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Cao Y, Balduf T, Beachy MD, Bennett MC, Bochevarov AD, Chien A, Dub PA, Dyall KG, Furness JW, Halls MD, Hughes TF, Jacobson LD, Kwak HS, Levine DS, Mainz DT, Moore KB, Svensson M, Videla PE, Watson MA, Friesner RA. Quantum chemical package Jaguar: A survey of recent developments and unique features. J Chem Phys 2024; 161:052502. [PMID: 39092934 DOI: 10.1063/5.0213317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024] Open
Abstract
This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar's development in more than thirty years of its existence.
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Affiliation(s)
- Yixiang Cao
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Ty Balduf
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Michael D Beachy
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - M Chandler Bennett
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Art D Bochevarov
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Alan Chien
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Pavel A Dub
- Schrödinger, Inc., 9868 Scranton Road, Suite 3200, San Diego, California 92121, USA
| | - Kenneth G Dyall
- Schrödinger, Inc., 101 SW Main St., Suite 1300, Portland, Oregon 97204, USA
| | - James W Furness
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Mathew D Halls
- Schrödinger, Inc., 9868 Scranton Road, Suite 3200, San Diego, California 92121, USA
| | - Thomas F Hughes
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Leif D Jacobson
- Schrödinger, Inc., 101 SW Main St., Suite 1300, Portland, Oregon 97204, USA
| | - H Shaun Kwak
- Schrödinger, Inc., 101 SW Main St., Suite 1300, Portland, Oregon 97204, USA
| | - Daniel S Levine
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Daniel T Mainz
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Kevin B Moore
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Mats Svensson
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Pablo E Videla
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Mark A Watson
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Richard A Friesner
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
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Wang K, Li S, Yang A, Chen D, Xu F, Zhang LL, Zhang J, Yang S. Near-Barrierless CO Oxidation Using Phosphotungstic Acid-Supported Single-Atom Catalysts. Inorg Chem 2024; 63:13253-13264. [PMID: 38984385 DOI: 10.1021/acs.inorgchem.4c00863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Efficient CO oxidation at ambient or low temperatures is essential for environmental purification and selective CO oxidation in H2, yet achieving this remains a challenge with current methodologies. In this research, we extensively evaluated the catalytic performance of phosphotungstic acid (PTA)-supported 11 M1/PTA single-atom catalysts (SACs) using density functional theory calculations across both gas phase and 12 common solvents. The Rh1/PTA, Pd1/PTA, and Pt1/PTA systems exhibit moderate CO adsorption energies, facilitating the feasibility of oxygen vacancy formation. Remarkably, the Pd1/PTA and Pt1/PTA catalysts exhibited negligible energy barriers and demonstrated exceptionally high catalytic rates, with values reaching up to (1 × 1010)11, markedly exceeding the threshold for room temperature reactions, set at 6.55 × 108. This phenomenon is attributed to a transition from the high-energy barrier processes of oxygen dissociation in O2 and N-O bond dissociation in N2O to the more efficient dissociation of H2O2. Orbital analysis and charge variations at metal sites throughout the reaction process provide deeper insights into the role of the three metal catalytic sites in CO activation. Our findings not only reveal key aspects of SACs in facilitating CO oxidation at low temperatures but also provide valuable insights for future catalytic reaction mechanism studies and environmental applications.
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Affiliation(s)
- Kaijie Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
- School of Chemistry and Chemical Engineering, Guizhou University, Guiyang 550025, PR China
| | - Shiyu Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Anqi Yang
- Institute of New Type Optoelectronic Materials and Technology, College of Big Data and Information Engineering, Guizhou University, Guiyang 550025, China
| | - Dandan Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Feng Xu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Li-Long Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Jian Zhang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Huazhong, University of Science and Technology, Wuhan 430074, PR China
| | - Song Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, State-Local Joint Laboratory for Comprehensive Utilization of Biomass, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
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Quan Z, Liu YJ. Mechanistic Investigation into Chemiluminescence from 1,4-Benzoquinone. J Phys Chem A 2024; 128:5659-5667. [PMID: 38953788 DOI: 10.1021/acs.jpca.4c03461] [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
Tetrahalogen-1,4-benzoquinone (THBQ) represents a category of H2O2-dependent substrates for chemiluminescence (CL), including tetrafluoro-, tetrachloro-, tetrabromo-, and tetraiodo-1,4-benzoquinone (TFBQ, TCBQ, TBBQ, and TIBQ). A deep understanding of the CL mechanism of THBQ is essential for all H2O2-dependent CL and even some bioluminescence. This article systematically investigates the CL process of THBQ by density functional theory and multireference state theory. The theoretical results confirm the generality of the CL mechanism previously proposed in studies on TCBQ and TBBQ. The dissociation steps producing the emitter of light from dihalogenquinone dioxetane (DHD) and its anion (DHD-), formed by the oxidation of THBQ, were carefully considered. Findings show that the dissociation of DHD/DHD- follows the entropy trap/gradually reversible charge-transfer-induced luminescence (GRCTIL) mechanisms. The dissociation of DHD- is kinetically more advantageous compared with that of DHD. At the practical experimental pH value, the decrease in the electron-withdrawing inductive effect from F to I substituents results in the decrease in the proportions of easily dissociated DHD-, and the increase in the heavy-atom effect from F to I substituents leads to the increase in the phosphorescence emission. These combined factors successively decrease the CL intensity from TFBQ to TCBQ, TBBQ, and TIBQ. The conclusions are verified by the previous experiments on TCBQ and TBBQ, and they are expected to be confirmed by future experiments on TFBQ and TIBQ.
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Affiliation(s)
- Zhuo Quan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
- Department of Chemistry, Faculty of Arts and Sciences, Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
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Dutra FR, Vasiliu M, Gomez AN, Xia D, Dixon DA. Prediction of Redox Potentials for U, Np, Pu, and Am in Aqueous Solution. J Phys Chem A 2024; 128:5612-5626. [PMID: 38959054 DOI: 10.1021/acs.jpca.4c02902] [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
The redox properties of the actinides in aqueous solution are important for fuel production/reprocessing and understanding the environmental impact of nuclear waste. The redox potentials for U, Np, Pu, and Am in oxidation states from 0 up to VII (as appropriate) in aqueous solutions have been predicted at the density functional theory level with the B3LYP functional, Stuttgart small core pseudopotential basis sets for the actinides, and explicit (30H2O molecules)/implicit treatment of the aqueous solvent using the self-consistent reaction field COSMO and SMD approaches for the implicit solvation. The predictions of the structural parameters of clusters incorporating first and second solvation shells are consistent with the available experimental data. Our results are typically within 0.2 V of the available experimental data using two explicit solvation shells with an implicit solvent model. The use of the PW91 functional substantially improved the prediction of the Pu(VI/V) redox couple. The redox couples for An(VI/IV) and An(V/IV) which involve the addition of protons and removal of the actinyl oxygens led to slightly larger differences from an experiment. The An(IV/0) and An(III/0) couples were reliably predicted with our approach. Predictions of the unknown An(II/I) redox potentials were negative, consistent with expectations, and predictions for unknown An(VII/VI), An(III/II), and An(II/0) redox couples improve prior estimates.
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Affiliation(s)
- Felipe R Dutra
- Instituto de Química, Universidade Estadual de Campinas, Barão Geraldo, P.O. Box 6154, Campinas 13083-970, São Paulo, Brazil
- Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, United States
| | - Monica Vasiliu
- Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, United States
| | - Amber N Gomez
- Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, United States
| | - Donna Xia
- Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, United States
| | - David A Dixon
- Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, United States
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Wang Y, Teng C, Begin E, Bussiere M, Bao JL. PW-SMD: A Plane-Wave Implicit Solvation Model Based on Electron Density for Surface Chemistry and Crystalline Systems in Aqueous Solution. J Chem Theory Comput 2024. [PMID: 39024317 DOI: 10.1021/acs.jctc.4c00594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Electron density-based implicit solvation models are a class of techniques for quantifying solvation effects and calculating free energies of solvation without an explicit representation of solvent molecules. Integral to the accuracy of solvation modeling is the proper definition of the solvation shell separating the solute molecule from the solvent environment, allowing for a physical partitioning of the free energies of solvation. Unlike state-of-the-art implicit solvation models for molecular quantum chemistry calculations, e.g., the solvation model based on solute electron density (SMD), solvation models for systems under periodic boundary conditions with plane-wave (PW) basis sets have been limited in their accuracy. Furthermore, a unified implicit solvation model with both homogeneous solution-phase and heterogeneous interfacial structures treated on equal footing is needed. In order to address this challenge, we developed a high-accuracy solvation model for periodic PW calculations that is applicable to molecular, ionic, interfacial, and bulk-phase chemistry. Our model, PW-SMD, is an extension of the SMD molecular solvation model to periodic systems in water. The free energy of solvation is partitioned into the electrostatic and cavity-dispersion-solvent structure (CDS) contributions. The electrostatic contributions of the solvation shell surrounding solute structures are parametrized based on their geometric and physical properties. In addition, the nonelectrostatic contribution to the solvation energy is accounted for by extending the CDS formalism of SMD to incorporate periodic boundary conditions. We validate the accuracy and robustness of our solvation model by comparing predicted solvation free energies against experimental data for molecular and ionic systems, carved-cluster composite energetic models of solvated reaction energies and barriers on surface systems, and deep-learning-accelerated ab initio molecular dynamics (AIMD). Our developed periodic implicit solvation model shows significantly improved accuracy compared to previous work (namely, solvation models in aqueous solution) and can be applied to simulate solvent effects in a wide range of surface and crystalline materials.
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Affiliation(s)
- Yang Wang
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Chong Teng
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Elijah Begin
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Mason Bussiere
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Junwei Lucas Bao
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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Liu X, Zhu R, Yang Y, Xue Y, Xu D. Theoretical insights into enantioselective [2 + 1] cyclopropanation reactions of diazo compounds with electron-deficient olefins. J Mol Model 2024; 30:274. [PMID: 39023638 DOI: 10.1007/s00894-024-06079-9] [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: 06/25/2024] [Accepted: 07/14/2024] [Indexed: 07/20/2024]
Abstract
CONTEXT The cyclopropane skeleton plays a significant role in bioactive molecules due to its distinctive structural properties. This has sparked keen interest and in-depth exploration in the field of stereoselective synthesis of cyclopropane derivatives. In the present study, the mechanism and the origin of stereoselectivity of diastereodivergent synthesis of cyclopropane derivatives via the catalyst-free [2 + 1]-cyclopropanation reactions of 3-diazo-N-methylindole (R1) with two types of electron-deficient olefins (R2 and R3) in both aqueous and toluene media have been studied using the DFT calculations. The findings indicate that these [2 + 1] cycloaddition reactions proceed in two stages, where the first step is not only the rate-determining step but also critically dictates the stereoselectivity of the product. The calculated diastereomeric ratios are in agreement with the experimental results. Furthermore, by utilizing non-covalent interaction (NCI) analysis and energy decomposition analysis based on molecular force fields (EDA-FF), we elucidated that the electrostatic interactions between reactant fragments in the transition state TS1s for the first step are the predominant factors determining the stereoselectivity, as opposed to the experimentally hypothesized steric hindrance and π-π stacking interactions. METHODS The geometrical structures of all minima and transition states on the potential energy surface (PES) in solvents water and toluene were fully optimized using the DFT method at the M06-2X(D3)/SMD/6-31 + G(d,p) level of theory. Single-point energy calculations were carried out based on the optimized geometries in the solution at the M06-2X(D3)/6-311 + G(d,p) level. All the DFT calculations were performed using the Gaussian 09 software. The optimized molecular structures were visualized using CYLview software. NCI analysis was performed using the Multiwfn and VMD softwares. The Multiwfn program was also used for CDFT and EDA-FF analyses.
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Affiliation(s)
- Xudong Liu
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Ruyu Zhu
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Yongsheng Yang
- School of Pharmacy and Institute of Pharmacy, North Sichuan Medical College, Nanchong, 637100, People's Republic of China
| | - Ying Xue
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu, 610064, People's Republic of China.
| | - Dingguo Xu
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu, 610064, People's Republic of China
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7
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Kania MJ, Reyes A, Neufeldt SR. Oxidative Addition of (Hetero)aryl (Pseudo)halides at Palladium(0): Origin and Significance of Divergent Mechanisms. J Am Chem Soc 2024; 146:19249-19260. [PMID: 38959060 DOI: 10.1021/jacs.4c04496] [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
Two limiting mechanisms are possible for oxidative addition of (hetero)aryl (pseudo)halides at Pd(0): a 3-centered concerted and a nucleophilic displacement mechanism. Until now, there has been little understanding about when each mechanism is relevant. Prior investigations to distinguish between these pathways were limited to a few specific combinations of the substrate and ligand. Here, we computationally evaluated over 180 transition structures for oxidative addition in order to determine mechanistic trends based on substrate, ligand(s), and coordination number. Natural abundance 13C kinetic isotope effects provide experimental results consistent with computational predictions. Key findings include that (1) differences in highest occupied molecular orbital (HOMO) symmetries dictate that, although 12e- PdL is strongly biased toward a 3-centered concerted mechanism, 14e- PdL2 often prefers a nucleophilic displacement mechanism; (2) ligand electronics and sterics, including ligand bite angle, influence the preferred mechanism of the reaction at PdL2; (3) phenyl triflate always reacts through a displacement mechanism regardless of the catalyst structure due to the stability of a triflate anion and the inability of oxygen to effectively donate electron density to Pd; and (4) the high reactivity of C-X bonds adjacent to nitrogen in pyridine substrates relates to stereoelectronic stabilization of a nucleophilic displacement transition state. This work has implications for controlling rate and selectivity in catalytic couplings, and we demonstrate application of the mechanistic insight toward chemodivergent cross-couplings of bromochloroheteroarenes.
