1
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Denjean AEF, Rio J, Ciofini I, Perrin MEL, Payard PA. Computed versus experimental energy barriers in solution: Influence of the type of the density functional approximation. J Comput Chem 2024; 45:2284-2293. [PMID: 38847601 DOI: 10.1002/jcc.27436] [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: 03/20/2024] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 08/15/2024]
Abstract
Mechanistic investigations at the density functional theory level of organic and organometallic reactions in solution are now broadly accessible and routinely implemented to complement experimental investigations. The selection of an appropriate functional among the plethora of developed ones is the first challenge on the way to reliable energy barrier calculations. To provide guidelines for the choice of an initial and reliable computational level, the performances of commonly used non-empirical (PBE, PBE0, PBE0-DH) and empirical density functionals (BLYP, B3LYP, B2PLYP) were evaluated relative to experimental activation enthalpies. Most reactivity databases to assess density functional performances are primarily based on high level calculations, here a set of experimental activation enthalpies of organic and organometallic reactions performed in solution were selected from the literature. As a general trend, the non-empirical functionals outperform the empirical ones. The most accurate energy barriers are obtained with hybrid PBE0 and double-hybrid PBE0-DH density functionals, both providing similar performance. Regardless of the functional under consideration, the addition of the GD3-BJ empirical dispersion correction does not enhance the accuracy of computed energy barriers.
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Affiliation(s)
- Aurore E F Denjean
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
- Universite Claude Bernard Lyon I, CNRS, CPE-Lyon, INSA-Lyon, UMR 5246, ICBMS Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Villeurbanne, France
| | - Jordan Rio
- Universite Claude Bernard Lyon I, CNRS, CPE-Lyon, INSA-Lyon, UMR 5246, ICBMS Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Villeurbanne, France
| | - Ilaria Ciofini
- i-CLeHS (UMR 8060), CNRS Chimie Paris-Tech-PSL, Université Paris Sciences et Lettres, Paris, France
| | - Marie-Eve L Perrin
- Universite Claude Bernard Lyon I, CNRS, CPE-Lyon, INSA-Lyon, UMR 5246, ICBMS Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Villeurbanne, France
| | - Pierre-Adrien Payard
- Universite Claude Bernard Lyon I, CNRS, CPE-Lyon, INSA-Lyon, UMR 5246, ICBMS Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Villeurbanne, France
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2
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Mashhadimoslem H, Abdol MA, Karimi P, Zanganeh K, Shafeen A, Elkamel A, Kamkar M. Computational and Machine Learning Methods for CO 2 Capture Using Metal-Organic Frameworks. ACS NANO 2024; 18:23842-23875. [PMID: 39173133 DOI: 10.1021/acsnano.3c13001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Machine learning (ML) using data sets of atomic and molecular force fields (FFs) has made significant progress and provided benefits in the fields of chemistry and material science. This work examines the interactions between chemistry and materials computational science at the atomic and molecular scales for metal-organic framework (MOF) adsorbent development toward carbon dioxide (CO2) capture. Herein, a connection will be drawn between atomic forces predicted by ML algorithms and the structures of MOFs for CO2 adsorption. Our study also takes into account the successes of atomic computational screening in the field of materials science, especially quantum ML, and its relationship to ML algorithms that clarify advancements in the area of CO2 adsorption by MOFs. Additionally, we reviewed the processes for supplying data to ML algorithms for algorithm training, including text mining from scientific articles, and MOF's formula processing linked to the chemical properties of MOFs. To create ML algorithms for future research, we recommend that the digitization of scientific records can help efficiently synthesize advanced MOFs. Finally, a future vision for developing pioneer MOF synthesis routes for CO2 capture is presented in this review article.
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Affiliation(s)
- Hossein Mashhadimoslem
- Chemical Engineering Department, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Mohammad Ali Abdol
- Chemical Engineering Department, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Peyman Karimi
- Chemical Engineering Department, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Kourosh Zanganeh
- Natural Resources Canada (NRCan), Canmet ENERGY-Ottawa (CE-O), 1 Haanel Dr., Ottawa, ON K1A 1M1 Canada
| | - Ahmed Shafeen
- Natural Resources Canada (NRCan), Canmet ENERGY-Ottawa (CE-O), 1 Haanel Dr., Ottawa, ON K1A 1M1 Canada
| | - Ali Elkamel
- Chemical Engineering Department, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Department of Chemical Engineering, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Milad Kamkar
- Chemical Engineering Department, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Shupletsov L, Topal S, Schieck A, Helten S, Grünker R, Deka A, De A, Werheid M, Bon V, Weidinger I, Pöppl A, Senkovska I, Kaskel S. Linker Conformation Controls Oxidation Potentials and Electrochromism in Highly Stable Zr-Based Metal-Organic Frameworks. J Am Chem Soc 2024. [PMID: 39226465 DOI: 10.1021/jacs.4c04653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
The development of tailor-made electrochromic (EC) materials requires a large variety of available substances with properties that precisely match the task. Since the inception of electrochromic metal-organic frameworks (MOFs), the field relies only on a limited set of building blocks, providing the desired electrochromic effect. Herein, we demonstrate for the first time the implementation of a Piccard-type system (N,N,N',N'-benzidinetetrabenzoate) into Zr-MOFs to obtain electrochromic materials. With fast switching rates, high contrast ratio, long-life stability, and exceptional chemical and physical stability, the novel material is on par with inorganic EC material. The new EC system exhibits an ultrahigh contrast from the bleaching state, with transmittance in the visible region >53%, to the colored state with a transmittance of ca. 3%. The 5 μm thick film attained up to 90% of the coloring in 12.5 s and exhibited high electrochemical reversibility. Moreover, the conformational lability of the electrochromic ligand chosen is locked via the topology design of the framework, which is not attainable in the solution. Locked conformations of the redox active linker in distinct polymorphous frameworks (DUT-65 and DUT-66) feature different redox characteristics and opens the door to the overarching control of the oxidation pathway in the Piccard-type systems.
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Affiliation(s)
- Leonid Shupletsov
- Chair of Inorganic Chemistry I, Technische Universität Dresden, 01069 Dresden, Germany
| | - Sebahat Topal
- Chair of Inorganic Chemistry I, Technische Universität Dresden, 01069 Dresden, Germany
| | - Alina Schieck
- Chair of Inorganic Chemistry I, Technische Universität Dresden, 01069 Dresden, Germany
| | - Stella Helten
- Chair of Inorganic Chemistry I, Technische Universität Dresden, 01069 Dresden, Germany
| | - Ronny Grünker
- Chair of Inorganic Chemistry I, Technische Universität Dresden, 01069 Dresden, Germany
| | - Antareekshya Deka
- Felix Bloch Institute for Solid State Physics, Leipzig University, 04103 Leipzig, Germany
| | - Ankita De
- Chair of Inorganic Chemistry I, Technische Universität Dresden, 01069 Dresden, Germany
| | - Matthias Werheid
- Chair of Electrochemistry, Technische Universität Dresden, 01069 Dresden, Germany
| | - Volodymyr Bon
- Chair of Inorganic Chemistry I, Technische Universität Dresden, 01069 Dresden, Germany
| | - Inez Weidinger
- Chair of Electrochemistry, Technische Universität Dresden, 01069 Dresden, Germany
| | - Andreas Pöppl
- Felix Bloch Institute for Solid State Physics, Leipzig University, 04103 Leipzig, Germany
| | - Irena Senkovska
- Chair of Inorganic Chemistry I, Technische Universität Dresden, 01069 Dresden, Germany
| | - Stefan Kaskel
- Chair of Inorganic Chemistry I, Technische Universität Dresden, 01069 Dresden, Germany
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4
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Kumar A, Verma H, Gangwar P, Jangid K, Kumar V, Dhiman M, Jaitak V. Estrogen receptor alpha (ER-α) antagonistic activity of phytoconstituents from Potentilla atrosanguinea and Potentilla fulgens in breast cancer. Fitoterapia 2024; 177:106123. [PMID: 39004288 DOI: 10.1016/j.fitote.2024.106123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/07/2024] [Accepted: 07/08/2024] [Indexed: 07/16/2024]
Abstract
The Potentilla genus has long been used traditionally as food and a folklore medicine. In the present study, aerial parts of two Potentilla species, Potentilla fulgens and Potentilla atrosanguinea, of western Himalayan origin, were studied for their anti-breast cancer activity. Ethyl acetate (PAA-EA, PFA-EA), methanolic (PAA-ME, PFA-ME) and hydro-methanolic extract (PAA-HM, PFA-HM) of the plants were tested for their antiproliferative activities against MCF-7 and T-47D breast cancer cell lines. The extracts showed good antiproliferative activity against ER-α dominant breast cancer cell line T-47D, having IC50 values 6.19 ± 0.01 to 33.23 ± 0.04 μg/ml. Eight compounds were isolated, characterized, and quantified from ethyl acetate and methanolic extracts by column chromatography, 1D, 2D-NMR, HRMS and TLC densitometric analysis. Two compounds (4 and 6) have shown better antiproliferative activity than standard bazedoxifene and were further evaluated for their ER-α binding affinity via-fluorescence polarization-based competitive binding assay. The antiestrogenic properties of both compounds were assessed using western blotting. Compounds 4 and 6 were found to have significant affinity for the ER-α and managed to decrease its expression by 38 and 54% respectively. Compounds 4 and 6 also had good stability and reactivity as measured by minimal fluctuations in molecular dynamic simulation analysis, a good dock score in molecular docking, and a respectable HOMO-LUMO energy gap in DFT calculations. Compounds 4 and 6 have shown reliable results and can be used in the development of natural product-based anti-breast cancer agents.
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Affiliation(s)
- Amit Kumar
- Natural Products Chemistry Lab, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Harkomal Verma
- Department of Zoology, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Prabhakar Gangwar
- Department of Zoology, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Kailash Jangid
- Department of Chemistry, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Vinod Kumar
- Department of Chemistry, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Monisha Dhiman
- Department of Microbiology, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Vikas Jaitak
- Natural Products Chemistry Lab, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India..
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5
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Faraji S, Liu M. Transferable machine learning interatomic potential for carbon hydrogen systems. Phys Chem Chem Phys 2024; 26:22346-22358. [PMID: 39140158 DOI: 10.1039/d4cp02300e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
In this study, we developed a machine learning interatomic potential based on artificial neural networks (ANN) to model carbon-hydrogen (C-H) systems. The ANN potential was trained on a dataset of C-H clusters obtained through density functional theory (DFT) calculations. Through comprehensive evaluations against DFT results, including predictions of geometries and formation energies across 0D-3D systems comprising C and C-H, as well as modeling various chemical processes, the ANN potential demonstrated exceptional accuracy and transferability. Its capability to accurately predict lattice dynamics, crucial for stability assessment in crystal structure prediction, was also verified through phonon dispersion analysis. Notably, its accuracy and computational efficiency in calculating force constants facilitated the exploration of complex energy landscapes, leading to the discovery of a novel C polymorph. These results underscore the robustness and versatility of the ANN potential, highlighting its efficacy in advancing computational materials science by conducting precise atomistic simulations on a wide range of C-H materials.
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Affiliation(s)
- Somayeh Faraji
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.
| | - Mingjie Liu
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.
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6
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Romero M, Kushnir JS, Mochi B, Velez C, Acevedo O. Monte Carlo QM/MM simulation studies of the Cannizzaro reaction in ionic liquids for improved biofuel production. J Chem Phys 2024; 161:084117. [PMID: 39206828 DOI: 10.1063/5.0222092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
The conversion of biomass to 5-hydroxymethylfurfural (HMF) holds substantial promise as a renewable energy source. Notably, HMF can be transformed into 2,5-bis(hydroxymethyl)furan (BHMF), a crucial reactant in biofuel production, but requires harsh operating conditions, H2, and precious metal catalysts. A recently reported Cannizzaro reaction of HMF to BHMF, characterized by its efficiency, mild conditions, and eco-friendliness, instead employed ionic liquids (ILs) to achieve high yields. In this study, combined quantum mechanical and molecular mechanical (QM/MM) simulations in conjunction with Metropolis Monte Carlo statistical mechanics and free-energy perturbation theory utilized M06-2X/6-31+G(d), PDDG/PM3, and the OPLS-VSIL force field to uncover important solute-solvent interactions present in the HMF to BHMF reaction pathway. The Cannizzaro reaction was examined in water and in five ILs composed of the 1-butyl-3-methylimidazolium [BMIM] cation coupled to hexafluorophosphate, tetrafluoroborate, thiocyanate, chloride, and bromide. Energetic and structural analysis of the rate-determining hydride transfer between HMF and the hydride-donor anion HMFOH- attributed the enhanced reactivity to highly organized solvent interactions featuring (1) hydrogen bonding between the ring protons of [BMIM] and the negatively charged carbonyl oxygen atoms on the transition structure, (2) favorable electrostatic interactions between the IL anions and solute hydroxyl groups, and (3) beneficial π-π stacking interactions between [BMIM] and the two aromatic rings present in HMF and HMFOH-.
