51
|
Zhao D, He X, Ayers PW, Liu S. Excited-State Polarizabilities: A Combined Density Functional Theory and Information-Theoretic Approach Study. Molecules 2023; 28:molecules28062576. [PMID: 36985548 PMCID: PMC10058485 DOI: 10.3390/molecules28062576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
Accurate and efficient determination of excited-state polarizabilities (α) is an open problem both experimentally and computationally. Following our previous work, (Phys. Chem. Chem. Phys. 2023, 25, 2131−2141), in which we employed simple ground-state (S0) density-related functions from the information-theoretic approach (ITA) to accurately and efficiently evaluate the macromolecular polarizabilities, in this work we aimed to predict the lowest excited-state (S1) polarizabilities. The philosophy is to use density-based functions to depict excited-state polarizabilities. As a proof-of-principle application, employing 2-(2′-hydroxyphenyl)benzimidazole (HBI), its substituents, and some other commonly used ESIPT (excited-state intramolecular proton transfer) fluorophores as model systems, we verified that either with S0 or S1 densities as an input, ITA quantities can be strongly correlated with the excited-state polarizabilities. When transition densities are considered, both S0 and S1 polarizabilities are in good relationships with some ITA quantities. The transferability of the linear regression model is further verified for a series of molecules with little or no similarity to those molecules in the training set. Furthermore, the excitation energies can be predicted based on multivariant linear regression equations of ITA quantities. This study also found that the nature of both the ground-state and excited-state polarizabilities of these species are due to the spatial delocalization of the electron density.
Collapse
Affiliation(s)
- Dongbo Zhao
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Xin He
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao 266237, China
| | - Paul W. Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
- Correspondence: (P.W.A.); (S.L.)
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, NC 27599-3420, USA
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
- Correspondence: (P.W.A.); (S.L.)
| |
Collapse
|
52
|
Cedillo–Cruz A, Villalobos–López DC, Aguilar MI, Trejo–Soto PJ, Hernández–Campos A, Jung–Cook H. Praziquanamine enantiomers: crystal structure, Hirshfeld surface analysis, and quantum chemical studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
|
53
|
Klyukin IN, Kolbunova AV, Novikov AS, Nelyubin AV, Zhdanov AP, Kubasov AS, Selivanov NA, Bykov AY, Zhizhin KY, Kuznetsov NT. Synthesis of Disubstituted Carboxonium Derivatives of Closo-Decaborate Anion [2,6-B 10H 8O 2CC 6H 5] -: Theoretical and Experimental Study. Molecules 2023; 28:molecules28041757. [PMID: 36838745 PMCID: PMC9966448 DOI: 10.3390/molecules28041757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
A comprehensive study focused on the preparation of disubstituted carboxonium derivatives of closo-decaborate anion [2,6-B10H8O2CC6H5]- was carried out. The proposed synthesis of the target product was based on the interaction between the anion [B10H11]- and benzoic acid C6H5COOH. It was shown that the formation of this product proceeds stepwise through the formation of a mono-substituted product [B10H9OC(OH)C6H5]-. In addition, an alternative one-step approach for obtaining the target derivative is postulated. The structure of tetrabutylammonium salts of carboxonium derivative ((C4H9)4N)[2,6-B10H8O2CC6H5] was established with the help of X-ray structure analysis. The reaction pathway for the formation of [2,6-B10H8O2CC6H5]- was investigated with the help of density functional theory (DFT) calculations. This process has an electrophile induced nucleophilic substitution (EINS) mechanism, and intermediate anionic species play a key role. Such intermediates have a structure in which one boron atom coordinates two hydrogen atoms. The regioselectivity for the process of formation for the 2,6-isomer was also proved by theoretical calculations. Generally, in the experimental part, the simple and available approach for producing disubstituted carboxonium derivative was introduced, and the mechanism of this process was investigated with the help of theoretical calculations. The proposed approach can be applicable for the preparation of a wide range of disubstituted derivatives of closo-borate anions.