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Affiliation(s)
- Matthew J Kania
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Albert Reyes
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Sharon R Neufeldt
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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Loudermilk A, Dixon DA. Prediction of the p Ka's of Hydrated Metal Carbonates and Bicarbonates for Mg, Ca, Mn, Fe, Co, Ni, Cu, and Zn Dications. J Phys Chem A 2024; 128:5331-5343. [PMID: 38950028 DOI: 10.1021/acs.jpca.4c02879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
The gas- and aqueous-phase acidities of hydrated metal dication carbonates, bicarbonates, and hydroxide complexes M(CO3)(H2O)n for n = 1 to 3, M(HCO3)2, M(HCO3)2(H2O)2, M(HCO3)(OH), and M(HCO3)(H2O)2(OH) for M = Mg, Ca, Mn, Fe, Co, Ni, Cu, and Zn were calculated at the CCSD(T)/aug-cc-pwCVDZ/cc-pwCVDZ level in the gas phase and at the B3LYP/aug-cc-pVTZ/cc-pVTZ(-PP) level with the COSMO self-consistent reaction field (SCRF) method in the aqueous phase. The composite correlated molecular orbital theory G3(MP2) and G3(MP2)B3 methods were used to predict the pKa's of the Mg structures and cis-cis carbonic acid to provide additional benchmarks. Using values scaled to experiment for H2CO3, the pKa's of bicarbonate ligands in group 2 and transition-metal complexes were compared to carbonic acid to gauge the effect of the metal complex on the bicarbonate. The group 2 metal complexes M(HCO3)2 and M(HCO3)(OH) decreased the acidity of the bicarbonate ligands, whereas their dihydrates were even less acidic. The transition-metal di-bicarbonate and bicarbonate hydroxide complexes generally made the bicarbonate more acidic especially when reduction of the metal occurs consistent with electron donation from the ligands; this is accompanied by spin transfer which typically increases in the order Mn < Fe < Co < Ni < Cu. The transition-metal dihydrates were less acidic than carbonic acid. Using values scaled to experiment for hydrated metal dications, the pKa's of water coordinated to group 2 and transition-metal complexes were generally more acidic than the hydrated metal dications, with the exception of Ca bicarbonate dihydrate, Co carbonate, Ni di-bicarbonate dihydrate, and Cu bicarbonate hydroxide di-bicarbonate.
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Affiliation(s)
- Amanda Loudermilk
- Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, United States
| | - David A Dixon
- Department of Chemistry and Biochemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, United States
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9
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Mittal K, Pham AV, Davis AG, Richardson AD, De Hoe C, Dean RT, Baird V, McDonald AR, Frantz DK. Intramolecular Diels-Alder Reaction of a Biphenyl Group in a Strained meta-Quaterphenylene Acetylene. J Org Chem 2024; 89:9620-9626. [PMID: 36701431 PMCID: PMC11232012 DOI: 10.1021/acs.joc.2c02280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Indexed: 01/27/2023]
Abstract
At elevated temperatures, a strained, cyclic meta-quaterphenylene acetylene undergoes an intramolecular cyclization reaction to form benz[e]indeno[1,2,3-hi]acephenanthrylene. This reaction represents an example of a Diels-Alder reaction at the 2-, 1-, 1'-, and 2'-positions of a biphenyl derivative, a region analogous to the bay regions of perylene and other periacenes. The reaction proceeds cleanly with high conversion. Kinetics studies of a methylated derivative reveal that the ΔG‡ for the reaction is ∼40-41 kcal/mol, and computational models predict a similar value of Grel for the transition state of a concerted [4 + 2]-cycloaddition.
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Affiliation(s)
- Komal Mittal
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Ashley V Pham
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Amanda G Davis
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Abigail D Richardson
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Clement De Hoe
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Ryan T Dean
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Vi Baird
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Ashley Ringer McDonald
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Derik K Frantz
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
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10
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Radoń M. Predicting spin states of iron porphyrins with DFT methods including crystal packing effects and thermodynamic corrections. Phys Chem Chem Phys 2024; 26:18182-18195. [PMID: 38899797 DOI: 10.1039/d4cp01327a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Accurate computational treatment of spin states for transition metal complexes, exemplified by iron porphyrins, lies at the heart of quantum bioinorganic chemistry, but at the same time represents a great challenge for approximate density functional theory (DFT) methods, which are predominantly used. Here, the accuracy of DFT methods for spin-state splittings in iron porphyrin is assessed by probing the ability to correctly predict the ground states for six FeIII or FeII complexes experimentally characterized in solid state. For each case, molecular and periodic DFT calculations are employed to quantify the effect of porphyrin side substituents and the crystal packing effect (CPE) on the spin-state splitting. It is proposed to partition the total CPE into additive components, the direct and structural one, the importance of which is shown to significantly vary from case to case. By knowing the substituent effect, the CPE, and the Gibbs free energy thermodynamic correction from calculations, one can employ the experimental ground-state information in order to derive a quantitative constraint on the electronic energy difference for a simplified (porphin) model of the experimentally characterized metalloporphyrin. The constraints derived in such a way-in the form of single or double inequalities-are used to assess the accuracy of dispersion-corrected DFT methods for 6 spin-state splittings of [FeIII(P)(2-MeIm)2]+, [FeIII(P)(2-MeIm)]+, [FeII(P)(THF)2] and [FeII(P)] models (where P is porphin, 2-MeIm is 2-methylimidazole, THF is tetrahydrofuran). These data constitute the new benchmark set of spin states for crystalline iron porphyrins (SSCIP6). The highest accuracy is obtained in the case of double-hybrid functionals (B2PLYP-D3, DSD-PBEB95-D3), whereas hybrid functionals, especially those with reduced admixture of the exact exchange (B3LYP*-D3, TPSSh-D3), are found to considerably overstabilize the intermediate spin state, leading to incorrect ground-state prediction in FeIII porphyrins. The present approach, which can be generalized to other transition metal complexes, is not only useful in method benchmarking, but also sheds light on the interpretations of experimental data for metalloporphyrins, which are important models to understand the electronic properties of heme proteins.
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Affiliation(s)
- Mariusz Radoń
- Faculty of Chemistry, Jagiellonian University, Kraków, Poland.
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Barakat M, Elhajj S, Yazji R, Miller AJM, Hasanayn F. Kinetic Isotope Effects and the Mechanism of CO 2 Insertion into the Metal-Hydride Bond of fac-(bpy)Re(CO) 3H. Inorg Chem 2024; 63:12133-12145. [PMID: 38901030 DOI: 10.1021/acs.inorgchem.4c01246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The 1,2-insertion reaction of CO2 into metal-hydride bonds of d6-octahedral complexes to give κ1-O-metal-formate products is the key step in various CO2 reduction schemes and as a result has attracted extensive mechanistic investigations. For many octahedral catalysts, CO2 insertion follows an associative mechanism in which CO2 interacts directly with the coordinated hydride ligand instead of the more classical dissociative mechanism that opens an empty coordination site to bind the substrate to the metal prior to a hydride migration step. To better understand the associative mechanism, we conducted a systematic quantum chemical investigation on the reaction between CO2 and fac-(bpy)Re(CO)3H (1-Re-H; bpy = 2,2'-bipyridine) starting with the gas phase and then moving to THF and other solvents with increased dielectric constants. Detailed analyses of the potential energy surfaces (PESs) and intrinsic reaction coordinates (IRCs) reveal that the reaction is enabled in all media by an initial stage of making a 3c-2e bond between the carbon of CO2 and the metal-hydride bond that is most consistent with an organometallic bridging hydride Re-H-CO2 species. Once CO2 is bent and anchored to the metal-hydride bond, the reaction proceeds by a rotation motion via a cyclic transition state TS2 that interchanges Re-H-CO2 and Re-O-CHO coordination. The combined stages provide an asynchronous-concerted pathway for CO2 insertion on the Gibbs free energy surface with TS2 as the highest energy point. Consideration of TS2 as a rate-determining TS gives activation barriers, inverse KIEs, substituent effects, and solvent effects that agree with the experimental data available in this system. An important new insight revealed by the analyses of the results is that the initial stage of the reaction is not a hydride transfer step as has been assumed in some studies. In fact, the loose vibration of the TS that can be identified for the first stage of the reaction in solution (TS1) does not involve the Re-H stretching vibrational mode. Accordingly, the imaginary frequency of TS1 is insensitive to deuteration, and therefore, TS1 leads to no significant KIE.
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Affiliation(s)
- Mariam Barakat
- Department of Chemistry, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Sarah Elhajj
- Department of Chemistry, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Riyad Yazji
- Department of Chemistry, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Alexander J M Miller
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Faraj Hasanayn
- Department of Chemistry, American University of Beirut, Beirut 1107 2020, Lebanon
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12
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Ma J, Qi S, Yan G, Kirillov AM, Yang L, Fang R. DFT Study on the Mechanisms and Selectivities in Rh (III)-Catalyzed [5 + 1] Annulation of 2-Alkenylanilides and 2-Alkylphenols with Allenyl Acetates. J Org Chem 2024; 89:8562-8577. [PMID: 38847049 DOI: 10.1021/acs.joc.4c00517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The mechanisms and regio-, chemo-, and stereoselectivity were theoretically investigated in the Rh(III)-catalyzed [5 + 1] annulation of 2-alkenylanilides and 2-alkylphenols with allenyl acetates. Two different reactants, 2-alkenylanilides and 2-alkylphenols, were selected as model systems in the density functional theory calculations. The obtained theoretical results show that both these reactants exhibit similar steps, namely, (1) N-H/O-H deprotonation and C-H activation, (2) allenyl acetate migratory insertion, (3) β-oxygen elimination, (4) intramolecular nucleophilic addition of the nitrogen/oxygen-rhodium bond resulting in [5 + 1]-annulation, and (5) protonation with the formation of the desired product and regeneration of the Rh(III) catalyst. The theoretical evidence suggests that the selectivity is determined at the step of allenyl acetate's migratory insertion. Moreover, the regioselectivity is driven by electronic effects, while the interaction energies (C-H···π and C-H···O interactions) play a more imperative role in controlling the stereoselectivity. The obtained theoretical results not only well rationalize the experimental observations but also provide important mechanistic insights for related types of [5 + 1]-annulation reactions.
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Affiliation(s)
- Ji Ma
- Key Laboratory of Chemical Additives for China National Light Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, P. R. China
| | - Simeng Qi
- Key Laboratory of Chemical Additives for China National Light Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, P. R. China
| | - Guowei Yan
- Key Laboratory of Chemical Additives for China National Light Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, P. R. China
| | - Alexander M Kirillov
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, Lisbon 1049-001, Portugal
| | - Lizi Yang
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Ran Fang
- Key Laboratory of Chemical Additives for China National Light Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, P. R. China
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13
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Spiegel M. Unveiling the Antioxidative Potential of Galangin: Complete and Detailed Mechanistic Insights through Density Functional Theory Studies. J Org Chem 2024; 89:8676-8690. [PMID: 38861646 PMCID: PMC11197094 DOI: 10.1021/acs.joc.4c00611] [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: 03/09/2024] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024]
Abstract
A comprehensive quantum mechanical investigation delved into the antioxidative activity of galangin (Glg). Thermochemical and kinetic data were used to assess antiradical, chelating, and renewal potential under physiological conditions. A brief comparison with reference antioxidants and other flavonoids characterized Glg as a moderate antioxidative agent. The substance showed significantly lower performance in lipid compared to aqueous solvent─the reaction rates for scavenging •OOH in both media were established at 3.77 × 103 M-1 s-1 and 6.21 × 104 M-1 s-1, respectively, accounting for the molar fraction of both interacting molecules at the given pH. The impact of pH value on the kinetics was assessed. Although efficient at chelating Cu(II) ions, the formed complexes can still undergo the Fenton reaction. On the other hand, they persistently scavenge •OH in statu nascendi. The flavonoid effectively repairs oxidatively damaged biomolecules except model lipid acids. All Glg radicals are readily restored by physiologically prevailing O2•-. Given this, the polyphenol is expected to participate in antiradical and regenerating activities multiple times, amplifying its antioxidative potential.
