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Nemčovičová I, Lopušná K, Štibrániová I, Benedetti F, Berti F, Felluga F, Drioli S, Vidali M, Katrlík J, Pažitná L, Holazová A, Blahutová J, Lenhartová S, Sláviková M, Klempa B, Ondrejovič M, Chmelová D, Legerská B, Miertuš S, Klacsová M, Uhríková D, Kerti L, Frecer V. Identification and evaluation of antiviral activity of novel compounds targeting SARS-CoV-2 virus by enzymatic and antiviral assays, and computational analysis. J Enzyme Inhib Med Chem 2024; 39:2301772. [PMID: 38221792 PMCID: PMC10791089 DOI: 10.1080/14756366.2024.2301772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 12/18/2023] [Indexed: 01/16/2024] Open
Abstract
The viral genome of the SARS-CoV-2 coronavirus, the aetiologic agent of COVID-19, encodes structural, non-structural, and accessory proteins. Most of these components undergo rapid genetic variations, though to a lesser extent the essential viral proteases. Consequently, the protease and/or deubiquitinase activities of the cysteine proteases Mpro and PLpro became attractive targets for the design of antiviral agents. Here, we develop and evaluate new bis(benzylidene)cyclohexanones (BBC) and identify potential antiviral compounds. Three compounds were found to be effective in reducing the SARS-CoV-2 load, with EC50 values in the low micromolar concentration range. However, these compounds also exhibited inhibitory activity IC50 against PLpro at approximately 10-fold higher micromolar concentrations. Although originally developed as PLpro inhibitors, the comparison between IC50 and EC50 of BBC indicates that the mechanism of their in vitro antiviral activity is probably not directly related to inhibition of viral cysteine proteases. In conclusion, our study has identified new potential noncytotoxic antiviral compounds suitable for in vivo testing and further improvement.
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Affiliation(s)
- Ivana Nemčovičová
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Katarína Lopušná
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Iveta Štibrániová
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Fabio Benedetti
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Federico Berti
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Fulvia Felluga
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Sara Drioli
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Mattia Vidali
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Jaroslav Katrlík
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lucia Pažitná
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Alena Holazová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jana Blahutová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Simona Lenhartová
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Monika Sláviková
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Boris Klempa
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miroslav Ondrejovič
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
- ICARST n.o, Bratislava, Slovakia
| | - Daniela Chmelová
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Barbora Legerská
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Stanislav Miertuš
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
- ICARST n.o, Bratislava, Slovakia
| | - Mária Klacsová
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
| | - Daniela Uhríková
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
| | - Lukáš Kerti
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
| | - Vladimír Frecer
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
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de Sousa DS, da Silva AP, Chiari LPA, de Angelo RM, de Sousa AG, Honorio KM, da Silva ABF. Predicting biological activity and design of 5-HT 6 antagonists through assessment of ANN-QSAR models in the context of Alzheimer's disease. J Mol Model 2024; 30:350. [PMID: 39325274 DOI: 10.1007/s00894-024-06134-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 09/03/2024] [Indexed: 09/27/2024]
Abstract
CONTEXT Alzheimer's disease (AD) is the leading cause of dementia around the world, totaling about 55 million cases, with an estimated growth to 74.7 million cases in 2030, which makes its treatment widely desired. Several studies and strategies are being developed considering the main theories regarding its origin since it is not yet fully understood. Among these strategies, the 5-HT6 receptor antagonism emerges as an auspicious and viable symptomatic treatment approach for AD. The 5-HT6 receptor belongs to the G protein-coupled receptor (GPCR) family and is closely implicated in memory loss processes. As a serotonin receptor, it plays an important role in cognitive function. Consequently, targeting this receptor presents a compelling therapeutic opportunity. By employing antagonists to block its activity, the 5-HT6 receptor's functions can be effectively modulated, leading to potential improvements in cognition and memory. METHODS Addressing this challenge, our research explored a promising avenue in drug discovery for AD, employing Artificial Neural Networks-Quantitative Structure-Activity Relationship (ANN-QSAR) models. These models have demonstrated great potential in predicting the biological activity of compounds based on their molecular structures. By harnessing the capabilities of machine learning and computational chemistry, we aimed to create a systematic approach for analyzing and forecasting the activity of potential drug candidates, thus streamlining the drug discovery process. We assembled a diverse set of compounds targeting this receptor and utilized density functional theory (DFT) calculations to extract essential molecular descriptors, effectively representing the structural features of the compounds. Subsequently, these molecular descriptors served as input for training the ANN-QSAR models alongside corresponding biological activity data, enabling us to predict the potential efficacy of novel compounds as 5-hydroxytryptamine receptor 6 (5-HT6) antagonists. Through extensive analysis and validation of ANN-QSAR models, we identified eight new promising compounds with therapeutic potential against AD.
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Affiliation(s)
- Daniel S de Sousa
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, 13560-970, São Paulo, Brazil.
| | - Aldineia P da Silva
- School of Arts, Sciences and Humanities, University of São Paulo, São Paulo, 03828-000, Brazil.
| | - Laise P A Chiari
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, 13560-970, São Paulo, Brazil
| | - Rafaela M de Angelo
- Center for Natural Sciences and Humanities, Federal University of ABC, Santo André, 09210-580, São Paulo, Brazil
| | - Alexsandro G de Sousa
- Department of Exact and Natural Sciences, Southwest Bahia State University, Itapetinga, 45700-000, Bahia, Brazil
| | - Kathia M Honorio
- School of Arts, Sciences and Humanities, University of São Paulo, São Paulo, 03828-000, Brazil
- Center for Natural Sciences and Humanities, Federal University of ABC, Santo André, 09210-580, São Paulo, Brazil
| | - Albérico B F da Silva
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, 13560-970, São Paulo, Brazil.
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Ren H, Zhou N, Ma W, Zhang P, Tu D, Lu CS, Yan H. Dative Bonding Activation Enables Precise Functionalization of the Remote B-H Bond of nido-Carborane Clusters. J Am Chem Soc 2024; 146:26543-26555. [PMID: 39267603 DOI: 10.1021/jacs.4c10728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2024]
Abstract
The innovation of synthetic strategies for selective B-H functionalization is a pivotal objective in the realm of boron cluster chemistry. However, the precise, efficient, and rapid functionalization of a B-H bond of carboranes that is distant from the existing functional groups remains intractable owing to the limited approaches for site-selective control from the established methods. Herein, we report a dative bonding activation strategy for the selective functionalization of a nonclassical remote B-H site of nido-carboranes. By leveraging the electronic effects brought by the exopolyhedral B(9)-dative bond, a cross-nucleophile B-H/S-H coupling protocol of the distal B(5)-H bond has been established. The dative bond not only amplifies the subtle reactivity difference among B-H bonds but also significantly changes the reactive sites, further infusing nido-carboranes with additional structural diversity. This reaction paradigm features mild conditions, rapid conversion, efficient production, broad scope, and excellent group tolerance, thus enabling the applicability to an array of complex bioactive molecules. The efficient and scalable reaction platform is amenable to the modular construction of photofunctional molecules and boron delivery agents for boron neutron capture therapy. This work not only provides an unprecedented solution for the selective diversification of distal B-H sites in nido-carboranes but also holds the potential for expediting the discovery of novel carborane-based functional molecules.
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Affiliation(s)
- Hongyuan Ren
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ningning Zhou
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wenli Ma
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ping Zhang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Deshuang Tu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Chang-Sheng Lu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hong Yan
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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Pang Z, Huang S, Li Y, Zhang Y, Qin R. Molecular Simulation Analysis of Polyurethane Molecular Structure under External Electric Field. Molecules 2024; 29:4329. [PMID: 39339326 PMCID: PMC11433814 DOI: 10.3390/molecules29184329] [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: 07/30/2024] [Revised: 08/23/2024] [Accepted: 09/10/2024] [Indexed: 09/30/2024] Open
Abstract
Polyurethane (PU) materials are extensively utilized in power equipment. This paper introduces a comprehensive evaluation method that combines electromagnetics and computational chemistry based on the Density Functional Theory (DFT) to elucidate the impact of external electric fields on the molecular structure of PU during electrical contact. The study focuses on the microstructural and molecular energy changes in the hard (HS) and soft (SS) segments of PU under the influence of an electric field of uniform intensity. Findings indicate that the total energy of HS molecules decreases markedly as the electric field intensity increases, accompanied by a significant rise in both the dipole moment and polarizability. Conversely, the total energy and polarizability of the SS molecules decrease, while the dipole moment experiences a slight increase. Under the influence of a strong electric field, HS molecules tend to stretch towards the extremities of the main chain, leading to structural instability and the cleavage of hydroxyl O-H bonds. Meanwhile, the carbon chain of the SS molecules twists towards the center under the electric field, with no chemical bond rupture observed. At an electric field intensity of 8.227 V/nm, the HOMO-LUMO gap of the HS molecule narrows sharply, signifying a rapid decline in the molecular structure stability, corroborated by infrared spectroscopy analysis. These findings offer theoretical insights and guidance for the modification of PU materials in power equipment applications.
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Affiliation(s)
- Zhiyi Pang
- Faculty of Intelligent Manufacturing, Nanning University, Nanning 530200, China
| | - Shangshi Huang
- State Key Laboratory of Power System, Department of Electrical Engineering, Tsinghua University, Beijing 100084, China
| | - Yi Li
- School of Electrical Engineering, Guangxi University, Nanning 530004, China
| | - Yiyi Zhang
- School of Electrical Engineering, Guangxi University, Nanning 530004, China
| | - Rui Qin
- Liuzhou Power Supply Bur Guangxi Power Grid Co., Ltd., Liuzhou 545000, China
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Raffah BM, Knani S, Bouzid M, Alruqi AB, Vieira Y, Dotto GL, Lefi N, Ben Lamine A. Morphological, sterical, and localized thermodynamics in the adsorption of CO 2 by activated biocarbon from the white rot fungi Trametes gibbosa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 939:173326. [PMID: 38777051 DOI: 10.1016/j.scitotenv.2024.173326] [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: 03/25/2024] [Revised: 05/09/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
The capture of CO2 by biochar has recently become one of the cornerstones of circular economy models for a sustainable society. In this work, we synthesized an activated biocarbon using Trametes gibbosa (BioACTG) in a one-step synthesis. We investigated CO2 adsorption mechanisms under five different temperatures using a statistical physics approach. The data was better represented by the multilayer model with two distinguished energies, providing more accurate values for the estimated parameters. According to the number of carbon dioxide molecules per site (n) and the densities of the receptor sites (Dzif), the tendency to form a second layer increased as the temperature increased. The adsorption of CO2 on BioACTG was exothermic (the values of Qasat = 15.5 mmol/g at 273 K decrease to 10.5 mmol/g at 353 K), and the temperature influenced CO2 as well as the morphological features of the process. A computational approach was used to investigate the electronic properties of the adsorbate, showing that its lowest unoccupied orbital (LUMO) heavily contributed to the high efficiency of the process which was ruled by pore diffusion mechanisms driven by energetic fluctuations. Other molecules present in CO2-rich mixtures were also investigated, showing that their concentration limited their competitiveness with CO2.