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Affiliation(s)
- Maria Romero
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, USA
| | - Jamie S Kushnir
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, USA
| | - Bruno Mochi
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, USA
| | - Caroline Velez
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, USA
| | - Orlando Acevedo
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, USA
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7
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Gray M, Bowling PE, Herbert JM. Comment on "Benchmarking Basis Sets for Density Functional Theory Thermochemistry Calculations: Why Unpolarized Basis Sets and the Polarized 6-311G Family Should Be Avoided". J Phys Chem A 2024. [PMID: 39190891 DOI: 10.1021/acs.jpca.4c00283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Affiliation(s)
- Montgomery Gray
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Paige E Bowling
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M Herbert
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
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8
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Hintersatz C, Tsushima S, Kaufer T, Kretzschmar J, Thewes A, Pollmann K, Jain R. Efficient density functional theory directed identification of siderophores with increased selectivity towards indium and germanium. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135523. [PMID: 39178780 DOI: 10.1016/j.jhazmat.2024.135523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 08/06/2024] [Accepted: 08/13/2024] [Indexed: 08/26/2024]
Abstract
Siderophores are promising ligands for application in novel recycling and bioremediation technologies, as they can selectively complex a variety of metals. However, with over 250 known siderophores, the selection of suiting complexants in the wet lab is impractical. Thus, this study established a density functional theory (DFT) based approach to efficiently identify siderophores with increased selectivity towards target metals on the example of germanium and indium. Considering 239 structures, chemically similar siderophores were clustered, and their complexation reactions modeled utilizing DFT. The calculations revealed siderophores with, compared to the reference siderophore desferrioxamine B (DFOB), up to 128 % or 48 % higher selectivity for indium or germanium, respectively. Experimental validation of the method was conducted with fimsbactin A and agrobactin, demonstrating up to 40 % more selective indium binding and at least sevenfold better germanium binding than DFOB, respectively. The results generated in this study open the door for the utilization of siderophores in eco-friendly technologies for the recovery of many different critical metals from various industry waters and leachates or bioremediation approaches. This endeavor is greatly facilitated by applying the herein-created database of geometry-optimized siderophore structures as de novo modeling of the molecules can be omitted.
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Affiliation(s)
- Christian Hintersatz
- Helmholtz Institute Freiberg for Resource Technology, Department of Biotechnology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Satoru Tsushima
- Institute of Resource Ecology, Department of Biophysics, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Tobias Kaufer
- Helmholtz Institute Freiberg for Resource Technology, Department of Biotechnology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Jerome Kretzschmar
- Institute of Resource Ecology, Department of Actinide Thermodynamics, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Angela Thewes
- Helmholtz Institute Freiberg for Resource Technology, Department of Biotechnology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Katrin Pollmann
- Helmholtz Institute Freiberg for Resource Technology, Department of Biotechnology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Rohan Jain
- Helmholtz Institute Freiberg for Resource Technology, Department of Biotechnology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany.
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9
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De S, Das B. Dimerization of Fe(III) Ion in an Aqueous Medium: Mechanistic Modelling and Effects of Ligands. Chemphyschem 2024; 25:e202400144. [PMID: 38727608 DOI: 10.1002/cphc.202400144] [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: 02/07/2024] [Revised: 05/09/2024] [Indexed: 06/16/2024]
Abstract
Aqueous iron solutions generally undergo spontaneous hydrolysis followed by aggregation resulting in the precipitation of nanocrystalline oxyhydroxide minerals. The mechanism of nucleation of such multinuclear oxyhydroxide clusters are unclear due to limited experimental evidence. Here, we investigate the mechanistic pathway of dimerization of Fe(III) ions using density functional theory (DFT) in aqueous medium considering effects of other ligands. Two hydrolyzed monomeric Fe(III) ions in aqueous medium may react to form two closely related binuclear products, the μ-oxo and the dihydroxo Fe2 dimer. Our studies indicate that the water molecules in the second coordination sphere and those co-ordinated to the Fe(III) ion, both participate in the dimerization process. The proposed mechanism effectively explains the formation of dihydroxo and μ-oxo Fe2 dimers with interconversion possibilities, for the first time. Results show, with only water molecules present in the second co-ordination sphere, dihydroxo Fe2 dimer is the thermodynamically and kinetically favored product with a low activation free energy. We calculated the step-wise reaction free energies of dimerization in the presence of nitrate ions in the first and second coordination sphere of Fe(III) ion separately, which shows that with nitrate ions in the second co-ordination sphere, the μ-oxo Fe2 dimer is the kinetically favored product.
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Affiliation(s)
- Sharmistha De
- School of Applied and Interdisciplinary Sciences (SAIS), Indian Association for the Cultivation of Science (IACS), Jadavpur, 700032, Kolkata, India
| | - Bidisa Das
- Research Institute for Sustainable Energy (RISE), Center for Research and Education in Science and Technology (TCG-CREST), Salt Lake, 700091, Kolkata, India
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10
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Ramdhani D, Watabe H, Hardianto A, Janitra RS. Complexation of 3p- C-NETA with radiometal ions: A density functional theory study for targeted radioimmunotherapy. Heliyon 2024; 10:e34875. [PMID: 39144950 PMCID: PMC11320446 DOI: 10.1016/j.heliyon.2024.e34875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 07/13/2024] [Accepted: 07/17/2024] [Indexed: 08/16/2024] Open
Abstract
Bifunctional chelators (BFCs) are vital in the design of effective radiopharmaceuticals, as they are able to bind to both a radiometal ion and a targeting vector. The 3p-C-NETA or 4-[2-(bis-carboxy-methylamino)-5-(4-nitrophenyl)-entyl])-7-carboxymethyl-[1,4,7]tri-azonan-1-yl acetic acid is a novel and promising BFC, developed for diagnostic and therapeutic purposes. The binding affinity between the BFC and radiometal ion significantly impacts their effectiveness. Predicting the equilibrium constants for the formation of 1:1 radiometals/chelator complexes (log K1 values) is crucial for designing BFCs with improved affinity and selectivity for radiometals. The purpose of this study is to evaluate the complexation of Ga3+, Tb3+, Bi3+, and Ac3+ radiometal ions with 3p-C-NETA using density functional theory (B3LYP and M06-HF functional) and 6-311G(d)/SDD basis sets, where the 1,4,7,10-tetrazacyclodecane-1,4,7,10-tetracetic acid (DOTA) was employed as a benchmark. Formation of the [Ac3+(3p-C-NETA)(H2O)]- complexes is predicted to be markedly less stable compared to the other complexes, exhibiting the lowest chemical hardness and the highest chemical softness. Additionally, the chelation stability of the complexes is mainly determined by ligand-ion and ion-water interactions, which depend on the atomic charge and atomic radius of the metal ion.
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Affiliation(s)
- Danni Ramdhani
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
- Division of Radiation Protection and Safety Control, Cyclotron and Radioisotope Center (CYRIC), Tohoku University, Sendai, Japan
| | - Hiroshi Watabe
- Division of Radiation Protection and Safety Control, Cyclotron and Radioisotope Center (CYRIC), Tohoku University, Sendai, Japan
| | - Ari Hardianto
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Regaputra S. Janitra
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
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11
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Bogo N, Stein CJ. Benchmarking DFT-based excited-state methods for intermolecular charge-transfer excitations. Phys Chem Chem Phys 2024; 26:21575-21588. [PMID: 39082837 DOI: 10.1039/d4cp01866d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Intermolecular charge-transfer is a highly important process in biology and energy-conversion applications where generated charges need to be transported over several moieties. However, its theoretical description is challenging since the high accuracy required to describe these excited states must be accessible for calculations on large molecular systems. In this benchmark study, we identify reliable low-scaling computational methods for this task. Our reference results were obtained from highly accurate wavefunction calculations that restrict the size of the benchmark systems. However, the density-functional theory based methods that we identify as accurate can be applied to much larger systems. Since targeting charge-transfer states requires the unambiguous classification of an excited state, we first analyze several charge-transfer descriptors for their reliability concerning intermolecular charge-transfer and single out the charge-transfer distance calculated based on the variation of electron density upon excitation (DCT) as an optimal choice for our purposes. In general, best results are obtained for orbital-optimized methods and among those, the maximum overlap method proved to be the most numerically stable variant when using the initial MOs as reference orbitals. Favorable error cancellation with optimally-tuned range-separated hybrid functionals and a rather small basis set can provide an economical yet reasonable wavefunction when using time-dependent density functional theory, which provides relevant information about the excited-state character to be used in the orbital-optimized methods. The qualitative agreement makes these fast calculations attractive for high-throughput screening applications.
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Affiliation(s)
- Nicola Bogo
- Faculty of Physics, University of Duisburg-Essen, 47057 Duisburg, Germany
- Department of Chemistry and Catalysis Research Center, TUM School of Natural Sciences, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany.
| | - Christopher J Stein
- Department of Chemistry and Catalysis Research Center, TUM School of Natural Sciences, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany.
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12
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Nakajima Y, Ohmura T, Seino J. Using atomic clustering based on structural and electronic descriptors that consider surrounding environment to evaluate local properties of DFT functionals. J Comput Chem 2024; 45:1870-1879. [PMID: 38686778 DOI: 10.1002/jcc.27375] [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: 11/12/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
We developed a method for evaluating the accuracies of the local properties of DFT functionals in detail using a clustering method based on machine learning and structural/electronic descriptors. We generated 36 clusters consistent with human intuition using 30,436 carbon atoms from the QM9 dataset. The results were used to evaluate 13C NMR chemical shifts calculated using 84 DFT functionals. Carbon atoms were grouped based on their similar environments, reducing errors within these groups. This enables more accurate assessment of the accuracy using a specific DFT functional. Therefore, the present atomic clustering provides more detailed insight into accuracy verification.
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Affiliation(s)
- Yuya Nakajima
- Waseda Research Institute for Science and Engineering, Tokyo, Japan
| | - Takuto Ohmura
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Junji Seino
- Waseda Research Institute for Science and Engineering, Tokyo, Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
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13
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Piskor T, Pinski P, Mast T, Rybkin V. Multi-Level Protocol for Mechanistic Reaction Studies Using Semi-Local Fitted Potential Energy Surfaces. Int J Mol Sci 2024; 25:8530. [PMID: 39126098 PMCID: PMC11312657 DOI: 10.3390/ijms25158530] [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: 06/28/2024] [Revised: 07/18/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
In this work, we propose a multi-level protocol for routine theoretical studies of chemical reaction mechanisms. The initial reaction paths of our investigated systems are sampled using the Nudged Elastic Band (NEB) method driven by a cheap electronic structure method. Forces recalculated at the more accurate electronic structure theory for a set of points on the path are fitted with a machine learning technique (in our case symmetric gradient domain machine learning or sGDML) to produce a semi-local reactive potential energy surface (PES), embracing reactants, products and transition state (TS) regions. This approach has been successfully applied to a unimolecular (Bergman cyclization of enediyne) and a bimolecular (SN2 substitution) reaction. In particular, we demonstrate that with only 50 to 150 energy-force evaluations with the accurate reference methods (here complete-active-space self-consistent field, CASSCF, and coupled-cluster singles and doubles, CCSD) it is possible to construct a semi-local PES giving qualitative agreement for stationary-point geometries, intrinsic reaction coordinates and barriers. Furthermore, we find a qualitative agreement in vibrational frequencies and reaction rate coefficients. The key aspect of the method's performance is its multi-level nature, which not only saves computational effort but also allows extracting meaningful information along the reaction path, characterized by zero gradients in all but one direction. Agnostic to the nature of the TS and computationally economic, the protocol can be readily automated and routinely used for mechanistic reaction studies.