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Affiliation(s)
- Maciej Spiegel
- Department of Organic Chemistry and
Pharmaceutical Technology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland
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14
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Conboy A, Goodfellow AS, Kasten K, Dunne J, Cordes DB, Bühl M, Smith AD. De-epimerizing DyKAT of β-lactones generated by isothiourea-catalysed enantioselective [2 + 2] cycloaddition. Chem Sci 2024; 15:8896-8904. [PMID: 38873072 PMCID: PMC11168096 DOI: 10.1039/d4sc01410c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/17/2024] [Indexed: 06/15/2024] Open
Abstract
An enantioselective isothiourea-catalysed [2 + 2] cycloaddition of C(1)-ammonium enolates with pyrazol-4,5-diones is used to construct spirocyclic β-lactones in good yields, excellent enantioselectivity (99 : 1 er) but with modest diastereocontrol (typically 70 : 30 dr). Upon ring-opening with morpholine or alternative nucleophilic amines and alcohols β-hydroxyamide and β-hydroxyester products are generated with enhanced diastereocontrol (up to >95 : 5 dr). Control experiments show that stereoconvergence is observed in the ring-opening of diastereoisomeric β-lactones, leading to a single product (>95 : 5 dr, >99 : 1 er). Mechanistic studies and DFT analysis indicate a substrate controlled Dynamic Kinetic Asymmetric Transformation (DyKAT) involving epimerisation at C(3) of the β-lactone under the reaction conditions, coupled with a hydrogen bond-assisted nucleophilic addition to the Si-face of the β-lactone and stereodetermining ring-opening. The scope and limitations of a one-pot protocol consisting of isothiourea-catalysed enantio-determining [2 + 2] cycloaddition followed by diastereo-determining ring-opening are subsequently developed. Variation within the anhydride ammonium enolate precursor, as well as N(1) and C(3) within the pyrazol-4,5-dione scaffold is demonstrated, giving a range of functionalised β-hydroxyamides with high diastereo- and enantiocontrol (>20 examples, up to >95 : 5 dr and >99 : 1 er) via this DyKAT.
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Affiliation(s)
- Aífe Conboy
- EaStCHEM, School of Chemistry, University of St Andrews St Andrews Fife KY16 9ST UK
| | - Alister S Goodfellow
- EaStCHEM, School of Chemistry, University of St Andrews St Andrews Fife KY16 9ST UK
| | - Kevin Kasten
- EaStCHEM, School of Chemistry, University of St Andrews St Andrews Fife KY16 9ST UK
| | - Joanne Dunne
- EaStCHEM, School of Chemistry, University of St Andrews St Andrews Fife KY16 9ST UK
| | - David B Cordes
- EaStCHEM, School of Chemistry, University of St Andrews St Andrews Fife KY16 9ST UK
| | - Michael Bühl
- EaStCHEM, School of Chemistry, University of St Andrews St Andrews Fife KY16 9ST UK
| | - Andrew D Smith
- EaStCHEM, School of Chemistry, University of St Andrews St Andrews Fife KY16 9ST UK
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15
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Wang Z, Shi B, Zhao C, Zeng Y. Hypervalent Chalcogen Bonds Catalysis on the Intramolecular Aza-Michael Reaction of Aminochalcone: Catalytic Performance and Chalcogen Bond Properties. Chemistry 2024:e202401886. [PMID: 38857119 DOI: 10.1002/chem.202401886] [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: 05/14/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/12/2024]
Abstract
Chalcogen bond (ChB) catalysis, as a new type in the field of non-covalent bond catalysis, has become a hot research topic in the field of organocatalysis in recent years. In the present work, we investigated the catalytic performance of a series of hypervalent ChB catalysis based on the intramolecular Aza-Michael reaction of aminochalcone. The reaction includes the carbon-nitrogen bond coupling step (key step) and the proton transfer step. The catalytic performance of mono-dentate pentafluorophenyl chalcogen bond donor ChB1 was comparable to that of bis-dentate chalcogen bond donor ChB4, and stronger than that of mono-dentate chalcogen bond donors ChB2 and ChB3. The formation of the chalcogen bond between the catalyst and the carbonyl oxygen atom of the reactant, causing the charge rearrangement of the reactant and C(1) charge of the -C-Ph group to become more positive, thereby the ChB catalysis promoted the nucleophile reaction. The electron density of the chalcogen bond of the pre-complex, the most positive electrostatic potentials of the catalyst, and the NPA charge of the key atom are proportional to the Gibbs energy barrier of the C-N bond coupling process, which provides an idea to predict the catalytic activity of the ChB catalysis.
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Affiliation(s)
- Zhuo Wang
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-Materials, Hebei Normal University, Shijiazhuang, 050024, P. R. China
- Key Laboratory of Cluster Science, Ministry of Education of China, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Bo Shi
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-Materials, Hebei Normal University, Shijiazhuang, 050024, P. R. China
| | - Chang Zhao
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-Materials, Hebei Normal University, Shijiazhuang, 050024, P. R. China
| | - Yanli Zeng
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-Materials, Hebei Normal University, Shijiazhuang, 050024, P. R. China
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16
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Ivanchenko O, Odnoroh M, Rolle F, Kroeger AA, Mallet-Ladeira S, Mazières S, Guerre M, Coote ML, Destarac M. 2-Cyanopropan-2-yl versus 1-Cyanocyclohex-1-yl Leaving Group: Comparing Reactivities of Symmetrical Trithiocarbonates in RAFT Polymerization. Macromol Rapid Commun 2024:e2400317. [PMID: 38837466 DOI: 10.1002/marc.202400317] [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: 05/07/2024] [Revised: 05/29/2024] [Indexed: 06/07/2024]
Abstract
This study introduces bis(1-cyanocyclohex-1-yl)trithiocarbonate (TTC-bCCH) as a novel trithiocarbonate chain transfer agent and compares its reactivity with the previously described bis(2-cyanopropan-2-yl)trithiocarbonate (TTC-bCP) for the reversible addition-fragmentation chain transfer (RAFT) polymerization of styrene (St), n-butyl acrylate (nBA), and methyl methacrylate (MMA). Significant findings include the effective control of Mn and low dispersities from the onset of polymerization of St and nBA showing swift addition-fragmentation kinetics, leading to similar behaviors between the two RAFT agents. In contrast, a fourfold decrease of the chain transfer constant to MMA is established for TTC-bCCH over TTC-bCP. This trend is confirmed through density functional theory (DFT) calculations. Finally, the study compares thermoplastic elastomer properties of all-(meth)acrylic ABA block copolymers produced with both RAFT agents. The impact of dispersity of PMMA blocks on thermomechanical properties evaluated via rheological analysis reveals a more pronounced temperature dependence of the storage modulus (G') for the triblock copolymer synthesized with TTC-bCCH, indicating potential alteration of the phase separation.
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Affiliation(s)
- Oleksandr Ivanchenko
- Laboratoire SOFTMAT, Université Toulouse 3 - Paul Sabatier, CNRS UMR 5623, 118 route de Narbonne, Toulouse, 31062, France
| | - Maksym Odnoroh
- Laboratoire SOFTMAT, Université Toulouse 3 - Paul Sabatier, CNRS UMR 5623, 118 route de Narbonne, Toulouse, 31062, France
| | - Faustine Rolle
- Laboratoire SOFTMAT, Université Toulouse 3 - Paul Sabatier, CNRS UMR 5623, 118 route de Narbonne, Toulouse, 31062, France
| | - Asja A Kroeger
- Institute for Nanoscale Science & Technology, Flinders University, Adelaide, South Australia, 5042, Australia
| | - Sonia Mallet-Ladeira
- Institut de Chimie de Toulouse (UAR 2599) / Université Toulouse 3 - Paul Sabatier, 118 route de Narbonne, Toulouse, 31062, France
| | - Stéphane Mazières
- Laboratoire SOFTMAT, Université Toulouse 3 - Paul Sabatier, CNRS UMR 5623, 118 route de Narbonne, Toulouse, 31062, France
| | - Marc Guerre
- Laboratoire SOFTMAT, Université Toulouse 3 - Paul Sabatier, CNRS UMR 5623, 118 route de Narbonne, Toulouse, 31062, France
| | - Michelle L Coote
- Institute for Nanoscale Science & Technology, Flinders University, Adelaide, South Australia, 5042, Australia
| | - Mathias Destarac
- Laboratoire SOFTMAT, Université Toulouse 3 - Paul Sabatier, CNRS UMR 5623, 118 route de Narbonne, Toulouse, 31062, France
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17
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Collins S, Linnolahti M. Sheet Models for Methylaluminoxane (MAO) Activators? A Theoretical Case Study involving rac-Me 2Si(η 5-C 9H 6) 2Zr (SBIZr) Complexes. Chemphyschem 2024; 25:e202300856. [PMID: 38469662 DOI: 10.1002/cphc.202300856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/09/2024] [Accepted: 03/10/2024] [Indexed: 03/13/2024]
Abstract
Activation of SBIZrMe2 or SBIZrMeCl and a sheet model for an active component of hydrolytic MAO, (MeAlO)16(Me3Al)6, (16,6) has been studied by DFT. Contact ion-pair formation occurs through the intermediacy of SBIZrMe(Cl) or SBIZrMe2 reacting with sheet 16,6 to furnish SBIZrMe-μ-X(MeAlO)16(Me3Al)6 (2, X=Me, Cl). Contact ion-pairs 2 would be in equilibrium with heterodinuclear catalyst precursors [SBIZrMe2AlMe2][(MeAlO)16(Me3Al)6X] (3 (X=Me, Cl) through reversible binding of Me3Al at higher Al : Zr ratios. Calculations show that formation of ion-pairs 3 from contact ion-pairs 2 is more favourable for the SBIZr compared with the parent Cp2Zr complexes. TD-DFT calculations were conducted on relevant SBIZr complexes to relate the results to earlier spectroscopic studies of catalyst activation using UV-Vis spectroscopy. Finally, propene insertion into ion-pairs 2, SBIZrMe-μ-MeB(C6F5)3 (6) and [SBIZrMe][B(C6F5)4] (7) was studied at M06-2X/TZVP level of theory. These studies suggest that contact ion-pairs 2 are significantly less reactive towards insertion than 6 or 7, in disagreement with experiment.
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Affiliation(s)
- Scott Collins
- Department of Chemistry, University of Eastern Finland, Joensuu Campus, Yliopistokatu 7, FI-80100, Joensuu, Finland
| | - Mikko Linnolahti
- Department of Chemistry, University of Eastern Finland, Joensuu Campus, Yliopistokatu 7, FI-80100, Joensuu, Finland
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18
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Toro-González M, Akingbesote N, Bible A, Pal D, Sanders B, Ivanov AS, Jansone-Popova S, Popovs I, Benny P, Perry R, Davern S. Development of 225Ac-doped biocompatible nanoparticles for targeted alpha therapy. J Nanobiotechnology 2024; 22:306. [PMID: 38825717 PMCID: PMC11145892 DOI: 10.1186/s12951-024-02520-6] [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: 02/02/2024] [Accepted: 05/01/2024] [Indexed: 06/04/2024] Open
Abstract
Targeted alpha therapy (TAT) relies on chemical affinity or active targeting using radioimmunoconjugates as strategies to deliver α-emitting radionuclides to cancerous tissue. These strategies can be affected by transmetalation of the parent radionuclide by competing ions in vivo and the bond-breaking recoil energy of decay daughters. The retention of α-emitting radionuclides and the dose delivered to cancer cells are influenced by these processes. Encapsulating α-emitting radionuclides within nanoparticles can help overcome many of these challenges. Poly(lactic-co-glycolic acid) (PLGA) nanoparticles are a biodegradable and biocompatible delivery platform that has been used for drug delivery. In this study, PLGA nanoparticles are utilized for encapsulation and retention of actinium-225 ([225Ac]Ac3+). Encapsulation of [225Ac]Ac3+ within PLGA nanoparticles (Zave = 155.3 nm) was achieved by adapting a double-emulsion solvent evaporation method. The encapsulation efficiency was affected by both the solvent conditions and the chelation of [225Ac]Ac3+. Chelation of [225Ac]Ac3+ to a lipophilic 2,9-bis-lactam-1,10-phenanthroline ligand ([225Ac]AcBLPhen) significantly decreased its release (< 2%) and that of its decay daughters (< 50%) from PLGA nanoparticles. PLGA nanoparticles encapsulating [225Ac]AcBLPhen significantly increased the delivery of [225Ac]Ac3+ to murine (E0771) and human (MCF-7 and MDA-MB-231) breast cancer cells with a concomitant increase in cell death over free [225Ac]Ac3+ in solution. These results demonstrate that PLGA nanoparticles have potential as radionuclide delivery platforms for TAT to advance precision radiotherapy for cancer. In addition, this technology offers an alternative use for ligands with poor aqueous solubility, low stability, or low affinity, allowing them to be repurposed for TAT by encapsulation within PLGA nanoparticles.
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Affiliation(s)
- Miguel Toro-González
- Isotope Science and Engineering Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37830, USA
| | - Ngozi Akingbesote
- Isotope Science and Engineering Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37830, USA
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Amber Bible
- Biological and Environmental Systems Science Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37830, USA
| | - Debjani Pal
- Isotope Science and Engineering Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37830, USA
| | - Brian Sanders
- Biological and Environmental Systems Science Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37830, USA
| | - Alexander S Ivanov
- Physical Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37830, USA
| | - Santa Jansone-Popova
- Physical Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37830, USA
| | - Ilja Popovs
- Physical Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37830, USA
| | - Paul Benny
- Isotope Science and Engineering Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37830, USA
| | - Rachel Perry
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Sandra Davern
- Isotope Science and Engineering Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37830, USA.