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Affiliation(s)
- Bahaaludin M Raffah
- Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Salah Knani
- Department of Physics, College of Science, Northern Border University, Arar, Saudi Arabia.
| | - Mohamed Bouzid
- CRMN, Centre for Research on Microelectronics and Nanotechnology of Sousse, NANOMISENE, LR16CRMN01, Code Postal 4054, Sousse, Tunisia.
| | - Adel Bandar Alruqi
- Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Yasmin Vieira
- Department of Chemistry, Federal University of Santa Maria, Av. Roraima, 1000 - 9B, 97105-900 Santa Maria, RS, Brazil.
| | - Guilherme Luiz Dotto
- Research Group on Adsorptive and Catalytic Process Engineering (ENGEPAC), Federal University of Santa Maria, Av. Roraima, 1000-8, 97105-900 Santa Maria, RS, Brazil.
| | - Nizar Lefi
- Department of Physics, College of Science, Qassim University, Buraidah 51452, Saudi Arabia.
| | - Abdelmottaleb Ben Lamine
- Laboratory of Quantum and Statistical Physics LR 18 ES 18, Faculty of Sciences of Monastir, Environnement Street, 5019 Monastir, Tunisia
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Zhang WW, Feng Z, You SL, Zheng C. Electrophile-Arene Affinity: An Energy Scale for Evaluating the Thermodynamics of Electrophilic Dearomatization Reactions. J Org Chem 2024; 89:11487-11501. [PMID: 39077910 DOI: 10.1021/acs.joc.4c01168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Rational design and development of organic reactions are lofty goals in synthetic chemistry. Quantitative description of the properties of molecules and reactions by physical organic parameters plays an important role in this regard. In this Article, we report an energy scale, namely, electrophile-arene affinity (EAA), for evaluating the thermodynamics of electrophilic dearomatization reactions, a class of important transformations that can rapidly build up molecular complexity and structural diversity by converting planar aromatic compounds into three-dimensional cyclic molecules. The acquisition of EAA data can be readily achieved by theoretically calculating the enthalpy changes (ΔH) of the hypothetical reactions of various (cationic) electrophiles with aromatic systems (taking the 1-methylnaphthalen-2-olate ion as an example in this study). Linear correlations are found between the calculated ΔH values and established physical organic parameters such as the percentage of buried volume %VBur (steric effect), Hammett's σ or Brown's σ+ (electronic effect), and Mayr's E (reaction kinetics). Careful analysis of the ΔH values leads to the rational design of a dearomative alkynylation reaction using alkynyl hypervalent iodonium reagents as the electrophiles.
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Affiliation(s)
- Wen-Wen Zhang
- Chang-Kung Chuang Institute, East China Normal University, 3663 N. Zhongshan Road, Shanghai 200062, China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
| | - Zuolijun Feng
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
| | - Shu-Li You
- Chang-Kung Chuang Institute, East China Normal University, 3663 N. Zhongshan Road, Shanghai 200062, China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
| | - Chao Zheng
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
- Shanghai-Hong Kong Joint Laboratory of Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
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Lin X, Apostol P, Xu H, Bakuru VR, Guo X, Chen Z, Rambabu D, Pal S, Tie D, Zhang Y, Xie X, Kim SG, Li Y, Li Z, Du M, Yan S, Zhang X, Yuan R, Zheng M, Gauthy F, Finsy V, Zou J, Gohy JF, Dong Q, Vlad A. Design Principles of Quinone Redox Systems for Advanced Sulfide Solid-State Organic Lithium Metal Batteries. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2312908. [PMID: 38843480 DOI: 10.1002/adma.202312908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/18/2024] [Indexed: 06/12/2024]
Abstract
The emergence of solid-state battery technology presents a potential solution to the dissolution challenges of high-capacity small molecule quinone redox systems. Nonetheless, the successful integration of argyrodite-type Li6PS5Cl, the most promising solid-state electrolyte system, and quinone redox systems remains elusive due to their inherent reactivity. Here, a library of quinone derivatives is selected as model electrode materials to ascertain the critical descriptors governing the (electro)chemical compatibility and subsequently the performances of Li6PS5Cl-based solid-state organic lithium metal batteries (LMBs). Compatibility is attained if the lowest unoccupied molecular orbital level of the quinone derivative is sufficiently higher than the highest occupied molecular orbital level of Li6PS5Cl. The energy difference is demonstrated to be critical in ensuring chemical compatibility during composite electrode preparation and enable high-efficiency operation of solid-state organic LMBs. Considering these findings, a general principle is proposed for the selection of quinone derivatives to be integrated with Li6PS5Cl, and two solid-state organic LMBs, based on 2,5-diamino-1,4-benzoquinone and 2,3,5,6-tetraamino-1,4-benzoquinone, are successfully developed and tested for the first time. Validating critical factors for the design of organic battery electrode materials is expected to pave the way for advancing the development of high-efficiency and long cycle life solid-state organic batteries based on sulfides electrolytes.
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Affiliation(s)
- Xiaodong Lin
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
| | - Petru Apostol
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
| | - Hewei Xu
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
| | - Vasudeva Rao Bakuru
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
| | - Xiaolong Guo
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
| | - Zehan Chen
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
| | - Darsi Rambabu
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
| | - Shubhadeep Pal
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
| | - Da Tie
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
| | - Yan Zhang
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
| | - Xinlong Xie
- National Engineering Research Center of Light Alloy Net Forming, State Key Laboratory of Metal Matrix Composite, Center of Hydrogen Science, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Seung-Gi Kim
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
| | - Yi Li
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
| | - Zhao Li
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
- National Engineering Research Center of Light Alloy Net Forming, State Key Laboratory of Metal Matrix Composite, Center of Hydrogen Science, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mengyuan Du
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
| | - Shanshan Yan
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
| | - Xiaozhe Zhang
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
| | - Ruming Yuan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Mingsen Zheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Fernand Gauthy
- Syensqo SA, Battery Materials Platform, Solid State Battery Applicability Laboratory, Rue de la Fusée, 98, Brussels, 1130, Belgium
| | - Vincent Finsy
- Syensqo SA, Battery Materials Platform, Solid State Battery Applicability Laboratory, Rue de la Fusée, 98, Brussels, 1130, Belgium
| | - Jianxin Zou
- National Engineering Research Center of Light Alloy Net Forming, State Key Laboratory of Metal Matrix Composite, Center of Hydrogen Science, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jean-François Gohy
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
| | - Quanfeng Dong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Alexandru Vlad
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, B-1348, Belgium
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Islam MS, Kedziora G, Lee J, Stafford A, Varshney V, Nepal D, Baldwin LA, Roy AK. Efficiency and Mechanism of Catalytic Siloxane Exchange in Vitrimer Polymers: Modeling and Density Functional Theory Investigations. J Phys Chem A 2024; 128:5627-5636. [PMID: 38957945 DOI: 10.1021/acs.jpca.4c01394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Of late, siloxane-containing vitrimers have gained significant interest due to their fast dynamic characteristics over a reasonable temperature range (180-220 °C), making them well-suited for diverse applications. The exchange reaction pathway in the siloxane vitrimers is accountable for the covalent adaptive network, with the reaction's effectiveness being regulated by either organic or organometallic catalysts. However, directly studying the exchange reaction pathway in the bulk phase using experimental approaches is challenging because of the intricate and interconnected structure of these vitrimers. Here, we perform comprehensive density functional theory (DFT) and experimental investigations to discover the detailed catalytic efficacy of siloxane exchange and provide direction for the reaction process using a 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) catalyst. The calculated transition barrier energy and catalytic efficiency of hexamethyldisiloxane and dihydroxy-dimethylsilane exchange derived from the nudged elastic band with transition-state calculations strongly agree with the experimental findings. In addition, Fukui indices, along with partial charges, are employed to evaluate the nucleophilic and electrophilic behaviors of silanol and siloxane molecules. Our analysis revealed that by utilizing the Fukui indices of both the acid and the base, we can make an approximate estimation of the respective kinetics of the SN2 process in the siloxane exchange reaction mechanism. These findings establish a foundation for comprehending a crucial aspect of the exchange mechanism in siloxane vitrimer systems and could aid in the development of novel catalysts.
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Affiliation(s)
- Md Sherajul Islam
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
- Spectral Energies, LLC, Dayton, Ohio 45430, United States
| | - Gary Kedziora
- Inu Teq, LLC, NASA Ames Supercomputing Division, Moffet Field, Mountain View, California 94035, United States
- GDIT, AFRL/RC, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | - Jonghoon Lee
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
- ARCTOS Technology Solutions, Dayton, Ohio 45432, United States
| | - Alex Stafford
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | - Vikas Varshney
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | - Dhriti Nepal
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | - Luke A Baldwin
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | - Ajit K Roy
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
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9
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Hoffmann G, Chermette H, Morell C. Revisiting nucleophilicity: an index for chemical reactivity from a CDFT approach. J Mol Model 2024; 30:232. [PMID: 38937336 DOI: 10.1007/s00894-024-06020-0] [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: 04/12/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024]
Abstract
CONTEXT Understanding and predicting the nucleophilic reactivity are paramount in elucidating organic chemical reactions and designing new synthetic pathways. In this study, we propose a nucleophilicity index within the framework of Conceptual Density Functional Theory (CDFT). Through rigorous theoretical formulations, we introduce an original quantum reactivity descriptor that captures the nucleophilic propensity of molecules based on their electronic structure and chemical environment. Subsequently, this proposed index is applied to a series of nucleophiles (pyrrolidines derivatives), spanning a diverse range of chemical functionalities. Our computational assessments reveal insightful correlations between the predicted nucleophilicity index and experimental observations of nucleophilic behavior. Thereby, they offer a promising avenue for advancing the understanding of organic reactivity and guiding synthetic efforts. METHODS Experimentally, Mayr's experimental parameters accounting for nucleophilicity were selected for the pyrrolidines. This study used DFT calculations at the B3LYP/Aug-cc-pVTZ level of theory using the Gaussian 16 program. Geometry optimization was thus performed, and the methodology employed for the computation of quantum reactivity descriptor is presented. Solvent effect was also taken into account using IEFPCM, and empirical dispersion correction (GD3) was employed.
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Affiliation(s)
- Guillaume Hoffmann
- Universite Claude Bernard Lyon1, ISA, UMR5280, CNRS, 5 rue de la Doua, Villeurbanne, 69100, France.
| | - Henry Chermette
- Universite Claude Bernard Lyon1, ISA, UMR5280, CNRS, 5 rue de la Doua, Villeurbanne, 69100, France
| | - Christophe Morell
- Universite Claude Bernard Lyon1, ISA, UMR5280, CNRS, 5 rue de la Doua, Villeurbanne, 69100, France
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10
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McPherson PAC, McKenna N, Johnston BM. Physicochemical Properties of 4-(4-Hydroxyphenyl)-butan-2-one ("Raspberry Ketone") Evaluated Using a Computational Chemistry Approach. ACS OMEGA 2024; 9:23963-23970. [PMID: 38854552 PMCID: PMC11154730 DOI: 10.1021/acsomega.4c02293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/02/2024] [Accepted: 05/10/2024] [Indexed: 06/11/2024]
Abstract
Raspberry ketone (RK) is a product of the phenylpropanoid pathway in a variety of plants and is the second most expensive natural flavouring in the world. It is also widely used as a nutritional supplement due to its reported ability to promote lipolysis and fat oxidation in vivo. We have evaluated the thermodynamics of RK using the correlation consistent ccCA-CBS-2 approach which afforded calculation of (inter alia) the enthalpy of formation. To obtain pK a, log D, electrode potential, solubility, and reactivity indices, we used TPSS/def2-TZVP geometries followed by single-point energies obtained at the M06-2X/def2-TZVPP level of theory. We obtained Δf H o = -299.4 ± 0.17 kJ·mol-1; the pK a and logD were found to be 9.95 and 1.84, respectively, consistent with chemometric predictions. Using the enthalpy of fusion obtained from theory, we evaluated the aqueous solubility of RK to be in the region of 2.5 mg·mL-1 which is in agreement with limited literature reports. In terms of reactivity, we obtained a formal electrode potential of 1.29 V (vs SHE) at pH 7.4 and 298.15 K. The HOMO-LUMO energy separation in an aqueous environment was found to be ca. 7.8 eV, suggesting moderate chemical reactivity. Analysis of the frontier molecular orbitals using conceptual density functional theory supported this and revealed a reactivity pattern consistent with the metabolite profile obtained in mammals, namely, a propensity for nucleophilic attack at the carbonyl carbon and electrophilic addition of the benzene ring.
