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García-Argote W, Ruiz L, Inostroza D, Cardenas C, Yañez O, Tiznado W. Introducing KICK-MEP: exploring potential energy surfaces in systems with significant non-covalent interactions. J Mol Model 2024; 30:369. [PMID: 39377846 DOI: 10.1007/s00894-024-06155-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Accepted: 09/20/2024] [Indexed: 10/09/2024]
Abstract
CONTEXT Exploring potential energy surfaces (PES) is fundamental in computational chemistry, as it provides insights into the relationship between molecular energy, geometry, and chemical reactivity. We introduce Kick-MEP, a hybrid method for exploring the PES of atomic and molecular clusters, particularly those dominated by non-covalent interactions. Kick-MEP computes the Coulomb integral between the maximum and minimum electrostatic potential values on a 0.001 a.u. electron density isosurface for two interacting fragments. This approach efficiently estimates interaction energies and selects low-energy configurations at reduced computational cost. Kick-MEP was evaluated on silicon-lithium clusters, water clusters, and thymol encapsulated within Cucurbit[7]uril, consistently identifying the lowest energy structures, including global minima and relevant local minima. METHODS Kick-MEP generates an initial population of molecular structures using the stochastic Kick algorithm, which combines two molecular fragments (A and B). The molecular electrostatic potential (MEP) values on a 0.001 a.u. electron density isosurface for each fragment are used to compute the Coulomb integral between them. Structures with the lowest Coulomb integral are selected and refined through gradient-based optimization and DFT calculations at the PBE0-D3/Def2-TZVP level. Molecular docking simulations for the thymol-Cucurbit[7]uril complex using AutoDock Vina were performed for benchmarking. Kick-MEP was validated across different molecular systems, demonstrating its effectiveness in identifying the lowest energy structures, including global minima and relevant local minima, while maintaining a low computational cost.
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Affiliation(s)
- Williams García-Argote
- Centro de Química Teórica & Computacional (CQT&C), Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, Avenida República 275, 8370146, Santiago de Chile, Chile
- Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andres Bello, República 275, Santiago, Chile
| | - Lina Ruiz
- Centro de Investigación Biomédica, Universidad Autónoma de Chile, 7500912, Santiago, Chile
| | - Diego Inostroza
- Centro de Química Teórica & Computacional (CQT&C), Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, Avenida República 275, 8370146, Santiago de Chile, Chile
| | - Carlos Cardenas
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, 7800024, Ñuñoa, Santiago, Chile.
- Center for the Development of Nanoscience and Nanotechnology (CEDENNA), 9170124, Santiago, Chile.
| | - Osvaldo Yañez
- Núcleo de Investigación en Data Science, Facultad de Ingeniería y Negocios, Universidad de Las Américas, 7500975, Santiago, Chile.
| | - William Tiznado
- Centro de Química Teórica & Computacional (CQT&C), Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, Avenida República 275, 8370146, Santiago de Chile, Chile.
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Musatat AB, Durmuş T, Atahan A. Harnessing high potential benzothiazole chalcones against dengue virus NS5 protein: A multi-faceted theoretical study through molecular docking, ADME, and DFT. Arch Biochem Biophys 2024; 761:110171. [PMID: 39366630 DOI: 10.1016/j.abb.2024.110171] [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: 07/22/2024] [Revised: 09/13/2024] [Accepted: 09/30/2024] [Indexed: 10/06/2024]
Abstract
Chalcones bearing tetralone, indanone and benzothiazole cores were synthesized successfully using a general Claisen-Schmidt condensation protocol. The prepared compounds were purified and structurally analyzed by 1H, 13C NMR, and FT-IR techniques. A multi-faceted theoretical approach, combining Density Functional Theory (DFT), molecular docking, and ADME predictions, was employed to evaluate their therapeutic potential. DFT calculations at the B3LYP/def2-TZVP level revealed key electronic properties, with TD3 compound demonstrating the highest chemical reactivity. Molecular Electrostatic Potential (MEP) and Reduced Density Gradient (RDG) analyses provided insights into the compounds' non-covalent interactions and charge distributions. Molecular docking studies against the NS5 protein (PDB: 6KR2) showed superior binding affinities for all three compounds compared to the control ligand SAH, with TD3 exhibiting the lowest binding energy (-8.41 kcal/mol) and theoretical inhibition constant (689.31 nM). ADME predictions indicated favorable drug-like properties with concerns regarding aqueous solubility and potential P-glycoprotein interactions. Toxicity evaluations highlighted challenges, particularly in hepatotoxicity and carcinogenicity. The study identified TD3 as a promising lead compound for Dengue Virus NS5 inhibition, while also emphasizing the need for targeted modifications to address toxicity concerns. This research not only contributes to anti-dengue drug discovery efforts but also provides a robust methodological framework for the theoretical evaluation of similar small compounds in future investigations.
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Affiliation(s)
| | - Tülay Durmuş
- Department of Chemistry, Faculty of Art and Sciences, Düzce University, 81100, Düzce, Turkiye
| | - Alparslan Atahan
- Department of Chemistry, Faculty of Art and Sciences, Düzce University, 81100, Düzce, Turkiye
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Geetha Sadasivan Nair R, Narayanan Nair AK, Sun S. Adsorption of drugs on B 12N 12 and Al 12N 12 nanocages. RSC Adv 2024; 14:31756-31767. [PMID: 39380648 PMCID: PMC11459447 DOI: 10.1039/d4ra05586a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Accepted: 09/26/2024] [Indexed: 10/10/2024] Open
Abstract
The adsorption behavior of twelve drug molecules (5-fluorouracil, nitrosourea, pyrazinamide, sulfanilamide, ethionamide, 6-thioguanine, ciclopirox, 6-mercaptopurine, isoniazid, metformin, 4-aminopyridine, and cathinone) on B12N12 and Al12N12 nanocages was studied using density functional theory. In general, the drug molecules prefer to bind with the boron atom of the B12N12 nanocage and the aluminium atoms of the Al12N12 nanocage. However, a hydrogen atom is transferred from each of 5-fluorouracil, nitrosourea, 6-thioguanine, ciclopirox, and 6-mercaptopurine to the nitrogen atom of the Al12N12 nanocage. All the drug molecules are found to be chemisorbed on the B12N12 and Al12N12 nanocages. The adsorption energies of the drug/B12N12 system are linearly correlated with the molecular electrostatic potential minimum values of the drug molecules. The transfer of the hydrogen atom from the drug molecules to the nitrogen atom of the Al12N12 nanocage leads to relatively high adsorption energies. We observed significant changes in the reactivity parameters (e.g. electronic chemical potential) of the nanocages due to the chemisorption process. Overall, the QTAIM analysis indicates that the interactions between drug molecules and nanocages have a partial covalent character. Among the studied systems, the adsorption process was more spontaneous for the ciclopirox/Al12N12 system in water.
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Affiliation(s)
- Remya Geetha Sadasivan Nair
- Physical Science and Engineering Division (PSE), Computational Transport Phenomena Laboratory, King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia
| | - Arun Kumar Narayanan Nair
- Physical Science and Engineering Division (PSE), Computational Transport Phenomena Laboratory, King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia
| | - Shuyu Sun
- Physical Science and Engineering Division (PSE), Computational Transport Phenomena Laboratory, King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia
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Zaklika J, Ordon P, Komorowski L. Hyperhardness and hypersoftness of atoms and their ions. J Mol Model 2024; 30:344. [PMID: 39305376 PMCID: PMC11416423 DOI: 10.1007/s00894-024-06136-3] [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: 03/23/2024] [Accepted: 09/03/2024] [Indexed: 09/25/2024]
Abstract
CONTEXT The theory of reactivity based on cDFT has been supplemented with the new method of calculating the atomic and local indices. With the use of previously derived relationship of the electron density gradient to the softness kernel and to the linear response function, we deliver theoretical analysis to obtain significant reactivity indices-the electron density derivatives: local softness and local hypersoftness together with the global hyperhardness index and the derivative of the global softness with respect to the number of electrons. The local derivatives have been applied in the calculation of responses of atoms to perturbation by an external potential by the alchemical approach. The vital role of the local softness has been confirmed; the potential role of the hypersoftness has been indicated. METHOD Our original theoretical scheme has been numerically illustrated with the results obtained with electron density calculations with B3LYP method implemented in Gaussian 16 package. The aug-cc-pvqz basis set has been routinely applied, except for the Ca atom (cc-pvqz). Using the pVTZ basis set recommended by Sadlej was necessary for the potassium atom.
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Affiliation(s)
- Jarosław Zaklika
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Piotr Ordon
- Department of Physics and Biophysics, Wrocław University of Environmental and Life Sciences, Ul. Norwida 25, 50-373, Wrocław, Poland.
| | - Ludwik Komorowski
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370, Wrocław, Poland
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Maddheshiya AK, Kumar M, Tufail A, Yadav PS, Deswal Y, Yadav N, Yadav TP, Dubey A. Synergistic Activity of Noble Trimetallic Nanofluids: Unveiling Unprecedented Antimicrobial Potential and Computational Insights. ACS APPLIED BIO MATERIALS 2024; 7:5906-5924. [PMID: 38722351 DOI: 10.1021/acsabm.3c01268] [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] [Indexed: 08/27/2024]
Abstract
Nanofluids hold significant promise in diverse applications, particularly in biomedicine, where noble trimetallic nanofluids outperformed their monometallic counterparts. The composition, morphology, and size of these nanofluids play pivotal roles in their functionality. Controlled synthesis methods have garnered attention, focusing on precise morphology, content, biocompatibility, and versatile chemistry. Understanding how reaction parameters such as time, reducing agents, stabilizers, precursor concentration, temperature, and pH affect size and shape during synthesis is crucial. Trimetallic nanofluids, with their ideal composition, size, surface structure, and synergistic properties, are gaining traction in antimicrobial applications. These nanofluids were tested against seven microorganisms, demonstrating a heightened antimicrobial efficacy. Computational analyses, including molecular docking, dynamics, density functional theory (DFT), molecular electrostatic potential (MESP) analysis, and absorption, distribution, metabolism, elimination, and toxicology studies (ADMET) provided insights into binding interactions, energy, reactivity, and safety profiles, affirming the antimicrobial potential of trimetallic nanofluids. These findings emphasize the importance of controlled synthesis and computational validation in harnessing the unique properties of trimetallic nanofluids for biomedical applications.
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Affiliation(s)
- Ajit Kumar Maddheshiya
- Department of Physics, Faculty of Science, University of Allahabad, Prayagraj 211002, India
| | - Manish Kumar
- Department of Biochemistry, Iswar Saran Degree College (A Constituent PG College of University of Allahabad), Teliarganj, Prayagraj 211004, India
| | - Aisha Tufail
- Department of Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida 201310, India
| | - Phool Singh Yadav
- Department of Physics, Faculty of Science, University of Allahabad, Prayagraj 211002, India
| | - Yogesh Deswal
- Department of Chemistry, Guru Jambheshwar University of Science and Technology, Hisar 125001, India
| | - Navneet Yadav
- Department of Physics, Faculty of Science, University of Allahabad, Prayagraj 211002, India
| | - Thakur Prasad Yadav
- Department of Physics, Faculty of Science, University of Allahabad, Prayagraj 211002, India
| | - Amit Dubey
- Department of Pharmacology, Saveetha Dental College, and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
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Cárdenas C, Ayers PW, Chakraborty D, Gómez T, Echeverri A, Munoz F, Fuentealba P. On the link between the reaction force constant and conceptual DFT. J Mol Model 2024; 30:332. [PMID: 39276242 DOI: 10.1007/s00894-024-06137-2] [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: 05/24/2024] [Accepted: 09/03/2024] [Indexed: 09/16/2024]
Abstract
CONTEXT The reaction force constant ( κ ), introduced by Professor Alejandro Toro-Labbé, plays a pivotal role in characterizing the reaction pathway by assessing the curvature of the potential energy profile along the intrinsic reaction coordinate. This study establishes a novel link between κ and the reactivity descriptors of conceptual density functional theory (c-DFT). Specifically, we derive expressions that relate the reaction force constant to nuclear softness and variations in chemical potential. Our findings indicate that regions of the reaction pathway where κ is negative match with significant electronic structure rearrangements, while positive κ regions match mostly with geometric rearrangements. This correlation between κ and c-DFT reactivity descriptors enhances our understanding of the underlying forces driving chemical reactions and offers new perspectives for analyzing reaction mechanisms. METHODS The internal reaction path for the proton transfer in SNOH, chemical potential, and nuclear softness were computed using DFT with B3LYP exchange-correlation functional and 6-311++G(d,2p) basis set.
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Affiliation(s)
- Carlos Cárdenas
- Departmento de Física, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile.
- Center for the Development of Nanoscience and Nanotechnology (CEDENNA), Santiago, Chile.
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, L8S 4M1, Canada.
| | - Debajit Chakraborty
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27109, USA
| | - Tatiana Gómez
- Theoretical and Computational Chemistry Center, Institute of Applied Chemical Sciences, Faculty of Engineering, Universidad Autonoma de Chile, Avenida Pedro de Valdivia 425, Santiago, Chile
| | - Andrea Echeverri
- Departmento de Física, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - Francisco Munoz
- Departmento de Física, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
- Center for the Development of Nanoscience and Nanotechnology (CEDENNA), Santiago, Chile
| | - Patricio Fuentealba
- Departmento de Física, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
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Islam MR, Biswas S, Amena U, Rahman M, Islam S, Islam MA, Saleh MA, Hassan HM, Al‐Emam A, Zaki MEA. Modified oxymatrine as novel therapeutic inhibitors against Monkeypox and Marburg virus through computational drug design approaches. J Cell Mol Med 2024; 28:e70116. [PMID: 39340487 PMCID: PMC11437895 DOI: 10.1111/jcmm.70116] [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: 03/21/2024] [Revised: 08/06/2024] [Accepted: 09/17/2024] [Indexed: 09/30/2024] Open
Abstract
Global impact of viral diseases specially Monkeypox (mpox) and Marburg virus, emphasizing the urgent need for effective drug interventions. Oxymatrine is an alkaloid which has been selected and modified using various functional groups to enhance its efficacy. The modifications were evaluated using various computatioanal analysis such as pass prediction, molecular docking, ADMET, and molecular dynamic simulation. Mpox and Marburg virus were chosen as target diseases based on their maximum pass prediction spectrum against viral disease. After that, molecular docking, dynamic simulation, DFT, calculation and ADMET prediction were determined. The main objective of this study was to enhance the efficacy of oxymatrine derivatives through functional group modifications and computational analyses to develop effective drug candidates against mpox and Marburg viruses. The calculated binding affinities indicated strong interactions against both mpox virus and Marburg virus. After that, the molecular dynamic simulation was conducted at 100 ns, which confirmed the stability of the binding interactions between the modified oxymatrine derivatives and target proteins. Then, the modified oxymatrine derivatives conducted theoretical ADMET profiling, which demonstrated their potential for effective drug development. Moreover, HOMO-LUMO calculation was performed to understand the chemical reactivity and physicochemical properties of compounds. This computational analysis indicated that modified oxymatrine derivatives for the treatment of mpox and Marburg virus suggested effective drug candidates based on their binding affinity, drug-like properties, stability and chemical reactivity. However, further experimental validation is necessary to confirm their clinical value and efficacy as therapeutic candidates.