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19
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Zgrabik J, Bhowmick R, Eckstrom FD, Harrison AR, Fetrow TV, Blake AV, Vlaisavljevich B, Daly SR. The Influence of Phosphorus Substituents on the Structures and Solution Speciation of Trivalent Uranium and Lanthanide Phosphinodiboranates. Inorg Chem 2024; 63:9451-9463. [PMID: 38011639 PMCID: PMC11134491 DOI: 10.1021/acs.inorgchem.3c02773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/29/2023]
Abstract
Here, we report the mechanochemical synthesis and characterization of homoleptic uranium and lanthanide phosphinodiboranates with isopropyl and ethyl substituents attached to phosphorus. M(H3BPiPr2BH3)3 complexes with M = U, Nd, Sm, Tb, and Er were prepared by ball milling UI3(THF)4, SmBr3, or MI3 with three equivalents of K(H3BPiPr2BH3). M(H3BPEt2BH3)3 with M = U and Nd were prepared similarly using K(H3BPEt2BH3), and the complexes were purified by extraction and crystallization from Et2O or CH2Cl2. Single-crystal XRD studies revealed that all five M(H3BPiPr2BH3)3 crystallize as dimers, despite the significant differences in metal radii across the series. In contrast, Nd(H3BPEt2BH3)3 with smaller ethyl substituents crystallized as a coordination polymer. Crystals of U(H3BPEt2BH3)3 were not suitable for structural analysis, but crystals of U(H3BPMe2BH3)3 isolated in low yield by solution methods were isostructural with Nd(H3BPEt2BH3)3. 1H and 11B NMR studies in C6D6 revealed that all of the complexes form mixtures of monomer and oligomers when dissolved, and the extent of oligomerization was highly dependent on metal radius and phosphorus substituent size. A comprehensive analysis of all structurally characterized uranium and lanthanide phosphinodiboranate complexes reported to date, including those with larger Ph and tBu substituents, revealed that the degree of oligomerization in solution can be correlated to differences in B-P-B angles obtained from single-crystal XRD studies. Density functional theory calculations, which included structural optimizations in combination with conformational searches using tight binding methods, replicated the general experimental trends and revealed free energy differences that account for the different solution and solid-state structures. Collectively, these results reveal how steric changes to phosphorus substituents significantly removed from metal coordination sites can have a significant influence on solution speciation, deoligomerization energies, and the solid-state structure of homoleptic phosphinodiboranate complexes containing trivalent f-metals.
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Affiliation(s)
- Joshua
C. Zgrabik
- Department
of Chemistry, The University of Iowa, E331 Chemistry Building, Iowa City, Iowa 52242, United States
| | - Rina Bhowmick
- Department
of Chemistry, The University of South Dakota, 414 E Clark St., Vermillion, South Dakota 57069, United States
| | - Francesca D. Eckstrom
- Department
of Chemistry, The University of Iowa, E331 Chemistry Building, Iowa City, Iowa 52242, United States
| | - A. Rayford Harrison
- Department
of Chemistry, The University of Iowa, E331 Chemistry Building, Iowa City, Iowa 52242, United States
| | - Taylor V. Fetrow
- Department
of Chemistry, The University of Iowa, E331 Chemistry Building, Iowa City, Iowa 52242, United States
| | - Anastasia V. Blake
- Department
of Chemistry, The University of Iowa, E331 Chemistry Building, Iowa City, Iowa 52242, United States
| | - Bess Vlaisavljevich
- Department
of Chemistry, The University of South Dakota, 414 E Clark St., Vermillion, South Dakota 57069, United States
| | - Scott R. Daly
- Department
of Chemistry, The University of Iowa, E331 Chemistry Building, Iowa City, Iowa 52242, United States
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20
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Jiang N, Darù A, Kunstelj Š, Vitillo JG, Czaikowski ME, Filatov AS, Wuttig A, Gagliardi L, Anderson JS. Catalytic, Spectroscopic, and Theoretical Studies of Fe 4S 4-Based Coordination Polymers as Heterogenous Coupled Proton-Electron Transfer Mediators for Electrocatalysis. J Am Chem Soc 2024; 146:12243-12252. [PMID: 38651361 DOI: 10.1021/jacs.4c03726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Iron-sulfur clusters play essential roles in biological systems, and thus synthetic [Fe4S4] clusters have been an area of active research. Recent studies have demonstrated that soluble [Fe4S4] clusters can serve as net H atom transfer mediators, improving the activity and selectivity of a homogeneous Mn CO2 reduction catalyst. Here, we demonstrate that incorporating these [Fe4S4] clusters into a coordination polymer enables heterogeneous H atom transfer from an electrode surface to a Mn complex dissolved in solution. A previously reported solution-processable Fe4S4-based coordination polymer was successfully deposited on the surfaces of different electrodes. The coated electrodes serve as H atom transfer mediators to a soluble Mn CO2 reduction catalyst displaying good product selectivity for formic acid. Furthermore, these electrodes are recyclable with a minimal decrease in activity after multiple catalytic cycles. The heterogenization of the mediator also enables the characterization of solution-phase and electrode surface species separately. Surface enhanced infrared absorption spectroscopy (SEIRAS) reveals spectroscopic signatures for an in situ generated active Mn-H species, providing a more complete mechanistic picture for this system. The active species, reaction mechanism, and the protonation sites on the [Fe4S4] clusters were further confirmed by density functional theory calculations. The observed H atom transfer reactivity of these coordination polymer-coated electrodes motivates additional applications of this composite material in reductive H atom transfer electrocatalysis.
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Affiliation(s)
- Ningxin Jiang
- Department of Chemistry, University of Chicago, Chicago,Illinois 60637, United States
| | - Andrea Darù
- Department of Chemistry, University of Chicago, Chicago,Illinois 60637, United States
| | - Špela Kunstelj
- Department of Chemistry, University of Chicago, Chicago,Illinois 60637, United States
| | - Jenny G Vitillo
- Department of Science and High Technology and INSTM, Università degli Studi dell'Insubria, Como 22100, Italy
| | - Maia E Czaikowski
- Department of Chemistry, University of Chicago, Chicago,Illinois 60637, United States
| | - Alexander S Filatov
- Department of Chemistry, University of Chicago, Chicago,Illinois 60637, United States
| | - Anna Wuttig
- Department of Chemistry, University of Chicago, Chicago,Illinois 60637, United States
| | - Laura Gagliardi
- Department of Chemistry, University of Chicago, Chicago,Illinois 60637, United States
- Pritzker School of Molecular Engineering, James Franck Institute, University of Chicago, Chicago,Illinois 60637, United States
| | - John S Anderson
- Department of Chemistry, University of Chicago, Chicago,Illinois 60637, United States
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21
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Song Z, Zhu C, Gong K, Wang R, Zhang J, Zhao S, Li Z, Zhang X, Xie J. Deciphering the Microdroplet Acceleration Factors of Aza-Michael Addition Reactions. J Am Chem Soc 2024; 146:10963-10972. [PMID: 38567839 DOI: 10.1021/jacs.4c02312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Microdroplet chemistry is emerging as a great tool for accelerating reactions by several orders of magnitude. Several unique properties such as extreme pHs, interfacial electric fields (IEFs), and partial solvation have been reported to be responsible for the acceleration; however, which factor plays the key role remains elusive. Here, we performed quantum chemical calculations to explore the underlying mechanisms of an aza-Michael addition reaction between methylamine and acrylamide. We showed that the acceleration in methanol microdroplets results from the cumulative effects of several factors. The acidic surface of the microdroplet plays a dominating role, leading to a decrease of ∼9 kcal/mol in the activation barrier. We speculated that the dissociation of both methanol and trace water contributes to the surface acidity. An IEF of 0.1 V/Å can further decrease the barrier by ∼2 kcal/mol. Partial solvation has a negligible effect on lowering the activation barrier in microdroplets but can increase the collision frequency between reactants. With acidity revealed to be the major accelerating factor for methanol droplets, reactions on water microdroplets should have even higher rates because water is more acidic. Both theoretically and experimentally, we confirmed that water microdroplets significantly accelerate the aza-Michael reaction, achieving an acceleration factor that exceeds 107. This work elucidates the multifactorial influences on the microdroplet acceleration mechanism, and with such detailed mechanistic investigations, we anticipate that microdroplet chemistry will be an avenue rich in opportunities in the realm of green synthesis.
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Affiliation(s)
- Zhexuan Song
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Chenghui Zhu
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Ke Gong
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Ruijing Wang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Jianze Zhang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Supin Zhao
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Zesheng Li
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Xinxing Zhang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Renewable Energy Conversion and Storage Centre, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Centre for New Organic Matter, Nankai University, Tianjin 300071, China
| | - Jing Xie
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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22
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Fletcher LS, Tedder ML, Olayiwola SO, Joyner NA, Mason MM, Oliver AG, Ensor DD, Dixon DA, Carrick JD. Next-Generation 3,3'-AlkoxyBTPs as Complexants for Minor Actinide Separation from Lanthanides: A Comprehensive Separations, Spectroscopic, and DFT Study. Inorg Chem 2024; 63:4819-4827. [PMID: 38437739 DOI: 10.1021/acs.inorgchem.3c02061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Progress toward the closure of the nuclear fuel cycle can be achieved if satisfactory separation strategies for the chemoselective speciation of the trivalent actinides from the lanthanides are realized in a nonproliferative manner. Since Kolarik's initial report on the utility of bis-1,2,4-triazinyl-2,6-pyridines (BTPs) in 1999, a perfect complexant-based, liquid-liquid separation system has yet to be realized. In this report, a comprehensive performance assessment for the separation of 241Am3+ from 154Eu3+ as a model system for spent nuclear fuel using hydrocarbon-actuated alkoxy-BTP complexants is described. These newly discovered complexants realize gains that contemporary aryl-substituted BTPs have yet to achieve, specifically: long-term stability in highly concentrated nitric acid solutions relevant to the low pH of unprocessed spent nuclear fuel, high DAm over DEu in the economical, nonpolar diluent Exxal-8, and the demonstrated capacity to complete the separation cycle with high efficiency by depositing the chelated An3+ to the aqueous layer via decomplexation of the metal-ligand complex. These soft-N-donor BTPs are hypothesized to function as bipolar complexants, effectively traversing the organic/aqueous interface for effective chelation and bound metal/ligand complex solubility. Complexant design, separation assays, spectroscopic analysis, single-crystal X-ray crystallographic data, and DFT calculations are reported.
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Affiliation(s)
- Lesta S Fletcher
- Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505-0001, United States
| | - Mariah L Tedder
- Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505-0001, United States
| | - Samiat O Olayiwola
- Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505-0001, United States
| | - Nickolas A Joyner
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Marcos M Mason
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Allen G Oliver
- Department of Chemistry, The University of Notre Dame, Notre Dame, Indiana 46656, United States
| | - Dale D Ensor
- Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505-0001, United States
| | - David A Dixon
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Jesse D Carrick
- Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee 38505-0001, United States
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23
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Chirila A, Hu Y, Linehan JC, Dixon DA, Wiedner ES. Thermodynamic and Kinetic Activity Descriptors for the Catalytic Hydrogenation of Ketones. J Am Chem Soc 2024; 146:6866-6879. [PMID: 38437011 DOI: 10.1021/jacs.3c13876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
Activity descriptors are a powerful tool for the design of catalysts that can efficiently utilize H2 with minimal energy losses. In this study, we develop the use of hydricity and H- self-exchange rates as thermodynamic and kinetic descriptors for the hydrogenation of ketones by molecular catalysts. Two complexes with known hydricity, HRh(dmpe)2 and HCo(dmpe)2, were investigated for the catalytic hydrogenation of ketones under mild conditions (1.5 atm and 25 °C). The rhodium catalyst proved to be an efficient catalyst for a wide range of ketones, whereas the cobalt catalyst could only hydrogenate electron-deficient ketones. Using a combination of experiment and electronic structure theory, thermodynamic hydricity values were established for 46 alkoxide/ketone pairs in both acetonitrile and tetrahydrofuran solvents. Through comparison of the hydricities of the catalysts and substrates, it was determined that catalysis was observed only for catalyst/ketone pairs with an exergonic H- transfer step. Mechanistic studies revealed that H- transfer was the rate-limiting step for catalysis, allowing for the experimental and computation construction of linear free-energy relationships (LFERs) for H- transfer. Further analysis revealed that the LFERs could be reproduced using Marcus theory, in which the H- self-exchange rates for the HRh/Rh+ and ketone/alkoxide pairs were used to predict the experimentally measured catalytic barriers within 2 kcal mol-1. These studies significantly expand the scope of catalytic reactions that can be analyzed with a thermodynamic hydricity descriptor and firmly establish Marcus theory as a valid approach to develop kinetic descriptors for designing catalysts for H- transfer reactions.