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Affiliation(s)
- Peter A. C. McPherson
- School
of Pharmacy & Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, U.K.
| | - Niamh McKenna
- School
of Pharmacy, University of North Carolina, Chapel Hill 27599, North Carolina, United
States
| | - Ben M. Johnston
- School
of Science, Engineering & Construction, Belfast Metropolitan College, Belfast BT3 9DT, U.K.
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11
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Zhang P, Yu ZX. Dynamically or Kinetically Controlled? Computational Study of the Mechanisms of Electrophilic Aminoalkenylation of Heteroaromatics with Keteniminium Ions. J Org Chem 2024; 89:4326-4335. [PMID: 38506441 DOI: 10.1021/acs.joc.3c02379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Quantum chemical calculations and molecular dynamics simulations were applied to study the electrophilic aminoalkenylation of heteroaromatics with keniminium ions. Post-transition state bifurcation (PTSB) was found in the electrophilic addition step for the aminoalkenylation of pyrroles and indoles, and the selectivity for these reactions was dynamically controlled. However, the aminoalkenylation of furan was kinetically controlled because no apparent PTSB was found in the electrophilic addition step. The substituents on the keteniminium ions can also affect the dynamic results for the aminoalkenylations to pyrroles: the C2-aminoalkenylated product is much more favored over the C3-aminoalkenylated product for keteniminium ions with electron-donating substituents, while the product ratio (C2 product/C3 product) decreased when stronger electron-withdrawing substituents were applied.
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Affiliation(s)
- Pan Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, China
| | - Zhi-Xiang Yu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, China
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12
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Tian H, Lee W, Li Y, Dweck MJ, Mendoza A, Harran PG, Houk KN. Origin of Octafluorocyclopentene Polyelectrophilicity. J Am Chem Soc 2024; 146:5375-5382. [PMID: 38354320 DOI: 10.1021/jacs.3c12690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Octafluorocyclopentene (OFCP) has found utility as a polyelectrophile in substitution cascades that form complex macrocyclic compounds. The Harran group synthesis of macrocyclic polypeptides depends on OFCP as a linker, combining with four different nucleophilic units of a polypeptide. We report a computational investigation of the origins of OFCP reactivity and a rationale for controlled mono-, di-, tri-, and tetrasubstitution of fluoride ions by heteroatomic nucleophiles. The roles of inductive, negative hyperconjugative, and resonance electron-donation by fluoride substituents are explored for the reaction of OFCP, less-fluorinated analogues, and common electrophilic alkenes with several different nucleophiles.
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Affiliation(s)
- Haowen Tian
- College of Chemistry, Nankai University, 94 Weijin Road, Tianjin 300071, China
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - William Lee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Yuli Li
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Morris J Dweck
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Angel Mendoza
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Patrick G Harran
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
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13
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Gharbi C, Louis H, Essghaier B, Ubah CB, Benjamin I, Kaminsky W, Nasr CB, Khedhiri L. Single crystal X-ray diffraction analysis, spectroscopic measurement, quantum chemical studies, antimicrobial potency and molecular docking of a new [Co(NCS)4]2(C6H17N3)2·4H2O coordination compound based on piperazine-thiocyanate as co-ligand. J Mol Struct 2024; 1298:136997. [DOI: 10.1016/j.molstruc.2023.136997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
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14
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Savino DF, Silva JV, da Silva Santos S, Lourenço FR, Giarolla J. How do physicochemical properties contribute to inhibitory activity of promising peptides against Zika Virus NS3 protease? J Mol Model 2024; 30:54. [PMID: 38289526 DOI: 10.1007/s00894-024-05843-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024]
Abstract
CONTEXT AND RESULTS Flavivirus diseases' cycles, especially Dengue and Yellow Fever, can be observed all over Brazilian territory, representing a great health concern. Additionally, there are no drugs available in therapy. In this scenario, in silico methodologies were applied to obtain physicochemical properties, as well as to better understand the ligand-biological target interaction mode of 20 previously reported NS2B/NS3 protease inhibitors of Dengue virus. Since catalytic site of flavivirus hold similarities, such as the same catalytic triad (His51, Asp75 e Ser135), the ability of this series of molecules to fit in Zika NS3 domains can be achieved. We performed an exploratory data analysis, using statistical methodologies, such as PCA (Principal Component Analysis) and HCA (Hierarchical Component Analysis), to assist the comprehension of how physicochemical properties impact the interaction observed by the docking studies, as well as to build a correlation between the respective ranked characteristics. Based on these previous studies, peptides were selected for the dynamics simulations, which were useful to better understand the ligand-protein interactions. Information relating to, for instance, energy, ΔG, average number of hydrogen bonds and distance from Ser135 (one of the main amino acids in the catalytic pocket) were discussed. In this sense, peptides 15 (considering ΔG value and Hbond number), 7 (ΔG and energy) and 1, 6, 7 and 15 (the proximity to Ser135 throughout the dynamics simulation) were highlighted as promising. Those interesting results could contribute to future studies regarding Zika virus drug design, since this infection represents a great concern in neglected populations. METHODS The models were constructed in the ChemDraw software. The ligand parametrization was performed in the CHEM3D 17.0, UCSF Chimera. Docking simulations were carried out in the GOLD software, after the redocking validation. We used ASP as the function score. Additionally, for dynamics simulations we applied GROMACS software, exploring, mainly, free binding energy calculations. Exploratory analysis was carried out in Minitab 17.3.1 statistical software. Prior to the exploratory analysis, data of quantum chemical properties of the peptides were collected in Microsoft Excel spreadsheet and organized to obtain Hierarchical Cluster Analysis (HCA) and Principal Component Analysis (PCA).
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Affiliation(s)
- Débora Feliciano Savino
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil
| | - João Vitor Silva
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil
| | - Soraya da Silva Santos
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil
| | - Felipe Rebello Lourenço
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil
| | - Jeanine Giarolla
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil.
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15
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Eckhoff M, Diedrich JV, Mücke M, Proppe J. Quantitative Structure-Reactivity Relationships for Synthesis Planning: The Benzhydrylium Case. J Phys Chem A 2024; 128:343-354. [PMID: 38113457 PMCID: PMC10788916 DOI: 10.1021/acs.jpca.3c07289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023]
Abstract
Selective and feasible reactions are among the top targets in synthesis planning. Mayr's approach to quantifying chemical reactivity has greatly facilitated the planning process, but reactivity parameters for new compounds require time-consuming experiments. In the past decade, data-driven modeling has been gaining momentum in the field, as it shows promise in terms of efficient reactivity prediction. However, state-of-the-art models use quantum chemical data as input, which prevent access to real-time planning in organic synthesis. Here, we present a novel data-driven workflow for predicting reactivity parameters of molecules that takes only structural information as input, enabling de facto real-time reactivity predictions. We use the well-understood chemical space of benzhydrylium ions as an example to demonstrate the functionality of our approach and the performance of the resulting quantitative structure-reactivity relationships (QSRRs). Our results suggest that it is straightforward to build low-cost QSRR models that are accurate, interpretable, and transferable to unexplored systems within a given scope of application. Moreover, our QSRR approach suggests that Hammett σ parameters are only approximately additive.
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Affiliation(s)
- Maike Eckhoff
- Institute
of Physical and Theoretical Chemistry, TU
Braunschweig, Braunschweig 38106, Germany
| | - Johannes V. Diedrich
- Institute
of Physical and Theoretical Chemistry, TU
Braunschweig, Braunschweig 38106, Germany
- Institute
of Physical Chemistry, University of Göttingen, Göttingen 37077, Germany
| | - Maike Mücke
- Institute
of Physical and Theoretical Chemistry, TU
Braunschweig, Braunschweig 38106, Germany
- Institute
of Physical Chemistry, University of Göttingen, Göttingen 37077, Germany
| | - Jonny Proppe
- Institute
of Physical and Theoretical Chemistry, TU
Braunschweig, Braunschweig 38106, Germany
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16
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Iftikhar R, Irshad R, Zahid WA, Akram W, Shehzad RA, Abdelmohsen SAM, Alanazi MM, Shahzad N, Iqbal J. Designing of fluorine-substituted benzodithiophene-based small molecules with efficient photovoltaic parameters. J Mol Graph Model 2023; 125:108588. [PMID: 37557026 DOI: 10.1016/j.jmgm.2023.108588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/17/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023]
Abstract
In this study, four hole-transporting materials (JY-M1, JY-M2, JY-M3, and JY-M4) are designed by modifying benzothiadiazole-based core with diphenylamine-based carbazole via acceptors through thiophene linkers. The designed molecules exhibited deeper HOMO energy with smaller energy gaps than the reference JY molecule which enhance their hole mobility. The absorption spectra of the JY-M1, JY-M2, JY-M3, and JY-M4 molecules are located at 380 nm to 407 nm in the gaseous phase and 397 nm to 433 nm in the solvent phase, which is red-shifted and higher than the reference molecule, demonstrating that designed molecules possess improved light absorption properties and enhanced effective hole transfer. The dipole moments of the designed molecules (14.74 D to 26.12 D) indicate a greater ability for charge separation, solubility and will be beneficial to produce multilayer films. Moreover, the results of hole reorganization energy (0.38198 eV to 0.45304 eV) and charge transfer integral (0.14315 eV to 0.14665 eV) of designing molecules show improved hole mobility and lower recombination losses compared to the JY molecule. Overall, we suggested that the structural modifications in the designed molecules contributed to their enhanced efficiency in converting light energy into electrical energy and have the potential for utilization in solar devices, paving the way for future advancements in the field of photovoltaics.
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Affiliation(s)
- Rabia Iftikhar
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Rabiya Irshad
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Waqar Ali Zahid
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Waqas Akram
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Rao Aqil Shehzad
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Shaimaa A M Abdelmohsen
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Meznah M Alanazi
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Nabeel Shahzad
- Department of Chemistry, Government College University, Faisalabad, Pakistan
| | - Javed Iqbal
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan.
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17
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Li W, Han J, Zhang X, Chen G, Yang Y. Contributions of Pharmaceuticals to DBP Formation and Developmental Toxicity in Chlorination of NOM-containing Source Water. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:18775-18787. [PMID: 37505917 DOI: 10.1021/acs.est.3c00742] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Pharmaceuticals have been considered a priority group of emerging micropollutants in source waters in recent years, while their role in the formation and toxicity of disinfection byproducts (DBPs) during chlorine disinfection remains largely unclear. In this study, the contributions of natural organic matter (NOM) and pharmaceuticals (a mixture of ten representative pharmaceuticals) to the overall DBP formation and toxicity during drinking water chlorination were investigated. By innovatively "normalizing" chlorine exposure and constructing a kinetic model, we were able to differentiate and evaluate the contributions of NOM and pharmaceuticals to the total organic halogen (TOX) formation for source waters that contained different levels of pharmaceuticals. It was found that at a chlorine contact time of 1.0 h, NOM (2 mg/L as C) and pharmaceuticals (total 0.0062-0.31 mg/L as C) contributed 79.8-99.5% and 0.5-20.2%, respectively, of TOX. The toxicity test results showed that the chlorination remarkably increased the toxicity of the pharmaceutical mixture by converting the parent compounds into more toxic pharmaceutical-derived DBPs, and these DBPs might contribute significantly to the overall developmental toxicity of chlorinated waters. This study highlights the non-negligible role of pharmaceuticals in the formation and toxicity of overall DBPs in chlorinated drinking water.