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Affiliation(s)
- Md. Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health SciencesDaffodil International UniversityAshuliaDhakaBangladesh
| | - Suvro Biswas
- Department of Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | - Ummy Amena
- Department of Pharmacy, Faculty of Life & Earth SciencesJagannath UniversityDhakaBangladesh
| | - Miadur Rahman
- Department of Pharmaceutical SciencesNorth South UniversityDhakaBangladesh
| | - Shirmin Islam
- Department of Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | - Md. Ariful Islam
- Department of Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | - Md. Abu Saleh
- Department of Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | - Hesham M. Hassan
- Department of Pathology, College of MedicineKing Khalid UniversityAsirSaudi Arabia
| | - Ahmed Al‐Emam
- Department of Pathology, College of MedicineKing Khalid UniversityAsirSaudi Arabia
| | - Magdi E. A. Zaki
- Department of Chemistry, College of ScienceImam Mohammad Ibn Saud Islamic University RiyadhRiyadhSaudi Arabia
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Lu T. Theoretical Prediction and Comprehensive Characterization of an All-Nitrogenatomic Ring, Cyclo[18]Nitrogen (N 18). Chemphyschem 2024; 25:e202400377. [PMID: 38722092 DOI: 10.1002/cphc.202400377] [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: 04/01/2024] [Revised: 05/07/2024] [Indexed: 06/20/2024]
Abstract
The cyclic molecule cyclo[18]carbon composed of 18 carbon atoms has been observed in condensed phase experiment in recent years and has attracted great attention. Through state-of-art quantum chemistry calculation, this study found that 18 nitrogen atoms can also form a macrocyclic system, cyclo[18]nitrogen (N18), though its lifetime is very short at room temperature and can only exist for a relatively long time at very low temperatures. We comprehensively theoretically studied properties of N18, including geometric configurations, thermal decomposition mechanism and rate, molecular dynamics behavior, energetic properties, vibrational and electronic spectra. We also discussed in depth the electronic structure of N18, including nature of the N-N bonds, lone-pairs, charge distribution characteristics, electronic delocalization, and aromaticity. This work is not only the first exploration of the macrocyclic N18 molecule, but also the first time to systematically examine a very long-chain substance fully composed of nitrogen atoms in isolated state.
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Affiliation(s)
- Tian Lu
- Beijing Kein Research Center for Natural Sciences, Beijing, 100024, P. R. China
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Gayraud O, Guégan F. Charge transfer interaction revisited by a Fermi-Dirac derived approach. J Mol Model 2024; 30:307. [PMID: 39136856 DOI: 10.1007/s00894-024-06097-7] [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: 05/22/2024] [Accepted: 07/26/2024] [Indexed: 09/11/2024]
Abstract
CONTEXT In this article, we adapt a recent proposition to use a Fermi-Dirac-type population scheme on Kohn-Sham molecular orbitals to the case of an interaction with a thermalised electrode. This allows to derive a fundamental non-linear equation linking the chemical potential of the electrode and the amount of charge transferred to the system under study, hence allows to quantify the propensity to charge transfer (philicity). This methodology is applied to a large set of common electrophiles and nucleophiles, showing decent relation with more standard philicity descriptors. Chemical hardness is also revisited by this approach. METHODS All calculations were performed using the Gaussian 16 software package at the M062X/aug-cc-pvtz level of theory. Data analysis was then performed through a Python3 dedicated program (relying on the fsolve numerical solver from the SciPy package), using Gaussian output files, and available as supplementary material.
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Affiliation(s)
- Oscar Gayraud
- IC2MP UMR 7285, Université de Poitiers - CNRS, 4, Rue Michel Brunet, TSA 51106-86073 Cedex 9, Poitiers, France.
- Spectrometry, Interaction and Theoretical Chemistry Team, DCM UMR 5250, Université Grenoble Alpes - CNRS, Grenoble, 38058, France.
| | - Frédéric Guégan
- IC2MP UMR 7285, Université de Poitiers - CNRS, 4, Rue Michel Brunet, TSA 51106-86073 Cedex 9, Poitiers, France
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Guerra C, Burgos J, Ayarde-Henríquez L, Chamorro E. Formulating Reduced Density Gradient Approaches for Noncovalent Interactions. J Phys Chem A 2024; 128:6158-6166. [PMID: 39042821 DOI: 10.1021/acs.jpca.4c01667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
This work elucidates several forms of reduced electron density gradient (RDG) to describe noncovalent interactions (NCIs). By interpreting the RDG as a local moment function, we systematically leveraged Weizacker's and Fermi's local moments. This resulted in high-fidelity RDG representations consistent with the NCI analysis. In addition, the RDG version derived from the Lagrangian kinetic energy density is conveniently normalized. These results suggest the nonexistence of a particular RDG formulation when performing NCI analysis. Thus, an in-depth examination of the theoretical foundations connecting the RDG function with the nature of noncovalent interactions is necessary.
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Affiliation(s)
- Cristian Guerra
- Facultad de Ciencias Exactas. Departamento de Ciencias Químicas, Universidad Andrés Bello. Avenida República 275, 8370146 Santiago de Chile, Chile
| | - José Burgos
- Facultad de Ciencias Exactas. Departamento de Ciencias Químicas, Universidad Andrés Bello. Avenida República 275, 8370146 Santiago de Chile, Chile
| | - Leandro Ayarde-Henríquez
- School of Physics, Trinity College Dublin, Dublin 2, Ireland
- AMBER, Advanced Materials and BioEngineering Research Centre, Dublin 2, Ireland
| | - Eduardo Chamorro
- Facultad de Ciencias Exactas. Departamento de Ciencias Químicas, Universidad Andrés Bello. Avenida República 275, 8370146 Santiago de Chile, Chile
- Centro de Química Teórica y Computacional (CQTC), Facultad de Ciencias Exactas, Departamento de Ciencias Químicas, Universidad Andrés Bello. Avenida República 275, 8370146 Santiago de Chile, Chile
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Hoffmann G, Guégan F, Labet V, Joubert L, Chermette H, Morell C, Tognetti V. Expanding horizons in conceptual density functional theory: Novel ensembles and descriptors to decipher reactivity patterns. J Comput Chem 2024; 45:1716-1726. [PMID: 38580454 DOI: 10.1002/jcc.27363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 04/07/2024]
Abstract
Conceptual density functional theory (CDFT) and the quantum reactivity descriptors stemming from it have proven to be valuable tools for understanding the chemical behavior of molecules. This article is presented as being intrinsically of dual character. In a first part, it briefly reviews, in a deliberately didactical way, the main ensembles in CDFT, while the second half presents two additional ensembles, where the chemical hardness acts as a natural variable, and their respective reactivity descriptors. The evaluation of these reactivity descriptors on common organic chemical reagents are presented and discussed.
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Affiliation(s)
- Guillaume Hoffmann
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Villeurbanne, France
| | - Frédéric Guégan
- IC2MP UMR 7285, Université de Poitiers - CNRS, Poitiers, France
| | - Vanessa Labet
- Sorbonne Université CNRS, MONARIS, UMR8233, Paris, France
| | - Laurent Joubert
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, Rouen, France
| | - Henry Chermette
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Villeurbanne, France
| | - Christophe Morell
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Villeurbanne, France
| | - Vincent Tognetti
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, Rouen, France
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Savić M, Pevec A, Stevanović N, Novaković I, Matić IZ, Petrović N, Stanojković T, Milčić K, Zlatar M, Turel I, Čobeljić B, Milčić M, Gruden M. Synergy of experimental and computational chemistry: structure and biological activity of Zn(II) hydrazone complexes. Dalton Trans 2024. [PMID: 39058304 DOI: 10.1039/d4dt01353k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
In this paper, three different Zn(II) complexes with (E)-2-(2-(1-(6-bromopyridin-2-yl)ethylidene)hydrazinyl)-N,N,N-trimethyl-2-oxoethan-1-aminium chloride (HLCl) have been synthesized and characterized by single crystal X-ray diffraction, elemental analysis, IR and NMR spectroscopy. All complexes are mononuclear, with the ligand (L) coordinated in a deprotonated formally neutral zwitterionic form via NNO donor set atoms. Complex 1 forms an octahedral geometry with the composition [ZnL2](BF4)2, while complexes 2 [ZnL(NCO)2] and 3 [ZnL(N3)2] form penta-coordinated geometry. Density functional theory (DFT) calculations were performed to enhance our understanding of the structures of the synthesized complexes and the cytotoxic activity of the complexes was tested against five human cancer cell lines (HeLa, A549, MDA-MB-231, K562, LS 174T) and normal human fibroblasts MRC-5. Additionally, antibacterial and antifungal activity of these complexes was tested against a panel of Gram-negative and Gram-positive bacteria, two fungal strains, and a yeast strain. It is noteworthy that all three complexes show selective antifungal activity comparable to that of amphotericin B. Molecular docking analysis predicted that geranylgeranyl pyrophosphate synthase, an enzyme essential for sterol biosynthesis, is the most likely target for inhibition by the tested complexes.
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Affiliation(s)
- Milica Savić
- University of Belgrade - Institute of chemistry, technology and metallurgy Department of chemistry, Njegoševa 12, P.O. Box 815, 11001 Belgrade, Serbia
| | - Andrej Pevec
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Nevena Stevanović
- University of Belgrade - Faculty of Chemistry Studentski trg 12-16, 11000 Belgrade, Serbia.
| | - Irena Novaković
- University of Belgrade - Institute of chemistry, technology and metallurgy Department of chemistry, Njegoševa 12, P.O. Box 815, 11001 Belgrade, Serbia
| | - Ivana Z Matić
- Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | - Nina Petrović
- Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
- "VINČA" Institute of Nuclear Sciences-National Institute of the Republic of Serbia, University of Belgrade, Belgrade 11000, Serbia
| | - Tatjana Stanojković
- Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | - Karla Milčić
- University of Belgrade - Faculty of Chemistry Studentski trg 12-16, 11000 Belgrade, Serbia.
| | - Matija Zlatar
- University of Belgrade - Institute of chemistry, technology and metallurgy Department of chemistry, Njegoševa 12, P.O. Box 815, 11001 Belgrade, Serbia
| | - Iztok Turel
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Božidar Čobeljić
- University of Belgrade - Faculty of Chemistry Studentski trg 12-16, 11000 Belgrade, Serbia.
| | - Miloš Milčić
- University of Belgrade - Faculty of Chemistry Studentski trg 12-16, 11000 Belgrade, Serbia.
| | - Maja Gruden
- University of Belgrade - Faculty of Chemistry Studentski trg 12-16, 11000 Belgrade, Serbia.
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13
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Cedillo A, Martínez-Aguilar JR. The use of constrained methods to analyze the molecular reactivity and to define a new type of pseudo atoms. J Mol Model 2024; 30:269. [PMID: 39012379 PMCID: PMC11252233 DOI: 10.1007/s00894-024-06071-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/09/2024] [Indexed: 07/17/2024]
Abstract
CONTEXT Constrained methods in electronic structure methodologies add terms to the variational equations and generate solutions that represent distorted electronic distributions. In some cases, the new solutions can be used to study the chemical reactivity of parts of the molecule. Additionally, this contribution presents the use of population constraints to define pseudo atoms in a molecule. The effects of the pseudo atom on the molecular properties are analyzed. The pseudo atoms are used to simulate the inductive effect of the substituent in a group of carbonyl molecules and their effect on the stability of the complexes between these organic species and one molecule of water. A discussion on the assumptions involved in the present definition of pseudo atoms is also included. METHOD The constrained RHF computations are done in a modified Hartree-Fock code for Gaussian basis sets. The selected basis set is STO-6 G.
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Affiliation(s)
- Andrés Cedillo
- Departamento de Química, Universidad Autónoma Metropolitana - Iztapalapa, Av. Ferrocarril San Rafael Atlixco 186, Iztapalapa, 09310, CDMX, México.
| | - José-Remy Martínez-Aguilar
- Departamento de Química, Universidad Autónoma Metropolitana - Iztapalapa, Av. Ferrocarril San Rafael Atlixco 186, Iztapalapa, 09310, CDMX, México
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14
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Hussain M, Adnan M, Irshad Z, Hussain R, Darwish HW. Systematic Engineering of Near-Infrared Small Molecules Based on 4H-Cyclopenta[1,2-b:5,4-b']dithiophene Acceptors for Organic Solar Cells. ACS OMEGA 2024; 9:28791-28805. [PMID: 38973890 PMCID: PMC11223142 DOI: 10.1021/acsomega.4c03181] [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: 04/03/2024] [Revised: 06/06/2024] [Accepted: 06/11/2024] [Indexed: 07/09/2024]
Abstract
Nonfullerene acceptors (NFAs) have emerged as tremendous materials, efficiently advancing bulk-heterojunction organic solar cells (OSCs) technology. Unlike their fullerene counterparts, NFAs offer the unique advantage of finely tunable electronic energy levels and optical characteristics, which correspond to substantial enhancement in power conversion efficiency of OSCs. Herein, we have introduced a new series of near-infrared NFAs (AY1-AY8) to advance this technology further. Our research deeply investigates the structure-property relationship and thoroughly explores the optical, optoelectronics, photophysical, and photovoltaic characteristics of a synthetic reference molecule (R) and the modeled AY1-AY8 NFAs series. We performed advanced quantum chemical simulations using density functional theory (DFT) and time-dependent DFT methods. Additionally, we also estimated key geometric characteristics such as frontier molecular orbitals, hole-electron overlap, density of states, molecular electrostatic potential, molecular excitation and binding energies, transition density matrix, and reorganizational energy of electrons and holes and compared them with those of a synthetic reference molecule (R). Our findings show that all designed materials (AY1-AY8) exhibit red-shift absorption, improved electronic charge mobility, and low binding and excitation energies compared to R. Notably, these designed materials (AY1-AY8) display significantly narrower electronic energy gaps (E g 1.89-1.71 eV), indicating enhanced charge shifting from the highest occupied molecular orbital to lowest unoccupied molecular orbital and broadening of the absorption spectrum. Moreover, we also revealed a comprehensive study of the donor/acceptor complex of PTB7-Th/AY8 to understand charge shifting between donor and acceptor molecules. Therefore, we strongly recommend this designed (AY1-AY8) series to the experimentalists for the future development of highly efficient OSC devices.