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Affiliation(s)
- Tomislav Piskor
- HQS Quantum Simulations GmbH, Rintheimer Straße 23, 76131 Karlsruhe, Germany
- Theoretical Physics, Saarland University, 66123 Saarbrücken, Germany
| | - Peter Pinski
- HQS Quantum Simulations GmbH, Rintheimer Straße 23, 76131 Karlsruhe, Germany
| | - Thilo Mast
- HQS Quantum Simulations GmbH, Rintheimer Straße 23, 76131 Karlsruhe, Germany
| | - Vladimir Rybkin
- HQS Quantum Simulations GmbH, Rintheimer Straße 23, 76131 Karlsruhe, Germany
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14
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Camarillo-Cisneros J, Ramirez-Alonso G, Arzate-Quintana C, Varela-Rodríguez H, Guzman-Pando A. MolGC: molecular geometry comparator algorithm for bond length mean absolute error computation on molecules. Mol Divers 2024:10.1007/s11030-024-10945-2. [PMID: 39097550 DOI: 10.1007/s11030-024-10945-2] [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: 05/30/2024] [Accepted: 07/22/2024] [Indexed: 08/05/2024]
Abstract
Density Functional Theory (DFT) is extensively used in theoretical and computational chemistry to study molecular and crystal properties across diverse fields, including quantum chemistry, materials physics, catalysis, biochemistry, and surface science. Despite advances in DFT hardware and software for optimized geometries, achieving consensus in molecular structure comparisons with experimental counterparts remains a challenge. This difficulty is exacerbated by the lack of automated bond length comparison tools, resulting in labor-intensive and error-prone manual processes. To address these challenges, we propose MolGC, a Molecular Geometry Comparator algorithm that automates the comparison of optimized geometries from different theoretical levels. MolGC calculates the mean absolute error (MAE) of bond lengths by integrating data from various DFT software. It provides interactive and customizable visualization of geometries, enabling users to explore different views for enhanced analysis. In addition, it saves MAE computations for further analysis and offers a comprehensive statistical summary of the results. MolGC effectively addresses complex graph labeling challenges, ensuring accurate identification and categorization of bonds in diverse chemical structures. It achieves a 98.91% average rate in correct bond label assignments on an antibiotics dataset, showcasing its effectiveness for comparing molecular bond lengths across geometries of varying complexity and size. The executable file and software resources for running MolGC can be downloaded from https://github.com/AbimaelGP/MolGC/tree/main .
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Affiliation(s)
- Javier Camarillo-Cisneros
- Computational Chemistry Physics Laboratory, Facultad de Medicina y Ciencias Biomedicas, Universidad Autonoma de Chihuahua, Campus II, 31125, Chihuahua, Mexico
| | - Graciela Ramirez-Alonso
- Faculty of Engineering, Universidad Autonoma de Chihuahua, Campus II, 31125, Chihuahua, Mexico
| | - Carlos Arzate-Quintana
- Computational Chemistry Physics Laboratory, Facultad de Medicina y Ciencias Biomedicas, Universidad Autonoma de Chihuahua, Campus II, 31125, Chihuahua, Mexico
| | - Hugo Varela-Rodríguez
- Computational Chemistry Physics Laboratory, Facultad de Medicina y Ciencias Biomedicas, Universidad Autonoma de Chihuahua, Campus II, 31125, Chihuahua, Mexico
| | - Abimael Guzman-Pando
- Computational Chemistry Physics Laboratory, Facultad de Medicina y Ciencias Biomedicas, Universidad Autonoma de Chihuahua, Campus II, 31125, Chihuahua, Mexico.
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15
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Ermakova E, Tsyrendorzhieva I, Mareev A, Pavlov D, Maslova O, Shayapov V, Maksimovskiy E, Yushina I, Kosinova M. Carbon-Rich Plasma-Deposited Silicon Oxycarbonitride Films Derived from 4-(Trimethylsilyl)morpholine as a Novel Single-Source Precursor. Chempluschem 2024; 89:e202400094. [PMID: 38659085 DOI: 10.1002/cplu.202400094] [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: 02/02/2024] [Revised: 04/09/2024] [Accepted: 04/24/2024] [Indexed: 04/26/2024]
Abstract
4-(trimethylsilyl)morpholine O(CH2CH2)2NSi(CH3)3 (TMSM) was investigated as a single-source precursor for SiCNO films synthesis. Optical emission spectroscopy of plasma generated from TMSM/He, TMSM/H2, and TMSM/NH3 gas mixtures revealed the presence of N2, CH, H, CN, and CO species. The last two are suggested to be responsible for the lowering of carbon concentration in the films in comparison with the precursor. The refractive index ranged from 1.5 to 2.0, and bandgap varied from 2.0 to 4.6 eV, which pointed that some of the films can be used as antireflective coatings in silicon photovoltaic cell technologies and dielectric layers in electronic devices.
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Affiliation(s)
- Evgeniya Ermakova
- Nikolaev Institute of Inorganic Chemistry, SB RAS, 3 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Irina Tsyrendorzhieva
- Favorsky Irkutsk Institute of Chemistry, SB RAS, 1 Favorskogo str., Irkutsk, 664033, Russia
| | - Alexander Mareev
- Favorsky Irkutsk Institute of Chemistry, SB RAS, 1 Favorskogo str., Irkutsk, 664033, Russia
| | - Dmitry Pavlov
- Favorsky Irkutsk Institute of Chemistry, SB RAS, 1 Favorskogo str., Irkutsk, 664033, Russia
| | - Olga Maslova
- Nikolaev Institute of Inorganic Chemistry, SB RAS, 3 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Vladimir Shayapov
- Nikolaev Institute of Inorganic Chemistry, SB RAS, 3 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Eugene Maksimovskiy
- Nikolaev Institute of Inorganic Chemistry, SB RAS, 3 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Irina Yushina
- Nikolaev Institute of Inorganic Chemistry, SB RAS, 3 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Marina Kosinova
- Nikolaev Institute of Inorganic Chemistry, SB RAS, 3 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia
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16
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Kunze L, Froitzheim T, Hansen A, Grimme S, Mewes JM. ΔDFT Predicts Inverted Singlet-Triplet Gaps with Chemical Accuracy at a Fraction of the Cost of Wave Function-Based Approaches. J Phys Chem Lett 2024:8065-8077. [PMID: 39083761 DOI: 10.1021/acs.jpclett.4c01649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Efficient OLEDs need to quickly convert singlet and triplet excitons into photons. Molecules with an inverted singlet-triplet energy gap (INVEST) are promising candidates for this task. However, typical INVEST molecules have drawbacks like too low oscillator strengths and excitation energies. High-throughput screening could identify suitable INVEST molecules, but existing methods are problematic: The workhorse method TD-DFT cannot reproduce gap inversion, while wave function-based methods are too slow. This study proposes a state-specific method based on unrestricted Kohn-Sham DFT with common hybrid functionals. Tuned on the new INVEST15 benchmark set, this method achieves an error of less than 1 kcal/mol, which is traced back to error cancellation between spin contamination and dynamic correlation. Applied to the larger and structurally diverse NAH159 set in a black-box fashion, the method maintains a small error (1.2 kcal/mol) and accurately predicts gap signs in 83% of cases, confirming its robustness and suitability for screening workflows.
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Affiliation(s)
- Lukas Kunze
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Thomas Froitzheim
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Jan-Michael Mewes
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
- beeOLED GmbH, Niedersedlitzer Str. 75c, 01257 Dresden, Germany
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17
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Phan Dang CT, Truong DH, Nguyen TLA, Taamalli S, El Bakali A, Louis F, Dao DQ. Oxidation of metazachlor herbicide by ozone in the gas and aqueous phases: mechanistic, kinetics, and ecotoxicity studies. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-34453-w. [PMID: 39073716 DOI: 10.1007/s11356-024-34453-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
The atmospheric and aqueous ozonolysis of metazachlor (MTZ) is investigated using high-level quantum chemical and kinetic calculations (M06-2X/6-311 + + G(3df,3pd)//M06-2X/6-31 + G(d,p) level of theory). The ozone (O3)-initiated degradation pathways of MTZ under three different mechanisms, namely cycloaddition, oxygen-addition, and single electron transfer (SET), are explored in the temperature range of 283-333 K and 1 atm pressure. As a result, the cycloaddition reaction at the C16C18 double bond of the benzene ring of MTZ is found to be the most dominant channel in the atmosphere with the standard Gibbs free energy of reaction (ΔrG0g) of - 129.13 kJ mol-1 and the highest branching ratio of 95.18%. In the aqueous phase, the main reaction channel turns into the SET mechanism, which owns the lowest Gibbs free energy of activation (ΔG#aq) of 73.8 kJ mol-1 and contributes 87.8% to the ktotal. Over the temperature range of 283-333 K, the total rate constant (ktotal) significantly increases from 8.42 to 5.82 × 101 M-1 s-1 in the atmosphere and from 4.10 × 102 to 2.40 × 104 M-1 s-1 in the aqueous environment. Remarkably, the ecotoxicity assessment shows that MTZ may be harmful to fish and chronically harmful to daphnia. In contrast, its main ozonolysis products exhibit no acute or chronic toxicity or mutagenic effects.
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Affiliation(s)
- Cam-Tu Phan Dang
- Institute of Research and Development, Duy Tan University, Da Nang, 550000, Vietnam
- School of Engineering and Technology, Duy Tan University, Da Nang, 550000, Vietnam
| | - Dinh Hieu Truong
- Institute of Research and Development, Duy Tan University, Da Nang, 550000, Vietnam
- School of Engineering and Technology, Duy Tan University, Da Nang, 550000, Vietnam
| | - Thi Le Anh Nguyen
- Institute of Research and Development, Duy Tan University, Da Nang, 550000, Vietnam
- School of Engineering and Technology, Duy Tan University, Da Nang, 550000, Vietnam
| | - Sonia Taamalli
- UMR 8522 - PC2A - PhysicoChimie des Processus de Combustion et de l'Atmosphère, Université de Lille, CNRS, 590000, Lille, France
| | - Abderrahman El Bakali
- UMR 8522 - PC2A - PhysicoChimie des Processus de Combustion et de l'Atmosphère, Université de Lille, CNRS, 590000, Lille, France
| | - Florent Louis
- UMR 8522 - PC2A - PhysicoChimie des Processus de Combustion et de l'Atmosphère, Université de Lille, CNRS, 590000, Lille, France
| | - Duy Quang Dao
- Institute of Research and Development, Duy Tan University, Da Nang, 550000, Vietnam.
- School of Engineering and Technology, Duy Tan University, Da Nang, 550000, Vietnam.
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18
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Schwarting M, Seifert NA, Davis MJ, Blaiszik B, Foster I, Prozument K. Twins in rotational spectroscopy: Does a rotational spectrum uniquely identify a molecule? J Chem Phys 2024; 161:044309. [PMID: 39051838 DOI: 10.1063/5.0212632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/03/2024] [Indexed: 07/27/2024] Open
Abstract
Rotational spectroscopy is the most accurate method for determining structures of molecules in the gas phase. It is often assumed that a rotational spectrum is a unique "fingerprint" of a molecule. The availability of large molecular databases and the development of artificial intelligence methods for spectroscopy make the testing of this assumption timely. In this paper, we pose the determination of molecular structures from rotational spectra as an inverse problem. Within this framework, we adopt a funnel-based approach to search for molecular twins, which are two or more molecules, which have similar rotational spectra but distinctly different molecular structures. We demonstrate that there are twins within standard levels of computational accuracy by generating rotational constants for many molecules from several large molecular databases, indicating that the inverse problem is ill-posed. However, some twins can be distinguished by increasing the accuracy of the theoretical methods or by performing additional experiments.