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Affiliation(s)
- Wanxin Li
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR 00000, China
| | - Jiarui Han
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR 00000, China
| | - Xiangru Zhang
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR 00000, China
| | - Guanghao Chen
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution (Hong Kong Branch), and Water Technology Center, The Hong Kong University of Science and Technology, Hong Kong SAR 00000, China
| | - Yun Yang
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR 00000, China
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18
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Tananta VL, Costa EV, Mary YS, Mary YS, S Al-Otaibi J, Costa RA. DFT, ADME studies and evaluation of the binding with HSA and MAO-B inhibitory potential of protoberberine alkaloids from Guatteria friesiana: theoretical insights of promising candidates for the treatment of Parkinson's disease. J Mol Model 2023; 29:353. [PMID: 37907772 DOI: 10.1007/s00894-023-05756-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/13/2023] [Indexed: 11/02/2023]
Abstract
CONTEXT Parkinson's disease is a chronic neurodegenerative condition that has no cure, characterized by the progressive degeneration of specific brain cells responsible for producing dopamine, a crucial neurotransmitter for controlling movement and muscle coordination. Parkinson's disease is estimated to affect around 1% of the world's population over the age of 60, but it can be diagnosed at younger ages. One of the treatment strategies for Parkinson's disease involves the use of drugs that aim to increase dopamine levels or simulate the action of dopamine in the brain. A class of commonly prescribed drugs are the so-called monoamine oxidase B (MAO-B) inhibitors due to the fact that this enzyme is responsible for metabolizing dopamine, thus reducing its levels in the brain. Studies have shown that berberine-derived alkaloids have the ability to selectively inhibit MAO-B activity, resulting in increased dopamine availability in the brain. In this context, berberine derivatives 13-hydroxy-discretinine and 7,8-dihydro-8-hydroxypalmatine, isolated from Guatteria friesiana, were evaluated via density functional theory followed by ADME studies, docking and molecular dynamic simulations with MAO-B, aiming to evaluate their anti-Parkinson potential, which have not been reported yet. Docking simulations with HSA were carried out aiming to evaluate the transport of these molecules through the circulatory system. METHODS The 3D structures of the berberine-derived alkaloids were modeled via the DFT approach at B3LYP-D3(BJ)/6-311 + + G(2df, 2pd) theory level using Gaussian 09 software. Solvation free energies were determined through Truhlar's solvation model. MEP and ALIE maps were generated with Multiwfn software. Autodock Vina software was used for molecular docking simulations and analysis of the interactions in the binding sites. The 3D structure of MAO-B was obtained from the Protein Data Bank website under PDB code 2V5Z. For the interaction of studied alkaloids with human serum albumin (HSA) drug sites, 3D structures with PDB codes 2BXD, 2BXG, and 4L9K were used. Molecular dynamics simulations were carried out using GROMACS 2019.4 software, with the GROMOS 53A6 force field at 100 ns simulation time. The estimation of the ligand's binding free energies was obtained via molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method.
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Affiliation(s)
- Victor L Tananta
- Department of Chemistry, Federal University of Amazonas (DQ-UFAM), Manaus, AM, 69080-900, Brazil
| | - Emmanoel V Costa
- Department of Chemistry, Federal University of Amazonas (DQ-UFAM), Manaus, AM, 69080-900, Brazil
| | | | | | - Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 8442811671, Riyadh, Saudi Arabia
| | - Renyer A Costa
- Department of Chemistry, Federal University of Amazonas (DQ-UFAM), Manaus, AM, 69080-900, Brazil.
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19
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Alrokayan S, Hussain T, Alamery S, Mohammed AA, Mahmood A, Ejaz SA, Langer P, Iqbal J. [1, 8]-Naphthyridine derivatives as dual inhibitor of alkaline phosphatase and carbonic anhydrase. BMC Chem 2023; 17:142. [PMID: 37880684 PMCID: PMC10599030 DOI: 10.1186/s13065-023-01052-8] [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: 06/05/2023] [Accepted: 10/02/2023] [Indexed: 10/27/2023] Open
Abstract
[1,8]-Naphthyridine derivatives have been reported to possess important biological activities and may serve as attractive pharmacophores in the drug discovery process. [1,8]-Naphthyridine derivatives (1a-1l) were evaluated for inhibitory potential for isozymes of carbonic anhydrase (CA) and alkaline phosphatase (ALP). CAs have been reported to carry out reversible hydration of CO2 into HCO3-, secretion of electrolytes, acid-base regulation, bone resorption, calcification, and biosynthetic reactions. Whereas ALPs hydrolyze monophosphate esters with the release of inorganic phosphate and play an important role in bone mineralization. Both enzymes have been found to be over-expressed and raised functional activities in patients suffering from rheumatoid arthritis. The discovery of dual inhibitors of these enzymes may provide a synergistic effect to cure bone disorders such as rheumatoid arthritis and ankylosing spondylitis. Among the test compounds, the most potent inhibitors for CA-II, CA-IX, and CA-XII were 1e, 1g, and 1a with IC50 values of 0.44 ± 0.19, 0.11 ± 0.03 and 0.32 ± 0.07 µM, respectively. [1,8]-Naphthyridine derivatives (1a-1l) were approximately 4 folds more potent than standard CA inhibitor acetazolamide. While in the case of ALPs, the most potent compounds for b-TNAP and c-IAP were 1b and 1e with IC50 values of 0.122 ± 0.06 and 0.107 ± 0.02 µM, respectively. Thus, synthesized derivatives proved to be 100 to 800 times more potent as compared to standard inhibitors of b-TNAP and c-IAP (Levamisole and L-phenyl alanine, respectively). In addition, selectivity and dual inhibition of [1,8]-Naphthyridine derivatives confer precedence over known inhibitors. Molecular docking and molecular simulation studies were also conducted in the present studies to define the type of interactions between potential inhibitors and enzyme active sites.
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Affiliation(s)
- Salman Alrokayan
- Research Chair for Biomedical Application of Nanomaterials, Biochemistry Department, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
- Biochemistry Department, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Tajamul Hussain
- Research Chair for Biomedical Application of Nanomaterials, Biochemistry Department, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
- Centre of Excellence in Biotechnology Research, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Salman Alamery
- Biochemistry Department, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Arif Ahmed Mohammed
- Biochemistry Department, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Abid Mahmood
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Syeda Abida Ejaz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacv, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Peter Langer
- Institut Für Chemie, Universität Rostock, A.-Einstein-Str. 3a, 18059, Rostock, Germany
| | - Jamshed Iqbal
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan.
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20
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Hadi H, Louis H, Gber TE, Ogungbemiro FO. Molecular modeling of the structural, electronic, excited state dynamic, and the photovoltaic properties of the oligomers of n-corannulene (n = 1-4). Heliyon 2023; 9:e20706. [PMID: 37860554 PMCID: PMC10582301 DOI: 10.1016/j.heliyon.2023.e20706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/01/2023] [Accepted: 10/04/2023] [Indexed: 10/21/2023] Open
Abstract
Despite the fact that n-corannulene oligomers (n = 1-4) have a variety of electronic and optical properties, including the ability to be tuned and the potential to be used as light-harvesting materials, there has not been a computational assessment of their structural, electronic, and optical properties. Herein, a computational evaluation of the concerned materials regarding their potent use in solar cell technology has been conducted via DFT/CAM-B3LYP and M062X/6-311+G level of theory. It was observed that the calculated 1st frequency of the n-Corannulene (n = 1-4) were 144.15, 106.36, 48.96 and 42.21 respectively. Notably, the computed cohesive energy value increased as the number of Corannulene units increases while the electronic characteristics revealed that the chemical activity of the structures increased as the number of oligomers rose. Both calculation techniques demonstrate that the number of n-Corannulene oligomers increases the HOMO energy while decreasing the LUMO energy based on the external electric field (EF) effect. The findings demonstrated that as EF intensity increases, the energy gap (Eg/eV = |EHOMO-ELUMO|) of these molecular systems decreases which can be attributed to a decrease in the electron transfer potential barrier. The 4-Corannulene systems showed the highest wave length of adsorption for the investigated compound at 546.18 nm, with the highest oscillator strength of 0.2708 and the lowest transition energy of 2.2700 eV, arising from S0-S1 (H-L) and the highest major percentage contribution of 93.34 % in comparison to the investigated compounds. We are hopeful that this research will help experimental researchers understand the potential of n-Corannulene, specifically 4-corannulene, as powerful material for a variety of applications ranging from solar cell, photovoltaic properties and many others.
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Affiliation(s)
- Hamid Hadi
- Department of Chemistry, Physical Chemistry group, Lorestan University, Khorramabad, Iran
| | - Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India
| | - Terkumbur E. Gber
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
| | - Festus O. Ogungbemiro
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
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21
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Ren P, Li H, Nie T, Jian X, Yu C, Li J, Su H, Zhang X, Li S, Yang X, Peng C, Yin Y, Zhang L, Xu Y, Liu H, Bai F. Discovery and Mechanism Study of SARS-CoV-2 3C-like Protease Inhibitors with a New Reactive Group. J Med Chem 2023; 66:12266-12283. [PMID: 37594952 DOI: 10.1021/acs.jmedchem.3c00818] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
3CLpro is an attractive target for the treatment of COVID-19. Using the scaffold hopping strategy, we identified a potent inhibitor of 3CLpro (3a) that contains a thiocyanate moiety as a novel warhead that can form a covalent bond with Cys145 of the protein. Tandem mass spectrometry (MS/MS) and X-ray crystallography confirmed the mechanism of covalent formation between 3a and the protein in its catalytic pocket. Moreover, several analogues of compound 3a were designed and synthesized. Among them, compound 3h shows the best inhibition of 3CLpro with an IC50 of 0.322 μM and a kinact/Ki value of 1669.34 M-1 s-1, and it exhibits good target selectivity for 3CLpro against host proteases. Compound 3c inhibits SARS-CoV-2 in Vero E6 cells (EC50 = 2.499 μM) with low cytotoxicity (CC50 > 200 μM). These studies provide ideas and insights to explore and develop new 3CLpro inhibitors in the future.
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Affiliation(s)
- Pengxuan Ren
- School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Hui Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tianqing Nie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiaoqin Jian
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Changyue Yu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jian Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xianglei Zhang
- School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Shiwei Li
- School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Xin Yang
- School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Yue Yin
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Leike Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Hong Liu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Fang Bai
- School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
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22
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Gupta SM, Behera A, Jain NK, Tripathi A, Rishipathak D, Singh S, Ahemad N, Erol M, Kumar D. Development of substituted benzylidene derivatives as novel dual cholinesterase inhibitors for Alzheimer's treatment. RSC Adv 2023; 13:26344-26356. [PMID: 37671344 PMCID: PMC10476022 DOI: 10.1039/d3ra03224h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/26/2023] [Indexed: 09/07/2023] Open
Abstract
Leading pathological markers of Alzheimer's disease (AD) include Acetylcholinesterase (AChE), Butyrylcholinesterase (BuChE), Amyloid beta (Aβ) and reactive oxygen species (ROS). Indole derivatives were identified and optimized to improve the potency against AChE, BuChE, Aβ and ROS. The lead molecule IND-30 was found to be selective for AChE (selectivity ratio: 22.92) in comparison to BuChE and showed maximum inhibition potential for human AChE (IC50: 4.16 ± 0.063 μM). IND-30 was found to be safe on the SH-SY5Y cell line until the dose of 30 mM. Further, molecule IND-30 was evaluated for its ability to inhibit AChE-induced Aβ aggregation at 0.5, 10 and 20 μM doses. Approximately, 50% of AChE-induced Aβ aggregation was inhibited by IND-30. Thus, IND-30 was found to be multitargeting for AD.