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Affiliation(s)
- Muzammil Hussain
- Department
of Chemistry, University of Okara, Okara 56300, Pakistan
| | - Muhammad Adnan
- Graduate
School of Energy Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Zobia Irshad
- Graduate
School of Energy Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Riaz Hussain
- Department
of Chemistry, University of Okara, Okara 56300, Pakistan
| | - Hany W. Darwish
- Department
of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
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15
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Hoffmann G, Chermette H, Morell C. Revisiting nucleophilicity: an index for chemical reactivity from a CDFT approach. J Mol Model 2024; 30:232. [PMID: 38937336 DOI: 10.1007/s00894-024-06020-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024]
Abstract
CONTEXT Understanding and predicting the nucleophilic reactivity are paramount in elucidating organic chemical reactions and designing new synthetic pathways. In this study, we propose a nucleophilicity index within the framework of Conceptual Density Functional Theory (CDFT). Through rigorous theoretical formulations, we introduce an original quantum reactivity descriptor that captures the nucleophilic propensity of molecules based on their electronic structure and chemical environment. Subsequently, this proposed index is applied to a series of nucleophiles (pyrrolidines derivatives), spanning a diverse range of chemical functionalities. Our computational assessments reveal insightful correlations between the predicted nucleophilicity index and experimental observations of nucleophilic behavior. Thereby, they offer a promising avenue for advancing the understanding of organic reactivity and guiding synthetic efforts. METHODS Experimentally, Mayr's experimental parameters accounting for nucleophilicity were selected for the pyrrolidines. This study used DFT calculations at the B3LYP/Aug-cc-pVTZ level of theory using the Gaussian 16 program. Geometry optimization was thus performed, and the methodology employed for the computation of quantum reactivity descriptor is presented. Solvent effect was also taken into account using IEFPCM, and empirical dispersion correction (GD3) was employed.
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Affiliation(s)
- Guillaume Hoffmann
- Universite Claude Bernard Lyon1, ISA, UMR5280, CNRS, 5 rue de la Doua, Villeurbanne, 69100, France.
| | - Henry Chermette
- Universite Claude Bernard Lyon1, ISA, UMR5280, CNRS, 5 rue de la Doua, Villeurbanne, 69100, France
| | - Christophe Morell
- Universite Claude Bernard Lyon1, ISA, UMR5280, CNRS, 5 rue de la Doua, Villeurbanne, 69100, France
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16
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Ferrer M, Elguero J, Alkorta I, Azofra LM. Understanding the coupling of non-metallic heteroatoms to CO 2 from a Conceptual DFT perspective. J Mol Model 2024; 30:201. [PMID: 38853233 PMCID: PMC11162977 DOI: 10.1007/s00894-024-05992-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/23/2024] [Indexed: 06/11/2024]
Abstract
CONTEXT A Conceptual DFT (CDFT) study has been carry out to analyse the coupling reactions of the simplest amine (CH3NH2), alcohol (CH3OH), and thiol (CH3SH) compounds with CO2 to form the corresponding adducts CH3NHCO2H, CH3OCO2H, and CH3SCO2H. The reaction mechanism takes place in a single step comprising two chemical events: nucleophilic attack of the non-metallic heteroatoms to CO2 followed by hydrogen atom transfer (HAT). According to our calculations, the participation of an additional nucleophilic molecule as HAT assistant entails important decreases in activation electronic energies. In such cases, the formation of a six-membered ring in the transition state (TS) reduces the angular stress with respect to the non-assisted paths, characterised by four-membered ring TSs. Through the analysis of the energy and reaction force profiles along the intrinsic reaction coordinate (IRC), the ratio of structural reorganisation and electronic rearrangement for both activation and relaxation energies has been computed. In addition, the analysis of the electronic chemical potential and reaction electronic flux profiles confirms that the highest electronic activity as well as their changes take place in the TS region. Finally, the distortion/interaction model using an energy decomposition scheme based on the electron density along the reaction coordinate has been carried out and the relative energy gradient (REG) method has been applied to identify the most important components associated to the barriers. METHODS The theoretical calculation were performed with Gaussian-16 scientific program. The B3LYP-D3(BJ)/aug-cc-pVDZ level was used for optimization of the minima and TSs. IRC calculations has also been carried out connecting the TS with the associated minima. Conceptual-DFT (CDFT) calculations have been carried out with the Eyringpy program and in-house code. The distortion/interaction model along the reaction coordinate have used the decomposition scheme of Mandado et al. and the analysis of the importance of each components have been done with the relative energy gradient (REG) method.
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Affiliation(s)
- Maxime Ferrer
- Instituto de Química Médica, CSIC, Juan de La Cierva,3, 28006, Madrid, Spain
- PhD Program in Theoretical Chemistry and Computational Modelling, Doctoral School, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - José Elguero
- Instituto de Química Médica, CSIC, Juan de La Cierva,3, 28006, Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica, CSIC, Juan de La Cierva,3, 28006, Madrid, Spain.
| | - Luis Miguel Azofra
- Instituto de Estudios Ambientales y Recursos Naturales (iUNAT), Universidad de Las Palmas de Gran Canaria (ULPGC), Campus de Tafira, 35017, Las Palmas de Gran Canaria, Spain.
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17
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Hussein EM, Moussa Z, Al-Fahemi JH, Al-Rooqi MM, Obaid RJ, Malik MS, Abd-El-Aziz AS, Ahmed SA. Study on Regio- and Diastereoselectivity of the 1,3-Dipolar Cycloaddition Reaction of Azomethine Ylide with 2-(Benzo[ d]thiazol-2-yl)-3-(aryl)acrylonitrile: Synthesis, Spectroscopic, and Computational Approach. ACS OMEGA 2024; 9:23802-23821. [PMID: 38854577 PMCID: PMC11154954 DOI: 10.1021/acsomega.4c01552] [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: 02/24/2024] [Revised: 04/23/2024] [Accepted: 05/08/2024] [Indexed: 06/11/2024]
Abstract
An unprecedented and efficient three-component 1,3-dipolar cycloaddition reaction using (E)-2-(benzo[d]thiazol-2-yl)-3-(aryl)acrylonitriles 4a-g and an in situ generated azomethine ylide 3 from isatin and N-methylglycine is described. The reaction exhibits exclusive regioselectivity, resulting in the formation of 3'-(benzo[d]thiazol-2-yl)-1'-methyl-2-oxo-4'-(aryl)spiro[indoline-3,2'-pyrrolidine]-3'-carbonitriles regioisomers through exo/endo approaches. The diastereoselectivity of the reaction is highly dependent on the substitution pattern of the phenyl ring in dipolarophiles 4a-g, leading to the formation of exo-/endo-cycloadducts in varying ratios. To understand the stereoselectivity, the transition state structures were optimized using the TS guess geometry with the QST3-based method. The reaction mechanism and regioselectivity were elucidated by evaluating global and local electrophilicity and nucleophilicity descriptors at the B3LYP/cc-pVTZ level of theory, along with considerations based on the HSAB principle. The analysis of global electron density transfer (GEDT) showed that the reactions are polar and electron density fluxes from azomethine ylide 3 toward dipolarophile 4a-g. It was found from the molecular electrostatic potential map (MESP) that at the more favorable transition state, approach of reactants locates the oppositely charged regions over each other resulting in attractive forces between the two fragments. The computational results are consistent with the experimental observations, confirming that the reactions proceed through an asynchronous one-step mechanism.
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Affiliation(s)
- Essam M. Hussein
- Department
of Chemistry, Faculty of Science, Umm Al-Qura
University, 21955 Makkah, Saudi
Arabia
- Department
of Chemistry, Faculty of Science, Assiut
University, 71516 Assiut, Egypt
| | - Ziad Moussa
- Department
of Chemistry, College of Science, United
Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Jabir H. Al-Fahemi
- Department
of Chemistry, Faculty of Science, Umm Al-Qura
University, 21955 Makkah, Saudi
Arabia
| | - Munirah M. Al-Rooqi
- Department
of Chemistry, Faculty of Science, Umm Al-Qura
University, 21955 Makkah, Saudi
Arabia
| | - Rami J. Obaid
- Department
of Chemistry, Faculty of Science, Umm Al-Qura
University, 21955 Makkah, Saudi
Arabia
| | - M. Shaheer Malik
- Department
of Chemistry, Faculty of Science, Umm Al-Qura
University, 21955 Makkah, Saudi
Arabia
| | - Alaa S. Abd-El-Aziz
- Qingdao
Innovation and Development Center, Harbin
Engineering University, Qingdao, 266400, China
| | - Saleh A. Ahmed
- Department
of Chemistry, Faculty of Science, Umm Al-Qura
University, 21955 Makkah, Saudi
Arabia
- Department
of Chemistry, Faculty of Science, Assiut
University, 71516 Assiut, Egypt
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18
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Gu Z, Bo M, Gao Z, Xu J, Chen J, Xiao T, Ma P. Theoretical study on different substituent-modified derivatives of 6-dinitrophenyl-5,6,7,8-tetrahydro-4-imidazo [4,5-e]furazano[3,4-b] pyrazine. J Mol Model 2024; 30:192. [PMID: 38814476 DOI: 10.1007/s00894-024-05993-2] [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: 04/12/2024] [Accepted: 05/24/2024] [Indexed: 05/31/2024]
Abstract
CONTEXT The compounds of the "565" parent ring structure have received much attention from researchers because of their excellent detonation performance. In the present study, 81 derivatives were designed by introducing different substituents based on 6-dinitrophenyl-5,6,7,8-tetrahydro-4-imidazo[4,5-e]furazano[3,4-b] pyrazine (DIOP), which is a compound of the parent ring structure of 565, and the performance of these derivatives, such as the electronic structure, energy gap, heat of formation, and detonation performance, were investigated. Among these energy-containing derivatives, the density ranges from 1.70 to 2.17 g/cm3, the detonation velocity ranges from 8.01 to 10.26 km/s, and the detonation pressure ranges from 27.99 to 49.88 GPa. Through comprehensive analysis of several properties of DIOP derivatives, it was found that the oxygen balance of derivatives with the -ONO2 group was greater than zero and close to zero, while the oxygen balance of derivatives with other groups was almost all less than zero. Among them, G8 (D = 10.1 km/s, P = 47.72 GPa), H8 (D = 10.11 km/s, P = 47.92 GPa), and I8 (D = 10.26 km/s, P = 49.88 GPa) had higher detonation velocity and pressure among all derivatives, and their impact sensitivity was better than RDX. Therefore, three potential high-energy and less sensitive energy-containing derivatives, G8, H8, and I8, were screened out. The intramolecular interactions of the three derivatives were further analyzed, and it was found that there were intensive van der Waals interactions and significant spatial steric effects within the molecules, which had a positive effect on reducing the shock sensitivity of the compounds. Moreover, the three derivatives have a large degree of stacking, which leads to a high density. METHODS All calculations in this paper are performed using Gaussian16 based on density functional theory. Firstly, the structures of the derivatives were optimized at the level of B3LYP-D3/6-311G**, and then single-site energy calculations were carried out at the level of M06-2X-D3/def2-TZVPP, to reveal the effects of single substituents versus multiple substituents and isomerism on the properties of the DIOP-based energetic derivatives. Multiwfn was used to plot the density of states (DOS) of the derivatives and to calculate the molecular surface electrostatic potential at 0.001 e/Bohr3 electron density, 0.25 Bohr lattice spacing surface.
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Affiliation(s)
- Zhihui Gu
- College of Safety Science and Engineering, Nanjing Tech University, Nanjing, 210009, China
| | - Mengjie Bo
- College of Safety Science and Engineering, Nanjing Tech University, Nanjing, 210009, China
| | - Zikai Gao
- College of Safety Science and Engineering, Nanjing Tech University, Nanjing, 210009, China
| | - Jiani Xu
- College of Safety Science and Engineering, Nanjing Tech University, Nanjing, 210009, China
| | - Jun Chen
- College of Safety Science and Engineering, Nanjing Tech University, Nanjing, 210009, China
| | - Tingting Xiao
- College of Safety Science and Engineering, Nanjing Tech University, Nanjing, 210009, China
| | - Peng Ma
- College of Safety Science and Engineering, Nanjing Tech University, Nanjing, 210009, China.