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Affiliation(s)
- Andrei Chirila
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yiqin Hu
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - John C Linehan
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - David A Dixon
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Eric S Wiedner
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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24
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Wang J, Wang Y. Strategies to Improve the Quantum Computation Accuracy for Electrochemical Windows of Ionic Liquids. J Phys Chem B 2024; 128:1943-1952. [PMID: 38354327 DOI: 10.1021/acs.jpcb.3c08127] [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
Rational design of ionic liquids (ILs) with wide electrochemical windows (ECWs) for high-voltage cathodes is essential to elevating the energy density of current rechargeable batteries. It is significant to determine appropriate strategies for accurately predicting the ECWs of ILs. In this study, we compare the calculated ECWs based on three quantum methods, including the highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) method, the ionization potential-electron affinity (IP-EA) method, and the thermodynamic method, under four unique combinations of simulation environments, and assess the discrepancies between the calculated and the experimental results of ECWs. For the three quantum methods, although HOMO-LUMO and IP-EA methods show limited prediction accuracy compared to the experimental values, they can qualitatively rank the anodic limits of anions and the cathodic limits of cations. For the thermodynamic method, we demonstrate that the highest accuracy can be achieved by considering the most rational redox reaction process. By varying the calculation environments, the calculated ECWs tend to be underestimated by considering separate cations and anions of ILs under gas phase, whereas they always exhibit overestimated results when calculating based on the cation-anion pairs. When the computation considers isolated ions with the solvent model plus proper thermodynamic corrections, we observe improved consistency with the experimental results. Though all methods have limitations to achieving perfect predictions of ECWs, we believe rational selection of calculation methods based on application-oriented scenarios can balance the efficiency and accuracy of the results for the development of a high-throughput and accurate database of ECWs for ILs.
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Affiliation(s)
- Jifeng Wang
- Department of Macromolecular Science, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Ying Wang
- Department of Macromolecular Science, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
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25
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Chakraborty R, Talbot JJ, Shen H, Yabuuchi Y, Carsch KM, Jiang HZH, Furukawa H, Long JR, Head-Gordon M. Quantum chemical modeling of hydrogen binding in metal-organic frameworks: validation, insight, predictions and challenges. Phys Chem Chem Phys 2024; 26:6490-6511. [PMID: 38324335 DOI: 10.1039/d3cp05540j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
A detailed chemical understanding of H2 interactions with binding sites in the nanoporous crystalline structure of metal-organic frameworks (MOFs) can lay a sound basis for the design of new sorbent materials. Computational quantum chemical calculations can aid in this quest. To set the stage, we review general thermodynamic considerations that control the usable storage capacity of a sorbent. We then discuss cluster modeling of H2 ligation at MOF binding sites using state-of-the-art density functional theory (DFT) calculations, and how the binding can be understood using energy decomposition analysis (EDA). Employing these tools, we illustrate the connections between the character of the MOF binding site and the associated adsorption thermodynamics using four experimentally characterized MOFs, highlighting the role of open metal sites (OMSs) in accessing binding strengths relevant to room temperature storage. The sorbents are MOF-5, with no open metal sites, Ni2(m-dobdc), containing Lewis acidic Ni(II) sites, Cu(I)-MFU-4l, containing π basic Cu(I) sites and V2Cl2.8(btdd), also containing π-basic V(II) sites. We next explore the potential for binding multiple H2 molecules at a single metal site, with thermodynamics useful for storage at ambient temperature; a materials design goal which has not yet been experimentally demonstrated. Computations on Ca2+ or Mg2+ bound to catecholate or Ca2+ bound to porphyrin show the potential for binding up to 4 H2; there is precedent for the inclusion of both catecholate and porphyrin motifs in MOFs. Turning to transition metals, we discuss the prediction that two H2 molecules can bind at V(II)-MFU-4l, a material that has been synthesized with solvent coordinated to the V(II) site. Additional calculations demonstrate binding three equivalents of hydrogen per OMS in Sc(I) or Ti(I)-exchanged MFU-4l. Overall, the results suggest promising prospects for experimentally realizing higher capacity hydrogen storage MOFs, if nontrivial synthetic and desolvation challenges can be overcome. Coupled with the unbounded chemical diversity of MOFs, there is ample scope for additional exploration and discovery.
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Affiliation(s)
- Romit Chakraborty
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Justin J Talbot
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Hengyuan Shen
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Yuto Yabuuchi
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Kurtis M Carsch
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Henry Z H Jiang
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Hiroyasu Furukawa
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Jeffrey R Long
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
- Department of Chemical and Biomedical Engineering, University of California, Berkeley, CA 94720, USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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26
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Šebesta F, Sovová Ž, Burda JV. Determination of Amino Acids' p Ka: Importance of Cavity Scaling within Implicit Solvation Models and Choice of DFT Functionals. J Phys Chem B 2024; 128:1627-1637. [PMID: 38345944 PMCID: PMC10895671 DOI: 10.1021/acs.jpcb.3c07007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Protonation states of molecules significantly influence the thermodynamics and kinetics of chemical reactions. This is especially important in biochemical processes, where appropriate protonation states of amino acids control the exo/endoergicity of practically all biochemical cycles. This paper is focused on appraisal of the impact of DFT functionals and PCM solvation models on the accuracy of pKa evaluations for all proteinogenic amino acids. Eight functionals (B3LYP, PBE0, revPBE0, M06-2X, M11, M11-L, TPSSh, and ωB97X-D) and four basis sets are considered, together with four kinds of implicit solvation models when additional attention is paid to a cavity construction. An influence of nonelectrostatic contributions and Wertz's corrections on Gibbs free energy is investigated together with accuracy of provided proton solvation energy. The best model is based on the M06-2X/6-311++G**/D-PCM/UAKS computational level. The fitting procedure is utilized to improve the accuracy of the evaluated models. All of these results are also compared with values obtained from the COSMOtherm program and CCSD(T) calculations. Results for cysteine and histidine are discussed individually, as they can be found in different protonation states at neutral pH.
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Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Žofie Sovová
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Jaroslav V. Burda
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
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27
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Tang M, Draper F, Pham LN, Ho CC, Huang H, Sun J, Thickett SC, Coote ML, Connell TU, Bissember AC. Photochemical Povarov-type Reactions: Electron Donor-Acceptor Photoactivation by Visible Light. J Org Chem 2024; 89:2683-2690. [PMID: 38314706 DOI: 10.1021/acs.joc.3c02746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
This report investigates the mechanism of photochemical Povarov-type reactions of N,N-dialkylanilines and maleimides in polar solvents (DMF or dioxane) in the presence of light. Fundamental aspects of the electron donor-acceptor (EDA) photoactivation pathway proposed to underpin this chemistry are examined through integrated experimental and computational studies. This approach provided evidence supporting the involvement of an EDA complex in facilitating this chemistry via a reaction mechanism that does not involve a triplet manifold. Most notably, our findings indicate that relying solely on UV-vis absorption spectroscopic data to either account for or predict reactivity in synthetic experiments may not always provide the complete picture. More specifically, this relates to considering UV-vis absorption spectroscopic data, calculated values for association constants (KEDA) and molar extinction coefficients (ε), with the reactivity observed in associated synthetic reactions in practice.
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Affiliation(s)
- Meiqiong Tang
- School of Natural Sciences - Chemistry, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Felicity Draper
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia
| | - Le Nhan Pham
- Institute for Nanoscale Science and Technology, Flinders University, Adelaide, South Australia 5042, Australia
| | - Curtis C Ho
- School of Natural Sciences - Chemistry, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Hai Huang
- Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China
| | - Jianwei Sun
- Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, School of Petrochemical Engineering, Changzhou University, Changzhou 213164, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Stuart C Thickett
- School of Natural Sciences - Chemistry, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Michelle L Coote
- Institute for Nanoscale Science and Technology, Flinders University, Adelaide, South Australia 5042, Australia
| | - Timothy U Connell
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia
| | - Alex C Bissember
- School of Natural Sciences - Chemistry, University of Tasmania, Hobart, Tasmania 7001, Australia
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28
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Prasanthkumar KP, Valayankadan F, Aravindakumar CT, P A, Babu A, Alvarez-Idaboy JR. Identifying the Transients and Transformation Products in Hydroxyl Radical-Methimazole Reactions Using DFT and UPLC-Q-TOF MS/MS Approaches. J Phys Chem B 2024; 128:1448-1460. [PMID: 38320124 DOI: 10.1021/acs.jpcb.3c07913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Oxidative reactions of the hydroxyl radical (·OH) with methimazole (MMI), an antithyroid drug, are crucial for understanding its fate in oxidizing environments. By synergistically integrating density functional theory and ultraperformance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (UPLC-Q-TOF MS/MS) techniques, we elucidated the transients and transformation products (TPs) arising from the ·OH-MMI reactions. We probed two hydrogen-atom abstraction (HA) reactions, three radical adduct formation reactions, and single electron transfer (SET) at the M06-2X/6-311++G(d,p)/SMD(water) level. All proposed reaction channels, except for HA from the methyl group and SET, were found to be barrier-free. SET is the dominant oxidation pathway, accounting for 44% of oxidations, as determined by branching ratio analysis. The selenium analogue, MSeI, exhibited minor reactivity differences compared to MMI, yet its overall patterns resembled those of ·OH-MMI reactions. TPs were generated experimentally by reacting MMI with ·OH produced by UV-photolysis of H2O2. Eight TPs were identified from an approximately 24% degradation of MMI using UPLC-Q-TOF MS/MS analysis, and an additional two TPs were identified from the approximately 52% degraded MMI sample. The exact identities of all of the TPs were established through their corresponding fragmentation patterns. This study elucidates the drug's susceptibility to free radical species under physiologically relevant conditions.
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Affiliation(s)
- Kavanal P Prasanthkumar
- Post Graduate and Research Department of Chemistry, Maharaja's College, Ernakulam 682 011, India
| | - Faseelath Valayankadan
- Post Graduate and Research Department of Chemistry, Maharaja's College, Ernakulam 682 011, India
| | - Charuvila T Aravindakumar
- School of Environmental Sciences, Mahatma Gandhi University, Kottayam 686 560, India
- Inter-University Instrumentation Centre, Mahatma Gandhi University, Kottayam 686 560, India
| | - Arun P
- Inter-University Instrumentation Centre, Mahatma Gandhi University, Kottayam 686 560, India
| | - Aswathy Babu
- Post Graduate and Research Department of Chemistry, Maharaja's College, Ernakulam 682 011, India
| | - Juan R Alvarez-Idaboy
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, México D. F. 04510, Mexico
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29
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Hegedüsová L, Blaise N, Pašteka LF, Budzák Š, Medveď M, Filo J, Mravec B, Slavov C, Wachtveitl J, Grabarz AM, Cigáň M. Enhancing the Potential of Fused Heterocycle-Based Triarylhydrazone Photoswitches. Chemistry 2024; 30:e202303509. [PMID: 38212244 DOI: 10.1002/chem.202303509] [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: 10/24/2023] [Indexed: 01/13/2024]
Abstract
Triarylhydrazones represent an attractive class of photochromic compounds offering many interesting features including high molar absorptivity, good addressability, and extraordinary thermal stability. In addition, unlike most other hydrazone-based photoswitches, they effectively absorb light above 365 nm. However, previously prepared triaryhydrazones suffer from low quantum yields of the Z→E photoisomerization. Here, we have designed a new subclass of naphthoyl-benzothiazole hydrazones that balance the most beneficial features of previously reported naphthoyl-quinoline and benzoyl-pyridine triarylhydrazones. These preserve the attractive absorption characteristics, exhibit higher thermal stability of the metastable form than the former and enhance the rate of the Z→E photoisomerization compared to the later, as a result of the weakening of the intramolecular hydrogen bonding between the hydrazone hydrogen and the benzothiazole moiety. Introducing the benzothiazole motif extends the tunability of the photochromic behaviour of hydrazone-based switches.
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Affiliation(s)
- Lea Hegedüsová
- Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, 84215, Slovakia
| | - Nadine Blaise
- Institute of Physical and Theoretical Chemistry, Faculty of Biochemistry, Chemistry, Pharmacy, Goethe University, Frankfurt am Main, 60438, Germany
| | - Lukáš F Pašteka
- Van Swinderen Institute for Particle Physics and Gravity, University of Groningen, Groningen, 9747AG, The Netherlands
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, 84215, Slovakia
| | - Šimon Budzák
- Department of Chemistry, Faculty of Natural Sciences, Matej Bel University, Banská Bystrica, 97400, Slovakia
| | - Miroslav Medveď
- Department of Chemistry, Faculty of Natural Sciences, Matej Bel University, Banská Bystrica, 97400, Slovakia
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, 77900, Czechia
| | - Juraj Filo
- Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, 84215, Slovakia
| | - Bernard Mravec
- Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, 84215, Slovakia
| | - Chavdar Slavov
- Department of Chemistry, University of South Florida, Tampa, FL 33620, Florida, US
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Faculty of Biochemistry, Chemistry, Pharmacy, Goethe University, Frankfurt am Main, 60438, Germany
| | - Anna M Grabarz
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, 84215, Slovakia
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, 50370, Poland
| | - Marek Cigáň
- Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, 84215, Slovakia
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30
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Selaković S, Rodić MV, Novaković I, Matić IZ, Stanojković T, Pirković A, Živković L, Spremo-Potparević B, Milčić M, Medaković V, Dimiza F, Psomas G, Anđelković K, Šumar-Ristović M. Cu(II) complexes with a salicylaldehyde derivative and α-diimines as co-ligands: synthesis, characterization, biological activity. Experimental and theoretical approach. Dalton Trans 2024; 53:2770-2788. [PMID: 38226867 DOI: 10.1039/d3dt03862a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Copper(II) complexes with an α-diimine show a wide variety of biological activities, such as antibacterial, antifungal, antioxidant and anticancer. In this work, we synthesized and structurally characterized two novel Cu(II) complexes with methyl 3-formyl-4-hydroxybenzoate (HL) and α-diimines: 2,2'-bipyridine (bipy) and 1,10-phenanthroline (phen). Crystal structure analysis shows that the formulas of the compounds are [Cu(bipy)(L)(BF4)] (1) and [Cu(phen)(L)(H2O)](BF4)·H2O (2), with BF4- as a ligand in complex 1, which is rarely coordinated to metals. Both complexes have a square pyramidal geometry, while DFT calculations showed that the most stable structures of complexes 1 and 2 in a water/DMSO mixture are square-planar derivatives [Cu(bipy)(L)]+ and [Cu(phen)(L)]+. The antibacterial activity of compounds was evaluated in vitro on four Gram-negative and four Gram-positive bacterial strains. Complex 2 showed greater antibacterial activity towards all bacterial strains comparable to the control compound Amikacin. Complex 2 exerted a strong cytotoxic effect against the tested cancer cell lines (IC50 values ranging from 0.32 to 0.44 μM). Both complexes caused apoptotic cell death in HeLa cells and a noticeable in vitro antiangiogenic effect. In the concentration range of 5 to 100 μM, the complexes showed the absence of a genotoxic effect and displayed a protective effect against oxidative DNA damage induced by H2O2 in human peripheral blood cells. The interaction between the compounds and calf-thymus DNA was evaluated by diverse techniques suggesting a tight binding, which was also confirmed by molecular docking. In addition, it was found that the complexes bind tightly and reversibly to bovine and human serum albumin.