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Affiliation(s)
- Shraddha Manish Gupta
- Faculty of Pharmacy, Oriental University Indore 453555 Madhya Pradesh India
- Department of Pharmaceutical Sciences, School of Health Sciences and Technology, University of Petroleum and Energy Studies (UPES) Dehradun 48007 India
| | - Ashok Behera
- Faculty of Pharmacy, School of Pharmacy and Population Health Informatics, DIT University Makkawala Dehradun Uttarakhand India
| | - Neetesh K Jain
- Faculty of Pharmacy, Oriental University Indore 453555 Madhya Pradesh India
| | - Avanish Tripathi
- Institute of Pharmaceutical Research, GLA University Mathura 281 406 U.P. India
| | - Dinesh Rishipathak
- Department of Pharmaceutical Chemistry, MET's Institute of Pharmacy Nasik Maharashtra India
| | - Siddharth Singh
- Department of Pharmaceutical Sciences, School of Health Sciences and Technology, University of Petroleum and Energy Studies (UPES) Dehradun 48007 India
| | - Nafees Ahemad
- School of Pharmacy, Monash University Jalan Lagoon Selatan, Bandar Sunway Petaling Jaya 47500 Selangor DE Malaysia
| | - Meryem Erol
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University Kayseri Turkey
| | - Devendra Kumar
- School of Pharmacy & Technology Management, SVKM's NMIMS (Deemed-to-be) University Mukesh Patel Technology Park Shirpur 425405 India +91 542 368428 +91 9455714362
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23
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Guan T, Bian C, Ma Z. In vitro and in silico perspectives on the activation of antioxidant responsive element by citrus-derived flavonoids. Front Nutr 2023; 10:1257172. [PMID: 37674886 PMCID: PMC10478098 DOI: 10.3389/fnut.2023.1257172] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023] Open
Abstract
Introduction Oxidative stress plays an essential role in the pathogenesis of chronic diseases. Disrupting the Keap1-Nrf2 pathway by binding Keap1 is identified as a potential strategy to prevent oxidative stress-related chronic diseases. Therefore, of special interest is the utilization of dietary antioxidations from citrus, including narirutin, naringenin, hesperetin, hesperidin, naringin, neohesperidin dihydrochalcone, neohesperidin, and nobiletin, has been exploited as a prospective way to treat or prevent several human pathologies as Keap1-Nrf2 inhibitors for modulation of antioxidant properties. Methods To probe into the structural foundation of the molecular identification of citrus-derived antioxidations, we calculated the antioxidant responsive element activation ability of citrus-derived flavonoids after binding with Keap1. Also, the quantum chemistry properties and binding mode were performed theoretically with frontier molecular orbitals, molecular electrostatic potential analysis, molecular docking, and absorption, distribution, metabolism, excretion (ADME) calculation. Results and discussion Experimental findings combining computational assays revealed that the tested citrus-derived flavonoids can be grouped into strong agonists and weak agonists. The citrus-derived antioxidations were well housed in the bound zone of Keap1 via stable hydrogen bonding and hydrophobic interaction. Eventually, three of eight antioxidations were identified after ADME and physicochemical evaluations. The citrus-derived flavonoids were identified as potential dietary antioxidants of the Keap1-Nrf2 interaction, and can be used to improve oxidative stress-related chronic diseases.
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Affiliation(s)
- Tianzhu Guan
- School of Food Science and Engineering, Yangzhou University, Yangzhou, China
| | - Canfeng Bian
- School of Food Science and Engineering, Yangzhou University, Yangzhou, China
| | - Zheng Ma
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan, China
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24
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Wan X, Zhang Z, Wang A, Su J, Zhou W, Robertson J, Peng Y, Zheng Y, Guo Y. Deep-learning-assisted theoretical insights into the compatibility of environment friendly insulation medium with metal surface of power equipment. J Colloid Interface Sci 2023; 648:317-326. [PMID: 37301156 DOI: 10.1016/j.jcis.2023.05.188] [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: 03/22/2023] [Revised: 05/05/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Exploring a new generation of eco-friendly gas insulation medium to replace greenhouse gas sulphur hexafluoride (SF6) in power industry is significant for reducing the greenhouse effect and building a low-carbon environment. The gas-solid compatibility of insulation gas with various electrical equipment is also of significance before practical applications. Herein, take a promising SF6 replacing gas trifluoromethyl sulfonyl fluoride (CF3SO2F) for example, one strategy to theoretically evaluate the gas-solid compatibility between insulation gas and the typical solid surfaces of common equipment was raised. Firstly, the active site where the CF3SO2F molecule is prone to interact with other compounds was identified. Secondly, the interaction strength and charge transfer between CF3SO2F and four typical solid surfaces of equipment were studied by first-principles calculations and further analysis was conducted, with SF6 as the control group. Then, the dynamic compatibility of CF3SO2F with solid surfaces was investigated by large-scale molecular dynamics simulations with the aid of deep learning. The results indicate that CF3SO2F has excellent compatibility similar to SF6, especially in the equipment whose contact surface is Cu, CuO, and Al2O3 due to their similar outermost orbital electronic structures. Besides, the dynamic compatibility with pure Al surfaces is poor. Finally, preliminary experimental verifications indicate the validity of the strategy.
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Affiliation(s)
- Xuhao Wan
- School of Electrical Engineering and Automation, Wuhan University, Wuhan, Hubei 430072, China; Department of Engineering, Cambridge University, Cambridge CB2 1PZ, United Kingdom
| | - Zhaofu Zhang
- The Institute of Technological Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Anyang Wang
- School of Electrical Engineering and Automation, Wuhan University, Wuhan, Hubei 430072, China
| | - Jinhao Su
- School of Electrical Engineering and Automation, Wuhan University, Wuhan, Hubei 430072, China
| | - Wenjun Zhou
- School of Electrical Engineering and Automation, Wuhan University, Wuhan, Hubei 430072, China
| | - John Robertson
- Department of Engineering, Cambridge University, Cambridge CB2 1PZ, United Kingdom
| | - Yuan Peng
- China Electronics Technology Group Taiji Corporation, Beijing 100846, China
| | - Yu Zheng
- School of Electrical Engineering and Automation, Wuhan University, Wuhan, Hubei 430072, China.
| | - Yuzheng Guo
- School of Electrical Engineering and Automation, Wuhan University, Wuhan, Hubei 430072, China.
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25
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Soro DM, Roque JB, Rackl JW, Park B, Payer S, Shi Y, Ruble JC, Kaledin AL, Baik MH, Musaev DG, Sarpong R. Photo- and Metal-Mediated Deconstructive Approaches to Cyclic Aliphatic Amine Diversification. J Am Chem Soc 2023; 145:11245-11257. [PMID: 37171220 DOI: 10.1021/jacs.3c01318] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Described herein are studies toward the core modification of cyclic aliphatic amines using either a riboflavin/photo-irradiation approach or Cu(I) and Ag(I) to mediate the process. Structural remodeling of cyclic amines is explored through oxidative C-N and C-C bond cleavage using peroxydisulfate (persulfate) as an oxidant. Ring-opening reactions to access linear aldehydes or carboxylic acids with flavin-derived photocatalysis or Cu salts, respectively, are demonstrated. A complementary ring-opening process mediated by Ag(I) facilitates decarboxylative Csp3-Csp2 coupling in Minisci-type reactions through a key alkyl radical intermediate. Heterocycle interconversion is demonstrated through the transformation of N-acyl cyclic amines to oxazines using Cu(II) oxidation of the alkyl radical. These transformations are investigated by computation to inform the proposed mechanistic pathways. Computational studies indicate that persulfate mediates oxidation of cyclic amines with concomitant reduction of riboflavin. Persulfate is subsequently reduced by formal hydride transfer from the reduced riboflavin catalyst. Oxidation of the cyclic aliphatic amines with a Cu(I) salt is proposed to be initiated by homolysis of the peroxy bond of persulfate followed by α-HAT from the cyclic amine and radical recombination to form an α-sulfate adduct, which is hydrolyzed to the hemiaminal. Investigation of the pathway to form oxazines indicates a kinetic preference for cyclization over more typical elimination pathways to form olefins through Cu(II) oxidation of alkyl radicals.
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Affiliation(s)
- David M Soro
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jose B Roque
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jonas W Rackl
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Bohyun Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Stefan Payer
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Yuan Shi
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - J Craig Ruble
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Alexey L Kaledin
- Cherry L. Emerson Center for Scientific Computation, and Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Mu-Hyun Baik
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Djamaladdin G Musaev
- Cherry L. Emerson Center for Scientific Computation, and Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Richmond Sarpong
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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26
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Horwitz MA, Dürr AB, Afratis K, Chen Z, Soika J, Christensen KE, Fushimi M, Paton RS, Gouverneur V. Regiodivergent Nucleophilic Fluorination under Hydrogen Bonding Catalysis: A Computational and Experimental Study. J Am Chem Soc 2023; 145:9708-9717. [PMID: 37079853 PMCID: PMC10161234 DOI: 10.1021/jacs.3c01303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
The controlled programming of regiochemical outcomes in nucleophilic fluorination reactions with alkali metal fluoride is a problem yet to be solved. Herein, two synergistic approaches exploiting hydrogen bonding catalysis are presented. First, we demonstrate that modulating the charge density of fluoride with a hydrogen-bond donor urea catalyst directly influences the kinetic regioselectivity in the fluorination of dissymmetric aziridinium salts with aryl and ester substituents. Moreover, we report a urea-catalyzed formal dyotropic rearrangement, a thermodynamically controlled regiochemical editing process consisting of C-F bond scission followed by fluoride rebound. These findings offer a route to access enantioenriched fluoroamine regioisomers from a single chloroamine precursor, and more generally, new opportunities in regiodivergent asymmetric (bis)urea-based organocatalysis.
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Affiliation(s)
- Matthew A Horwitz
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Alexander B Dürr
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Konstantinos Afratis
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Zijun Chen
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Julia Soika
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Kirsten E Christensen
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Makoto Fushimi
- Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Robert S Paton
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80528, United States
| | - Véronique Gouverneur
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
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27
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Ratzenböck K, Fischer SM, Slugovc C. Poly(ether)s derived from oxa-Michael polymerization: a comprehensive review. MONATSHEFTE FUR CHEMIE 2023. [DOI: 10.1007/s00706-023-03049-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
AbstractPoly(ether)s represent an important class of polymers and are typically formed by ring-opening polymerization, Williamson ether synthesis, or self-condensation of alcohols. The oxa-Michael reaction presents another method to form poly(ether)s with additional functional groups in the polymer backbone starting from di- or triols and electron deficient olefins such as acrylates, sulfones, or acrylamides. However, research on oxa-Michael polymerization is still limited. Herein, we outline the principles of the oxa-Michael polymerization and focus on the synthesis and preparation of poly(ether-sulfone)s, poly(ether-ester)s, poly(ether)s, and poly(ether-amide)s. Further, challenges as well as future perspectives of the oxa-Michael polymerization are discussed.