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19
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Barrera Y, Anderson JSM. Does the radical GPRI strongly depend on the population scheme? A comparative study to predict radical attack on unsaturated molecules with the radical general-purpose reactivity indicator. J Comput Chem 2024; 45:1152-1159. [PMID: 38299704 DOI: 10.1002/jcc.27314] [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: 05/21/2023] [Revised: 07/15/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024]
Abstract
The reactivity of 22 unsaturated molecules undergoing attack by a methyl radical (⋅CH3) have been elucidated using the condensed radical general-purpose reactivity indicator (condensed radical GPRI) appropriate for relatively nucleophilic or electrophilic molecules. Using the appropriate radical GPRI equation for electrophilic attack or nucleophilic radical attack, seven different population schemes were used to assign the most reactive atoms in each of the 22 molecules. The results show that the condensed radical GPRI is sensitive to the population scheme chosen, but less sensitive than the radical Fukui function. Therefore, the reliability of these methods depends on the population scheme. Our investigation indicates that the condensed radical GPRI is most accurate in predicting the dominant products of the methyl radical addition reactions on a variety of unsaturated molecules when the Hirshfeld, Merz-Singh-Kollman, or Voronoi deformation density population schemes are used. Furthermore, for all populations schemes in the majority of instances where the radical Fukui function failed the radical GPRI was able to identify the most reactive atom under certain reactivity conditions.
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Affiliation(s)
- Yoshio Barrera
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Mexico City, Mexico
| | - James S M Anderson
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Mexico City, Mexico
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20
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Wibowo-Teale M, Huynh BC, Wibowo-Teale AM, De Proft F, Geerlings P. Symmetry and reactivity of π-systems in electric and magnetic fields: a perspective from conceptual DFT. Phys Chem Chem Phys 2024; 26:15156-15180. [PMID: 38747576 PMCID: PMC11135622 DOI: 10.1039/d4cp00799a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/30/2024] [Indexed: 05/30/2024]
Abstract
The extension of conceptual density-functional theory (conceptual DFT) to include external electromagnetic fields in chemical systems is utilised to investigate the effects of strong magnetic fields on the electronic charge distribution and its consequences on the reactivity of π-systems. Formaldehyde, H2CO, is considered as a prototypical example and current-density-functional theory (current-DFT) calculations are used to evaluate the electric dipole moment together with two principal local conceptual DFT descriptors, the electron density and the Fukui functions, which provide insight into how H2CO behaves chemically in a magnetic field. In particular, the symmetry properties of these quantities are analysed on the basis of group, representation, and corepresentation theories using a recently developed automatic program for symbolic symmetry analysis, QSYM2. This allows us to leverage the simple symmetry constraints on the macroscopic electric dipole moment components to make profound predictions on the more nuanced symmetry transformation properties of the microscopic frontier molecular orbitals (MOs), electron densities, and Fukui functions. This is especially useful for complex-valued MOs in magnetic fields whose detailed symmetry analyses lead us to define the new concepts of modular and phasal symmetry breaking. Through these concepts, the deep connection between the vanishing constraints on the electric dipole moment components and the symmetry of electron densities and Fukui functions can be formalised, and the inability of the magnetic field in all three principal orientations considered to induce asymmetry with respect to the molecular plane of H2CO can be understood from a molecular perspective. Furthermore, the detailed forms of the Fukui functions reveal a remarkable reversal in the direction of the dipole moment along the CO bond in the presence of a parallel or perpendicular magnetic field, the origin of which can be attributed to the mixing between the frontier MOs due to their subduced symmetries in magnetic fields. The findings in this work are also discussed in the wider context of a long-standing debate on the possibility to create enantioselectivity by external fields.
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Affiliation(s)
- Meilani Wibowo-Teale
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Bang C Huynh
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Andrew M Wibowo-Teale
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Frank De Proft
- Research group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Paul Geerlings
- Research group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium.
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21
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Shafiq I, Khalid M, Maria G, Raza N, Braga AAC, Bullo S, Khairy M. Use of benzothiophene ring to improve the photovoltaic efficacy of cyanopyridinone-based organic chromophores: a DFT study. RSC Adv 2024; 14:12841-12852. [PMID: 38645518 PMCID: PMC11027887 DOI: 10.1039/d3ra06817j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 04/08/2024] [Indexed: 04/23/2024] Open
Abstract
The benzothiophene based chromophores (A1D1-A1D5) with A-π-A configuration were designed via end-capped tailoring with benzothiophene type acceptors using reference compound (A1R). Quantum chemical calculations were accomplished at M06/6-311G(d,p) level to probe optoelectronic and photophysical properties of designed chromophores. Therefore, frontier molecular orbitals (FMOs), binding energy (Eb), open circuit voltage (Voc), transition density matrix (TDM), density of state (DOS) and UV-Vis analyses of A1R and A1D1-A1D5 were accomplished. The designed compounds (A1D1-A1D5) exhibited absorption values in the visible region as 616.316-649.676 nm and 639.753-665.508 nm in gas and chloroform phase, respectively, comparing with reference chromophore. An efficient charge transference from HOMO towards LUMO was found in A1D1-A1D5 chromophores which was further supported by TDM and DOS analyses. Among all chromophores, A1D2 exhibited unique characteristics such as reduced band gap (2.354 eV), higher softness (σ = 0.424 eV), lower exciton binding energy (0.491 eV) and maximum value of open circuit voltage (Voc = 1.981 V). Consequently, A1D2 may be considered as potential candidate for the development of optoelectronic devices. These analyses revealed that the studied compounds exhibited promising findings. They may be utilized in the realm of organic solar cells.
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Affiliation(s)
- Iqra Shafiq
- Institute of Chemistry, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
- Centre for Theoretical and Computational Research, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
| | - Muhammad Khalid
- Institute of Chemistry, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
- Centre for Theoretical and Computational Research, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
| | - Gul Maria
- Institute of Chemistry, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
- Centre for Theoretical and Computational Research, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
| | - Nadeem Raza
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU) Riyadh Saudi Arabia
| | - Ataualpa A C Braga
- Departamento de Qu'ımica Fundamental, Instituto de Qu'ımica, Universidade de Saõ Paulo Av. Prof. Lineu Prestes, 748 Sao Paulo 05508-000 Brazil
| | - Saifullah Bullo
- Department of Human and Rehabilitation Sciences, Begum Nusrat Bhutto Women University Sukkur Sindh Pakistan
| | - Mohamed Khairy
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU) Riyadh Saudi Arabia
- Chemistry Department, Faculty of Science, Benha University Egypt
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22
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Damin A, Bonomo M, Centrella B, Signorile M, Barolo C, Bordiga S. Modulation of [CuOH/O] + Properties in [2,2'-Bipyridine] 2 Homoleptic Complexes through Substitution at the 6,6' Position by Methyl Groups. ACS OMEGA 2024; 9:16610-16620. [PMID: 38617660 PMCID: PMC11007709 DOI: 10.1021/acsomega.4c00598] [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: 01/18/2024] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 04/16/2024]
Abstract
In this paper, data from a DFT-based computational study on the reactivity of [Cu(2,2'-S-bpy)2]+PF6- (S indicating substitution by methyl groups at the 6 and/or 6' position and ranging from 0 to 100% through 50%) homoleptic complexes based toward tButOOH were presented. Computational results, supported by cyclic voltammetry analysis, prove the feasibility of finely tuning the chemical properties of the complexes and their reactivity by means of insertion of methyl moieties in selected positions within the bipyridine scaffold.
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Affiliation(s)
- Alessandro Damin
- Department of Chemistry,
NIS and INSTM Reference Centre, University
of Turin, Via G. Quarello 15/A, Turin 10135, Italy
| | - Matteo Bonomo
- Department of Chemistry,
NIS and INSTM Reference Centre, University
of Turin, Via G. Quarello 15/A, Turin 10135, Italy
| | - Barbara Centrella
- Department of Chemistry,
NIS and INSTM Reference Centre, University
of Turin, Via G. Quarello 15/A, Turin 10135, Italy
| | - Matteo Signorile
- Department of Chemistry,
NIS and INSTM Reference Centre, University
of Turin, Via G. Quarello 15/A, Turin 10135, Italy
| | - Claudia Barolo
- Department of Chemistry,
NIS and INSTM Reference Centre, University
of Turin, Via G. Quarello 15/A, Turin 10135, Italy
| | - Silvia Bordiga
- Department of Chemistry,
NIS and INSTM Reference Centre, University
of Turin, Via G. Quarello 15/A, Turin 10135, Italy
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Gadali KE, Rafya M, El Mansouri AE, Maatallah M, Vanderlee A, Mehdi A, Neyts J, Jochmans D, De Jonghe S, Benkhalti F, Sanghvi YS, Taourirte M, Lazrek HB. Design, synthesis, and molecular modeling studies of novel 2-quinolone-1,2,3-triazole-α-aminophosphonates hybrids as dual antiviral and antibacterial agents. Eur J Med Chem 2024; 268:116235. [PMID: 38377828 DOI: 10.1016/j.ejmech.2024.116235] [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: 12/21/2023] [Revised: 02/01/2024] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
With the aim to identify new antiviral agents with antibacterial properties, a series of 2-quinolone-1,2,3-triazole derivatives bearing α-aminophosphonates was synthesized and characterized by 1H NMR, 13C NMR, 31P NMR, single crystal XRD and HRMS analyses. These compounds were examined against five RNA viruses (YFV, ZIKV, CHIKV, EV71 and HRV) from three distinct families (Picornaviridae, Togaviridae and Flaviviridae) and four bacterial strains (S. aureus, E. feacalis, E. coli and P. aeruginosa). The α-aminophosphonates 4f, 4i, 4j, 4k, 4p and 4q recorded low IC50 values of 6.8-10.91 μM, along with elevated selectivity indices ranging from 2 to more than 3, particularly against YFV, CHIKV and HRV-B14. Besides, the synthesized compounds were generally more sensitive toward Gram-positive bacteria, with the majority of them displaying significant potency against E. feacalis. Specifically, an excellent anti-enterococcus activity was obtained by compound 4q with MIC and MBC values of 0.03 μmol/mL, which were 8.7 and 10 times greater than those of the reference drugs ampicillin and rifampicin, respectively. Also, compounds 4f, 4p and 4q showed potent anti-staphylococcal activity with MIC values varying between 0.11 and 0.13 μmol/mL, compared to 0.27 μmol/mL for ampicillin. The results from DFT and molecular docking simulations were in agreement with the biological assays, proving the binding capability of hybrids 4f, 4i, 4j, 4k, 4p and 4q with viral and bacterial target enzymes through hydrogen bonds and other non-covalent interactions. The in silico ADME/Tox prediction revealed that these molecules possess moderate to good drug-likeness and pharmacokinetic properties, with a minimal chance of causing liver toxicity or carcinogenic effects.
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Affiliation(s)
- Khadija El Gadali
- Laboratoire de Recherche en Développement Durable et Santé, Faculty of Sciences and Technology Gueliz (FSTG), BP549, Marrakech 40000, Morocco; Laboratory of Molecular Chemistry, Department of Chemistry, Faculty of Sciences Semlalia, Marrakech 40000, Morocco
| | - Meriem Rafya
- Laboratoire de Recherche en Développement Durable et Santé, Faculty of Sciences and Technology Gueliz (FSTG), BP549, Marrakech 40000, Morocco
| | - Az-Eddine El Mansouri
- University of the Free State Faculty of Natural and Agricultural Sciences Chemistry Department 205 Nelson Mandela, Bloemfontein, 9301, South Africa
| | - Mohamed Maatallah
- Laboratory of Molecular Chemistry, Department of Chemistry, Faculty of Sciences Semlalia, Marrakech 40000, Morocco
| | - Arie Vanderlee
- Institut Européen des Membranes, IEM, UMR 5635, Univ. Montpellier, CNRS, ENSCM, 34095 Montpellier, France
| | - Ahmad Mehdi
- ICGM, UMR5253 1919, Route de Mende 34293 Montpellier cedex 5, France
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Box 1043, B-3000 Leuven, Belgium
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Box 1043, B-3000 Leuven, Belgium
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Box 1043, B-3000 Leuven, Belgium
| | - Fatiha Benkhalti
- Laboratoire de Recherche en Développement Durable et Santé, Faculty of Sciences and Technology Gueliz (FSTG), BP549, Marrakech 40000, Morocco
| | - Yogesh S Sanghvi
- Rasayan Inc, 2802 Crystal Ridge Road, Encinitas, CA 92024-6615, USA
| | - Moha Taourirte
- Laboratoire de Recherche en Développement Durable et Santé, Faculty of Sciences and Technology Gueliz (FSTG), BP549, Marrakech 40000, Morocco.
| | - Hassan B Lazrek
- Laboratory of Molecular Chemistry, Department of Chemistry, Faculty of Sciences Semlalia, Marrakech 40000, Morocco.
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24
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Barreto MSC, Elzinga EJ, Kubicki JD, Sparks DL. A multi-scale assessment of the impact of salinity on the desorption of chromate from hematite: Sea level rise implications. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133041. [PMID: 38043423 DOI: 10.1016/j.jhazmat.2023.133041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/08/2023] [Accepted: 11/17/2023] [Indexed: 12/05/2023]
Abstract
The solubility and transport of Cr(VI) is primarily controlled by adsorption-desorption reactions at the surfaces of soil minerals such as iron oxides. Environmental properties such as pH, ionic strength, and ion competition are expected to affect the mobility and fate of Cr(VI). Sea level rise (SLR), and consequent seawater intrusion, is creating a new biogeochemical soil environment at coastal margins, potentially impacting Cr(VI) retention at contaminated sites. We employed in-situ ATR-FTIR spectroscopy and DFT calculations to investigate at the molecular level the adsorption of Cr(VI) on the hematite surface and its desorption by sulfate, as a function of pH and ionic strength. We further used a batch experiment to assess Cr(VI) desorption at varying artificial seawater (ASW) concentrations. IR results demonstrate the complexity of Cr(VI) adsorption, showing a combination of monodentate inner-sphere complexation at high pH and dichromate outer-sphere (∼75%) at low pH. The Cr(VI)-complexes exhibited desorption induced by increasing pH values (58% of desorption) and sulfate competition (∼40% desorption). ASW desorbed ∼20% more Cr(VI), even at just 1% concentration. Our findings provide insight into Cr(VI)-adsorption complexation that controls the retention and remobilization of Cr(VI) on Fe-oxide minerals. The results point to an elevated risk of Cr(VI) mobilization in contaminated soils affected by SLR.