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Affiliation(s)
- Marcus Schwarting
- Department of Computer Science, University of Chicago, Chicago, Illinois 60637, USA
| | - Nathan A Seifert
- Department of Chemistry and Chemical and Biomedical Engineering, University of New Haven, West Haven, Connecticut 06516, USA
| | - Michael J Davis
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Ben Blaiszik
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Ian Foster
- Department of Computer Science, University of Chicago, Chicago, Illinois 60637, USA
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Kirill Prozument
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
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19
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Korb M, Ghazvini SMBH, Low PJ. Migration of Condensed Aromatic Hydrocarbons During Alkyne-Vinylidene Rearrangements. Chemistry 2024; 30:e202400930. [PMID: 38780030 DOI: 10.1002/chem.202400930] [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: 03/07/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 05/25/2024]
Abstract
Diarylacetylenes ArC≡CAr featuring condensed aromatic hydrocarbon fragments (Ar) such as naphthalene, anthracene, phenanthrene and pyrene were converted into vinylidene ligands by 1,2-migration reactions within the coordination sphere of half-sandwich complexes [MII(dppe)Cp]+ (MII = RuII, FeII). Comparison of the extent of conversion of the alkyne substrates to the vinylidene complexes [Ru{=C=CAr2}(dppe)Cp]+ with those obtained from acetylenes functionalized by smaller groups (H, CH3, Ph) show that the molecular volume (VM) of the migrating group and relief of steric congestion plays a role during the rearrangement process. Conversely, the H-atoms from the larger condensed ring aryl groups that are in close proximity to the migrating sites also have a significant influence on the efficacy and extent of the reaction by restricting access of the alkyne to the metal center, resulting in a less effective migration reaction. This combination of competing steric factors (acceleration due to relief of steric congestion and restricted access of the alkyne moiety to the reaction site) is exemplified by the facile migration of 1-pyryl entities and the low yields of vinylidene products formed from 1,2-bis(9-anthryl)acetylene.
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Affiliation(s)
- Marcus Korb
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Seyed M B H Ghazvini
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Paul J Low
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
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20
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Piskorz T, Perez-Chirinos L, Qiao B, Sasselli IR. Tips and Tricks in the Modeling of Supramolecular Peptide Assemblies. ACS OMEGA 2024; 9:31254-31273. [PMID: 39072142 PMCID: PMC11270692 DOI: 10.1021/acsomega.4c02628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/30/2024]
Abstract
Supramolecular peptide assemblies (SPAs) hold promise as materials for nanotechnology and biomedicine. Although their investigation often entails adapting experimental techniques from their protein counterparts, SPAs are fundamentally distinct from proteins, posing unique challenges for their study. Computational methods have emerged as indispensable tools for gaining deeper insights into SPA structures at the molecular level, surpassing the limitations of experimental techniques, and as screening tools to reduce the experimental search space. However, computational studies have grappled with issues stemming from the absence of standardized procedures and relevant crystal structures. Fundamental disparities between SPAs and protein simulations, such as the absence of experimentally validated initial structures and the importance of the simulation size, number of molecules, and concentration, have compounded these challenges. Understanding the roles of various parameters and the capabilities of different models and simulation setups remains an ongoing endeavor. In this review, we aim to provide readers with guidance on the parameters to consider when conducting SPA simulations, elucidating their potential impact on outcomes and validity.
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Affiliation(s)
| | - Laura Perez-Chirinos
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 182, 20014 Donostia-San Sebastián, Spain
| | - Baofu Qiao
- Department
of Natural Sciences, Baruch College, City
University of New York, New York, New York 10010, United States
| | - Ivan R. Sasselli
- Centro
de Física de Materiales (CFM), CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
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21
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Salikov RF, Belyy AY, Ilyushchenko MK, Platonov DN, Sokolova AD, Tomilov YV. Antiaromaticity of Cycloheptatrienyl Anions: Structure, Acidity, and Magnetic Properties. Chemistry 2024; 30:e202401041. [PMID: 38785416 DOI: 10.1002/chem.202401041] [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: 03/14/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 05/25/2024]
Abstract
Investigations of the nature and degree of antiaromaticity of cycloheptatrienyl anion derivatives using both experimental and computational tools are presented. The ground state of cycloheptatrienyl anion in the gas phase is triplet, planar and Baird-aromatic. In DMSO, it assumes a singlet distorted allylic form with a paratropic ring current. The other derivatives in both phases assume either allylic or diallylic conformations depending on the substituent pattern. A combination of experimental and computational methods was used to determine the pKa values of 16 derivatives in DMSO, which ranged from 36 to -10.7. We revealed that the stronger stabilization of the anionic system, which correlates with acidity, does not necessarily imply a lower degree of antiaromaticity in terms of magnetic properties. Conversely, the substitution pattern first affects the geometry of the ring through the bulkiness of the substituents and their better conjugation with a more distorted system. Consequently, the distortion reduces the cyclic conjugation in the π-system and thereby decreases the paratropic current in a magnetic field, which manifests itself as a decrease in the NICS. The triplet-state geometries and magnetic properties are nearly independent on the substitution pattern, which is typical for simple aromatic systems.
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Affiliation(s)
- Rinat F Salikov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., Moscow, 119991, Russian Federation
- Department of Chemistry, Higher School of Economics National Research University, Moscow, 101000, Russian Federation
| | - Alexander Y Belyy
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., Moscow, 119991, Russian Federation
| | - Matvey K Ilyushchenko
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., Moscow, 119991, Russian Federation
| | - Dmitry N Platonov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., Moscow, 119991, Russian Federation
| | - Alena D Sokolova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., Moscow, 119991, Russian Federation
| | - Yury V Tomilov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., Moscow, 119991, Russian Federation
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22
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Göller AH, Johanssen S, Zalewski A, Ziegler V. Quantum chemical calculations of nitrosamine activation and deactivation pathways for carcinogenicity risk assessment. Front Pharmacol 2024; 15:1415266. [PMID: 39086387 PMCID: PMC11288830 DOI: 10.3389/fphar.2024.1415266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 06/21/2024] [Indexed: 08/02/2024] Open
Abstract
N-nitrosamines and nitrosamine drug substance related impurities (NDSRIs) became a critical topic for the development and safety of small molecule medicines following the withdrawal of various pharmaceutical products from the market. To assess the mutagenic and carcinogenic potential of different N-nitrosamines lacking robust carcinogenicity data, several approaches are in use including the published carcinogenic potency categorization approach (CPCA), the Enhanced Ames Test (EAT), in vivo mutagenicity studies as well as read-across to analogue molecules with robust carcinogenicity data. We employ quantum chemical calculations as a pivotal tool providing insights into the likelihood of reactive ion formation and subsequent DNA alkylation for a selection of molecules including e.g., carcinogenic N-nitrosopiperazine (NPZ), N-nitrosopiperidine (NPIP), together with N-nitrosodimethylamine (NDMA) as well as non-carcinogenic N-nitrosomethyl-tert-butylamine (NTBA) and bis (butan-2-yl) (nitros)amine (BBNA). In addition, a series of nitroso-methylaminopyridines is compared side-by-side. We draw comparisons between calculated reaction profiles for structures representing motifs common to NDSRIs and those of confirmed carcinogenic and non-carcinogenic molecules with in vivo data from cancer bioassays. Furthermore, our approach enables insights into reactivity and relative stability of intermediate species that can be formed upon activation of several nitrosamines. Most notably, we reveal consistent differences between the free energy profiles of carcinogenic and non-carcinogenic molecules. For the former, the intermediate diazonium ions mostly react, kinetically controlled, to the more stable DNA adducts and less to the water adducts via transition-states of similar heights. Non-carcinogenic molecules yield stable carbocations as intermediates that, thermodynamically controlled, more likely form the statistically preferred water adducts. In conclusion, our data confirm that quantum chemical calculations can contribute to a weight of evidence approach for the risk assessment of nitrosamines.
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Affiliation(s)
- Andreas H. Göller
- Computational Molecular Design, Bayer AG, Pharmaceuticals, Wuppertal, Germany
| | - Sandra Johanssen
- Industrial Chemicals and Marketed Products, Bayer AG, Pharmaceuticals, Berlin, Germany
| | - Adam Zalewski
- Genetic and Computational Toxicology, Bayer AG, Pharmaceuticals, Berlin, Germany
| | - Verena Ziegler
- Genetic and Computational Toxicology, Bayer AG, Pharmaceuticals, Berlin, Germany
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23
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Karagiannis A, Neugebauer H, Lalancette RA, Grimme S, Hansen A, Prokopchuk DE. Pushing the Limits of Organometallic Redox Chemistry with an Isolable Mn(-I) Dianion. J Am Chem Soc 2024; 146:19279-19285. [PMID: 38976843 DOI: 10.1021/jacs.4c04561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
We report an incredibly reducing and redox-active Mn-I dianion, [Mn(CO)3(Ph2B(tBuNHC)2)]2- (NHC = N-heterocyclic carbene), furnished via 2e- reduction of the parent 16e- MnI complex with Na0 or K0. Cyclic voltammograms show a Mn0/-I redox couple at -3.13 V vs Fc+/0 in tetrahydrofuran (THF), -3.06 V in 1,2-dimethoxyethane, and -2.85 V in acetonitrile. The diamagnetic Mn-I dianion is stable in solution and solid-state at room temperature, tolerating a wide range of countercations ([M(2.2.2)crypt]+, [M(18-crown-6)]+, [nBu4N]+; M = Na, K). Countercation identity does not significantly alter 13C NMR spectral signatures with [nBu4N]+ and Na+, suggesting minimal ion pairing in solution. IR spectroscopy reveals a significant decrease in CO stretching frequencies from MnI to Mn-I (ca. 240 cm-1), consistent with a drastic increase in electron density at Mn. State-of-the-art DFT calculations are in excellent agreement with the observed IR spectral data. Moreover, the Mn-I dianion behaves as a chemical reductant, smoothly releasing 1e- or 2e- to regenerate the oxidized Mn0 or MnI species in solution. The reducing potential of [Mn(CO)3(Ph2B(tBuNHC)2)]2- surpasses the naphthalenide anion in THF (-3.09 V) and represents one of the strongest isolable chemical redox agents.
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Affiliation(s)
- Ageliki Karagiannis
- Department of Chemistry, Rutgers University-Newark, 73 Warren Street, Newark, New Jersey 07102, United States
| | - Hagen Neugebauer
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Bonn 53115, Germany
| | - Roger A Lalancette
- Department of Chemistry, Rutgers University-Newark, 73 Warren Street, Newark, New Jersey 07102, United States
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Bonn 53115, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Bonn 53115, Germany
| | - Demyan E Prokopchuk
- Department of Chemistry, Rutgers University-Newark, 73 Warren Street, Newark, New Jersey 07102, United States
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24
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Han JT, Tsuji N, Zhou H, Leutzsch M, List B. Organocatalytic asymmetric synthesis of Si-stereogenic silacycles. Nat Commun 2024; 15:5846. [PMID: 38992000 PMCID: PMC11239892 DOI: 10.1038/s41467-024-49988-2] [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: 03/23/2024] [Accepted: 06/27/2024] [Indexed: 07/13/2024] Open
Abstract
A strong and confined Brønsted acid catalyzed enantioselective cyclization of bis(methallyl)silanes provides enantioenriched Si-stereogenic silacycles. High enantioselectivities of up to 96.5:3.5 er were obtained for a range of bis(methallyl)silanes. NMR and ESI-MS studies reveal that the formation of a covalent adduct irreversibly inhibits turnover. Remarkably, we found that acetic acid as an additive promotes the collapse of this adduct, enabling full turnover. Experimental investigation and density functional theory (DFT) calculations were conducted to elucidate the origin of this phenomenon and the observed enantioselectivity.
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Affiliation(s)
- Jung Tae Han
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
- Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Nobuya Tsuji
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan
| | - Hui Zhou
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Markus Leutzsch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Benjamin List
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, 001-0021, Japan.
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25
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Scaringi S, Leforestier B, Mazet C. Remote Functionalization by Pd-Catalyzed Isomerization of Alkynyl Alcohols. J Am Chem Soc 2024; 146:18606-18615. [PMID: 38941513 PMCID: PMC11240579 DOI: 10.1021/jacs.4c05136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/30/2024]
Abstract
In recent years, progress has been made in the development of catalytic methods that allow remote functionalizations based on alkene isomerization. In contrast, protocols based on alkyne isomerization are comparatively rare. Herein, we report a general Pd-catalyzed long-range isomerization of alkynyl alcohols. Starting from aryl-, heteroaryl-, or alkyl-substituted precursors, the optimized system provides access preferentially to the thermodynamically more stable α,β-unsaturated aldehydes and is compatible with potentially sensitive functional groups. We showed that the migration of both π-components of the carbon-carbon triple bond can be sustained over several methylene units. Computational investigations served to shed light on the key elementary steps responsible for the reactivity and selectivity. These include an unorthodox phosphine-assisted deprotonation rather than a more conventional β-hydride elimination in the final tautomerization event.