Graphical abstract
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28
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Li L, Mayer RJ, Ofial AR, Mayr H. One-Bond-Nucleophilicity and -Electrophilicity Parameters: An Efficient Ordering System for 1,3-Dipolar Cycloadditions. J Am Chem Soc 2023; 145:7416-7434. [PMID: 36952671 DOI: 10.1021/jacs.2c13872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Diazoalkanes are ambiphilic 1,3-dipoles that undergo fast Huisgen cycloadditions with both electron-rich and electron-poor dipolarophiles but react slowly with alkenes of low polarity. Frontier molecular orbital (FMO) theory considering the 3-center-4-electron π-system of the propargyl fragment of diazoalkanes is commonly applied to rationalize these reactivity trends. However, we recently found that a change in the mechanism from cycloadditions to azo couplings takes place due to the existence of a previously overlooked lower-lying unoccupied molecular orbital. We now propose an alternative approach to analyze 1,3-dipolar cycloaddition reactions, which relies on the linear free energy relationship lg k2(20 °C) = sN(N + E) (eq 1) with two solvent-dependent parameters (N, sN) to characterize nucleophiles and one parameter (E) for electrophiles. Rate constants for the cycloadditions of diazoalkanes with dipolarophiles were measured and compared with those calculated for the formation of zwitterions by eq 1. The difference between experimental and predicted Gibbs energies of activation is interpreted as the energy of concert, i.e., the stabilization of the transition states by the concerted formation of two new bonds. By linking the plot of lg k2 vs N for nucleophilic dipolarophiles with that of lg k2 vs E for electrophilic dipolarophiles, one obtains V-shaped plots which provide absolute rate constants for the stepwise reactions on the borderlines. These plots furthermore predict relative reactivities of dipolarophiles in concerted, highly asynchronous cycloadditions more precisely than the classical correlations of rate constants with FMO energies or ionization potentials. DFT calculations using the SMD solvent model confirm these interpretations.
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Affiliation(s)
- Le Li
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Robert J Mayer
- CNRS, ISIS, Université de Strasbourg, 8 Allee Gaspard Monge, 67000 Strasbourg, France
| | - Armin R Ofial
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Herbert Mayr
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
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29
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Ren P, Yu C, Zhang R, Nie T, Hu Q, Li H, Zhang X, Zhang X, Li S, Liu L, Dai W, Li J, Xu Y, Su H, Zhang L, Liu H, Bai F. Discovery, synthesis and mechanism study of 2,3,5-substituted [1,2,4]-thiadiazoles as covalent inhibitors targeting 3C-Like protease of SARS-CoV-2. Eur J Med Chem 2023; 249:115129. [PMID: 36702052 PMCID: PMC9847367 DOI: 10.1016/j.ejmech.2023.115129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/04/2023] [Accepted: 01/15/2023] [Indexed: 01/19/2023]
Abstract
The 3C-like protease (3CLpro) is essential for the replication and transcription of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), making it a promising target for the treatment of corona virus disease 2019 (COVID-19). In this study, a series of 2,3,5-substituted [1,2,4]-thiadiazole analogs were discovered to be able to inhibit 3CLpro as non-peptidomimetic covalent binders at submicromolar levels, with IC50 values ranging from 0.118 to 0.582 μM. Interestingly, these compounds were also shown to inhibit PLpro with the same level of IC50 values, but had negligible effect on proteases such as chymotrypsin, cathepsin B, and cathepsin L. Subsequently, the antiviral abilities of these compounds were evaluated in cell-based assays, and compound 6g showed potent antiviral activity with an EC50 value of 7.249 μM. It was proposed that these compounds covalently bind to the catalytic cysteine 145 via a ring-opening metathesis reaction mechanism. To understand this covalent-binding reaction, we chose compound 6a, one of the identified hit compounds, as a representative to investigate the reaction mechanism in detail by combing several computational predictions and experimental validation. The process of ring-opening metathesis was theoretically studied using quantum chemistry calculations according to the transition state theory. Our study revealed that the 2,3,5-substituted [1,2,4]-thiadiazole group could covalently modify the catalytic cysteine in the binding pocket of 3CLpro as a potential warhead. Moreover, 6a was a known GPCR modulator, and our study is also a successful computational method-based drug-repurposing study.
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Affiliation(s)
- Pengxuan Ren
- School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Changyue Yu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Ruxue Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Tianqing Nie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qiaoyu Hu
- School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China,East China Normal University, Innovation Center for AI and Drug Discovery, Shanghai, 200062, China
| | - Hui Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xianglei Zhang
- School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Xueyuan Zhang
- School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Shiwei Li
- School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Lu Liu
- School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Wenhao Dai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jian Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Leike Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China.
| | - Hong Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
| | - Fang Bai
- School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; School of Information Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Shanghai Clinical Research and Trial Center, Shanghai, 201210, China.
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30
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Sharma S, Vashishtha M. Evaluation of optimized molecular structure-antimicrobial and antioxidant efficacy relationship of Schiff bases. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:20874-20886. [PMID: 36260232 DOI: 10.1007/s11356-022-23633-1] [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: 06/29/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The synthesis, reactivity, structure, antimicrobial potential, and antioxidant property of some Schiff bases were extensively studied experimentally and theoretically using the B3LYP method of DFT (density functional theory). Schiff bases formed with the interaction of salicylaldehyde and amino alcohols in a 1:1 molar ratio in ethanol. The physicochemical and spectroscopic investigations decide the plausible structure of these newly synthesized Schiff bases. The computational study can assess the molecular orbitals, chemical reactivity, stability, and molecular electrostatic potential of Schiff bases. The thermodynamic parameters and optimized structures of Schiff bases in the gaseous state investigated by the B3LYP method of DFT. The evaluation of Schiff bases possesses antimicrobial resistance against gram-negative (Pseudomonas aeruginosa) and (Bacillus cereus)gram-positive bacterial strains as well as fungal strains (Candida albicans and Penicillium chrysogeum). The MIC (minimum inhibitory concentration) of all Schiff bases against Bacillus cereus was found in the range of 250 to 1200 µg. The MIC values of L1H, L2H, and L3H against Penicillium chrysogeum were 400, 600, and 800 µg, respectively, whereas the MIC value of L1H against Candida albicans was 600 µg. The free radical scavenging activity by the DPPH method was used to access potential antioxidant activity in Schiff bases.
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Affiliation(s)
- Shobhana Sharma
- Department of Chemistry, S.S. Jain Subodh P.G. College, Jaipur, 302004, India
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Abstract
Reactivity scales are useful research tools for chemists, both experimental and computational. However, to determine the reactivity of a single molecule, multiple measurements need to be carried out, which is a time-consuming and resource-intensive task. In this Tutorial Review, we present alternative approaches for the efficient generation of quantitative structure-reactivity relationships that are based on quantum chemistry, supervised learning, and uncertainty quantification. First published in 2002, we observe a tendency for these relationships to become not only more predictive but also more interpretable over time.
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Affiliation(s)
- Maike Vahl
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany.
| | - Jonny Proppe
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany.
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Barqi MM, Abdellah IM, Eletmany MR, Ali NM, Elhenawy AA, Abd El Latif FM. Synthesis, Characterization, Bioactivity Screening and Computational Studies of Diphenyl−malonohydrazides and Pyridines Derivatives. ChemistrySelect 2023. [DOI: 10.1002/slct.202203913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Mashael M. Barqi
- Chemistry Department, Faculty of Science Albaha University Albaha 65731 Saudi Arabia
| | - Islam M. Abdellah
- Chemistry Department, Faculty of Science Aswan University Aswan 81528 Egypt
| | - Mohamed R. Eletmany
- Chemistry Department, Faculty of Science South Valley University Qena 83523 Egypt
- TECS Department, Wilson College of Textiles NC State University Raleigh 27606 USA
| | - Nada M. Ali
- Chemistry Department, Faculty of Science Albaha University Albaha 65731 Saudi Arabia
| | - Ahmed A. Elhenawy
- Chemistry Department, Faculty of Science Albaha University Albaha 65731 Saudi Arabia
- Chemistry Department, Faculty of Science Al-Azar University Cairo 11884 Egypt
| | - Fawy M. Abd El Latif
- Chemistry Department, Faculty of Science Albaha University Albaha 65731 Saudi Arabia
- Chemistry Department, Faculty of Science Aswan University Aswan 81528 Egypt
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Huang W, Du X, Zhang C, Zhang S, Zhang J, Yang XF. Rational Design of a Dual-Channel Fluorescent Probe for the Simultaneous Imaging of Hypochlorous Acid and Peroxynitrite in Living Organisms. Anal Chem 2022; 94:17485-17493. [PMID: 36480597 DOI: 10.1021/acs.analchem.2c03661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hypochlorous acid (HOCl) and peroxynitrite (ONOO-) are two important highly reactive oxygen/nitrogen species, which commonly coexist in biosystems and play pivotal roles in many physiological and pathological processes. To investigate their function and correlations, it is urgently needed to construct chemical tools that can track the production of HOCl and ONOO- in biological systems with distinct fluorescence signals. Here, we found that the coumarin fluorescence of coumarin-benzopyrylium (CB) hydrazides (spirocyclic form) is dim, and their fluorescence properties are controlled by their benzopyran moiety via an intramolecular photo-induced electron transfer (PET) process. Based on this mechanism, we report the development of a fluorescent probe CB2-H for the simultaneous detection of HOCl and ONOO-. ONOO- can selectively oxidize the hydrazide group of CB2-H to afford the parent dye CB2 (Absmax/Emmax = 631/669 nm). In the case of HOCl, it undergoes an electrophilic attack on the benzopyran moiety of CB2-H to give a chlorinated product CB2-H-Cl, which inhibits the PET process within the probe and thus affords a turn-on fluorescence response at the coumarin channel (Absmax/Emmax = 407/468 nm). Due to the marked differences in absorption/emission wavelengths between the HOCl and ONOO- products, CB2-H enables the concurrent detection of HOCl and ONOO- at two independent channels without spectral cross-interference. CB2-H has been applied for dual-channel fluorescence imaging of endogenously produced HOCl and ONOO- in living cells and zebrafish under different stimulants. The present probe provides a useful tool for further exploring the distribution and correlation of HOCl and ONOO- in more biosystems.
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Affiliation(s)
- Wenming Huang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| | - Xinmei Du
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| | - Congjie Zhang
- School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xian, Shaanxi 710062, P. R. China
| | - Shengrui Zhang
- School of Chemistry and Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, P. R. China
| | - Jianjian Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| | - Xiao-Feng Yang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
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Stieger CE, Park Y, de Geus MAR, Kim D, Huhn C, Slenczka JS, Ochtrop P, Müchler JM, Süssmuth RD, Broichhagen J, Baik M, Hackenberger CPR. DFT-Guided Discovery of Ethynyl-Triazolyl-Phosphinates as Modular Electrophiles for Chemoselective Cysteine Bioconjugation and Profiling. Angew Chem Int Ed Engl 2022; 61:e202205348. [PMID: 35792701 PMCID: PMC9804898 DOI: 10.1002/anie.202205348] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Indexed: 01/09/2023]
Abstract
We report the density functional theory (DFT) guided discovery of ethynyl-triazolyl-phosphinates (ETPs) as a new class of electrophilic warheads for cysteine selective bioconjugation. By using CuI -catalysed azide alkyne cycloaddition (CuAAC) in aqueous buffer, we were able to access a variety of functional electrophilic building blocks, including proteins, from diethynyl-phosphinate. ETP-reagents were used to obtain fluorescent peptide-conjugates for receptor labelling on live cells and a stable and a biologically active antibody-drug-conjugate. Moreover, we were able to incorporate ETP-electrophiles into an azide-containing ubiquitin under native conditions and demonstrate their potential in protein-protein conjugation. Finally, we showcase the excellent cysteine-selectivity of this new class of electrophile in mass spectrometry based, proteome-wide cysteine profiling, underscoring the applicability in homogeneous bioconjugation strategies to connect two complex biomolecules.