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Affiliation(s)
| | - Evert J Elzinga
- Department of Earth & Environmental Sciences, Rutgers University, Newark, NJ, USA
| | - James D Kubicki
- Department of Earth, Environmental & Resource Sciences, The University of Texas at El Paso, El Paso, TX, USA
| | - Donald L Sparks
- Department of Plant & Soil Sciences, University of Delaware, Newark, DE, USA
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25
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Benítez FJ, Gutiérrez-Oliva S, Herrera B, Toro-Labbé A. Basis Electronic Activity of Molecular Systems. A Theory of Bond Reactivity. J Phys Chem A 2024. [PMID: 38437616 DOI: 10.1021/acs.jpca.4c00359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
In this paper, we present a new finding, the basis electronic activity (BEA) of molecular systems; it corresponds to the significant, although nonreactive, vibrationally induced electronic activity that takes place in any molecular system. Although the molecule's BEA is composed of an equal number of local contributions as the vibrational degrees of freedom, our results indicate that only stretching modes contribute to it. To account for this electronic activity, a new descriptor, the bond electronic flux (BEF), is introduced. The BEF combined with the force constant of the potential well hosting the electronic activity gives rise to the effective bond reactivity index (EBR), which turns out to be the first density functional theory-based descriptor that simultaneously accounts for structural and electronic effects. Besides quantifying the bond reactivity, EBR provides a basis to compare the reactivities of bonds inserted in different chemical environments and paves the way for the exertion of selective control to enhance or inhibit their reactivities. The new concepts formulated in this paper and the associated computational tools are illustrated with characterization of the BEA of a set of representative molecules. In all cases, the BEFs follow the same linear pattern, whose slopes indicate the intensity of the electronic activity and quantify the reactivity of chemical bonds.
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Affiliation(s)
- Francisca J Benítez
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860 Macul, Santiago 7820436, Chile
| | - Soledad Gutiérrez-Oliva
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860 Macul, Santiago 7820436, Chile
| | - Bárbara Herrera
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860 Macul, Santiago 7820436, Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna 4860 Macul, Santiago 7820436, Chile
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26
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Wang B, Geerlings P, Liu S, De Proft F. Extending the Scope of Conceptual Density Functional Theory with Second Order Analytical Methodologies. J Chem Theory Comput 2024. [PMID: 38310523 DOI: 10.1021/acs.jctc.3c01184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
In the context of the growing impact of conceptual density functional theory (DFT) as one of the most successful chemical reactivity theories, response functions up to second order have now been widely applied; in recent years, among others, particular attention has been focused on the linear response function and also extensions to higher order have been put forward. As the larger part of these studies have been carried using a finite difference approach to compute these concepts, we now embarked on (an extension of) an analytical approach to conceptual DFT. With the ultimate aim of providing a complete set of analytically computable second order properties, including the softness and hardness kernels, the hardness as the simplest second order response function is scrutinized again with numerical results highlighting the difference in nature between the analytical hardness (referred to as hardness condition) and the Parr-Pearson absolute chemical hardness. The hardness condition is investigated for its capability to gauge the (de)localization error of density functional approximations (DFAs). The analytical Fukui function, besides overcoming the difficulties in the finite difference approach in treating negatively charged systems, also showcases the errors of deviating from the straight-line behavior using fractional occupation number calculations. Subsequently, the softness kernel and its atom-condensed inverse, the hardness matrix, are accessed through the Berkowitz-Parr relation. Revisiting the softness kernel confirms and extends previous discussions on how Kohn's Nearsightedness of Electronic Matter principle can be retrieved and identified as the physicist's version of the chemist's "transferability of functional groups" concept. The accurate, analytical hardness matrix evaluation on the other hand provides further support for the basics of Nalewajski's charge sensitivity analysis. Based on Parr and Liu's functional expansion of the energy functional, a new energy decomposition is introduced with an order of magnitude analysis of the different terms for a series of simple molecules both at their equilibrium geometry and upon variation in bond length and dihedral angle. Finally, for the first time, the perturbation expansion of the energy functional is studied numerically up to second order now that all response functions and integration techniques are at hand. The perturbation expansion energies are in excellent agreement with those obtained directly from DFA calculations giving confidence in the convergence of the perturbation series and its use in judging the importance of the different terms in reactivity investigations.
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Affiliation(s)
- Bin Wang
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - Paul Geerlings
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
| | - Frank De Proft
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
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Souza MAD, Rodrigues LG, Rocha JE, de Freitas TS, Bandeira PN, Marinho MM, Nunes da Rocha M, Marinho ES, Honorato Barreto AC, Coutinho HDM, Silva LMA, Julião MSDS, Marques Canuto K, Marques da Fonseca A, Teixeira AMR, Dos Santos HS. Synthesis, structural, characterization, antibacterial and antibiotic modifying activity, ADMET study, molecular docking and dynamics of chalcone ( E)-1-(4-aminophenyl)-3-(4-nitrophenyl)prop-2-en-1-one in strains of Staphylococcus aureus carrying NorA and MepA efflux pumps. J Biomol Struct Dyn 2024; 42:1670-1691. [PMID: 37222682 DOI: 10.1080/07391102.2023.2213777] [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: 11/15/2022] [Accepted: 04/05/2023] [Indexed: 05/25/2023]
Abstract
Chalcones have an open chain flavonoid structure that can be obtained from natural sources or by synthesis and are widely distributed in fruits, vegetables, and tea. They have a simple and easy to handle structure due to the α-β-unsaturated bridge responsible for most biological activities. The facility to synthesize chalcones combined with its efficient in combating serious bacterial infections make these compounds important agents in the fight against microorganisms. In this work, the chalcone (E)-1-(4-aminophenyl)-3-(4-nitrophenyl)prop-2-en-1-one (HDZPNB) was characterized by spectroscopy and electronic methods. In addition, microbiological tests were performed to investigate the modulator potential and efflux pump inhibition on S. aureus multi-resistant strains. The modulating effect of HDZPNB chalcone in association with the antibiotic norfloxacin, on the resistance of the S. aureus 1199 strain, resulted in increase the MIC. In addition, when HDZPNB was associated with ethidium bromide (EB), it caused an increase in the MIC value, thus not inhibiting the efflux pump. For the strain of S. aureus 1199B, carrying the NorA pump, the HDZPNB associated with norfloxacin showed no modulatory, and when the chalcone was used in association with EB, it had no inhibitory effect on the efflux pump. For the tested strain of S. aureus K2068, which carries the MepA pump, it can be observed that the chalcone together the antibiotic resulted in an increase the MIC. On the other hand, when chalcone was used in association with EB, it caused a decrease in bromide MIC, equal to the reduction caused by standard inhibitors. Thus, these results indicate that the HDZPNB could also act as an inhibitor of the S. aureus gene overexpressing pump MepA. The molecular docking reveals that chalcone has a good binding energies -7.9 for HDZPNB/MepA complexes, molecular dynamics simulations showed that Chalcone/MetA complexes showed good stability of the structure in an aqueous solution, and ADMET study showed that the chalcone has a good oral bioavailability, high passive permeability, low risk of efflux, low clearance rate and low toxic risk by ingestion. The microbiological tests show that the chalcone can be used as a possible inhibitor of the Mep A efflux pump.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mikael Amaro de Souza
- Graduate Program in Biological Chemistry, Department of Biological Chemistry, Regional University of Cariri, Crato, CE, Brazil
| | - Leilane Gomes Rodrigues
- Science and Technology Centre, Course of Chemistry, State University Vale do Acaraú, Sobral, CE, Brazil
| | - Janaina Esmeraldo Rocha
- Graduate Program in Biological Chemistry, Department of Biological Chemistry, Regional University of Cariri, Crato, CE, Brazil
| | - Thiago Sampaio de Freitas
- Graduate Program in Biological Chemistry, Department of Biological Chemistry, Regional University of Cariri, Crato, CE, Brazil
| | - Paulo Nogueira Bandeira
- Science and Technology Centre, Course of Chemistry, State University Vale do Acaraú, Sobral, CE, Brazil
| | - Márcia Machado Marinho
- Science and Technology Centre, Course of Chemistry, State University Vale do Acaraú, Sobral, CE, Brazil
| | | | | | | | - Henrique Douglas Melo Coutinho
- Graduate Program in Biological Chemistry, Department of Biological Chemistry, Regional University of Cariri, Crato, CE, Brazil
| | | | - Murilo Sergio da Silva Julião
- Science and Technology Centre, Course of Chemistry, State University Vale do Acaraú, Sobral, CE, Brazil
- Graduate Program in Natural Science, State University of Ceará, Fortaleza, CE, Brazil
| | - Kirley Marques Canuto
- Multiusuary Laboratory of Natural Products Chemistry, Embrapa Tropical Agroindustry, Fortaleza, CE, Brazil
| | - Aluísio Marques da Fonseca
- Academic Master's Degree in Sociobiodiversity and Sustainable Technologies - MASTS, Institute of Engineering and Development Sustainable, University of International Integration of Afro-Brazilian Lusofonia, Acarape, CE, Brazil
| | - Alexandre Magno Rodrigues Teixeira
- Graduate Program in Biological Chemistry, Department of Biological Chemistry, Regional University of Cariri, Crato, CE, Brazil
- Graduate Program in Natural Science, State University of Ceará, Fortaleza, CE, Brazil
| | - Hélcio Silva Dos Santos
- Graduate Program in Biological Chemistry, Department of Biological Chemistry, Regional University of Cariri, Crato, CE, Brazil
- Science and Technology Centre, Course of Chemistry, State University Vale do Acaraú, Sobral, CE, Brazil
- Graduate Program in Natural Science, State University of Ceará, Fortaleza, CE, Brazil
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28
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Gómez S, Gómez S, Rojas-Valencia N, Hernández JG, Ardila-Fierro KJ, Gómez T, Cárdenas C, Hadad C, Cappelli C, Restrepo A. Interactions and reactivity in crystalline intermediates of mechanochemical cyclorhodation reactions. Phys Chem Chem Phys 2024; 26:2228-2241. [PMID: 38165158 DOI: 10.1039/d3cp04201d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
There is experimental evidence that solid mixtures of the rhodium dimer [Cp*RhCl2]2 and benzo[h] quinoline (BHQ) produce two different polymorphic molecular cocrystals called 4α and 4β under ball milling conditions. The addition of NaOAc to the mixture leads to the formation of the rhodacycle [Cp*Rh-(BHQ)Cl], where the central Rh atom retains its tetracoordinate character. Isolate 4β reacts with NaOAc leading to the same rhodacycle while isolate 4α does not under the same conditions. We show that the puzzling difference in reactivity between the two cocrystals can be traced back to fundamental aspects of the intermolecular interactions between the BHQ and [Cp*RhCl2]2 fragments in the crystalline environment. To support this view, we report a number of descriptors of the nature and strength of chemical bonds and intermolecular interactions in the extended solids and in a cluster model. We calculate formal quantum mechanical descriptors based on electronic structure, electron density, and binding and interaction energies including an energy decomposition analysis. Without exception, all descriptors point to 4β being a transient structure higher in energy than 4α with larger local and global electrophilic and nucleophilic powers, a more favorable spatial and energetic distribution of the frontier orbitals, and a more fragile crystal structure.
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Affiliation(s)
- Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
| | - Santiago Gómez
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - Natalia Rojas-Valencia
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - José G Hernández
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - Karen J Ardila-Fierro
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - Tatiana Gómez
- Theoretical and Computational Chemistry Center, Institute of Applied Chemical Sciences, Faculty of Engineering, Universidad Autonoma de Chile, Avenida Pedro de Valdivia 425, Santiago, Chile
| | - Carlos Cárdenas
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
- Centro para el desarrollo de las Nanociencias y Nanotecnología, CEDENNA, Av. Ecuador 3493, Santiago, Chile
| | - Cacier Hadad
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
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29
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Miranda-Quintana RA, Chen L, Smiatek J. Insights into Hildebrand Solubility Parameters - Contributions from Cohesive Energies or Electrophilicity Densities? Chemphyschem 2024; 25:e202300566. [PMID: 37883736 DOI: 10.1002/cphc.202300566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 10/28/2023]
Abstract
We introduce certain concepts and expressions from conceptual density functional theory (DFT) to study the properties of the Hildebrand solubility parameter. The original form of the Hildebrand solubility parameter is used to qualitatively estimate solubilities for various apolar and aprotic substances and solvents and is based on the square root of the cohesive energy density. Our results show that a revised expression allows the replacement of cohesive energy densities by electrophilicity densities, which are numerically accessible by simple DFT calculations. As an extension, the reformulated expression provides a deeper interpretation of the main contributions and, in particular, emphasizes the importance of charge transfer mechanisms. All calculated values of the Hildebrand parameters for a large number of common solvents are compared with experimental values and show good agreement for non- or moderately polar aprotic solvents in agreement with the original formulation of the Hildebrand solubility parameters. The observed deviations for more polar and protic solvents define robust limits from the original formulation which remain valid. Likewise, we show that the use of machine learning methods leads to only slightly better predictability.
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Affiliation(s)
| | - Lexin Chen
- Department of Chemistry, University of Florida, Gainesville, FL 32603, USA
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569, Stuttgart, Germany
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30
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Halim SA, El-Meligy AB, El-Nahas AM, El-Demerdash SH. DFT study, and natural bond orbital (NBO) population analysis of 2-(2-Hydroxyphenyl)-1-azaazulene tautomers and their mercapto analouges. Sci Rep 2024; 14:219. [PMID: 38168481 PMCID: PMC10762136 DOI: 10.1038/s41598-023-50660-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024] Open
Abstract
Theoretical research on the keto-enol tautomerization of 2-(2-Hydroxyphenyl)-1-aza azulene (2HPhAZ) and its thiol-thione (2MPhAZ) analouge has been performed using the density functional B3LYP method with the 6-311 + + G(2d,2p) basis set in gas and ethanol phases. The findings of the MO computation on the energy scale and the prediction of the frontier molecular orbital (FMO) energies demonstrate that the tautomeric structures exist in a static mixture in the ground state, with the enol and thiol structure being more stable than the keto and thione structures in gas phase. The ethanol solvent causes some reordering of the relative stability of 2HPhAZ and 2MPhAZ conformers. The geometries created at the B3LYP/6-311 + + G(2d,2p) level of theory were used for NBO analysis. In the tautomerization of 2HPhAZ and its mercapto analogue 2-(2-Mercaptophenyl)-1-azaazulene (2MPhAZ), it has been found that the O(S)-C sigma bond is weak due to nO(S) -> σ*C25-O26(S26) and nO(S) -> σ*C15-N16 delocalization. It is also noted that the resulting p character of the corresponding oxygen (sulfur) natural hybrid orbital (NHO) of σO(S)-C bond orbital is related to the decreased occupancy of the localized σO(S)-C orbital in the idealized Lewis structure or the increased occupancy of σ*O(S)-C of the non-Lewis orbital and their subsequent impact on molecular stability and geometry (bond lengths) in gas phase and ethanol. Additionally, the energy of charge transfer decreases as the potential rotamers' Hammett constants (R1-R3 for O(S) atoms) increase. The partial charge distribution on the skeleton atoms demonstrates that the intra- and intermolecular interactions can be significantly influenced by the electrostatic attraction or repulsion between atoms. Lastly, the currently applied NBO-based HB strength indicator enables a fair prediction of the frequency of the proton donor NH stretching mode, but this simple picture is hidden by abundant hype conjugative effects.