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Affiliation(s)
| | | | - Clément Mazet
- Department of Organic Chemistry, University of Geneva, 30 Quai Ernest Ansermet, 1211 Geneva, Switzerland
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26
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Salta Z, Schaefer T, Tasinato N, Kieninger M, Katz A, Herrmann H, Ventura ON. Energetics of the OH radical H-abstraction reactions from simple aldehydes and their geminal diol forms. J Mol Model 2024; 30:253. [PMID: 38970670 DOI: 10.1007/s00894-024-06058-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024]
Abstract
CONTEXT Carbonyl compounds, especially aldehydes, emitted to the atmosphere, may suffer hydration in aerosols or water droplets in clouds. At the same time, they can react with hydroxyl radicals which may add or abstract hydrogen atoms from these species. The interplay between hydration and hydrogen abstraction is studied using density functional and quantum composite theoretical methods, both in the gas phase and in simulated bulk water. The H-abstraction from the aldehydic and geminal diol forms of formaldehyde, acetaldehyde, glycolaldehyde, glyoxal, methylglyoxal, and acrolein is studied to determine whether the substituent has any noticeable effect in the preference for the abstraction of one form or another. It is found that abstraction of the H-atom adjacent to the carbonyl group gives a more stable radical than same abstraction from the geminal diol in the case of formaldehyde, acetaldehyde, and glycolaldehyde. The presence of a delocalizing group in the Cα (a carbonyl group in glyoxal and methylglyoxal, and a vinyl group in acrolein), reverts this trend, and now the abstraction of the H-atom from the geminal diol gives more stable radicals. A further study was conducted abstracting hydrogen atoms from the other different positions in the species considered, both in the aldehydic and geminal diol forms. Only in the case of glycolaldehyde, the radical formed by H-abstraction from the -CH2OH group is more stable than any of the other radical species. Abstraction of the hydrogen atom in one of the hydroxyl groups in the geminal diol is equivalent to the addition of the •OH radical to the aldehyde. It leads, in some cases, to decomposition into a smaller radical and a neutral molecule. In these cases, some interesting theoretical differences are observed between the results in gas phase and (simulated) bulk solvent, as well as with respect to the method of calculation chosen. METHODS DFT (M06-2X, B2PLYP, PW6B95), CCSD(T), and composite (CBS-QB3, jun-ChS, SCVECV-f12) methods using Dunning basis sets and extrapolation to the CBS limit were used to study the energetics of closed shell aldehydes in their keto and geminal-diol forms, as well as the radical derived from them by hydrogen abstraction. Both gas phase and simulated bulk solvent calculations were performed, in the last case using the Polarizable Continuum Model.
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Affiliation(s)
- Zoi Salta
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, 56126, Pisa, Italy
| | - Thomas Schaefer
- Atmospheric Chemistry Department (ACD), Leibniz Institute for Tropospheric Research (TROPOS), Permoserstr. 15, 04318, Leipzig, Germany
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, 56126, Pisa, Italy
| | - Martina Kieninger
- Computational Chemistry and Biology Group, Facultad de Química, CCBG, Universidad de La República, 11400, Montevideo, DETEMA, Uruguay
| | - Aline Katz
- Computational Chemistry and Biology Group, Facultad de Química, CCBG, Universidad de La República, 11400, Montevideo, DETEMA, Uruguay
| | - Hartmut Herrmann
- Atmospheric Chemistry Department (ACD), Leibniz Institute for Tropospheric Research (TROPOS), Permoserstr. 15, 04318, Leipzig, Germany
| | - Oscar N Ventura
- Computational Chemistry and Biology Group, Facultad de Química, CCBG, Universidad de La República, 11400, Montevideo, DETEMA, Uruguay.
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27
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Lalith N, Singh AR, Gauthier JA. The Importance of Reaction Energy in Predicting Chemical Reaction Barriers with Machine Learning Models. Chemphyschem 2024; 25:e202300933. [PMID: 38517585 DOI: 10.1002/cphc.202300933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 03/24/2024]
Abstract
Improving our fundamental understanding of complex heterocatalytic processes increasingly relies on electronic structure simulations and microkinetic models based on calculated energy differences. In particular, calculation of activation barriers, usually achieved through compute-intensive saddle point search routines, remains a serious bottleneck in understanding trends in catalytic activity for highly branched reaction networks. Although the well-known Brønsted-Evans-Polyani (BEP) scaling - a one-feature linear regression model - has been widely applied in such microkinetic models, they still rely on calculated reaction energies and may not generalize beyond a single facet on a single class of materials, e. g., a terrace sites on transition metals. For highly branched and energetically shallow reaction networks, such as electrochemical CO2 reduction or wastewater remediation, calculating even reaction energies on many surfaces can become computationally intractable due to the combinatorial explosion of states that must be considered. Here, we investigate the feasibility of activation barrier prediction without knowledge of the reaction energy using linear and nonlinear machine learning (ML) models trained on a new database of over 500 dehydrogenation activation barriers. We also find that inclusion of the reaction energy significantly improves both classes of ML models, but complex nonlinear models can achieve performance similar to the simplest BEP scaling when predicting activation barriers on new systems. Additionally, inclusion of the reaction energy significantly improves generalizability to new systems beyond the training set. Our results suggest that the reaction energy is a critical feature to consider when building models to predict activation barriers, indicating that efforts to reliably predict reaction energies through, e. g., the Open Catalyst Project and others, will be an important route to effective model development for more complex systems.
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Affiliation(s)
- Nithin Lalith
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX 79409, USA
| | | | - Joseph A Gauthier
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX 79409, USA
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28
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Fischer M, Brauer J. Studying the adsorption of emerging organic contaminants in zeolites with dispersion-corrected density functional theory calculations: From numbers to recommendations. ChemistryOpen 2024; 13:e202300273. [PMID: 38385822 PMCID: PMC11230941 DOI: 10.1002/open.202300273] [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: 11/21/2023] [Revised: 01/10/2024] [Indexed: 02/23/2024] Open
Abstract
Adsorption energies obtained from dispersion-corrected density functional theory (DFT) calculations show a considerable dependence on the choice of exchange-correlation functional and dispersion correction. A number of investigations have employed different approaches to compute adsorption energies of small molecules in zeolites, using reference values from high-level calculations and/or experiments. Such comparative studies are lacking for larger functional organic molecules such as pharmaceuticals or personal care products, despite their potential relevance for applications, e. g., in contaminant removal or drug delivery. The present study aims to fill this gap by comparing adsorption energies and, for selected cases, equilibrium structures of emerging organic contaminants adsorbed in MOR- and FAU-type all-silica zeolites. A total of 13 dispersion-corrected DFT approaches are compared, including methods using a pairwise dispersion correction as well as non-local van der Waals density functionals. While absolute values of adsorption energies vary widely, qualitative trends across the set of zeolite-guest combinations are not strongly dependent on the choice of functional. For selected cluster models, DFT adsorption energies are compared to reference values from coupled cluster (DLPNO-CCSD(T)) calculations. Although all DFT approaches deliver systematically more negative adsorption energies than the coupled cluster reference, this tendency is least pronounced for the rev-vdW-DF2 functional.
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Affiliation(s)
- Michael Fischer
- Crystallography and GeomaterialsFaculty of GeosciencesUniversity of BremenKlagenfurter Straße 2–428359BremenGermany
- Bremen Center for Computational Materials Science and MAPEX Center for Materials and ProcessesUniversity of Bremen28359BremenGermany
| | - Jakob Brauer
- Crystallography and GeomaterialsFaculty of GeosciencesUniversity of BremenKlagenfurter Straße 2–428359BremenGermany
- Bremen Center for Computational Materials Science and MAPEX Center for Materials and ProcessesUniversity of Bremen28359BremenGermany
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29
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Zenner A, Steinmetzer J, Ueberschaar N, Freesmeyer M, Weigand W, Greiser J. The synthesis of N,1,4-tri(alkoxy-hydroxybenzyl)-1,4-diazepane-amines: investigations on reaction characteristics and mechanism. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240293. [PMID: 39076358 PMCID: PMC11285842 DOI: 10.1098/rsos.240293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 07/31/2024]
Abstract
1,4-Diazepane-6-amine (DAZA) can be alkylated with three 2-hydroxybenzyl pendant arms, resulting in hexadentate chelators suitable for coordination of radiometals like 68Ga. These chelators, N,1,4-tri(alkoxy-2-hydroxybenzyl)-DAZA, can be produced via a one-pot synthesis, with the first step being a carbonyl amine condensation of DAZA with two respective 4-alkoxy-2-hydroxybenzaldehydes, followed by reductive amination with sodium borohydride. While the first step of this reaction is predictable, the subsequent reductive amination can result in either mono-, di- or tri(alkoxy-hydroxybenzyl)-DAZA compounds. Seeking to identify dependencies that might allow a specific reaction control towards the formation of either of the three possible products, and particularly towards the favoured trialkylated DAZA compounds, a variety of synthesis trials were performed. Additionally, computational methods were employed to evaluate the underlying reaction mechanism. Synthesis trials verified that the trialkylated DAZA compounds are formed via direct reductive amination of the dialkylated DAZA compounds. Subsequently, a synthetic method was established, leading to an increase in the percentage of the trialkylated DAZA compounds, which allowed the successful isolation of those hexadentate chelators. Additionally, an alternative pathway proceeding via aminal C-N bond insertion of an attacking third carbonyl moiety was evaluated by means of quantum chemical calculations but so far remains entirely hypothetical.
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Affiliation(s)
- Anne Zenner
- Working Group for Translational Nuclear Medicine and Radiopharmacy, Clinic of Nuclear Medicine, Jena University Hospital, Jena, Germany
| | - Johannes Steinmetzer
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
| | - Nico Ueberschaar
- Mass Spectrometry Platform, Friedrich Schiller University Jena, Jena, Germany
| | - Martin Freesmeyer
- Working Group for Translational Nuclear Medicine and Radiopharmacy, Clinic of Nuclear Medicine, Jena University Hospital, Jena, Germany
| | - Wolfgang Weigand
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Julia Greiser
- Working Group for Translational Nuclear Medicine and Radiopharmacy, Clinic of Nuclear Medicine, Jena University Hospital, Jena, Germany
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30
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Zhang D, Kishimoto N. Theoretical Analysis of Coordination Geometries in Transition Metal-Histidine Complexes Using Quantum Chemical Calculations. Molecules 2024; 29:3003. [PMID: 38998956 PMCID: PMC11243457 DOI: 10.3390/molecules29133003] [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: 06/13/2024] [Accepted: 06/22/2024] [Indexed: 07/14/2024] Open
Abstract
A theoretical investigation utilizing density functional theory (DFT) calculations was conducted to explore the coordination complexes formed between histidine (His) ligands and various divalent transition metal ions (Mn2+, Fe2+, Co2+, Ni2+, Cu2+, and Zn2+). Conformational exploration of the His ligand was initially performed to assess its stability upon coordination. Both 1:1 and 1:2 of metal-to-ligand complexes were scrutinized to elucidate their structural features and the relative stability of the complexes. This study examined the ability of His to act as a bidentate or tridentate coordinating ligand, along with the differences in coordination geometry when solvent effects were incorporated. The reduced density gradient (RDG) analysis and local electron attachment energy (LEAE) analysis were employed to elucidate the interaction planes and the nucleophilic and electrophilic properties. The electronic properties were analyzed through electrostatic potential (ESP) maps and natural population analysis (NPA) of atomic charge distributions. This computational study provides valuable insights into the diverse coordination modes of His and its interactions with divalent transition metal ions, contributing to a better understanding of the role of this amino acid ligand in the formation of transition metal complexes. The findings can aid in the design and construction of self-assembled structures involving His-metal coordination.
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Affiliation(s)
- Dapeng Zhang
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Naoki Kishimoto
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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31
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Mészáros BB, Kubicskó K, Németh DD, Daru J. Emerging Conformational-Analysis Protocols from the RTCONF55-16K Reaction Thermochemistry Conformational Benchmark Set. J Chem Theory Comput 2024. [PMID: 38899777 DOI: 10.1021/acs.jctc.4c00565] [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
RTCONF55-16K is a new, reactive conformational data set based on cost-efficient methods to assess different conformational analysis protocols. Our reference calculations underpinned the accuracy of the CENSO (Grimme et al. J. Phys. Chem. A, 2021, 125, 4039) procedure and resulted in alternative recipes with different cost-accuracy compromises. Our general-purpose and economical protocols (CENSO-light and zero, respectively) were found to be 10-30 times faster than the original algorithm, adding only 0.4-0.7 kcal/mol absolute error to the relative free energy estimates.