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Affiliation(s)
- Snežana Selaković
- University of Belgrade - Faculty of Pharmacy, Department of General and Inorganic Chemistry, 11000 Belgrade, Serbia
| | - Marko V Rodić
- University of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, 21102 Novi Sad, Serbia
| | - Irena Novaković
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, Department of Chemistry, 11000 Belgrade, Serbia
| | - Ivana Z Matić
- Institute of Oncology and Radiology of Serbia, Belgrade, Serbia
| | | | - Andrea Pirković
- Institute for the Application of Nuclear Energy-INEP, Department for Biology of Reproduction, Serbia
| | - Lada Živković
- University of Belgrade - Faculty of Pharmacy, Department of Pathobiology, 11000 Belgrade, Serbia
| | | | - Miloš Milčić
- University of Belgrade - Faculty of Chemistry, 11000 Belgrade, Serbia.
| | - Vesna Medaković
- University of Belgrade - Faculty of Chemistry, 11000 Belgrade, Serbia.
| | - Filitsa Dimiza
- Laboratory of Inorganic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki GR-54124, Greece
| | - George Psomas
- Laboratory of Inorganic Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki GR-54124, Greece
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31
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Ma YZ, Premadasa UI, Bryantsev VS, Miles AR, Ivanov IN, Elgattar A, Liao Y, Doughty B. Unravelling photoisomerization dynamics in a metastable-state photoacid. Phys Chem Chem Phys 2024; 26:4062-4070. [PMID: 38224171 DOI: 10.1039/d3cp04454h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Direct access to trans-cis photoisomerization in a metastable state photoacid (mPAH) remains challenging owing to the presence of competing excited-state relaxation pathways and multiple transient isomers with overlapping spectra. Here, we reveal the photoisomerization dynamics in an indazole mPAH using time-resolved fluorescence (TRF) spectroscopy by exploiting a unique property of this mPAH having fluorescence only from the trans isomer. The combination of these experimental results with time-dependent density function theory (TDDFT) calculations enables us to gain mechanistic insight into this key dynamical process.
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Affiliation(s)
- Ying-Zhong Ma
- Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.
| | - Uvinduni I Premadasa
- Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.
| | - Vyacheslav S Bryantsev
- Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.
| | - Audrey R Miles
- Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Ilia N Ivanov
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Adnan Elgattar
- Department of Biomedical and Chemical Engineering, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - Yi Liao
- Department of Biomedical and Chemical Engineering, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - Benjamin Doughty
- Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.
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32
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Le TH, Ferro-Costas D, Fernández-Ramos A, Ortuño MA. Combined DFT and Kinetic Monte Carlo Study of UiO-66 Catalysts for γ-Valerolactone Production. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2024; 128:1049-1057. [PMID: 38293690 PMCID: PMC10823797 DOI: 10.1021/acs.jpcc.3c06053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/21/2023] [Accepted: 01/02/2024] [Indexed: 02/01/2024]
Abstract
Zr-based metal-organic frameworks (MOFs) are excellent heterogeneous porous catalysts due to their thermal stability. Their tunability via node and linker modifications makes them amenable for theoretical studies on catalyst design. However, detailed benchmarks on MOF-based reaction mechanisms combined with kinetics analysis are still scarce. Thus, we here evaluate different computational models and density functional theory (DFT) methods followed by kinetic Monte Carlo studies for a case reaction relevant in biomass upgrading, i.e., the conversion of methyl levulinate to γ-valerolactone catalyzed by UiO-66. We show the impact of cluster versus periodic models, the importance of the DF of choice, and the direct comparison to experimental data via simulated kinetics data. Overall, we found that Perdew-Burke-Ernzerhof (PBE), a widely employed method in plane-wave periodic calculations, greatly overestimates reaction rates, while M06 with cluster models better fits the available experimental data and is recommended whenever possible.
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Affiliation(s)
- Thanh-Hiep
Thi Le
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Universidade
de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - David Ferro-Costas
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Universidade
de Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Departamento
de Química Física, Facultade de Química, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Antonio Fernández-Ramos
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Universidade
de Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Departamento
de Química Física, Facultade de Química, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Manuel A. Ortuño
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Universidade
de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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33
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Wang Y, Zhang B, Wang W, Yuan P, Hu K, Zhang L, Yang D, Lu Y, Du G. Improvement of the Thermal Stability and Aqueous Solubility of Three Matrine Salts Assembled by the Similar Structure Salt Formers. Pharmaceuticals (Basel) 2024; 17:94. [PMID: 38256926 PMCID: PMC10818515 DOI: 10.3390/ph17010094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/31/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Matrine (MAT), a natural Chinese herbal medicine, has a unique advantage in the treatment of various chronic diseases. However, its low melting point, low bioavailability, and high dosage restrict its subsequent development into new drugs. In this study, three kinds of MAT salts, namely, MAT-2,5-dihydroxybenzoic acid (MAT-25DHB), MAT-2,6-dihydroxybenzoic acid (MAT-26DHB), and MAT-salicylic acid-hydrate (MAT-SAL-H2O), were designed and synthesized to improve the drugability of MAT. The three salts were characterized by using various analytical techniques, including single-crystal X-ray diffractometry, powder X-ray diffractometry, differential scanning calorimetry, thermogravimetry, and infrared spectroscopy. The results of the thermal stability evaluation showed that the formation of salts improved the stability of MAT; MAT-25DHB is the most stable salt reported at present. The results of aqueous solubility showed that the solubility of MAT-25DHB was higher than that of MAT, while that of MAT-26DHB and MAT-SAL-H2O were less. Given that the MAT-25DHB salt further improved the solubility of MAT, it is expected to be subjected to further research as an optimized salt. Lattice energy and solvation free energy are important factors affecting the solubility of salts; the reasons for the changes of solubility and stability of three kinds of salts are explained by calculating them.
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Affiliation(s)
- Yeyang Wang
- Beijing City Key Laboratory of Polymorphic Drugs, Center of Pharmaceutical Polymorphs, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Baoxi Zhang
- Beijing City Key Laboratory of Polymorphic Drugs, Center of Pharmaceutical Polymorphs, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Wenwen Wang
- Beijing City Key Laboratory of Polymorphic Drugs, Center of Pharmaceutical Polymorphs, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Penghui Yuan
- Beijing City Key Laboratory of Polymorphic Drugs, Center of Pharmaceutical Polymorphs, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Kun Hu
- Beijing City Key Laboratory of Polymorphic Drugs, Center of Pharmaceutical Polymorphs, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Li Zhang
- Beijing City Key Laboratory of Polymorphic Drugs, Center of Pharmaceutical Polymorphs, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Shandong Province Key Laboratory of Polymorphic Drugs, Shandong Yikang Pharmaceutical Co., Ltd., Tengzhou 277500, China
| | - Dezhi Yang
- Beijing City Key Laboratory of Polymorphic Drugs, Center of Pharmaceutical Polymorphs, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yang Lu
- Beijing City Key Laboratory of Polymorphic Drugs, Center of Pharmaceutical Polymorphs, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Guanhua Du
- Beijing City Key Laboratory of Drug Target and Screening Research, National Center for Pharmaceutical Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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34
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Multem AJH, Delaney AR, Kroeger AA, Coote ML, Colebatch AL. Utilising a Proton-Responsive 1,8-Naphthyridine Ligand for the Synthesis of Bimetallic Palladium and Platinum Complexes. Chem Asian J 2023:e202301071. [PMID: 38161148 DOI: 10.1002/asia.202301071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
We present four proton-responsive palladium and platinum complexes, [MCl2 (R PONNHO)] (M=Pd, Pt; R=i Pr, t Bu) synthesised by complexation of PdCl2 or PtCl2 (COD) with the 1,8-naphthyridine ligand R PONNHO. Deprotonation of [MCl2 (tBu PONNHO)] switches ligand coordination from mono- to dinucleating, offering a synthetic pathway to bimetallic PdII and PtII complexes [M2 Cl2 (tBu PONNO)2 ]. Two-electron reduction gives planar MI -MI complexes [M2 (tBu PONNO)2 ] (M=Pd, Pt) containing a metal-metal bond. In contrast to the related nickel system that forms a metallophosphorane [Ni2 (tBu PONNOPONNO)], an unusual phosphinite binding mode is observed in [M2 (tBu PONNO)2 ] containing close phosphinite-naphthyridinone P⋅⋅⋅O interactions, which is investigated spectroscopically, crystallographically and computationally. The presented proton-responsive and structurally-responsive R PONNHO and bimetallic R PONNO complexes offer a novel platform for future explorations of metal-ligand and metal-metal cooperativity with palladium and platinum.
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Affiliation(s)
- Arie J H Multem
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Andie R Delaney
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Asja A Kroeger
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
- Institute for Nanoscale Science & Technology, Flinders University, Adelaide, South Australia, 5042, Australia
| | - Michelle L Coote
- Institute for Nanoscale Science & Technology, Flinders University, Adelaide, South Australia, 5042, Australia
| | - Annie L Colebatch
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
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35
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Wang Y, Zhao C, Chen WK, Zeng Y. Chalcogen Bond Catalysis with Telluronium Cations for Bromination Reaction: Importance of Electrostatic and Polarization Effects. Chemistry 2023; 29:e202302749. [PMID: 37747101 DOI: 10.1002/chem.202302749] [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: 08/22/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 09/26/2023]
Abstract
Recently, chalcogen bond catalysts with telluronium cations have garnered considerable attention in organic reactions. In this work, chalcogen bond catalysis on the bromination reaction of anisole with N-bromosuccinimide (NBS) with the telluronium cationic catalysts has been explored with density functional theory (DFT). The catalytic reaction is divided into two stages: the bromine transfer step and the proton transfer step. Based on the computational results, one can find the rate-determining step is the bromine transfer step. Moreover, the present study elucidates that a stronger chalcogen bond between catalysts and NBS will give better catalytic performance. Additionally, this work also clarified the importance of the electrostatic and polarization effects in the chalcogen bond between the oxygen atom of NBS and the Te atom of the catalyst in this bromination reaction. The electrostatic and polarization effects are significantly influenced by the electron-withdrawing ability of the substitution groups on the catalysts. Moreover, the structure-property relationship between the strength of chalcogen bond, electrostatic effect, polarization effect and catalytic performance are established for the design of more efficient chalcogen bond catalysts.
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Affiliation(s)
- Yanjiang Wang
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, China
| | - Chang Zhao
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, China
| | - Wen-Kai Chen
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, China
| | - Yanli Zeng
- College of Chemistry and Materials Science, Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, 050024, China
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36
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Confer MP, Dixon DA. Acid Gas Capture by Nitrogen Heterocycle Ring Expansion. J Phys Chem A 2023; 127:10171-10183. [PMID: 37991507 DOI: 10.1021/acs.jpca.3c06094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Acid gases including CO2, OCS, CS2, and SO2 are emitted by industrial processes such as natural gas production or power plants, leading to the formation of acid rain and contributing to global warming as greenhouse gases. An important technological challenge is to capture acid gases and transform them into useful products. The capture of CO2, CS2, SO2, and OCS by ring expansion of saturated and unsaturated substituted nitrogen-strained ring heterocycles was computationally investigated at the G3(MP2) level. The effects of fluorine, methyl, and phenyl substituents on N and/or C were explored. The reactions for the capture CO2, CS2, SO2, and OCS by 3- and 4-membered N-heterocycles are exothermic, whereas ring expansion reactions with 5-membered rings are thermodynamically unfavorable. Incorporation of an OCS into the ring leads to the amide product being thermodynamically favored over the thioamide. CS2 and OCS capture reactions are more exothermic and exergonic than the corresponding CO2 and SO2 capture reactions due to bond dissociation enthalpy differences. Selected reaction energy barriers were calculated and correlated with the reaction thermodynamics for a given acid gas. The barriers are highest for CO2 and OCS and lowest for CS2 and SO2. The ability of a ring to participate in acid gas capture via ring expansion is correlated to ring strain energy but is not wholly dependent upon it. The expanded N-heterocycles produced by acid gas capture should be polymerizable, allowing for upcycling of these materials.