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Affiliation(s)
- Shimaa Abdel Halim
- Chemistry Department, Faculty of Education, Ain Shams University, Cairo, 1171, Egypt.
| | - Asmaa B El-Meligy
- Chemistry Department, Faculty of Science, Menoufia University, Shebin El-Kom, 32512, Egypt.
| | - Ahmed M El-Nahas
- Chemistry Department, Faculty of Science, Menoufia University, Shebin El-Kom, 32512, Egypt
| | - Safinaz H El-Demerdash
- Chemistry Department, Faculty of Science, Menoufia University, Shebin El-Kom, 32512, Egypt
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31
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Li X, Anderson JSM, Jobst KJ. Bioaccumulative chemicals are either too hard or too soft: Conceptual density functional theory as a screening tool for emerging pollutants. ENVIRONMENT INTERNATIONAL 2024; 183:108388. [PMID: 38159370 DOI: 10.1016/j.envint.2023.108388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/29/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
Conceptual density functional theory (CDFT) descriptors were computed to predict the environmental fate of approximately 6,000 widely used industrial chemicals. CDFT descriptors aligned with a molecule's possible bioaccumulation mechanism, i.e., soft chemicals are lipophilic, whereas hard chemicals may bioaccumulate by other mechanisms such as protein binding. The results have provided us with a new "rule of thumb" to guide risk assessment of chemical hazards: suspected persistent organic pollutants are either too hard (η > 0.40 hartree) or too soft (α > 200 Å3). This offers a novel approach to environmental risk assessment using two fundamental properties of a molecule.
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Affiliation(s)
- Xiaolei Li
- Department of Chemistry, Memorial University of Newfoundland, 45 Arctic Ave., St. John's, Canada A1C 5S7
| | - James S M Anderson
- Institute of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico 04510.
| | - Karl J Jobst
- Department of Chemistry, Memorial University of Newfoundland, 45 Arctic Ave., St. John's, Canada A1C 5S7.
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32
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Alonso M, Bettens T, Eeckhoudt J, Geerlings P, De Proft F. Wandering through quantum-mechanochemistry: from concepts to reactivity and switches. Phys Chem Chem Phys 2023; 26:21-35. [PMID: 38086672 DOI: 10.1039/d3cp04907h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Mechanochemistry has experienced a renaissance in recent years witnessing, at the molecular level, a remarkable interplay between theory and experiment. Molecular mechanochemistry has welcomed a broad spectrum of quantum-chemical methods to evaluate the influence of an external mechanical force on molecular properties. In this contribution, an overview is given on recent work on quantum mechanochemistry in the Brussels Quantum Chemistry group (ALGC). The effect of an external force was scrutinized both in fundamental topics, like reactivity descriptors in Conceptual DFT, and in applied topics, such as designing molecular force probes and tuning the stereoselectivity of certain types of reactions. In the conceptual part, a brief overview of the techniques introducing mechanical forces into a quantum-mechanical description of a molecule is followed by an introduction to conceptual DFT. The evolution of the electronic chemical potential (or electronegativity), chemical hardness and electrophilicity are investigated when a chemical bond in a series of diatomics is put under mechanical stress. Its counterpart, the influence of mechanical stress on bond angles, is analyzed by varying the strain present in alkyne triple bonds by applying a bending force, taking the strain promoted alkyne-azide coupling cycloaddition as an example. The increase of reactivity of the alkyne upon bending is probed by Fukui functions and the local softness. In the applied part, a new molecular force probe is presented based on an intramolecular 6π-electrocyclization in constrained polyenes operating under thermal conditions. A cyclic process is conceived where ring opening and closure are triggered by applying or removing an external pulling force. The efficiency of mechanical activation strongly depends on the magnitude of the applied force and the distance between the pulling points. The idea of pulling point distances as a tool to identify new mechanochemical processes is then tested in [28]hexaphyrins with an intricate equilibrium between Möbius aromatic and Hückel antiaromatic topologies. A mechanical force is shown to trigger the interconversion between the two topologies, using the distance matrix as a guide to select appropriate pulling points. In a final application, the Felkin-Anh model for the addition of nucleophiles to chiral carbonyls under the presence of an external mechanical force is scrutinized. By applying a force for restricting the conformational freedom of the chiral ketone, otherwise inaccessible reaction pathways are promoted on the force-modified potential energy surfaces resulting in a diastereoselectivity different from the force-free reaction.
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Affiliation(s)
- Mercedes Alonso
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium.
| | - Tom Bettens
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium.
| | - Jochen Eeckhoudt
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium.
| | - Paul Geerlings
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium.
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium.
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Joshi S, Srivastava R. Effect of "magic chlorine" in drug discovery: an in silico approach. RSC Adv 2023; 13:34922-34934. [PMID: 38035236 PMCID: PMC10687521 DOI: 10.1039/d3ra06638j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023] Open
Abstract
The chlorine atom plays a vital role in drug design, yet the benefits of chlorine in 250 FDA-approved chlorine-containing drugs have not been studied properly. To see the "magic chloro" effect, computational studies have been carried out for 35 inhibitors, which are numbered as 12 complexes with (parent (-H), one chlorine, or two chlorine) substituents. The physicochemical properties are studied by conceptual density functional theory (CDFT). The pharmacokinetics, toxicity and metabolic properties of the studied inhibitors are estimated using chemoinformatics tools. SwissTargetPrediction is used to predict the multitarget activities of the studied inhibitors. Four FDA-approved drugs, diazepam, chloroquine, chloramphenicol, and bendamustine, are referenced to validate the studies. A higher HOMO-LUMO gap predicted high stability for the studied one and two chlorine-substituted analogues. Most of the studied inhibitors show "drug likeliness", nontoxicity, and high gastrointestinal (GI) absorption. The addition of one or two chloro substituents has increased the physicochemical properties and stability of most of the inhibitors compared to the parent analogues, whereas the toxicity is not affected. No change in metabolic properties is observed on addition of one or two chlorine substituents. The multi-target activities of all the studied inhibitors are validated by the reference drugs and experimental results.
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Affiliation(s)
- Sravani Joshi
- Centre for Cellular and Molecular Biology-CSIR Hyderabad India
| | - Ruby Srivastava
- Centre for Cellular and Molecular Biology-CSIR Hyderabad India
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Laftani Y, Chatib B, Boussaoud A, Hachkar M. Theoretical study of Ponceau S oxidation using the electro-Fenton process under optimal operational conditions. RSC Adv 2023; 13:32217-32222. [PMID: 37928836 PMCID: PMC10620643 DOI: 10.1039/d3ra04677j] [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: 07/12/2023] [Accepted: 09/30/2023] [Indexed: 11/07/2023] Open
Abstract
Electrochemical methods as one of the Advanced Oxidation Processes (AOPs) have been applied effectively to the degradation of recalcitrant organic molecules in aqueous solutions. In the present study, the performance of the electro-Fenton (EF) process on the oxidation of Ponceau S(PS) dye was studied. The experimental study performed at the optimal factors like the solution pH, the PS concentration and the ferrous ions dose provided 74.35% of PS degradation. The results, however, showed a decreased removal efficiency of PS when using sodium sulphate as the supporting electrolyte. From a theoretical point of view, the hydroxyl radical being an electron acceptor and the PS dye an electron donor, from a theoretical point of view, the hydroxyl radical being an electron acceptor and the PS dye an electron donor, furthermore, the nitrogen atom 2N being the most nucleophilic site of the PS dye with the most electrophilic site of the hydroxyl radical being the oxygen atom, the first stage of the reaction between PS and the hydroxyl radical was suggested.
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Affiliation(s)
- Yasmine Laftani
- Laboratory of Process, Signals, Industrial Systems and Computer Science, Graduate School of Technology, Cadi Ayyad University Morocco +21-2639941253
| | - Baylassane Chatib
- Laboratory of Process, Signals, Industrial Systems and Computer Science, Graduate School of Technology, Cadi Ayyad University Morocco +21-2639941253
| | - Abdelghani Boussaoud
- Laboratory of Process, Signals, Industrial Systems and Computer Science, Graduate School of Technology, Cadi Ayyad University Morocco +21-2639941253
| | - Mohsine Hachkar
- Laboratory of Process, Signals, Industrial Systems and Computer Science, Graduate School of Technology, Cadi Ayyad University Morocco +21-2639941253
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35
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Flores-Holguín N, Salas-Leiva JS, Glossman-Mitnik D. Talarolide A and Talaropeptides A-D: Potential Marine-Derived Therapeutic Peptides with Interesting Chemistry and Biological Activity Studied through Density Functional Theory (DFT) and Conceptual DFT. Molecules 2023; 28:6708. [PMID: 37764483 PMCID: PMC10536153 DOI: 10.3390/molecules28186708] [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: 08/29/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Molecules sourced from marine environments hold immense promise for the development of novel therapeutic drugs, owing to their distinctive chemical compositions and valuable medicinal attributes. Notably, Talarolide A and Talaropeptides A-D have gained recent attention as potential candidates for pharmaceutical applications. This study aims to explore the chemical reactivity of Talarolide A and Talaropeptides A-D through the application of molecular modeling and computational chemistry techniques, specifically employing Conceptual Density Functional Theory (CDFT). By investigating their chemical behaviors, the study seeks to contribute to the understanding of the potential pharmacological uses of these marine-derived compounds. The molecular geometry optimizations and frequency calculations were conducted using the Density Functional Tight Binding (DFTBA) method. This was followed by a subsequent round of geometry optimization, frequency analysis, and computation of electronic properties and chemical reactivity descriptors. We employed the MN12SX/Def2TZVP/H2O model chemistry, utilizing the Gaussian 16 program and the SMD solvation model. The analysis of the global reactivity descriptors arising from CDFT was achieved as well as the graphical comparison of the dual descriptor DD revealing the areas of the molecules with more propensity to suffer a nucleophilic or electrophilic attack. Additionally, Molinspiration and SwissTargetPrediction were considered for the calculation of molecular characteristics and predicted biological targets. These include enzymes, nuclear receptors, kinase inhibitors, GPCR ligands, and ion channel modulators. The graphical results show that Talarolide A and the Talaropeptides A-D are likely to behave as protease inhibitors.
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Cador A, Tognetti V, Joubert L, Popelier PLA. Aza-Michael Addition in Explicit Solvent: A Relative Energy Gradient-Interacting Quantum Atoms Study. Chemphyschem 2023:e202300529. [PMID: 37728125 DOI: 10.1002/cphc.202300529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/09/2023] [Accepted: 09/17/2023] [Indexed: 09/21/2023]
Abstract
Aza-Michael additions are key reactions in organic synthesis. We investigate, from a theoretical and computational point of view, several examples ranging from weak to strong electrophiles in dimethylsulfoxide treated as explicit solvent. We use the REG-IQA method, which is a quantum topological energy decomposition (Interacting Quantum Atoms, IQA) coupled to a chemical-interpretation calculator (Relative Energy Gradient, REG). We focus on the rate-limiting addition step in order to unravel the different events taking place in this step, and understand the influence of solvent on the reaction, with an eye on predicting the Mayr electrophilicity. For the first time, a link is established between an REG-IQA analysis and experimental values.
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Affiliation(s)
- Aël Cador
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, 76821, Mont St, Aignan Cedex, France
| | - Vincent Tognetti
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, 76821, Mont St, Aignan Cedex, France
| | - Laurent Joubert
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, 76821, Mont St, Aignan Cedex, France
| | - Paul L A Popelier
- Department of Chemistry, The University of Manchester, Manchester, M13 9PL, Great Britain
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Hernández JG, Ardila-Fierro KJ, Gómez S, Stolar T, Rubčić M, Topić E, Hadad CZ, Restrepo A. The Role of Crystalline Intermediates in Mechanochemical Cyclorhodation Reactions Elucidated by in-Situ X-ray Powder Diffraction and Computation. Chemistry 2023; 29:e202301290. [PMID: 37347170 DOI: 10.1002/chem.202301290] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 06/23/2023]
Abstract
The occurrence of crystalline intermediates in mechanochemical reactions might be more widespread than previously assumed. For example, a recent study involving the acetate-assisted C-H activation of N-Heterocycles with [Cp*RhCl2 ]2 by ball milling revealed the formation of transient cocrystals between the reagents prior to the C-H activation step. However, such crystalline intermediates were only observed through stepwise intervallic ex-situ analysis, and their exact role in the C-H activation process remained unclear. In this study, we monitored the formation of discrete, stoichiometric cocrystals between benzo[h]quinoline and [Cp*RhCl2 ]2 by ball milling using in-situ synchrotron X-ray powder diffraction. This continuous analysis revealed an initial cocrystal that transformed into a second crystalline form. Computational studies showed that differences in noncovalent interactions made the [Cp*RhCl2 ]2 unit in the later-appearing cocrystal more reactive towards NaOAc. This demonstrated the advantage of cocrystal formation before the acetate-assisted metalation-deprotonation step, and how the net cooperative action of weak interactions between the reagents in mechanochemical experiments can lead to stable supramolecular assemblies, which can enhance substrate activation under ball-milling conditions. This could explain the superiority of some mechanochemical reactions, such as acetate-assisted C-H activation, compared to their solution-based counterparts.
