of hydration for model compounds that mimic the side chains of Arg+, Lys+, Asp-, and Glu-. Irrespective of the choice made for the hydration free energy of the proton, the TCPD approach reveals clear trends regarding the free energies of hydration for Arg+, Lys+, Asp-, and Glu-. These trends include asymmetries between the hydration free energies of acidic (Asp- and Glu-) and basic (Arg+ and Lys+) residues. Further, the TCPD analysis, which relies on a combination of experimental data, shows that the free energy of hydration of Arg+ is less favorable than that of Lys+. We sought a physical explanation for the TCPD-derived trends in free energies of hydration. To this end, we performed temperature-dependent calculations of free energies of hydration and analyzed hydration structures from simulations that use the polarizable Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field and water model. At 298 K, the AMOEBA model generates estimates of free energies of hydration that are consistent with TCPD values with a free energy of hydration for the proton of ca. -259 kcal/mol. Analysis of temperature-dependent simulations leads to a structural explanation for the observed differences in free energies of hydration of ionizable residues and reveals that the heat capacity of hydration is positive for Arg+ and Lys+ and negative for Asp- and Glu-.
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Affiliation(s)
| | | | - Rohit V. Pappu
- Department of Biomedical Engineering
and Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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7
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Kozlov VA, Ivanov SN, Koifman OI. Solvated proton as the main reagent and a catalyst in the single-stage aromatic sulfonation and protodesulfonation of sulfonic acids. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Vladimir A. Kozlov
- Department of Chemistry and Technology of Macromolecular Compounds; Ivanovo State University of Chemistry and Technology; Ivanovo Russia
| | - Sergey N. Ivanov
- Department of Organic and Physical Chemistry; Ivanovo State University; Ivanovo Russia
| | - Oskar I. Koifman
- Department of Chemistry and Technology of Macromolecular Compounds; Ivanovo State University of Chemistry and Technology; Ivanovo Russia
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8
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Bodnarchuk MS, Doncom KEB, Wright DB, Heyes DM, Dini D, O'Reilly RK. Polyelectrolyte pKa from experiment and molecular dynamics simulation. RSC Adv 2017. [DOI: 10.1039/c6ra27785c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The pKa of a polyelectrolyte has been determined experimentally by potentiometric titration and computed using Molecular Dynamics (MD) constant pH (CpH) methodology, which allows the pKa of each titratable site along the polymer backbone.
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Affiliation(s)
| | | | | | - David M. Heyes
- Department of Mechanical Engineering
- Imperial College
- London SW7 2AZ
- UK
| | - Daniele Dini
- Department of Mechanical Engineering
- Imperial College
- London SW7 2AZ
- UK
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9
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Yu D, Du R, Xiao JC. pK
a prediction for acidic phosphorus-containing compounds using multiple linear regression with computational descriptors. J Comput Chem 2016; 37:1668-71. [DOI: 10.1002/jcc.24381] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/12/2016] [Accepted: 03/05/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Donghai Yu
- Key Laboratory of Organofluorine Chemistry; Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences; Shanghai China
| | - Ruobing Du
- Key Laboratory of Organofluorine Chemistry; Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences; Shanghai China
| | - Ji-Chang Xiao
- Key Laboratory of Organofluorine Chemistry; Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences; Shanghai China
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10
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Cukrowski I, Mangondo P. Interacting quantum fragments-rooted preorganized-interacting fragments attributed relative molecular stability of the Be(II) complexes of nitrilotriacetic acid and nitrilotri-3-propionic acid. J Comput Chem 2016; 37:1373-87. [PMID: 26993356 DOI: 10.1002/jcc.24346] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 01/26/2016] [Accepted: 01/26/2016] [Indexed: 11/11/2022]
Abstract
A method designed to investigate, on a fundamental level, the origin of relative stability of molecular systems using Be(II) complexes with nitrilotriacetic acid (NTA) and nitrilotri-3-propionic acid (NTPA) is described. It makes use of the primary and molecular fragment energy terms as defined in the IQA/F (Interacting Quantum Atoms/Fragments) framework. An extensive classical-type investigation, focused on single descriptors (bond length, density at critical point, the size of metal ion or coordination ring, interaction energy between Be(II) and a donor atom, etc.) showed that it is not possible to explain the experimental trend. The proposed methodology is fundamentally different in that it accounts for the total energy contributions coming from all atoms of selected molecular fragments, and monitors changes in defined energy terms (e.g., fragment deformation, inter- and intra-fragment interaction) on complex formation. By decomposing combined energy terms we identified the origin of relative stability of Be(II) (NTA) and Be(II) (NTPA) complexes. We found that the sum of coordination bonds' strength, as measured by interaction energies between Be(II) ion and donor atoms, favours Be(II) (NTA) but the binding energy of Be(II) ion to the entire ligand correlates well with experimental trend. Surprisingly, the origin of Be(II) (NTPA) being more stable is due to less severe repulsive interactions with the backbone of NTPA (C and H-atoms). This general purpose protocol can be employed not only to investigate the origin of relative stability of any molecular system (e.g., metal complexes) but, in principle, can be used as a predictive tool for, e.g., explaining reaction mechanism. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ignacy Cukrowski
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, 0002, South Africa
| | - Paidamwoyo Mangondo
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, 0002, South Africa
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11
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Mirzaei S, Taherpour AA, Mohamadi S. Mechanistic study of allopurinol oxidation using aldehyde oxidase, xanthine oxidase and cytochrome P450 enzymes. RSC Adv 2016. [DOI: 10.1039/c6ra19197e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The oxidation reaction of allopurinol to its active metabolite (oxypurinol) is investigated using the AO and P450 enzymes. To the contrary of AO (and XO), the P450 enzyme can metabolize the allopurinol with a not self-inhibitory mechanism.
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Affiliation(s)
- Saber Mirzaei
- Department of Organic Chemistry
- Faculty of Chemistry
- Razi University
- Kermanshah
- Iran
| | - Avat Arman Taherpour
- Department of Organic Chemistry
- Faculty of Chemistry
- Razi University
- Kermanshah
- Iran
| | - Shahryar Mohamadi
- Department of Organic Chemistry
- Faculty of Chemistry
- Razi University
- Kermanshah
- Iran
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