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Affiliation(s)
- Christian E. Stieger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
- Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Yerin Park
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- Center for Catalytic Hydrocarbon FunctionalizationsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
| | - Mark A. R. de Geus
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
| | - Dongju Kim
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- Center for Catalytic Hydrocarbon FunctionalizationsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
| | - Christiane Huhn
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
- Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - J. Sophia Slenczka
- Institut für ChemieTechnische Universität BerlinStrasse des 17. Juni 12410623BerlinGermany
| | - Philipp Ochtrop
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
- Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Judith M. Müchler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
- Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Roderich D. Süssmuth
- Institut für ChemieTechnische Universität BerlinStrasse des 17. Juni 12410623BerlinGermany
| | - Johannes Broichhagen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
| | - Mu‐Hyun Baik
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- Center for Catalytic Hydrocarbon FunctionalizationsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
| | - Christian P. R. Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
- Department of ChemistryHumboldt Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
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35
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Nie W, Liu D, Li S, Yu H, Fu Y. Nucleophilicity Prediction Using Graph Neural Networks. J Chem Inf Model 2022; 62:4319-4328. [PMID: 36097394 DOI: 10.1021/acs.jcim.2c00696] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The quantitative description between chemical reaction rates and nucleophilicity parameters plays a crucial role in organic chemistry. In this regard, the formula proposed by Mayr et al. and the constructed reactivity database are important representatives. However, the determination of Mayr's nucleophilicity parameter N often requires time-consuming experiments with reference electrophiles in the solvent. Several machine learning (ML)-based models have been proposed to realize the data-driven prediction of N in recent years. However, in addition to DFT-calculated electronic descriptors, most of them also use a set of artificially predefined structural descriptors as input, which may result in a biased representation of the nucleophile's structural information depending on descriptors' definition preference. Compared with traditional ML algorithms, graph neural networks (GNNs) can naturally take the molecule's structural information into account by applying the message passing technique. We herein proposed a SchNet-based GNN model that only takes the molecular conformation and solvent type as input. The model achieves a comparable performance to the previous benchmark study on 10-fold cross-validation of 894 data points (R2 = 0.91, RMSE = 2.25). To enhance the model's ability to capture the molecule's electronic information, some DFT-calculated parameters are then incorporated into the model via graph global features, and substantial improvement is achieved in the prediction precision (R2 = 0.95, RMSE = 1.63). These results demonstrate that both structural and electronic information are important for the prediction of N, and GNN can integrate these two kinds of information more effectively.
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Affiliation(s)
- Wan Nie
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, Center for Excellence in Molecular Synthesis of CAS, Institute of Energy, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230026, China.,Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Deguang Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, Center for Excellence in Molecular Synthesis of CAS, Institute of Energy, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230026, China
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Haizhu Yu
- Department of Chemistry and Centre for Atomic Engineering of Advanced Materials, Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Anhui University, Hefei 230601, China
| | - Yao Fu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, Center for Excellence in Molecular Synthesis of CAS, Institute of Energy, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230026, China
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36
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Chandran K, Shane DI, Zochedh A, Sultan AB, Kathiresan T. Docking simulation and ADMET prediction based investigation on the phytochemical constituents of Noni ( Morinda citrifolia) fruit as a potential anticancer drug. In Silico Pharmacol 2022; 10:14. [PMID: 36034317 PMCID: PMC9411403 DOI: 10.1007/s40203-022-00130-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 08/05/2022] [Indexed: 02/02/2023] Open
Abstract
Morinda citrifolia is a traditional plant used in Asian and African countries for its wide nutraceutical and therapeutic effects for the treatment of various ailments. The fruit of M. citrifolia has various biological properties such as anti-bacterial, anti-oxidant, anti-cancer. Using the molecular docking based investigation; we explored around twenty three bioactive phytochemicals in M. citrifolia fruit against human cancer. MAPK6 (mitogen-activated protein kinase 6) was selected as target protein and these twenty three phytochemicals along with a known MAPK6 inhibitor were docked against the target protein. The docking scores of the bioactive phytochemicals against MAPK6 protein range between - 4.5 kcal/mol to - 7.9 kcal/mol and the docking score of the standard drug (CID: 447077) was - 7.3 kcal/mol. Based on the binding affinity five phytochemicals asperuloside (- 6.7 kcal/mol), asperulosidic acid (- 7.2 kcal/mol), deacetylasperulosidic acid (- 7.0 kcal/mol), eugenol (- 6.8 kcal/mol) and rutin (- 7.9 kcal/mol) were chosen for further evaluation. These five compounds were further investigated through RC plot analysis, density function theory and ADMET properties. Stable linkage of protein-ligand interaction was observed through RC plot, density function theory showed the structural stability and reactivity of bioactive compounds through the energy gap between HOMO and LUMO and the ADMET (adsorption, distribution, metabolism, excretion and toxicity) studies showed the safety profile of the bioactive compounds. These in silico results support the utilization of M. citrifolia fruit in the traditional medication and the initiation for the development of new drug against human cancer through in vivo and in vitro evaluation. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-022-00130-4.
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Affiliation(s)
- Kaliraj Chandran
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, Tamilnadu India
| | - Drose Ignatious Shane
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, Tamilnadu India
| | - Azar Zochedh
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, Tamilnadu India
| | - Asath Bahadur Sultan
- Department of Physics, Kalasalingam Academy of Research and Education, Krishnankoil, Tamilnadu India
| | - Thandavarayan Kathiresan
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, Tamilnadu India
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37
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Wei R, Ju S, Liu LL. Free Metallophosphines: Extremely Electron‐Rich Phosphorus Superbases That Are Electronically and Sterically Tunable**. Angew Chem Int Ed Engl 2022; 61:e202205618. [DOI: 10.1002/anie.202205618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Rui Wei
- Department of Chemistry Shenzhen Grubbs Institute and Guangdong Provincial Key Laboratory of Catalysis Southern University of Science and Technology Shenzhen 518055 China
| | - Shaoying Ju
- Department of Chemistry Shenzhen Grubbs Institute and Guangdong Provincial Key Laboratory of Catalysis Southern University of Science and Technology Shenzhen 518055 China
| | - Liu Leo Liu
- Department of Chemistry Shenzhen Grubbs Institute and Guangdong Provincial Key Laboratory of Catalysis Southern University of Science and Technology Shenzhen 518055 China
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38
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Stieger CE, Park Y, de Geus MAR, Kim D, Huhn C, Slenczka JS, Ochtrop P, Müchler JM, Süssmuth R, Broichhagen J, Baik MH, Hackenberger C. DFT‐Guided Discovery of Ethynyl‐Triazolyl‐Phosphinates as Modular Electrophiles for Chemoselective Cysteine Bioconjugation and Profiling. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Christian Ewald Stieger
- Leibniz Institute for Molecular Pharmacology: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chemical Biology GERMANY
| | - Yerin Park
- KAIST: Korea Advanced Institute of Science and Technology Department of Chemistry KOREA, REPUBLIC OF
| | - Mark A. R. de Geus
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin eV: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chemical Biology GERMANY
| | - Dongju Kim
- KAIST: Korea Advanced Institute of Science and Technology Department of Chemistry KOREA, REPUBLIC OF
| | - Christiane Huhn
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin eV: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chem Bio Probes GERMANY
| | - Julie Sophia Slenczka
- Technische Universität Berlin: Technische Universitat Berlin Institut für Chemie GERMANY
| | - Philipp Ochtrop
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin eV: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chemical Biology GERMANY
| | - Judith Maria Müchler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin eV: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chemical Biology GERMANY
| | - Roderich Süssmuth
- Technische Universität Berlin: Technische Universitat Berlin Institut für Chemie GERMANY
| | - Johannes Broichhagen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin eV: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV Chem Bio Probes GERMANY
| | - Mu-Hyun Baik
- KAIST: Korea Advanced Institute of Science and Technology Department of Chemistry KOREA, REPUBLIC OF
| | - Christian Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Deptm. of Chemical Biology Robert-Roessle Str. 10 13125 Berlin GERMANY
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39
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Zochedh A, Priya M, Shunmuganarayanan A, Thandavarayan K, Sultan AB. Investigation on structural, spectroscopic, DFT, biological activity and molecular docking simulation of essential oil Gamma-Terpinene. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133651] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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40
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Zhang Q, Chen J, Gao X, Che H, Ao Y, Wang P. Understanding the mechanism of interfacial interaction enhancing photodegradation rate of pollutants at molecular level: Intermolecular π-π interactions favor electrons delivery. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128386. [PMID: 35149492 DOI: 10.1016/j.jhazmat.2022.128386] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Uncovering the interaction between photocatalyst and reaction substrate as well as subsequent electron transfer process is critical to achieve high-performance photodegradation of pollutants. Herein, based on the reduced density gradient (RDG) method, we visualize the simulation of the π-π interactions between photocatalyst (g-C3N4) and pollutant molecule (flumequine, FLU). Results revealed that π-π interactions between g-C3N4 and FLU favor electrons delivery, resulting in enhanced charge separation efficiency and direct hole oxidation of FLU. Moreover, it is found that the charge transfer rate is determined by the valence band (VB) level of g-C3N4 and EHOMO of FLU, of which the deeper VB position of g-C3N4 favors faster charge transfer, leading to further enhancement in photocatalytic degradation rate of FLU. Additionally, the possible degradation pathways of FLU were proposed by theoretical calculation and the determined intermediates. Our work afforded a new insight into pollutants degradation and the rational design of highly efficient photocatalysts.
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Affiliation(s)
- Qiang Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, No.1, Xikang Road, Nanjing 210098, China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, No.1, Xikang Road, Nanjing 210098, China
| | - Xin Gao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, No.1, Xikang Road, Nanjing 210098, China
| | - Huinan Che
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, No.1, Xikang Road, Nanjing 210098, China
| | - Yanhui Ao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, No.1, Xikang Road, Nanjing 210098, China.
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, No.1, Xikang Road, Nanjing 210098, China
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41
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Wei R, Ju S, Liu LL. Free Metallophosphines: Extremely Electron‐Rich Phosphorus Superbases That Are Electronically and Sterically Tunable**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Rui Wei
- Department of Chemistry Shenzhen Grubbs Institute and Guangdong Provincial Key Laboratory of Catalysis Southern University of Science and Technology Shenzhen 518055 China
| | - Shaoying Ju
- Department of Chemistry Shenzhen Grubbs Institute and Guangdong Provincial Key Laboratory of Catalysis Southern University of Science and Technology Shenzhen 518055 China
| | - Liu Leo Liu
- Department of Chemistry Shenzhen Grubbs Institute and Guangdong Provincial Key Laboratory of Catalysis Southern University of Science and Technology Shenzhen 518055 China
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42
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Proppe J, Kircher J. Uncertainty Quantification of Reactivity Scales. Chemphyschem 2022; 23:e202200061. [PMID: 35189024 PMCID: PMC9314972 DOI: 10.1002/cphc.202200061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/16/2022] [Indexed: 11/09/2022]
Abstract
According to Mayr, polar organic synthesis can be rationalized by a simple empirical relationship linking bimolecular rate constants to as few as three reactivity parameters. Here, we propose an extension to Mayr's reactivity method that is rooted in uncertainty quantification and transforms the reactivity parameters into probability distributions. Through uncertainty propagation, these distributions can be transformed into uncertainty estimates for bimolecular rate constants. Chemists can exploit these virtual error bars to enhance synthesis planning and to decrease the ambiguity of conclusions drawn from experimental data. We demonstrate the above at the example of the reference data set released by Mayr and co-workers [J. Am. Chem. Soc. 2001, 123, 9500; J. Am. Chem. Soc. 2012, 134, 13902]. As by-product of the new approach, we obtain revised reactivity parameters for 36 π-nucleophiles and 32 benzhydrylium ions.