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Affiliation(s)
- Bence Balázs Mészáros
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
- Department of Organic Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Károly Kubicskó
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
- Department of Organic Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Dávid Dorián Németh
- Department of Organic Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - János Daru
- Department of Organic Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
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32
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Goll FD, Dießner N, Kuehne AJC, Ziener U. Dihedral Angles and Photoluminescence Quantum Yields: An NMR Analysis. Chemphyschem 2024:e202400288. [PMID: 38895805 DOI: 10.1002/cphc.202400288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/21/2024]
Abstract
The synthesis of two different series of donor-acceptor (D-A) molecules is reported, consisting of a series of four structurally related donors and two different acceptors. The subtle differences in the electron density of these D-A-D and D-A compounds are clearly reflected in the different chemical shifts of certain donor protons in the 1H NMR spectra. These shifts show a cosine squared correlation of the dihedral angle between the donor units and the neighbouring phenyl unit of the acceptor. This correlation is also related to optical properties such as the photoluminescence quantum yield, which shows a similar trend due to the different degree of charge transfer during excitation and relaxation processes. In this way, it is possible to directly correlate a molecular structural parameter with a material property on a purely experimental basis, which should be applicable to many donor-acceptor systems.
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Affiliation(s)
- Felix D Goll
- Institute of Organic Chemistry III - Macromolecular Chemistry and Organic Materials, Ulm University, 89081, Ulm, Germany
| | - Nicolas Dießner
- Institute of Organic Chemistry III - Macromolecular Chemistry and Organic Materials, Ulm University, 89081, Ulm, Germany
| | - Alexander J C Kuehne
- Institute of Organic Chemistry III - Macromolecular Chemistry and Organic Materials, Ulm University, 89081, Ulm, Germany
| | - Ulrich Ziener
- Institute of Organic Chemistry III - Macromolecular Chemistry and Organic Materials, Ulm University, 89081, Ulm, Germany
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33
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Misselwitz E, Spengler J, Rominger F, Kivala M. Indenoannulated Tridecacyclene: An All-Carbon Seven-Stage Redox-Amphoter. Chemistry 2024; 30:e202400696. [PMID: 38563636 DOI: 10.1002/chem.202400696] [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: 03/18/2024] [Accepted: 04/01/2024] [Indexed: 04/04/2024]
Abstract
We disclose an indenoannulated tridecacyclene comprising a central cyclooctatetraene moiety with multiple adjacent pentagonal rings which is accessible in a concise synthetic sequence. The saddle-shaped geometry of the non-benzenoid polycyclic scaffold and its unique packing behavior in the solid state were characterized by X-ray crystallography. In electrochemical studies, the compound undergoes seven reversible redox events comprising five reductions and two oxidations. The dicationic and dianionic species obtained by chemical oxidation and reduction, respectively, were characterized spectroscopically in solution. Density functional theory calculations were applied to provide insights into aromaticity evolution in the respective charged species, highlighting the beneficial effect of the non-benzenoid moieties on charge stabilization.
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Affiliation(s)
- Erik Misselwitz
- Organisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Jonas Spengler
- Organisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Frank Rominger
- Organisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Milan Kivala
- Organisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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34
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Antol I, Štrbac P, Murata Y, Margetić D. Theoretical Study of the Mechanism of the Formation of Azomethine Ylide from Isatine and Sarcosine and Its Reactivity in 1,3-Dipolar Cycloaddition Reaction with 7-Oxabenzonorbornadiene. Int J Mol Sci 2024; 25:6524. [PMID: 38928235 PMCID: PMC11203580 DOI: 10.3390/ijms25126524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
The reaction mechanism of tthe formation of azomethine ylides from isatins and sarcosine is addressed in the literature in a general manner. This computational study aims to explore the mechanistic steps for this reaction in detail and to assess the reactivity of formed ylide in a 1,3-dipolar cycloaddition reaction with 7-oxabenzonorbornadiene. For this purpose, density functional theory (DFT) calculations at the M06-2X(SMD,EtOH)/6-31G(d,p) level were employed. The results indicate that CO2 elimination is the rate-determining step, the activation barrier for 1,3-dipolar cycloaddition is lower, and the formed ylide will readily react with dipolarophiles. The substitution of isatine with electron-withdrawal groups slightly decreases the activation barrier for ylide formation.
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Affiliation(s)
- Ivana Antol
- Laboratory for Physical Organic Chemistry, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, HR-10002 Zagreb, Croatia
| | - Petar Štrbac
- Laboratory for Physical Organic Chemistry, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, HR-10002 Zagreb, Croatia
| | - Yasujiro Murata
- Structural Organic Chemistry Laboratory, Division of Synthetic Chemistry, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Davor Margetić
- Laboratory for Physical Organic Chemistry, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, HR-10002 Zagreb, Croatia
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35
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Rahrt R, Hein-Janke B, Amarasinghe KN, Shafique M, Feldt M, Guo L, Harvey JN, Pollice R, Koszinowski K, Mata RA. The Fe-MAN Challenge: Ferrates-Microkinetic Assessment of Numerical Quantum Chemistry. J Phys Chem A 2024; 128:4663-4673. [PMID: 38832568 PMCID: PMC11182345 DOI: 10.1021/acs.jpca.4c01361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Organometallic species, such as organoferrate ions, are prototypical nucleophiles prone to reacting with a wide range of electrophiles, including proton donors. In solution, the operation of dynamic equilibria and the simultaneous presence of several organometallic species severely complicate the analysis of these fundamentally important reactions. This can be overcome by gas-phase experiments on mass-selected ions, which allow for the determination of the microscopic reactivity of the target species. In this contribution, we focus on the reactivity of a series of trisarylferrate complexes toward 2,2,2-trifluoroethanol and 2,2-difluoroethanol. By means of mass-spectrometric measurements, we determined the experimental bimolecular rate constants kexp of the gas-phase protolysis reactions of the trisarylferrate anions FePh3- and FeMes3- with the aforementioned acids. Based on these experiments, we carried out a dual blind challenge, inviting theoretical groups to submit their best predictions for the activation barriers and/or theoretical rate constants ktheo. This provides a unique opportunity to evaluate different computational protocols under minimal bias and sets the stage for further benchmarking of quantum chemical methods and data-driven approaches in the future.
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Affiliation(s)
- Rene Rahrt
- Institut
für Organische und Biomolekulare Chemie, Universität Göttingen, Tammannstr. 2, Göttingen 37077, Germany
| | - Björn Hein-Janke
- Institut
für Physikalische Chemie, Universität
Göttingen, Tammannstr.
6, Göttingen 37077, Germany
| | - Kosala N. Amarasinghe
- Leibniz
Institute for Catalysis (LIKAT), Albert-Einstein-Str. 29A, Rostock 18059, Germany
| | - Muhammad Shafique
- Leibniz
Institute for Catalysis (LIKAT), Albert-Einstein-Str. 29A, Rostock 18059, Germany
| | - Milica Feldt
- Leibniz
Institute for Catalysis (LIKAT), Albert-Einstein-Str. 29A, Rostock 18059, Germany
| | - Luxuan Guo
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven B-3001, Belgium
| | - Jeremy N. Harvey
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven B-3001, Belgium
| | - Robert Pollice
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The
Netherlands
| | - Konrad Koszinowski
- Institut
für Organische und Biomolekulare Chemie, Universität Göttingen, Tammannstr. 2, Göttingen 37077, Germany
| | - Ricardo A. Mata
- Institut
für Physikalische Chemie, Universität
Göttingen, Tammannstr.
6, Göttingen 37077, Germany
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36
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Lackinger M. Possibilities and Limitations of Kinetic Studies in On-Surface Synthesis by Real Time X-ray Photoelectron Spectroscopy. Chemphyschem 2024; 25:e202400156. [PMID: 38528329 DOI: 10.1002/cphc.202400156] [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: 02/12/2024] [Revised: 03/07/2024] [Indexed: 03/27/2024]
Abstract
The kinetics of coupling reactions on surfaces can be quantitatively studied in real time by X-ray Photoelectron Spectroscopy (XPS). From fitting experimental data, kinetic reaction parameters such as the rate constant's pre-exponential and activation energy can be deduced and compared to quantum chemical simulations. To elucidate the possibilities and limitations of this approach, we propose studies in which experimental data are first simulated and subsequently fitted. Knowing the exact kinetic parameters used in the simulation allows one to evaluate the accuracy of the fit result. Here, several experimental influences, such as the data point density and the addition of noise, are explored for a model reaction with first-order kinetics. The proposed procedure sheds light on the accuracy with which kinetic parameters can be derived and may also help in the design of future experiments.
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Affiliation(s)
- Markus Lackinger
- Deutsches Museum, Museumsinsel 1, 80538, München, Germany
- Physics Department, Technical University of Munich, 85748, Garching, Germany
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Kairys V, Baranauskiene L, Kazlauskiene M, Zubrienė A, Petrauskas V, Matulis D, Kazlauskas E. Recent advances in computational and experimental protein-ligand affinity determination techniques. Expert Opin Drug Discov 2024; 19:649-670. [PMID: 38715415 DOI: 10.1080/17460441.2024.2349169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024]
Abstract
INTRODUCTION Modern drug discovery revolves around designing ligands that target the chosen biomolecule, typically proteins. For this, the evaluation of affinities of putative ligands is crucial. This has given rise to a multitude of dedicated computational and experimental methods that are constantly being developed and improved. AREAS COVERED In this review, the authors reassess both the industry mainstays and the newest trends among the methods for protein - small-molecule affinity determination. They discuss both computational affinity predictions and experimental techniques, describing their basic principles, main limitations, and advantages. Together, this serves as initial guide to the currently most popular and cutting-edge ligand-binding assays employed in rational drug design. EXPERT OPINION The affinity determination methods continue to develop toward miniaturization, high-throughput, and in-cell application. Moreover, the availability of data analysis tools has been constantly increasing. Nevertheless, cross-verification of data using at least two different techniques and careful result interpretation remain of utmost importance.
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Affiliation(s)
- Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Egidijus Kazlauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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Gómez S, Flórez E, Acelas N, Cappelli C, Hadad C, Restrepo A. Encapsulation of charged halogens by the 5 12 water cage. Phys Chem Chem Phys 2024; 26:15426-15436. [PMID: 38747303 DOI: 10.1039/d4cp01340a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
This study focuses on the encapsulation of the entire series of halides by the 512 cage of twenty water molecules and on the characterization of water to water and water to anion interactions. State-of-the-art computations are used to determine equilibrium geometries, energy related quantities, and thermal stability towards dissociation and to dissect the nature and strength of intermolecular interactions holding the clusters as stable units. Two types of structures are revealed: heavily deformed cages for F- indicating a preference for microsolvation, and slightly deformed cages for the remaining anions indicating a preference for encapsulation. The primary variable dictating the properties of the clusters is the charge density of the central halide, with the most severe effects observed for the F- case. For the remaining halides, the anion may be safely viewed as a sort of "big electron" with little local disruptive power, enough to affect the network of non-covalent hydrogen bonds in the cage, but not enough to break it. Gibbs energies for dissociation either into cavity and halide or into water molecules and halide suggest that, in a similar way as to methane clathrate, a more weakly bonded complex that has been detected in the gas phase, all halide containing clathrate-like structures should be amenable to experimental detection in the gas phase at moderate temperature and pressure conditions.
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Affiliation(s)
- Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
| | - Elizabeth Flórez
- Grupo de Materiales con Impacto, Mat&mpac. Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, 050026 Medellín, Colombia
| | - Nancy Acelas
- Grupo de Materiales con Impacto, Mat&mpac. Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, 050026 Medellín, Colombia
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
| | - Cacier Hadad
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
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Tampellini N, Mercado BQ, Miller SJ. Scaffold-Oriented Asymmetric Catalysis: Conformational Modulation of Transition State Multivalency during a Catalyst-Controlled Assembly of a Pharmaceutically Relevant Atropisomer. Chemistry 2024; 30:e202401109. [PMID: 38507249 PMCID: PMC11132932 DOI: 10.1002/chem.202401109] [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: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 03/22/2024]
Abstract
A new class of superbasic, bifunctional peptidyl guanidine catalysts is presented, which enables the organocatalytic, atroposelective synthesis of axially chiral quinazolinediones. Computational modeling unveiled the conformational modulation of the catalyst by a novel phenyl urea N-cap, that preorganizes the structure into the active, folded state. A previously unanticipated noncovalent interaction involving a difluoroacetamide acting as a hybrid mono- or bidentate hydrogen bond donor emerged as a decisive control element inducing atroposelectivity. These discoveries spurred from a scaffold-oriented project inspired from a fascinating investigational BTK inhibitor featuring two stable chiral axes and relies on a mechanistic framework that was foreign to the extant lexicon of asymmetric catalysis.