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Affiliation(s)
- José G Hernández
- Grupo Ciencia de los Materiales, Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Calle 70 No 52-21, Medellín, Colombia
| | - Karen J Ardila-Fierro
- Grupo Ciencia de los Materiales, Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Calle 70 No 52-21, Medellín, Colombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Tomislav Stolar
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
| | - Mirta Rubčić
- Faculty of Science Department of Chemistry, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - Edi Topić
- Faculty of Science Department of Chemistry, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - Cacier Z Hadad
- Instituto de Química, Facultad de Ciencias Exactas y Naturales Universidad de Antioquia, UdeA, Calle 70 No 52-21, Medellín, Colombia
| | - Albeiro Restrepo
- Instituto de Química, Facultad de Ciencias Exactas y Naturales Universidad de Antioquia, UdeA, Calle 70 No 52-21, Medellín, Colombia
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Dias LD, Aguiar ASN, de Melo NJ, Inada NM, Borges LL, de Aquino GLB, Camargo AJ, Bagnato VS, Napolitano HB. Structural basis of antibacterial photodynamic action of curcumin against S. aureus. Photodiagnosis Photodyn Ther 2023; 43:103654. [PMID: 37308043 DOI: 10.1016/j.pdpdt.2023.103654] [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: 03/26/2023] [Revised: 05/07/2023] [Accepted: 06/09/2023] [Indexed: 06/14/2023]
Abstract
Antimicrobial photodynamic therapy (aPDT) is an alternative tool to commercial antibiotics for the inactivation of pathogenic bacteria (e.g., S. aureus). However, there is still a lack of understanding of the molecular modeling of the photosensitizers and their mechanism of action through oxidative pathways. Herein, a combined experimental and computational evaluation of curcumin as a photosensitizer against S. aureus was performed. The radical forms of keto-enol tautomers and the energies of curcumin's frontier molecular orbitals were evaluated by density functional theory (DFT) to point out the photodynamic action as well as the photobleaching process. Furthermore, the electronic transitions of curcumin keto-enol tautomers were undertaken to predict the transitions as a photosensitizer during the antibacterial photodynamic process. Moreover, molecular docking was used to evaluate the binding affinity with the S. aureus tyrosyl-tRNA synthetase as the proposed a target for curcumin. In this regard, the molecular orbital energies show that the curcumin enol form has a character of 4.5% more basic than the keto form - the enol form is a more promising electron donor than its tautomer. Curcumin is a strong electrophile, with the enol form being 4.6% more electrophilic than its keto form. In addition, the regions susceptible to nucleophilic attack and photobleaching were evaluated by the Fukui function. Regarding the docking analysis, the model suggested that four hydrogen bonds contribute to the binding energy of curcumin's interaction with the ligand binding site of S. aureus tyrosyl-tRNA synthetase. Finally, residues Tyr36, Asp40, and Asp177 contact curcumin and may contribute to orienting the curcumin in the active area. Moreover, curcumin presented a photoinactivation of 4.5 log unit corroborating the necessity of the combined action of curcumin, light, and O2 to promote the photooxidation damage of S. aureus. These computational and experimental data suggest insights regarding the mechanism of action of curcumin as a photosensitizer to inactivate S. aureus bacteria.
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Affiliation(s)
- Lucas D Dias
- Laboratório de Novos Materiais, Universidade Evangélica de Goiás, Anápolis GO, Brazil; Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, Brazil.
| | - Antônio S N Aguiar
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, Brazil
| | - Nícolas J de Melo
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | - Natalia M Inada
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | - Leonardo L Borges
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, Brazil; Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Goiânia, GO, Brazil
| | - Gilberto L B de Aquino
- Laboratório de Pesquisa em Bioprodutos e Síntese, Universidade Estadual de Goiás, Anápolis, GO, Brazil
| | - Ademir J Camargo
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, Brazil
| | - Vanderlei S Bagnato
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil; Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | - Hamilton B Napolitano
- Laboratório de Novos Materiais, Universidade Evangélica de Goiás, Anápolis GO, Brazil; Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, Brazil.
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Bhat S, Pradeep S, Patil SS, Flores-Holguín N, Glossman-Mitnik D, Frau J, Sommano SR, Ali N, Mohany M, Shivamallu C, Prasad SK, Kollur SP. Preliminary Evaluation of Lablab purpureus Phytochemicals for Anti-BoHV-1 Activity Using In Vitro and In Silico Approaches. ACS OMEGA 2023; 8:22684-22697. [PMID: 37396248 PMCID: PMC10308559 DOI: 10.1021/acsomega.3c01478] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023]
Abstract
Lablab purpureus from the Fabaceae family has been reported to have antiviral properties and used in traditional medical systems like ayurveda and Chinese medicine and has been employed to treat a variety of illnesses including cholera, food poisoning, diarrhea, and phlegmatic diseases. The bovine alphaherpesvirus-1 (BoHV-1) is notorious for causing significant harm to the veterinary and agriculture industries. The removal of the contagious BoHV-1 from host organs, particularly in those reservoir creatures, has required the use of antiviral drugs that target infected cells. This study developed LP-CuO NPs from methanolic crude extracts, and FTIR, SEM, and EDX analyses were used to confirm their formation. SEM analysis revealed that the LP-CuO NPs had a spherical shape with particle sizes between 22 and 30 nm. Energy-dispersive X-ray pattern analysis revealed the presence of only copper and oxide ions. By preventing viral cytopathic effects in the Madin-Darby bovine kidney cell line, the methanolic extract of Lablab purpureus and LP-CuO NPs demonstrated a remarkable dose-dependent anti-BoHV-1 action in vitro. Furthermore, molecular docking and molecular dynamics simulation studies of bio-actives from Lablab purpureus against the BoHV-1 viral envelope glycoprotein disclosed effective interactions between all phytochemicals and the protein, although kievitone was found to have the highest binding affinity, with the greatest number of interactions, which was also validated with molecular dynamics simulation studies. Understanding the chemical reactivity qualities of the four ligands was taken into consideration facilitated by the global and local descriptors, which aimed to predict the chemical reactivity descriptors of the studied molecules through the conceptual DFT methodology, which, along with ADMET finding, support the in vitro and in silico results.
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Affiliation(s)
- Smitha
S. Bhat
- Department
of Biotechnology and Bioinformatics, JSS
Academy of Higher Education and Research, Mysuru 570 015, India
| | - Sushma Pradeep
- Department
of Biotechnology and Bioinformatics, JSS
Academy of Higher Education and Research, Mysuru 570 015, India
| | - Sharanagouda S. Patil
- ICAR-National
Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru 560 064, India
| | - Norma Flores-Holguín
- Laboratorio
Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Chihuahua 31136, Mexico
| | - Daniel Glossman-Mitnik
- Laboratorio
Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Chihuahua 31136, Mexico
| | - Juan Frau
- Departament
de Química, Facultat de Ciences, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Sarana Rose Sommano
- Plant
Bioactive Compound Laboratory, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Nemat Ali
- Department
of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohamed Mohany
- Department
of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Chandan Shivamallu
- Department
of Biotechnology and Bioinformatics, JSS
Academy of Higher Education and Research, Mysuru 570 015, India
| | - Shashanka K. Prasad
- Department
of Biotechnology and Bioinformatics, JSS
Academy of Higher Education and Research, Mysuru 570 015, India
- Plant
Bioactive Compound Laboratory, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Shiva Prasad Kollur
- School
of Physical Sciences, Amrita Vishwa Vidyapeetham,
Mysuru Campus, Mysuru, Karnataka 570 026, India
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Unsleber JP. Accelerating Reaction Network Explorations with Automated Reaction Template Extraction and Application. J Chem Inf Model 2023; 63:3392-3403. [PMID: 37216641 PMCID: PMC10268957 DOI: 10.1021/acs.jcim.3c00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Indexed: 05/24/2023]
Abstract
Autonomously exploring chemical reaction networks with first-principles methods can generate vast data. Especially autonomous explorations without tight constraints risk getting trapped in regions of reaction networks that are not of interest. In many cases, these regions of the networks are only exited once fully searched. Consequently, the required human time for analysis and computer time for data generation can make these investigations unfeasible. Here, we show how simple reaction templates can facilitate the transfer of chemical knowledge from expert input or existing data into new explorations. This process significantly accelerates reaction network explorations and improves cost-effectiveness. We discuss the definition of the reaction templates and their generation based on molecular graphs. The resulting simple filtering mechanism for autonomous reaction network investigations is exemplified with a polymerization reaction.
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Affiliation(s)
- Jan P. Unsleber
- Laboratory
of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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Halim SA, Abdel-Rahman MA. First-principles density functional theoretical study on the structures, reactivity and spectroscopic properties of (NH) and (OH) Tautomer's of 4-(methylsulfanyl)-3[(1Z)-1-(2-phenylhydrazinylidene) ethyl] quinoline-2(1H)-one. Sci Rep 2023; 13:8909. [PMID: 37264069 DOI: 10.1038/s41598-023-35933-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 05/25/2023] [Indexed: 06/03/2023] Open
Abstract
The tautomerizations mechanism of 4-(methylsulfanyl)-3[(1Z)-1-(2-phenylhydrazinylidene) ethyl] quinoline-2(1H)-one were inspected in the gas phase and ethanol using density function theory (DFT) M06-2X and B3LYP methods. Thermo-kinetic features of different conversion processes were estimated in temperature range 273-333 K using the Transition state theory (TST) accompanied with one dimensional Eckert tunneling correction (1D-Eck). Acidity and basicity were computed as well, and the computational results were compared against the experimental ones. Additionally, NMR, global descriptors, Fukui functions, NBO charges, and electrostatic potential (ESP) were discussed. From thermodynamics analysis, the keto form of 4-(methylsulfanyl)-3-[(1Z)-1-(2 phenylhydrazinylidene) quinoline-2(1H)-one is the most stable form in the gas phase and ethanol and the barrier heights required for tautomerization process were found to be high in the gas phase and ethanol ~ 38.80 and 37.35 kcal/mol, respectively. DFT methods were used for UV-Vis electronic spectra simulation and the time-dependent density functional theory solvation model (TDDFT-SMD) in acetonitrile compounds.
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Affiliation(s)
- Shimaa Abdel Halim
- Chemistry Department, Faculty of Education, Ain Shams University, Roxy, Cairo, 11711, Egypt.
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Miranda-Quintana RA, Vela A, De Proft F, Martínez González M, Gázquez JL. Can we predict ambident regioselectivity using the chemical hardness? Phys Chem Chem Phys 2023; 25:13611-13622. [PMID: 37144347 DOI: 10.1039/d3cp00876b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The hard/soft acid/base (HSAB) principle is a cornerstone in our understanding of chemical reactivity preferences. Motivated by the success of the original ("global") version of this rule, a "local" counterpart was readily proposed to account for regioselectivity preferences, in particular, in ambident reactions. However, ample experimental evidence indicates that the local HSAB principle often fails to provide meaningful predictions. Here we examine the assumptions behind the standard proof of the local HSAB rule, showing that it is based on a flawed premise. By solving this issue, we show that it is critical to consider not only the charge transferred between the different reacting centers but also the charge reorganization within the non-reacting parts of the molecule. We propose different reorganization models and derive the corresponding regioselectivity rules for each.
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Affiliation(s)
| | - Alberto Vela
- Departamento de Química, Centro de Investigacion y Estudios Avanzados, Av. Instituto Politécnico Nacional, 2508, Ciudad de, México 07360, Mexico
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC) Vrije Universiteit Brussel Pleinlaan 2, 1050 Brussels, Belgium
| | - Marco Martínez González
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, Ontario, L8S 4M1, Canada
| | - José L Gázquez
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Ave. San Rafael Atlixco 186, Ciudad de México 09340, Mexico
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Sobhi C, Merzoud L, Bouasla S, Nacereddine AK, Morell C, Chermette H. Understanding the mechanism and regio- and stereo selectivity of [3 + 2] cycloaddition reactions between substituted azomethine ylide and 3,3,3-trifluoro-1-nitroprop-1-ene, within the molecular electron density theory. J Comput Chem 2023; 44:1208-1220. [PMID: 36708224 DOI: 10.1002/jcc.27080] [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: 09/26/2022] [Revised: 12/10/2022] [Accepted: 01/04/2023] [Indexed: 01/29/2023]
Abstract
The selectivity and the nature of the molecular mechanism of the [3 + 2] cycloaddition (32CA) reaction between 2-(dimethylamino)-1H-indene-1,3(2H)-dione (AY11) and trans(E)-3,3,3-trifluoro-1-nitroprop-1-ene(FNP10) has been studied, in which the molecular electron density theory using density functional theory methods at the MPWB1K/6-31G(d) computational level was used. Analysis of the global reactivity indices permits us to characterize FNP10 as a strong electrophile and AY11 as a strong nucleophile. Four reactive pathways associated with the ortho/meta regioselective channels and endo/exo stereoselective approaches modes have been explored and characterized in the gas phase and in the benzene solvent. The analysis of the relative energies associated with the different reaction pathways indicates that the 32CA reactions of the azomethine ylide (AY) with the nitroalkene (FNP) is meta regioselective with high endo stereoselectivity. This result is in good agreement with the experimental observations. electron localization function topological analysis of the most favored reactive pathways allows for characterizing the mechanism of this 32CA reactions as a non-concerted two-stage one-step mechanism. Finally, non-covalent interactions and quantum theory of atoms in molecule analyses at the meta/endo transition state structure indicate that the presence of different several weak interactions, namely, CF and NH contributed in favoring the formation of a meta-endo cycloadduct.