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Affiliation(s)
- Jonny Proppe
- Georg-August UniversityInstitute of Physical ChemistryTammannstrasse 637077GöttingenGermany
- Present address: Technische Universität BraunschweigInstitute of Physical and Theoretical ChemistryGaussstrasse 1738106BraunschweigGermany
| | - Johannes Kircher
- Georg-August UniversityInstitute of Physical ChemistryTammannstrasse 637077GöttingenGermany
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Yadav S, Misra N, Khanna P, Mansi, Batra K, Khanna L. A DFT Study on Diels-Alder Reaction of Dibenzazepine and 2,5-Dimethylfuran Using Different Solvents and Temperature Conditions. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2056622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Shilpa Yadav
- University School of Basic & Applied Sciences, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Neeti Misra
- Department of Chemistry, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | - Pankaj Khanna
- Department of Chemistry, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | - Mansi
- University School of Basic & Applied Sciences, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Kriti Batra
- University School of Basic & Applied Sciences, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Leena Khanna
- University School of Basic & Applied Sciences, Guru Gobind Singh Indraprastha University, New Delhi, India
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Verma P, Srivastava A, Tandon P, Shimpi MR. Experimental and Quantum Chemical Studies of Nicotinamide-Oxalic Acid Salt: Hydrogen Bonding, AIM and NBO Analysis. Front Chem 2022; 10:855132. [PMID: 35372271 PMCID: PMC8965448 DOI: 10.3389/fchem.2022.855132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/08/2022] [Indexed: 11/18/2022] Open
Abstract
The computational modeling supported with experimental results can explain the overall structural packing by predicting the hydrogen bond interactions present in any cocrystals (active pharmaceutical ingredients + coformer) as well as salts. In this context, the hydrogen bonding synthons, physiochemical properties (chemical reactivity and stability), and drug-likeliness behavior of proposed nicotinamide-oxalic acid (NIC-OXA) salt have been reported by using vibrational spectroscopic signatures (IR and Raman spectra) and quantum chemical calculations. The NIC-OXA salt was prepared by reactive crystallization method. X-ray powder diffraction (XRPD) and differential scanning calorimetry (DSC) techniques were used for the characterization and validation of NIC-OXA salt. The spectroscopic signatures revealed that (N7-H8)/(N23-H24) of the pyridine ring of NIC, (C═O), and (C-O) groups of OXA were forming the intermolecular hydrogen bonding (N-H⋯O-C), (C-H⋯O═C), and (N-H⋯O═C), respectively, in NIC-OXA salt. Additionally, the quantum theory of atoms in molecules (QTAIM) showed that (C10-H22⋯O1) and (C26-H38⋯O4) are two unconventional hydrogen bonds present in NIC-OXA salt. Also, the natural bond orbital analysis was performed to find the charge transfer interactions and revealed the strongest hydrogen bonds (N7-H8⋯O5)/(N23-H24⋯O2) in NIC-OXA salt. The frontier molecular orbital (FMO) analysis suggested more reactivity and less stability of NIC-OXA salt in comparison to NIC-CA cocrystal and NIC. The global and local reactivity descriptors calculated and predicted that NIC-OXA salt is softer than NIC-CA cocrystal and NIC. From MESP of NIC-OXA salt, it is clear that electrophilic (N7-H8)/(N23-H24), (C6═O4)/(C3═O1) and nucleophilic (C10-H22)/(C26-H38), (C6-O5)/(C3-O2) reactive groups in NIC and OXA, respectively, neutralize after the formation of NIC-OXA salt, confirming the presence of hydrogen bonding interactions (N7-H8⋯O5-C6) and (N23-H24⋯O2-C3). Lipinski's rule was applied to check the activeness of salt as an orally active form. The results shed light on several features of NIC-OXA salt that can further lead to the improvement in the physicochemical properties of NIC.
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Affiliation(s)
- Priya Verma
- Department of Physics, University of Lucknow, Lucknow, India
| | | | - Poonam Tandon
- Department of Physics, University of Lucknow, Lucknow, India
| | - Manishkumar R. Shimpi
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
- Chemistry of Interfaces, Luleå University of Technology, Luleå, Sweden
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Li Y, Zhang L, Luo S. Bond Energies of Enamines. ACS OMEGA 2022; 7:6354-6374. [PMID: 35224397 PMCID: PMC8867489 DOI: 10.1021/acsomega.1c06945] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/25/2022] [Indexed: 05/11/2023]
Abstract
Energetics of reactive intermediates underlies their reactivity. The availability of these data provides a rational basis for understanding and predicting a chemical reaction. We reported here a comprehensive computational study on the energetics of enamine intermediates that are fundamental in carbonyl chemistry. Accurate density functional theory (DFT) calculations were performed to determine the bond energies of enamines and their derived radical intermediates. These efforts led to the compilation of a database of enamine energetics including a thermodynamic index such as free-energy stability, bond dissociation energy (BDE), and acid dissociation constant (pK a) as well as a kinetic index such as nucleophilicity and electrophilicity. These data were validated by relating to experimentally determined parameters and their relevance and utility were discussed in the context of modern enamine catalysis. It was found that pK a values of enamine radical cations correlated well with redox potentials of their parent enamines, the former could be used to rationalize the proton-transfer behavior of enamine radical cations. An analysis of the BDE of enamine radical cations indicated that these species underwent facile β-C-H hydrogen transfer, in line with the known oxidative enamine catalysis. The enamine energetics offers the possibility of a systematic evaluation of the reactivities of enamines and related radicals, which would provide useful guidance in exploring new enamine transformations.
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Geng S, Hu J, Yu J, Zhang C, Wang H, Zhong X. Rosin imidazoline as an eco-friendly corrosion inhibitor for the carbon steel in CO2-containing solution and its synergistic effect with thiourea. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Zhang K, Hu L, Wang C, Zhang K. Middle-low-temperature oxidation and adsorption of arsenic from flue gas by Fe-Ce-based composite catalyst. CHEMOSPHERE 2022; 288:132425. [PMID: 34606904 DOI: 10.1016/j.chemosphere.2021.132425] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
Fe-Ce-based composite catalysts were prepared and used for As2O3 catalytic oxidation and adsorption. They were characterized by XRD, BET, H2-TPR, Raman, SEM and XPS. The results suggests Fe, La and Zr can be partially doped into CeO2 lattice to form solid solutions. Compared with pure Fe2O3, the composite catalysts have stronger low-temperature reducibility, especially La3+ doping is beneficial to the formation of more low-temperature active sites. Raman and XPS measurements disclose the presence of oxygen vacancy and surface adsorbed oxygen in composite catalysts and these are more prominent in FeCeLaO. Ce3+ ratio increases to 18.30% after reaction, which confirms part of Ce4+ can participate in As2O3 oxidation and be reduced to Ce3+. The oxidation and adsorption capacity for As2O3 were investigated at different temperatures and O2 concentrations. The results show FeCeLaO exhibits excellent activity at middle-low-temperatures of 200-400 °C, the oxidation efficiency of As2O3 can reach 100%, the total adsorbed arsenic at 400 °C reaches 583.7 μg/g, which is 1.8 times of pure Fe2O3 at 600 °C. As2O3 oxidation mechanism over FeCeLaO with/without O2 was proposed through the Mars-Maessen theory with the aid of surface-active oxygen. The abundant oxygen vacancy defects and active chemisorbed oxygen play important roles and guarantee an efficient As2O3 oxidation, which is also the essential reason why the composite catalysts can effectively oxidize and adsorb As2O3 at middle-low-temperature of 200-400 °C, while pure Fe2O3 can only be at high temperature of 600-700 °C.
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Affiliation(s)
- Kaihua Zhang
- Beijing Key Laboratory of Pollutant Monitoring and Control in Thermoelectric Production Process, North China Electric Power University, Beijing, 102206, China; Department of Energy Power & Mechanical Engineering, North China Electric Power University, Beijing 102206, China.
| | - Lintao Hu
- Beijing Key Laboratory of Pollutant Monitoring and Control in Thermoelectric Production Process, North China Electric Power University, Beijing, 102206, China; Department of Energy Power & Mechanical Engineering, North China Electric Power University, Beijing 102206, China
| | - Chuanfeng Wang
- Department of Energy Power & Mechanical Engineering, North China Electric Power University, Beijing 102206, China
| | - Kai Zhang
- Beijing Key Laboratory of Pollutant Monitoring and Control in Thermoelectric Production Process, North China Electric Power University, Beijing, 102206, China; Department of Energy Power & Mechanical Engineering, North China Electric Power University, Beijing 102206, China
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Khalid I, Khera RA, Ali S, Shahid M. Design, synthesis, and comparative study of optoelectronic properties of arylated triazine-based sulfanilamide derivatives through Suzuki–Miyaura cross-coupling reactions. J Mol Model 2022; 28:44. [DOI: 10.1007/s00894-022-05027-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/05/2022] [Indexed: 10/19/2022]
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Huang M, Lu H, Wang M, Liu B, Ma Z, Wang Z, Yang J. Phenothiazine-Based Luminophores with AIE, Solvatochromism, and Mechanochromic Characteristics. J Phys Chem B 2021; 125:11548-11556. [PMID: 34615358 DOI: 10.1021/acs.jpcb.1c07304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aggregation-induced emission (AIE) fluorescent molecules with unique photoelectric properties have received extensive attention due to the wide range of applications. In this work, two novel phenothiazine-based luminophores DPE-PTZ-Cl and DPE-PTZ-CF3 were designed based on the frontier molecular orbital (FMO) theory and construction strategy of AIEgens. As expected, both of the luminophores displayed typical AIE behavior and realized the spatial separation of FMOs, which was confirmed by the positive solvatochromism behavior. Their AIE properties could be attributed to the twisted three-dimensional (3D) conformation. Such a conformation resulted from "butterfly-like" phenothiazine and a multirotor structure of diphenylethylene. The spatial separation of FMOs originated from the push-pull electronic synergistic effect of the donor-acceptor (D-A) architecture. Interestingly, DPE-PTZ-Cl also showed a rare blue-shifted mechanochromic (MC) luminescence property. Single-crystal X-ray diffraction (SCXRD) and powder X-ray diffraction (PXRD) experiments were carried out to reveal that the phase transformation between crystalline and amorphous states was responsible for the peculiar solid-state luminescence phenomenon.
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Affiliation(s)
- Mingming Huang
- Key Laboratory of Aerospace Advanced Materials and Performance, Ministry of Education, School of Materials Science and Engineering, Beihang University, Beijing 100191, China
| | - Hao Lu
- Key Laboratory of Aerospace Advanced Materials and Performance, Ministry of Education, School of Materials Science and Engineering, Beihang University, Beijing 100191, China
| | - Meng Wang
- Key Laboratory of Aerospace Advanced Materials and Performance, Ministry of Education, School of Materials Science and Engineering, Beihang University, Beijing 100191, China
| | - Beibei Liu
- Key Laboratory of Aerospace Advanced Materials and Performance, Ministry of Education, School of Materials Science and Engineering, Beihang University, Beijing 100191, China
| | - Zhiyong Ma
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Organic-Inorganic Composites, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zhijian Wang
- Key Laboratory of Aerospace Advanced Materials and Performance, Ministry of Education, School of Materials Science and Engineering, Beihang University, Beijing 100191, China
| | - Jiping Yang
- Key Laboratory of Aerospace Advanced Materials and Performance, Ministry of Education, School of Materials Science and Engineering, Beihang University, Beijing 100191, China
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50
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Guan Q, Wang H, Wang X. Theoretical research on molecular motors based on 4,5‐diazafluorenyl coordination motifs. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Qiuping Guan
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry Xiangtan University Xiangtan China
| | - Hailong Wang
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry Xiangtan University Xiangtan China
| | - Xueye Wang
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry Xiangtan University Xiangtan China
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