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Affiliation(s)
- Matthew P Confer
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - David A Dixon
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, United States
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37
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Delaney AR, Kroeger AA, Coote ML, Colebatch AL. Oxidative Addition and β-Hydride Elimination by a Macrocyclic Dinickel Complex: Observing Bimetallic Elementary Reactions. Chemistry 2023; 29:e202302366. [PMID: 37641804 DOI: 10.1002/chem.202302366] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
The dinickel(I) complex Ni2 (tBu PONNOPONNO), featuring a planar macrocyclic diphosphoranide ligand tBu PONNOPONNO, offers a unique architectural platform for observing bimetallic elementary reactions. Oxidative addition reactions of alkyl halides produce dinickel(II) complexes of the type Ni2 (μ-R)(μ-X)(tBu PONNOPONNO). However, when R=Et β-hydride elimination is observed to form a dinickel monohydride, with the rate dependent on the nature of X. DFT studies suggest a new mechanism for bimetallic β-hydride elimination, where the rate dependence arises from the steric pressure imposed by the X group on the opposing trans face of the dinickel macrocycle. This work enhances understanding of bimetallic elementary reactions, particularly β-hydride elimination, which have not been well-explored for dinuclear systems.
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Affiliation(s)
- Andie R Delaney
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Asja A Kroeger
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
- Institute for Nanoscale Science & Technology, Flinders University, Adelaide, South Australia, 5042, Australia
| | - Michelle L Coote
- Institute for Nanoscale Science & Technology, Flinders University, Adelaide, South Australia, 5042, Australia
| | - Annie L Colebatch
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
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38
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Ma Y, Li M, Huo Y, Zhou Y, Jiang J, Xie J, He M. Differences in the degradation behavior of disinfection by-products in UV/PDS and UV/H 2O 2 processes and the effect of their chemical properties. CHEMOSPHERE 2023; 345:140457. [PMID: 37839744 DOI: 10.1016/j.chemosphere.2023.140457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/17/2023]
Abstract
In this work, sixteen typical chlorinated and brominated aromatic disinfection by-products (DBPs) were selected as examples to investigate their different degradation mechanisms initiated by HO• and SO4•-. Addition reactions were the main mode of degradation of DBPs by HO•, while SO4•- dominated H-abstraction reactions and single electron transfer reactions. Chlorinated compounds had higher reactivity than brominated compounds. Furthermore, substituents with stronger electron-donating effects promoted the electrophilic reaction of DBPs with the two radicals. In addition, we developed a model based on the chemical properties LUMO, fmax-, and hardness for predicting the average reaction energy barriers for the initial reactions of DBPs with HO• and SO4•-. The model had good predictive performance for the difficulty of degradation of different DPBs by HO• and SO4•-, with R2 values of 0.85 and 0.87, respectively. Through the degradation efficiency simulation, we found that longer reaction times, higher oxidant concentrations and lower pollutant concentrations were more favorable for the removal of DBPs. The UV/PDS process showed better degradation of DBPs than the UV/H2O2 process. In addition, most degradation products of DBPs exhibited less toxicity to aquatic organisms than their parent compounds. This study provided theoretical guidance for the degradation and removal of other aromatic DBPs at the molecular level.
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Affiliation(s)
- Yuhui Ma
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
| | - Mingxue Li
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
| | - Yanru Huo
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
| | - Yuxin Zhou
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
| | - Jinchan Jiang
- Weihai Water Conservancy Service Center, Weihai, 264200, PR China
| | - Ju Xie
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225002, PR China
| | - Maoxia He
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China.
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39
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Kunchur HS, Sonawane SC, Saini P, Ramakrishnan S, Balakrishna MS. Copper(I) Complexes of Amide Functionalized Bisphosphine: Proximity Enhanced Metal-Ligand Cooperativity and Its Catalytic Advantage in C( sp3)-H Bond Activation of Unactivated Cycloalkanes in Dehydrogenative Carboxylation Reactions. Inorg Chem 2023. [PMID: 38031668 DOI: 10.1021/acs.inorgchem.3c01022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
The reactions of amide functionalized bisphosphine, o-Ph2PC6H4C-(O)N(H)C6H4PPh2-o (1) (BalaHariPhos), with copper salts is described. Treatment of 1 with CuX in a 1:1 molar ratio yielded chelate complexes of the type [CuX{(o-Ph2PC6H4C(O)N(H)C6H4PPh2-o)}-κ2-P,P] (X = Cl, 2; Br, 3; and I, 4), which on subsequent treatment with KOtBu resulted in a dimeric complex [Cu(o-Ph2PC6H4C(O)(N)C6H4PPh2-o)]2 (5). Interestingly, complexes 2-4 showed weak N-H···Cu interactions. These weak H-bonding interactions are studied in detail both experimentally and computationally. Also, CuI complexes 2-5 were employed in the oxidative dehydrogenative carboxylation (ODC) of unactivated cycloalkanes in the presence of carboxylic acids to form the corresponding allylic esters. Among complexes 2-5, halide-free dimeric CuI complex 5 showed excellent metal-ligand cooperativity in the oxidative dehydrogenative carboxylation (ODC) in the presence of carboxylic acids to form the corresponding allylic esters through C(sp3)-H bond activation of unactivated cycloalkanes. Mechanistic details of the catalytic process were established by isolating the precatalyst [Cu{(o-Ph2PC6H4C(O)(NH)C6H4PPh2-o)-κ2-P,P}(OOCPh)] (6) and fully characterized by mass spectrometry, NMR data, and single-crystal X-ray analysis. Density functional theory-based calculations further provided a quantitative understanding of the energetics of a series of H atom transfer steps occurring in the catalytic cycle.
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Affiliation(s)
- Harish S Kunchur
- Phosphorus Laboratory, Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sachin C Sonawane
- Phosphorus Laboratory, Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Prateek Saini
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | | - Maravanji S Balakrishna
- Phosphorus Laboratory, Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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40
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Qi S, Ma J, Yan G, Kirillov AM, Yang L, Fang R. Theoretical Analysis of a Three-Component Reaction between Two Diazo Compounds and a Hydroxylamine Derivative: Mechanism, Enantioselectivity, and Effect of Cooperative Catalysis. J Org Chem 2023. [PMID: 38032356 DOI: 10.1021/acs.joc.3c02061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
The mechanism, enantioselectivity, and effect of chiral phosphoric acid (CPA) cocatalyst were investigated by the density functional theory (DFT) for the three-component asymmetric aminohydroxylation between two diazo compounds and a hydroxylamine derivative. This type of cascade process is cooperatively catalyzed by Rh2(OAc)4 and CPA. The obtained results clearly indicate that the first step of the global reaction involves a nucleophilic attack at the nitrogen center of N-hydroxyaniline by rhodium-carbene intermediates producing imines. Subsequently, an enolate intermediate was recognized as the key species generated from the second diazo compound and the leaving benzyl alcohol (BnOH) fragment of the first step and in the presence of the same dirhodium catalyst. Then, the reaction is terminated by the asymmetric Mannich-type addition, delivering the aminohydroxylation products of an S-R conformation with the assistance of chiral phosphoric acid. The distortion/interaction analysis shows that the relative distortions of CPA and the enol play a vital role in the energy ordering of the stereocontrolling transition states (TSs). Furthermore, the influence of different substituents in CPA was fully rationalized by distortion/interaction analysis. This study opens up novel synthetic possibilities and improves the reaction predictability when exploring the related types of cooperatively catalyzed organic transformations.
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Affiliation(s)
- Simeng Qi
- Key Laboratory of Chemical Additives for China National Light Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, P. R. China
| | - Ji Ma
- Key Laboratory of Chemical Additives for China National Light Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, P. R. China
| | - Guowei Yan
- Key Laboratory of Chemical Additives for China National Light Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, P. R. China
| | - Alexander M Kirillov
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Lizi Yang
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
| | - Ran Fang
- Key Laboratory of Chemical Additives for China National Light Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, P. R. China
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41
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Lei X, Guan J, Lei Y, Yao L, Westerhoff P, Yang X. One-Electron Oxidant-Induced Transformations of Aromatic Alcohol to Ketone Moieties in Dissolved Organic Matter Increase Trichloromethane Formation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:18597-18606. [PMID: 36563128 DOI: 10.1021/acs.est.2c06425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Radicals in advanced oxidation processes (AOPs) degrade micropollutants during water and wastewater treatment, but the transformation of dissolved organic matter (DOM) may be equally important. Ketone moieties in DOM are known disinfection byproduct precursors, but ketones themselves are intermediates produced during AOPs. We found that aromatic alcohols in DOM underwent transformation to ketones by one-electron oxidants (using SO4•- as a representative), and the formed ketones significantly increased trichloromethane (CHCl3) formation potential (FP) upon subsequent chlorination. CHCl3-FPs from aromatic ketones (Ar-CO-CH3, average of 22 mol/mol) were 6-24 times of CHCl3-FPs from aromatic alcohols (Ar-CH(OH)-CH3, average of 0.85 mol/mol). At a typical SO4•- exposure of 7.0 × 10-12 M·s, CHCl3-FPs from aromatic alcohol transformation increased by 24.8%-112% with an average increase of 53.4%. Notably, SO4•- oxidation of aliphatic alcohols resulted in minute changes in CHCl3-FPs due to their low reactivities with SO4•- (∼107 M-1 s-1). Other one-electron oxidants (Cl2•-, Br2•-,and CO3•-) are present in AOPs and also lead to aromatic alcohol-ketone transformations similar to SO4•-. This study highlights that subtle changes in DOM physicochemical properties due to one-electron oxidants can greatly affect the reactivity with free chlorine and the formation of chlorinated byproducts.
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Affiliation(s)
- Xin Lei
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Jingmeng Guan
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Yu Lei
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Lu Yao
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Paul Westerhoff
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona 85287-3005, United States
| | - Xin Yang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
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42
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Radoń M. Benchmarks for transition metal spin-state energetics: why and how to employ experimental reference data? Phys Chem Chem Phys 2023; 25:30800-30820. [PMID: 37938035 DOI: 10.1039/d3cp03537a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Accurate prediction of energy differences between alternative spin states of transition metal complexes is essential in computational (bio)inorganic chemistry-for example, in characterization of spin crossover materials and in the theoretical modeling of open-shell reaction mechanisms-but it remains one of the most compelling problems for quantum chemistry methods. A part of this challenge is to obtain reliable reference data for benchmark studies, as even the highest-level applicable methods are known to give divergent results. This Perspective discusses two possible approaches to method benchmarking for spin-state energetics: using either theoretically computed or experiment-derived reference data. With the focus on the latter approach, an extensive general review is provided for the available experimental data of spin-state energetics and their interpretations in the context of benchmark studies, targeting the possibility of back-correcting the vibrational effects and the influence of solvents or crystalline environments. With a growing amount of experience, these effects can be now not only qualitatively understood, but also quantitatively modeled, providing the way to derive nearly chemically accurate estimates of the electronic spin-state gaps to be used as benchmarks and advancing our understanding of the phenomena related to spin states in condensed phases.
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Affiliation(s)
- Mariusz Radoń
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Krakow, Poland.
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43
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Mudge MN, Bhadbhade M, Ball GE, Colbran SB. Ruthenium(II) Complexes of a Xanthene-Spanned Dicarbene Ligand. Inorg Chem 2023; 62:18901-18914. [PMID: 37939015 DOI: 10.1021/acs.inorgchem.3c02348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Octahedral ruthenium(II) complexes of a xanthene-di(N-heterocyclic carbene) ancillary ligand (XdC) have been prepared and structurally characterized. Examples catalyze the transfer hydrogenation of ketones {[Ru(CO)I2(C,O,C'-XdC)] (1) and [Ru(CO)(MeCN)2(C,O,C'-XdC)]2+ (22+)} and the selective electrochemical reduction of CO2 to CO {[Ru(N,N'-bpy)(CO)(C,O,C'-XdC)]2+ (32+) at 0.40 V overpotential in MeCN-H2O (1 M)}. The reaction of 1 with KBEt3H afforded isomers of [(C,C'-XdC)Ru(μ-H)(H)]2 dimers, which are stable to reductive elimination of the XdC ligand, thereby suggesting similar (XdC)Rh(coligand)(H)x species may be viable intermediates in catalyses. The electrochemical reduction of CO2 involves a double reduction of 32+ to 3••, which has been characterized by IR-SEC and DFT calculations. The DFT calculations suggest the Ru-Oxanth bond breaks in 3••, opening a metal site for CO2 binding with selectivity over protons enabled by the diffuse nature of the HOMO delocalized over the metal and the bipyridine and carbonyl coligands. The results point to the promise of metal complexes of flexible and hemilabile xanthene-(NHC)2 ancillary ligands in catalysis.