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Affiliation(s)
- Chafia Sobhi
- Laboratoire Physico-Chimie Des Surfaces Et Interfaces, Université du 20 Août 1955, Skikda, Algeria
| | - Lynda Merzoud
- Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMRCNRS 5280, Université de Lyon, Lyon, France
| | - Souad Bouasla
- Laboratory of Materials and Energetic Engineering, Faculty of Technology, University 20 August 1955, Skikda, Algeria
| | - Abdelmalek Khorief Nacereddine
- Laboratory of Physical Chemistry and Biology of Materials, Department of Physics and Chemistry, Higher Normal School for Technological Education of Skikda, Azzaba, Skikda, Algeria
| | - Christophe Morell
- Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMRCNRS 5280, Université de Lyon, Lyon, France
| | - Henry Chermette
- Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMRCNRS 5280, Université de Lyon, Lyon, France
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da Silva LP, Almeida-Neto FWQ, Bezerra LL, Silva J, Monteiro NKV, Marinho MM, Dos Santos HS, Teixeira AMR, Marinho ES, de Lima-Neto P. Sulfonamide derived from anacardic acid as potential antichagasic: a theoretical approach based on molecular docking, molecular dynamics, and density functional theory calculations. J Mol Model 2023; 29:165. [PMID: 37117952 DOI: 10.1007/s00894-023-05566-9] [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: 10/24/2022] [Accepted: 04/19/2023] [Indexed: 04/30/2023]
Abstract
Chagas disease (CD) is a tropical disease caused by the parasite Trypanosoma cruzi, transmitted by the barber insect. Currently, there are approximately 7 million infected people in the world, and it is estimated that 70 million people could contract this disease. The anacardic acid (AA) showed effectiveness in in silico and in vitro tests. The antichagasic potential of five sulfonamide molecules, derived from anacardic acid, was evaluated from a molecular approach based on the density functional theory (DFT), molecular dynamics (MD), and molecular docking (docking) calculations. Methyl 2-methoxy-6- (8- (methylsulfonamide) octyl) benzoate (SA1); 2-methoxy-6- (8- (phenylsulfonamide) octyl) benzoate (SA2); methyl 2-methoxy-6- (8- (2methylphenyl sulfonamide) octyl) benzoate (SA3); methyl 2-methoxy-6- (8-(methylphenylsulfonamide)octyl)benzoate (SA4); methyl2-(8-(2,5-dimethylphenylsulfonamide)octyl)-6-methoxybenzoate (SA5) were the investigated molecules. The DFT calculations were performed using the B3LYP/6-311+G (d, p) level of theory. The global and local reactivity data showed that SA1 shows the highest molecular reactivity, while SA2 is the most stable derivative. In addition, the structures of investigated molecules were confirmed by the linear correlations higher than 0.98 displayed between the experimental and calculated spectroscopic data (IR and NMR). Molecular docking of the molecules showed a greater prominence for the SA1, SA2, and SA4 molecules in the results of distances of ligand-cruzain. In molecular dynamics, SA2 obtained better stability due to greater interactions with important amino acids of cruzain.
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Affiliation(s)
- Leonardo P da Silva
- Departamento de Química Analítica e Físico-Química, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, Brazil.
| | | | - Lucas L Bezerra
- Departamento de Química Analítica e Físico-Química, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, Brazil
| | - Jacilene Silva
- Departamento de Química Biológica, Universidade Regional do Cariri, Crato, Ceará, Brazil
| | - Norberto K V Monteiro
- Departamento de Química Analítica e Físico-Química, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, Brazil
| | - Márcia M Marinho
- Faculdade de Educação, Ciência e Letras de Iguatu, Universidade Estadual do Ceará, Iguatu, Ceará, Brazil
| | - Hélcio S Dos Santos
- Departamento de Química Biológica, Universidade Regional do Cariri, Crato, Ceará, Brazil
- Centro de Ciências e Tecnologia, Curso de Química, Universidade Vale do Acaraú, Sobral, Ceará, Brazil
| | - Alexandre M R Teixeira
- Departamento de Química Biológica, Universidade Regional do Cariri, Crato, Ceará, Brazil
- Departamento de Física, Universidade Regional do Cariri, Crato, Ceará, Brazil
| | - Emmanuel S Marinho
- Faculdade de Filosofia Dom Aureliano Matos, Universidade Estadual do Ceará, Limoeiro do Norte, CE, Brazil
| | - Pedro de Lima-Neto
- Departamento de Química Analítica e Físico-Química, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE, Brazil
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Hjouji MY, Almehdi AM, Elmsellem H, Seqqat Y, Ouzidan Y, Tebbaa M, Lfakir NA, Kandri Rodi Y, Chahdi FO, Chraibi M, Fikri Benbrahim K, Al-Omar MA, Almehizia AA, Naglah AM, El-Mowafi SA, Elhenawy AA. Exploring Antimicrobial Features for New Imidazo[4,5-b]pyridine Derivatives Based on Experimental and Theoretical Study. Molecules 2023; 28:molecules28073197. [PMID: 37049960 PMCID: PMC10096078 DOI: 10.3390/molecules28073197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023] Open
Abstract
5-bromopyridine-2,3-diamine reacted with benzaldehyde to afford the corresponding 6-Bromo-2-phenyl-3H-imidazo[4,5-b]pyridine (1). The reaction of the latter compound (1) with a series of halogenated derivatives under conditions of phase transfer catalysis solid–liquid (CTP) allows the isolation of the expected regioisomers compounds (2–8). The alkylation reaction of (1) gives, each time, two regioisomers, N3 and N4; in the case of ethyl bromoactate, the reaction gives, at the same time, the three N1, N3 and N4 regioisomers. The structures of synthesized compounds were elucidated on the basis of different spectral data (1H NMR, 13C NMR), X-Ray diffraction and theoretical study using the DFT method, and confirmed for each compound. Hirshfeld surface analysis was used to determine the intermolecular interactions responsible for the stabilization of the molecule. Density functional theory was used to optimize the compounds, and the HOMO-LUMO energy gap was calculated, which was used to examine the inter/intra molecular charge transfer. The molecular electrostatic potential map was calculated to investigate the reactive sites that were present in the molecule. In order to determine the potential mode of interactions with DHFR active sites, the three N1, N3 and N4 regioisomers were further subjected to molecular docking study. The results confirmed that these analogs adopted numerous important interactions, with the amino acid of the enzyme being targeted. Thus, the most docking efficient molecules, 2 and 4, were tested in vitro for their antibacterial activity against Gram-positive bacteria (Bacillus cereus) and Gram-negative bacteria (Escherichia coli). Gram-positive bacteria were more sensitive to the action of these compounds compared to the Gram-negative, which were much more resistant.
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Affiliation(s)
- Mohammed-yassin Hjouji
- Laboratory of Applied Organic Chemistry, Faculty of Science and Technology Saiss, Sidi Mohammed Ben Abdallah University, Fez 30050, Morocco
| | - Ahmed M. Almehdi
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Hicham Elmsellem
- Laboratory of Applied Chemistry and Environment (LCAE), Sciences Faculty, Oujda 60000, Morocco
| | - Yousra Seqqat
- Laboratory of Applied Organic Chemistry, Faculty of Science and Technology Saiss, Sidi Mohammed Ben Abdallah University, Fez 30050, Morocco
| | - Younes Ouzidan
- Laboratoire de Chimie-Physique et Biotechnologie des Biomolécules et Matériaux, Faculté des Sciences et Techniques, Université Hassan II, BP 146, Mohammedia 28800, Morocco
| | - Mohamed Tebbaa
- Laboratoire de Chimie-Physique et Biotechnologie des Biomolécules et Matériaux, Faculté des Sciences et Techniques, Université Hassan II, BP 146, Mohammedia 28800, Morocco
| | - Noura Ait Lfakir
- Laboratoire de Chimie-Physique et Biotechnologie des Biomolécules et Matériaux, Faculté des Sciences et Techniques, Université Hassan II, BP 146, Mohammedia 28800, Morocco
| | - Youssef Kandri Rodi
- Laboratory of Applied Organic Chemistry, Faculty of Science and Technology Saiss, Sidi Mohammed Ben Abdallah University, Fez 30050, Morocco
| | - Fouad Ouazzani Chahdi
- Laboratory of Applied Organic Chemistry, Faculty of Science and Technology Saiss, Sidi Mohammed Ben Abdallah University, Fez 30050, Morocco
| | - Marwa Chraibi
- Laboratory of Microbial Biotechnology, Faculty of Science and Technology Saïss, Sidi Mohamed Ben Abdellah University, Fez 30050, Morocco
| | - Kawtar Fikri Benbrahim
- Laboratory of Microbial Biotechnology, Faculty of Science and Technology Saïss, Sidi Mohamed Ben Abdellah University, Fez 30050, Morocco
| | - Mohamed A. Al-Omar
- Drug Exploration & Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdulrahman A. Almehizia
- Drug Exploration & Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed M. Naglah
- Drug Exploration & Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Shaima A. El-Mowafi
- Peptide Chemistry Department, Chemical Industries Research Institute, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Ahmed A. Elhenawy
- Chemistry Department, Faculty of Science, Al-Azhar University, Cairo 11884, Egypt
- Chemistry Department, Faculty of Science and Art, Albaha University, Albahah 65731, Saudi Arabia
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Camara AG, Almeida-Neto FW, Silva YL, Nunes FM, Mattos MC, Mafezoli J, Barbosa FG, Marinho ES, Lima-Neto P, Oliveira MC. IR and UV-VIS spectroscopic characterization of norbadione A and study of the electronic properties of other pigments derived from pulvinic acid. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Polo-Cuadrado E, Ferrer K, Osorio E, Brito I, Cisterna J, Espinoza L, Alderete JB, Gutiérrez M. Piperonal chalcone derivative incorporating the pyrazolo[3,4- b]pyridine moiety; crystal structure, spectroscopic characterization and quantum chemical investigations. RSC Adv 2023; 13:5197-5207. [PMID: 36777942 PMCID: PMC9910059 DOI: 10.1039/d2ra08101f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/26/2023] [Indexed: 02/11/2023] Open
Abstract
A single crystal of a piperonal chalcone derivative was obtained, fully characterized, and crystallized by a slow evaporation technique. The synthesized compound was characterized by UV-Visible, FT-IR, HRMS, 1H NMR, and 13C NMR spectroscopic studies and X-ray crystallography, revealing that the crystal belongs to a triclinic crystal system with a P1̄ space group, Z = 2. In the present work, we focus on molecular modeling studies such as Hirshfeld surface analysis, energy framework calculations, frontier molecular orbital analysis, natural bond orbital analysis, and NLO properties of a π-conjugate system combining the chalcone and the pyrazole[3,4-b]pyridine scaffolds to describe the in-depth structural analysis thereof. Good agreement was found between the calculated results and experimental data. In addition, Hirshfeld surface analysis of the crystal structure showed that the intermolecular stabilization in the crystal packing comes mainly from H⋯H bond interactions. The chalcone crystal exhibits significant NLO properties suggesting that it could be considered a potential candidate for application in nonlinear optical devices.
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Affiliation(s)
- Efraín Polo-Cuadrado
- Laboratorio Síntesis Orgánica y Actividad Biológica (LSO-Act-Bio), Instituto de Química de Recursos Naturales, Universidad de Talca Casilla 747 Talca 3460000 Chile
| | - Karoll Ferrer
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences, Palacký University Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Edison Osorio
- Facultad de Ciencias Naturales y Matemáticas, Universidad de Ibagué Carrera 22 Calle 67 Ibagué 730001 Colombia
| | - Iván Brito
- Departamento de Química, Facultad de Ciencias Básicas, Universidad de Antofagasta Campus Coloso Antofagasta 02800 Chile
| | - Jonathan Cisterna
- Departamento de Química, Facultad de Ciencias, Universidad Católica del Norte, Sede Casa Central Av. Angamos 0610 Antofagasta Chile
| | - Luis Espinoza
- Departamento de Química, Universidad Técnica Federico Santa María Av. España No. 1680 Valparaíso 2340000 Chile
| | - Joel B Alderete
- Instituto de Química de Recursos Naturales (IQRN), Universidad de Talca Avenida Lircay S/N, Casilla 747 Talca Chile
| | - Margarita Gutiérrez
- Laboratorio Síntesis Orgánica y Actividad Biológica (LSO-Act-Bio), Instituto de Química de Recursos Naturales, Universidad de Talca Casilla 747 Talca 3460000 Chile
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48
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Keskin E, Arslan H. Synthesis, crystal structure, DFT calculations, and Hirshfeld surface analysis of an NNN pincer type compound. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
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49
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Khaoua O, Benbellat N, Zeroual S, Mouffouk S, Golhen S, Gouasmia A, Chermette H, Haba H. Combined experimental, computational studies (synthesis, crystal structural, DFT calculations, spectral analysis) and biological evaluation of the new homonuclear complex Di-µ-benzoato-bis [benzoatodipyridine-cobalt (II)]. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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50
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Geerlings P, De Proft F. External fields in conceptual density functional theory. J Comput Chem 2023; 44:442-455. [PMID: 36054623 DOI: 10.1002/jcc.26978] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/30/2022] [Accepted: 07/13/2022] [Indexed: 12/31/2022]
Abstract
The necessity of the recent incorporation of new external variables in the context of conceptual DFT (CDFT) is discussed based on the ever-increasing portfolio of experimental reaction conditions in the endeavor of experimentalists to synthesize new molecules with unprecedented properties. Electric and magnetic fields (ε and B), mechanical forces (F), and confinement are proposed as valuable new variables, extending conventional CDFT and its associated response functions. A finite field approach is used to calculate the evolution of both global and local descriptors in a selected series of atomic and molecular applications, and from it derive new response function involving, with one exception, the first derivative to the field considered. The electric field results, displaying, for example, a case of a field-induced enantioselectivity in the Fukui function, may be instrumental in the recent upsurge of chemistry in oriented external electric fields. The study of atomic electronegativity and hardness in magnetic fields displays a piecewise behavior, associated to configurational jumps upon increasing field strength and reveals an overall compression of their ranges for stronger fields, which may be guiding upon investigating chemistry in extremely high fields like in white dwarfs. The evolution of the electronegativity and hardness of diatomics under mechanical force can elegantly be traced back to differences in their equilibrium distance in the neutral, cationic, and anionic state. The well-known reduction of the polarizability under confinement can be seen as a fore-runner of the increasing hardness of atoms under pressure, presently under investigation. Periodicity showing up in a spontaneous way in the variety of properties is a leitmotiv in this study, as well as the interconnections/analogies between the different response functions.
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Affiliation(s)
- Paul Geerlings
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel, Brussels, Belgium
| | - Frank De Proft
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel, Brussels, Belgium
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