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Affiliation(s)
- Nicolò Tampellini
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06511 (USA)
| | - Brandon Q. Mercado
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06511 (USA)
| | - Scott J. Miller
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06511 (USA)
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Kalita AJ, Rohman SS, Sahu PP, Guha AK. Reply to the Comments on Planar Tetracoordinate Hydrogen: Pushing the Limit of Multicentre Bonding. Angew Chem Int Ed Engl 2024; 63:e202403214. [PMID: 38517260 DOI: 10.1002/anie.202403214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Indexed: 03/23/2024]
Abstract
Recently, Huo et al. has commented on our communication (Angew. Chem. Int. Ed. 2024, 63, e202317312, DOI: 10.1002/anie.202317312), regarding the multireference character (MRC) of our proposed cluster. Their argument is based on small HOMO-LUMO gap, fractional occupation density (FOD) and CASPT2(12,13) calculations. They also proposed that the singlet planar In4H+ cluster cannot be observed. We present our calculations which reveals that some of their arguments are based on wrong interpretation of data and inadequate use of methodology. While we certainly agree with the strong physical ground of FOD, CASSF and CASPT2 methodology, we believe that such analysis for clusters is not adequate.
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Affiliation(s)
- Amlan J Kalita
- Advanced Computational Chemistry Centre, Cotton University, Panbazar, Guwahati, Assam, INDIA-, 781001
| | - Shahnaz S Rohman
- Department of Chemistry, National Institute of Technology, Calicut, Kerala, 673601, India
| | - Prem P Sahu
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, 502284, India
- Department of Chemistry "Ugo Schiff", University of Florence, Via della, Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Ankur Kanti Guha
- Advanced Computational Chemistry Centre, Cotton University, Panbazar, Guwahati, Assam, INDIA-, 781001
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Doveiko D, Kubiak-Ossowska K, Chen Y. Estimating Binding Energies of π-Stacked Aromatic Dimers Using Force Field-Driven Molecular Dynamics. Int J Mol Sci 2024; 25:5783. [PMID: 38891971 PMCID: PMC11171666 DOI: 10.3390/ijms25115783] [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: 03/27/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
π-π stacking are omnipresent interactions, crucial in many areas of chemistry, and often studied using quantum chemical methods. Here, we report a simple and computationally efficient method of estimating the binding energies of stacked polycyclic aromatic hydrocarbons based on steered molecular dynamics. This method leverages the force field parameters for accurate calculation. The presented results show good agreement with those obtained through DFT at the ωB97X-D3/cc-pVQZ level of theory. It is demonstrated that this force field-driven SMD method can be applied to other aromatic molecules, allowing insight into the complexity of the stacking interactions and, more importantly, reporting π-π stacking energy values with reasonable precision.
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Affiliation(s)
- Daniel Doveiko
- Photophysics Group, Department of Physics, University of Strathclyde, Scottish Universities Physics Alliance, Glasgow G4 0NG, UK;
| | | | - Yu Chen
- Photophysics Group, Department of Physics, University of Strathclyde, Scottish Universities Physics Alliance, Glasgow G4 0NG, UK;
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Doust Mohammadi M, Bhowmick S, Maisser A, Schmidt-Ott A, Biskos G. Electronic properties and collision cross sections of AgO kH m± ( k, m = 1-4) aerosol ionic clusters. Phys Chem Chem Phys 2024; 26:14547-14560. [PMID: 38721799 DOI: 10.1039/d3cp05499c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Experimental evidence shows that hydroxylated metal ions are often produced during cluster synthesis by atmospheric pressure spark ablation. In this work, we predict the ground state equilibrium structures of AgOkHm± clusters (k and m = 1-4), which are readily produced when spark ablating Ag, using the coupled cluster with singles and doubles (CCSD) method. The stabilization energy of these clusters is calculated with respect to the dissociation channel having the lowest energy, by accounting perturbative triples corrections to the CCSD method. The interatomic interactions in each of the systems have been investigated using the frontier molecular orbital (FMO), natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) methods. Many of the ground states of these ionic clusters are found to be stable, corroborating experimental observations. We find that clusters having singlet spin states are more stable in terms of dissociation than the clusters that have doublet or triplet spin states. Our calculations also indicate a strong affinity of the ionic and neutral Ag atom towards water and hydroxyl radicals or ions. Many 3-center, 4-electron (3c/4e) hyperbonds giving rise to more than one resonance structure are identified primarily for the anionic clusters. The QTAIM analysis shows that the O-H and O-Ag bonds in the clusters of both polarities are respectively covalent and ionic. The FMO analysis indicates that the anionic clusters are more reactive than the cationic ones. Using the cluster structures predicted by the CCSD method, we calculate the collision cross sections of the AgOkHm± family, with k and m ranging from 1 to 4, by the trajectory method. In turn, we predict the electrical mobilities of these clusters when suspended in helium at atmospheric pressure and compare them with experimental measurements.
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Affiliation(s)
- Mohsen Doust Mohammadi
- Climate & Atmosphere Research Centre, The Cyprus Institute, 20 Konstantinou Kavafi Street, Nicosia 2121, Cyprus.
| | - Somnath Bhowmick
- Climate & Atmosphere Research Centre, The Cyprus Institute, 20 Konstantinou Kavafi Street, Nicosia 2121, Cyprus.
| | - Anne Maisser
- Climate & Atmosphere Research Centre, The Cyprus Institute, 20 Konstantinou Kavafi Street, Nicosia 2121, Cyprus.
| | - Andreas Schmidt-Ott
- Climate & Atmosphere Research Centre, The Cyprus Institute, 20 Konstantinou Kavafi Street, Nicosia 2121, Cyprus.
- Faculty of Applied Sciences, Delft University of Technology, Delft, 2629 HZ, The Netherlands
| | - George Biskos
- Climate & Atmosphere Research Centre, The Cyprus Institute, 20 Konstantinou Kavafi Street, Nicosia 2121, Cyprus.
- Faculty of Civil Engineering and Geosciences, Delft University of Technology, Delft, 2628 CN, The Netherlands
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de Barros Leite NF, Marques RB, Macedo-Filho A, Rocha GB, Martins EPS. Evaluation of DFT methods for predicting geometries and NMR spectra of Bi(III) dithiocarbamate complexes with antitumor properties. J Mol Model 2024; 30:177. [PMID: 38775913 DOI: 10.1007/s00894-024-05969-2] [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: 01/29/2024] [Accepted: 05/09/2024] [Indexed: 06/07/2024]
Abstract
CONTEXT Bismuth complexes with dithiocarbamate ligands have attracted attention because of their biological applications, such as antimicrobial, antileishmanial, and anticancer properties. These complexes have high cytotoxic activity against cancer cells, being more active than the standard drugs cisplatin, doxorubicin, and tamoxifen. In the present study, we investigated the ability of some DFT methods to reproduce the geometries and NMR spectra of the Bi(III) dithiocarbamate complexes, selected based on their proven antitumor activity. Our investigation revealed that the M06-L/def2-TZVP/ECP/CPCM method presented good accuracy in predicting geometries, while the TPSSh/def2-SVP/ECP/CPCM method proved effective in analyzing the 13C NMR spectra of these molecules. In general, all examined methods exhibited comparable performance in predicting 1H NMR signals. METHODS Calculations were performed with the Gaussian 09 program using the def2-SVP and def2-TZVP basis sets, employing relativistic effective core potential (ECP) for Bi and using the CPCM solvent model. The exchange-correlation functionals BP86, PBE, OLYP, M06-L, B3LYP, B3LYP-D3, M06-2X, TPSSh, CAM-B3LYP, and ωB97XD were used in the study. Geometry optimizations were started from crystallographic structures available at the Cambridge Structural Database. The theoretical results were compared with experimental data using the mean root-mean-square deviation (RMSD), mean absolute deviations (MAD), and linear correlation coefficient (R2).
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Affiliation(s)
| | | | | | - Gerd Bruno Rocha
- Chemistry Department, Exact and Natural Sciences Center, Federal University of Paraíba, João Pessoa, Brazil
| | - Evandro P S Martins
- Graduate Program in Chemistry, State University of Piaui, Teresina, PI, Brazil.
- State University of Piauí, Piripiri, PI, 64260-000, Brazil.
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Guo H, Kirchhoff JL, Strohmann C, Grabe B, Loh CCJ. Asymmetric Pd/Organoboron-Catalyzed Site-Selective Carbohydrate Functionalization with Alkoxyallenes Involving Noncovalent Stereocontrol. Angew Chem Int Ed Engl 2024; 63:e202400912. [PMID: 38530140 DOI: 10.1002/anie.202400912] [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: 01/15/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 03/27/2024]
Abstract
Herein, we demonstrate the robustness of a synergistic chiral Pd/organoboron system in tackling a challenging suite of site-, regio-, enantio- and diastereoselectivity issues across a considerable palette of biologically relevant carbohydrate polyols, when prochiral alkoxyallenes were employed as electrophiles. In view of the burgeoning role of noncovalent interactions (NCIs) in stereoselective carbohydrate synthesis, our mechanistic experiments and DFT modeling of the reaction path unexpectedly revealed that NCIs such as hydrogen bonding and CH-π interactions between the resting states of the Pd-π-allyl complex and the borinate saccharide are critically involved in the stereoselectivity control. Our strategy thus illuminates the untapped potential of harnessing NCIs in the context of transition metal catalysis to tackle stereoselectivity challenges in carbohydrate functionalization.
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Affiliation(s)
- Hao Guo
- Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227, Dortmund, Germany
| | - Jan-Lukas Kirchhoff
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie Anorganische Chemie, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Carsten Strohmann
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie Anorganische Chemie, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Bastian Grabe
- NMR Department Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227, Dortmund, Germany
| | - Charles C J Loh
- Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227, Dortmund, Germany
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Hendra R, Agustha A, Frimayanti N, Abdulah R, Teruna HY. Antifungal Potential of Secondary Metabolites Derived from Arcangelisia flava (L.) Merr.: An Analysis of In Silico Enzymatic Inhibition and In Vitro Efficacy against Candida Species. Molecules 2024; 29:2373. [PMID: 38792233 PMCID: PMC11123860 DOI: 10.3390/molecules29102373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/12/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
Considering the escalating resistance to conventional antifungal medications, it is critical to identify novel compounds that can efficiently counteract this challenge. The purpose of this research was to elucidate the fungicidal properties of secondary metabolites derived from Arcangelisia flava, with a specific focus on their efficacy against Candida species. This study utilized a combination approach comprising laboratory simulations and experiments to discern and evaluate the biologically active constituents present in the dichloromethane extract of A. flava. The in vitro experiments demonstrated that compounds 1 (palmatine) and 2 (fibraurin) exhibited antifungal properties. The compounds exhibited minimum inhibitory concentrations (MICs) ranging from 15.62 to 62.5 µg/mL against Candida sp. Moreover, compound 1 demonstrated a minimum fungicidal concentration (MFC) of 62.5 µg/mL against Candida glabrata and C. krusei. In contrast, compound 2 exhibited an MFC of 125 µg/mL against both Candida species. Based on a molecular docking study, it was shown that compounds 1 and 2 have a binding free energy of -6.6377 and -6.7075 kcal/mol, respectively, which indicates a strong affinity and specificity for fungal enzymatic targets. This study utilized pharmacophore modeling and Density Functional Theory (DFT) simulations to better understand the interaction dynamics and structural properties crucial for antifungal activity. The findings underscore the potential of secondary metabolites derived from A. flava to act as a foundation for creating novel and highly efficient antifungal treatments, specifically targeting fungal diseases resistant to existing treatment methods. Thus, the results regarding these compounds can provide references for the next stage in antifungal drug design. Further investigation is necessary to thoroughly evaluate these natural substances' clinical feasibility and safety characteristics, which show great potential as antifungal agents.