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Affiliation(s)
- Matthew N Mudge
- School of Chemistry, University of New South Wales, Bedegal Country, Sydney, New South Wales 2052, Australia
| | - Mohan Bhadbhade
- Mark Wainwright Analytical Centre, University of New South Wales, Bedegal Country, Sydney, New South Wales 2052, Australia
| | - Graham E Ball
- School of Chemistry, University of New South Wales, Bedegal Country, Sydney, New South Wales 2052, Australia
| | - Stephen B Colbran
- School of Chemistry, University of New South Wales, Bedegal Country, Sydney, New South Wales 2052, Australia
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Yang G, Yun YJ, Peccati F, Jamhawi AM, Kamatham N, Jockusch S, Jiménez-Osés G, Ayitou AJL. Unraveling the Photophysical Characteristics, Aromaticity, and Stability of π-Extended Acene-Quinodimethyl Thioamides†. Chemphyschem 2023; 24:e202200906. [PMID: 37545345 DOI: 10.1002/cphc.202200906] [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: 12/12/2022] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/08/2023]
Abstract
Poly-aromatic systems that contain quinodimethyl (QDM) units are appealing for several photonic and spintronic applications owing to the unique electronic structure, aromaticity, and spin state(s) of the QDM ring. Herein, we report the synthesis and characterization of novel QDM-based chromophores 1-3, which exhibit unique photo-excited behavior and aromaticity. Extending the aromatic core with a biphenyl/phenanthryl- and a pyrrolo-fragment led to reducing the optoelectronic bandgap and modulating the photophysics QDM 1-3. Yet, QDM 2 and 3 suffer from "aromaticity imbalance" and become relatively unstable compared to the parent compound QDM 1. Further assessment of local aromaticity using computational tools revealed that the pseudo-quinoidal ring B is the main driving force allowing to easily populate the excited triplet state of these chromophores. The present study provides complementary guidelines for designing novel non-classical poly-aromatic systems.
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Affiliation(s)
- Guang Yang
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Young Ju Yun
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Francesca Peccati
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Spain
| | - Abdelqader M Jamhawi
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Nareshbabu Kamatham
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Steffen Jockusch
- Department of Chemistry & Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Spain
- Ikerbasque, Basque Foundation for Science, 48013, Bilbao, Spain
| | - A Jean-Luc Ayitou
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
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45
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Chao CBE, Pyne SG, Hyland CJT, Lee R. DFT Mechanistic Insights into the Ni(II)-Catalyzed Enantioselective Arylative Cyclization of Tethered Allene-Ketones. Chem Asian J 2023; 18:e202300724. [PMID: 37712336 DOI: 10.1002/asia.202300724] [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: 08/17/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023]
Abstract
Density functional theory (DFT) has provided a detailed mechanistic picture for the redox neutral nickel(II)-catalyzed arylative cyclization reactions of a tethered allene-ketone with arylboronic acids. A mechanistic rationale for the high diastereo- and enantioselectivity achieved experimentally at high reaction temperature was uncovered through modeling the reaction with a chiral ligand and the predicted stereochemical outcome corroborates with experimental results. An unprecedented mechanism for the base-free organoboron transmetalation was revealed and the regioselectivity of migratory insertion of tethered allene-ketones as well as the stability of the possible allylnickel isomers (σ-allyl vs π-allyl) were clarified. The multifaceted nature of the reaction is revealed with certain elementary steps preferring cationic compared to the neutral state.
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Affiliation(s)
- Chi Bong Eric Chao
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Stephen G Pyne
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Christopher J T Hyland
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Richmond Lee
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia
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46
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Mutsuji A, Saita K, Maeda S. An energy decomposition and extrapolation scheme for evaluating electron transfer rate constants: a case study on electron self-exchange reactions of transition metal complexes. RSC Adv 2023; 13:32097-32103. [PMID: 37920761 PMCID: PMC10619204 DOI: 10.1039/d3ra05784d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023] Open
Abstract
A simple approach to the analysis of electron transfer (ET) reactions based on energy decomposition and extrapolation schemes is proposed. The present energy decomposition and extrapolation-based electron localization (EDEEL) method represents the diabatic energies for the initial and final states using the adiabatic energies of the donor and acceptor species and their complex. A scheme for the efficient estimation of ET rate constants is also proposed. EDEEL is semi-quantitative by directly evaluating the seam-of-crossing region of two diabatic potentials. In a numerical test, EDEEL successfully provided ET rate constants for electron self-exchange reactions of thirteen transition metal complexes with reasonable accuracy. In addition, its energy decomposition and extrapolation schemes provide all the energy values required for activation-strain model (ASM) analysis. The ASM analysis using EDEEL provided rational interpretations of the variation of the ET rate constants as a function of the transition metal complexes. These results suggest that EDEEL is useful for efficiently evaluating ET rate constants and obtaining a rational understanding of their magnitudes.
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Affiliation(s)
- Akihiro Mutsuji
- Graduate School of Chemical Sciences and Engineering, Hokkaido University Sapporo Hokkaido 060-8628 Japan
| | - Kenichiro Saita
- Department of Chemistry, Graduate School of Science, Hokkaido University Sapporo Hokkaido 060-0810 Japan
| | - Satoshi Maeda
- Department of Chemistry, Graduate School of Science, Hokkaido University Sapporo Hokkaido 060-0810 Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University Sapporo Hokkaido 001-0021 Japan
- ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Hokkaido University Sapporo Hokkaido 060-0810 Japan
- Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS) Tsukuba Ibaraki 305-0044 Japan
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47
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Mendieta A, Álvarez-Idaboy JR, Ugalde-Saldívar VM, Flores-Álamo M, Armenta A, Ferrer-Sueta G, Gasque L. Role of Imidazole and Chelate Ring Size in Copper Oxidation Catalysts: An Experimental and Theoretical Study. Inorg Chem 2023; 62:16677-16690. [PMID: 37792328 DOI: 10.1021/acs.inorgchem.3c01236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
In this work, the structural, solution, electrochemical, and catalytic properties of the complexes with ligands derived from imidazole and pyridines were studied. A comparative study of five bioinspired copper catalysts with or without coordinated imidazole and with different chelate ring sizes is presented. Catalytic efficiency on the oxidation of 3,5-di-tert-butylcatechol (DTBC) and ortho-aminophenol (OAP) in a MeOH/H2O medium was assessed by means of the Michaelis-Menten model. Catalysts comprising imidazole-containing ligands and/or a six-membered chelate ring proved to be more efficient in both oxidation reactions. Determination of stability constants and electrochemical parameters of the copper complexes supported the explanation of the catalytic behavior. A catalytic cycle similar for both reactions has been proposed. The results of density functional theory (DFT) free energy calculations for all five complexes and both catalytic reactions agree with the experimental results.
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Affiliation(s)
- Alan Mendieta
- Facultad de Química, Universidad Nacional Autónoma de México, Avenida Universidad 3000, CDMX 04510, México
| | - Juan Raúl Álvarez-Idaboy
- Facultad de Química, Universidad Nacional Autónoma de México, Avenida Universidad 3000, CDMX 04510, México
| | - Víctor M Ugalde-Saldívar
- Facultad de Química, Universidad Nacional Autónoma de México, Avenida Universidad 3000, CDMX 04510, México
| | - Marcos Flores-Álamo
- Facultad de Química, Universidad Nacional Autónoma de México, Avenida Universidad 3000, CDMX 04510, México
| | - Alfonso Armenta
- Facultad de Química, Universidad Nacional Autónoma de México, Avenida Universidad 3000, CDMX 04510, México
| | - Gerardo Ferrer-Sueta
- Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, UY 11400, Uruguay
| | - Laura Gasque
- Facultad de Química, Universidad Nacional Autónoma de México, Avenida Universidad 3000, CDMX 04510, México
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Yang Y, Zhang C, Qian X, Jia F, Liang S. Computational study on the mechanisms of inhibition of SARS-CoV-2 M pro by aldehyde warheads based on DFT. Phys Chem Chem Phys 2023; 25:26308-26315. [PMID: 37747304 DOI: 10.1039/d3cp03394e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
SARS-CoV-2 main protease, Mpro, plays a crucial role in the virus replication cycle, making it an important target for antiviral research. In this study, a simplified model obtained through truncation is used to explore the reaction mechanism of aldehyde warhead compounds inhibiting Mpro at the level of density functional theory. According to the calculation results, proton transfer (P_T)-nucleophilic attack (N_A) is the rate-determining step in the entire reaction pathway. The water molecule that plays a catalytic role occupies the oxyanion hole, which is unfavorable for the aldehyde warhead to approach the Cys145 SH. Through a hypothetical study of substituting the main chain NH with methylene, it is further confirmed that the P_T-N_A is a proton transfer-dominated process accompanied by a nucleophilic attack reaction. In this process, the oxyanion hole serves only to stabilize the aldehyde oxygen anion and therefore does not have a significant impact on the activation free energy barrier of the step. Our research results provide a unique perspective for understanding the covalent inhibition reaction of the Mpro active site. This study also offers theoretical guidance for the design of new Mpro covalent inhibitors.
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Affiliation(s)
- Yongsheng Yang
- School of Pharmacy and Institute of Pharmacy, North Sichuan Medical College, Sichuan, China.
| | - Chenghua Zhang
- School of Pharmacy and Institute of Pharmacy, North Sichuan Medical College, Sichuan, China.
| | - Xingcan Qian
- School of Pharmacy and Institute of Pharmacy, North Sichuan Medical College, Sichuan, China.
| | - Feiyun Jia
- School of Pharmacy and Institute of Pharmacy, North Sichuan Medical College, Sichuan, China.
| | - Shiwei Liang
- School of Basic Medical Sciences and Forensic Medicine, North Sichuan Medical College, Sichuan, China
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Choi J, Kim Y, Eser BE, Han J. Theoretical study on the glycosidic C-C bond cleavage of 3''-oxo-puerarin. Sci Rep 2023; 13:16282. [PMID: 37770535 PMCID: PMC10539306 DOI: 10.1038/s41598-023-43379-1] [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: 07/01/2023] [Accepted: 09/22/2023] [Indexed: 09/30/2023] Open
Abstract
Puerarin, daidzein C-glucoside, was known to be biotransformed to daidzein by human intestinal bacteria, which is eventually converted to (S)-equol. The metabolic pathway of puerarin to daidzein by DgpABC of Dorea sp. PUE strain was reported as puerarin (1) → 3''-oxo-puerarin (2) → daidzein (3) + hexose enediolone (C). The second reaction is the cleavage of the glycosidic C-C bond, supposedly through the quinoid intermediate (4). In this work, the glycosidic C-C bond cleavage reaction of 3''-oxo-puerarin (2) was theoretically studied by means of DFT calculation to elucidate chemical reaction mechanism, along with biochemical energetics of puerarin metabolism. It was found that bioenergetics of puerarin metabolism is slightly endergonic by 4.99 kcal/mol, mainly due to the reaction step of hexose enediolone (C) to 3''-oxo-glucose (A). The result implied that there could be additional biochemical reactions for the metabolism of hexose enediolone (C) to overcome the thermodynamic energy barrier of 4.59 kcal/mol. The computational study focused on the C-C bond cleavage of 3''-oxo-puerarin (2) found that formation of the quinoid intermediate (4) was not accessible thermodynamically, rather the reaction was initiated by the deprotonation of 2''C-H proton of 3''-oxo-puerarin (2). The 2''C-dehydro-3''-oxo-puerarin (2a2C) anionic species produced hexose enediolone (C) and 8-dehydro-daidzein anion (3a8), and the latter quickly converted to daidzein through the daidzein anion (3a7). Our study also explains why the reverse reaction of C-glycoside formation from daidzein (3) and hexose enediolone (C) is not feasible.
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Affiliation(s)
- Jongkeun Choi
- Department of Chemical Engineering, Chungwoon University, 113, Sukgol-ro, Michuhol-gu, Incheon, 22100, Republic of Korea
| | - Yongho Kim
- Department of Applied Chemistry, Institute of Applied Sciences, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Bekir Engin Eser
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus, Denmark
| | - Jaehong Han
- Metalloenzyme Research Group, Department of Plant Science and Technology, Chung-Ang University, 4726 Seodong-daero, Anseong, 17546, Republic of Korea.
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Lorpaiboon W, Ho J. High-Level Quantum Chemical Prediction of C-F Bond Dissociation Energies of Perfluoroalkyl Substances. J Phys Chem A 2023; 127:7943-7953. [PMID: 37722129 DOI: 10.1021/acs.jpca.3c04750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
In this study, 550 C-F bond dissociation energies (BDEs) of a variety of per- and polyfluoroalkyl substances (PFASs) obtained from high-level DLPNO-CCSD(T)/CBS calculations were used to assess the accuracy of contemporary density functional theory (DFT) and semiempirical methods. DLPNO-CCSD(T)/CBS gas phase C-F BDEs fall between 404.9-550.7 kJ mol-1 and M06-2X and ωB97M-V in conjunction with the aug-cc-pVTZ basis set predicted BDEs closest to the benchmark level with a mean absolute deviation (MAD) of 7.3 and 8.3 kJ mol-1, respectively. It was observed that DFT prediction errors increase with the degree of fluorination and system size. As such, previous model chemistry recommendations based on smaller nonfluorinated systems may not be carried over to modeling the energetics of PFASs and related systems.
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Affiliation(s)
- Wanutcha Lorpaiboon
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Junming Ho
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
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