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Affiliation(s)
- Rudi Hendra
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Riau, Pekanbaru 28291, Indonesia; (A.A.); (H.Y.T.)
- Center of Excellence in Pharmaceutical Care Innovation, Universitas Padjadjaran, Bandung 40600, Indonesia;
| | - Aulia Agustha
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Riau, Pekanbaru 28291, Indonesia; (A.A.); (H.Y.T.)
| | - Neni Frimayanti
- Sekolah Tinggi Ilmu Farmasi Riau, Pekanbaru 28293, Indonesia;
| | - Rizky Abdulah
- Center of Excellence in Pharmaceutical Care Innovation, Universitas Padjadjaran, Bandung 40600, Indonesia;
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Jatinangor, Sumedang 45363, Indonesia
| | - Hilwan Yuda Teruna
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Riau, Pekanbaru 28291, Indonesia; (A.A.); (H.Y.T.)
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Kontodimas V, Yaman M, Greis K, Lettow M, Pagel K, Marianski M. Reinvestigation of the internal glycan rearrangement of Lewis a and blood group type H1 epitopes. Phys Chem Chem Phys 2024; 26:14160-14170. [PMID: 38712976 PMCID: PMC11147448 DOI: 10.1039/d3cp04491b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Protonated ions of fucose-containing oligosaccharides are prone to undergo internal glycan rearrangement which results in chimeric fragments that obfuscate mass-spectrometric analysis. Lack of accessible tools that would facilitate systematic analysis of glycans in the gas phase limits our understanding of this phenomenon. In this work, we use density functional theory modeling to interpret cryogenic IR spectra of Lewis a and blood group type H1 trisaccharides and to establish whether these trisaccharides undergo the rearrangement during gas-phase analysis. Structurally unconstrained search reveals that none of the parent ions constitute a thermodynamic global minimum. In contrast, predicted collision cross sections and anharmonic IR spectra provide a good match to available experimental data which allowed us to conclude that fucose migration does not occur in these antigens. By comparing the predicted structures with those obtained for Lewis x and blood group type H2 epitopes, we demonstrate that the availability of the mobile proton and a large difference in the relative stability of the parent ions and rearrangement products constitute the prerequisites for the rearrangement reaction.
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Affiliation(s)
- Vasilis Kontodimas
- Department of Chemistry, Hunter College, The City University of New York, New York, NY 10065, USA.
| | - Murat Yaman
- Department of Chemistry, Hunter College, The City University of New York, New York, NY 10065, USA.
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Kim Greis
- Fritz-Haber-Intitut der Max Planck Gesellschaft, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Maike Lettow
- Fritz-Haber-Intitut der Max Planck Gesellschaft, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Kevin Pagel
- Fritz-Haber-Intitut der Max Planck Gesellschaft, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Mateusz Marianski
- Department of Chemistry, Hunter College, The City University of New York, New York, NY 10065, USA.
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, The City University of New York, New York, NY 10016, USA
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Schlosser L, Rana D, Pflüger P, Katzenburg F, Glorius F. EnTdecker - A Machine Learning-Based Platform for Guiding Substrate Discovery in Energy Transfer Catalysis. J Am Chem Soc 2024; 146:13266-13275. [PMID: 38695558 DOI: 10.1021/jacs.4c01352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Due to the magnitude of chemical space, the discovery of novel substrates in energy transfer (EnT) catalysis remains a daunting task. Experimental and computational strategies to identify compounds that successfully undergo EnT-mediated reactions are limited by their time and cost efficiency. To accelerate the discovery process in EnT catalysis, we herein present the EnTdecker platform, which facilitates the large-scale virtual screening of potential substrates using machine-learning (ML) based predictions of their excited state properties. To achieve this, a data set is created containing more than 34,000 molecules aiming to cover a vast fraction of synthetically relevant compound space for EnT catalysis. Using this data predictive models are trained, and their aptitude for an in-lab application is demonstrated by rediscovering successful substrates from literature as well as experimental validation through luminescence-based screening. By reducing the computational effort needed to obtain excited state properties, the EnTdecker platform represents a tool to efficiently guide substrate selection and increase the experimental success rate for EnT catalysis. Moreover, through an easy-to-use web application, EnTdecker is made publicly accessible under entdecker.uni-muenster.de.
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Affiliation(s)
- Leon Schlosser
- Organisch-Chemisches Institut, University of Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Debanjan Rana
- Organisch-Chemisches Institut, University of Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Philipp Pflüger
- Organisch-Chemisches Institut, University of Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Felix Katzenburg
- Organisch-Chemisches Institut, University of Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Frank Glorius
- Organisch-Chemisches Institut, University of Münster, Corrensstraße 36, 48149 Münster, Germany
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Xu J, Hao J, Bu C, Meng Y, Xiao H, Zhang M, Li C. XMECP: Reaching State-of-the-Art MECP Optimization in Multiscale Complex Systems. J Chem Theory Comput 2024; 20:3590-3600. [PMID: 38651739 DOI: 10.1021/acs.jctc.4c00033] [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
The Python-based program, XMECP, is developed for realizing robust, efficient, and state-of-the-art minimum energy crossing point (MECP) optimization in multiscale complex systems. This article introduces the basic capabilities of the XMECP program by theoretically investigating the MECP mechanism of several example systems including (1) the photosensitization mechanism of benzophenone, (2) photoinduced proton-coupled electron transfer in the cytosine-guanine base pair in DNA, (3) the spin-flip process in oxygen activation catalyzed by an iron-containing 2-oxoglutarate-dependent oxygenase (Fe/2OGX), and (4) the photochemical pathway of flavoprotein adjusted by the intensity of an external electric field. MECPs related to multistate reaction and multistate reactivity in large-scale complex biochemical systems can be well-treated by workflows suggested by the XMECP program. The branching plane updating the MECP optimization algorithm is strongly recommended as it provides derivative coupling vector (DCV) with explicit calculation and can equivalently evaluate contributions from non-QM residues to DCV, which can be nonadiabatic coupling or spin-orbit coupling in different cases. In the discussed QM/MM examples, we also found that the influence on the QM region by DCV can occur through noncovalent interactions and decay with distance. In the example of DNA base pairs, the nonadiabatic coupling occurs across the π-π stacking structure formed in the double-helix system. In contrast to general intuition, in the example of Fe/2OGX, the central ferrous and oxygen part contribute little to the spin-orbit coupling; however, a nearby arginine residue, which is treated by molecular mechanics in the QM/MM method, contributes significantly via two hydrogen bonds formed with α-ketoglutarate (α-KG). This indicates that the arginine residue plays a significant role in oxygen activation, driving the initial triplet state toward the productive quintet state, which is more than the previous knowledge that the arginine residue can bind α-KG at the reaction site by hydrogen bonds.
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Affiliation(s)
- Jiawei Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jian Hao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Caijie Bu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350117, Fujian, P. R. China
| | - Yajie Meng
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Han Xiao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
| | - Minyi Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
| | - Chunsen Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, Fujian, P. R. China
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Milanović Ž, Marković Z, Kesić A, Jovanović Stević S, Petrović B, Avdović E. Influence of acid-base equilibrium on interactions of some monofunctional coumarin Pd(II) complexes with biologically relevant nucleophiles-comprehensive kinetic study. Dalton Trans 2024; 53:8275-8288. [PMID: 38659318 DOI: 10.1039/d4dt00789a] [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: 04/26/2024]
Abstract
This aimed to develop a comprehensive theoretical protocol for examining substitution reaction processes. The researchers used a theoretical quantum-mechanical protocol based on the QM-ORSA approach, which estimates the kinetic parameters of thermodynamically favourable reaction pathways. This theoretical protocol was validated by experimentally investigating substitution mechanisms in two previously synthesised Pd(II) complexes: chlorido-[(3-(1-(2-hydroxypropylamino)ethylidene)chroman-2,4-dione)]palladium(II) (C1) and chlorido-[(3-(1-(2-mercaptoethylamino)-ethylidene)-chroman-2,4dione)]palladium(II) (C2), along with biologically relevant nucleophiles, namely L-cysteine (l-Cys), L-methionine (l-Met), and guanosine-5'-monophosphate (5'-GMP). Reactions were investigated under pseudo-first-order conditions, monitoring nucleophile concentration and temperature changes using stopped-flow UV-vis spectrophotometry. All reactions were conducted under physiological conditions (pH = 7.2) at 37 °C. The reactivity of the studied nucleophiles follows the order: l-Cys > l-Met > 5'-GMP, and the reaction mechanism is associative based on the activation parameters. The experimental and theoretical data showed that C2 is more reactive than C1, confirming that the complexes' structural and electronic properties greatly affect their reactivity with selected nucleophiles. The study's findings have confirmed that the primary interaction occurs with the acid-base species L-Cys, mostly through the involvement of the partially negative sulfur atom (87.2%). On the other hand, C2 has a higher propensity for reacting with L-Cys-, primarily through the partially negative oxygen atom (92.6%). The implementation of this theoretical framework will significantly restrict the utilization of chemical substances, hence facilitating cost reduction and environmental protection.
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Affiliation(s)
- Žiko Milanović
- University of Kragujevac, Institute of Information Technologies, Department of Science, Jovana Cvijića bb, 34000 Kragujevac, Serbia
| | - Zoran Marković
- University of Kragujevac, Institute of Information Technologies, Department of Science, Jovana Cvijića bb, 34000 Kragujevac, Serbia
- Department of Natural Science and Mathematics, State University of Novi Pazar, Vuka Karadžića bb, 36300, Novi Pazar, Serbia
| | - Ana Kesić
- University of Kragujevac, Institute of Information Technologies, Department of Science, Jovana Cvijića bb, 34000 Kragujevac, Serbia
| | - Snežana Jovanović Stević
- University of Kragujevac, Faculty of Medical Sciences, Department of Pharmacy, Svetozara Markovića 69, 34000 Kragujevac, Serbia
| | - Biljana Petrović
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Edina Avdović
- University of Kragujevac, Institute of Information Technologies, Department of Science, Jovana Cvijića bb, 34000 Kragujevac, Serbia
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50
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Scholz AS, Massoth JG, Stoess L, Bolte M, Braun M, Lerner HW, Mewes JM, Wagner M, Froitzheim T. NBN- and BNB-Phenalenyls: the Yin and Yang of Heteroatom-doped π Systems. Chemistry 2024; 30:e202400320. [PMID: 38426580 DOI: 10.1002/chem.202400320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/02/2024]
Abstract
NBN- and BNB-doped phenalenyls are isoelectronic to phenalenyl anions and cations, respectively. They represent a pair of complementary molecules that have essentially identical structures but opposite properties as electron donors and acceptors. The NBN-phenalenyls 1-4 considered here were prepared from N,N'-dimethyl-1,8-diaminonaphthalene and readily available boron-containing building blocks (i. e., BH3⋅SMe2 (1), p-CF3-C6H4B(OH)2 (2), C6H5B(OH)2 (3), or MesBCl2/iPr2NEt (4)). Treatment of 1 with 4-Me2N-2,6-Me2-C6H2Li gave the corresponding NBN derivative 5. The BNB-phenalenyl 6 was synthesized from 1,8-naphthalenediyl-bridged diborane(6), PhNH2, and MesMgBr. A computational study reveals that the photoemission of 1, 4, and 5 originates from locally excited (LE) states at the NBN-phenalenyl fragments, while that of 2 is dominated by charge transfer (CT) from the NBN-phenalenyl to the p-CF3-C6H4 fragment. Depending on the dihedral angle θ between its Ph and NBN planes, compound 3 emits mainly from a less polar LE (θ >55°) or more polar CT state (θ <55°). In turn, the energetic preference for either state is governed by the polarity of the solvent used. An equimolar aggregate of the NBN- and BNB-phenalenyls 3 and 6 (in THF/H2O) shows a distinct red-shifted emission compared to that of the individual components, which originates from an intermolecular CT state.
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Affiliation(s)
- Alexander S Scholz
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Julian G Massoth
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Lennart Stoess
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Michael Bolte
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Markus Braun
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Hans-Wolfram Lerner
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Jan-M Mewes
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich Wilhelms-Universität Bonn, Beringstr. 4, 53115, Bonn, Germany
| | - Matthias Wagner
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Thomas Froitzheim
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich Wilhelms-Universität Bonn, Beringstr. 4, 53115, Bonn, Germany
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