Collapse
Affiliation(s)
- Ilya N. Klyukin
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
- Correspondence: (I.N.K.); (A.S.N.)
| | - Anastasia V. Kolbunova
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
| | - Alexander S. Novikov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia
- Research Institute of Chemistry, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya St. 6, 117198 Moscow, Russia
- Correspondence: (I.N.K.); (A.S.N.)
| | - Alexey V. Nelyubin
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
| | - Andrey P. Zhdanov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
| | - Alexey S. Kubasov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
| | - Nikita A. Selivanov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
| | - Alexander Yu. Bykov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
| | - Konstantin Yu. Zhizhin
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
| | - Nikolay T. Kuznetsov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Pr. 31, 117907 Moscow, Russia
| |
Collapse
|
54
|
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.
Collapse
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
| |
Collapse
|
55
|
Zhao D, Zhao Y, He X, Ayers PW, Liu S. Efficient and accurate density-based prediction of macromolecular polarizabilities. Phys Chem Chem Phys 2023; 25:2131-2141. [PMID: 36562468 DOI: 10.1039/d2cp04690c] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Accurately and efficiently predicting macromolecules' polarizabilities is an open problem. In this work, we employ a few simple density-based quantities from the information-theoretic approach (ITA) to predict polarizability of proteins. We first build quantitative structure/property relationships between molecular polarizabilities and ITA quantities. We then verify the broad applicability of ITA quantities for polarizability prediction for inorganic, organic, and biological systems with both localized and delocalized electronic structure. As a proof-of-concept application, we predict the molecular polarizabilities of complex proteins. Based on the linear regression equations for 20 natural amino acid residues, 400 dipeptides, and 8000 tripeptides, one then predicts the molecular polarizability of a larger peptide or even a protein once the molecular wavefunction is obtained. Because it is extremely costly to determine the wavefunction for a macromolecule like a protein, we propose to combine the ITA with the linear-scaling generalized energy-based fragmentation (GEBF) method to predict the macromolecular polarizability. In GEBF, the total molecular polarizability is obtained as a linear combination of the corresponding quantities from a series of small subsystems. We can predict them based on the subsystem wavefunction and linear regression equations rather than compute them from the nearly-intractable coupled-perturbed Hartree-Fock or Kohn-Sham equations for the whole macromolecule. Computational results showcase that the GEBF-ITA protocol should be an inexpensive yet accurate theoretical tool for predicting macromolecular polarizabilities.
Collapse
Affiliation(s)
- Dongbo Zhao
- Institute of Biomedical Research, Yunnan University, Kunming 650500, Yunnan, P. R. China
| | - Yilin Zhao
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ONL8S 4M1, Canada.
| | - Xin He
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao 266237, Shandong, P. R. China
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ONL8S 4M1, Canada.
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, USA. .,Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| |
Collapse
|
56
|
Li M, Wan X, He X, Rong C, Liu S. Impacts of external fields on aromaticity and acidity of benzoic acid: a density functional theory, conceptual density functional theory and information-theoretic approach study. Phys Chem Chem Phys 2023; 25:2595-2605. [PMID: 36602177 DOI: 10.1039/d2cp04557e] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The impact of external fields on the molecular structure and reactivity properties has been of considerable interest in the recent literature. Benzoic acid as one of the most widely used compounds in medicinal and materials sciences is known for its dual propensity in aromaticity and acidity. In this work, we systematically investigate the impact of a uniform external electric field on these properties. We apply density functional theory, conceptual density functional theory, and an information-theoretic approach to appreciate the change pattern of aromaticity and acidity properties in external fields with different strengths. Our results show that they possess different change patterns under external fields, which can be satisfactorily rationalized by variations in reactivity descriptors and partial charges. The surprising yet novel results from this study should enrich the body of our knowledge about the impact of external fields for different kinds of electronic properties and provide guidance and foundation for future studies of this phenomenon in other molecular systems.
Collapse
Affiliation(s)
- Meng Li
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P. R. China.
| | - Xinjie Wan
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P. R. China.
| | - Xin He
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Chunying Rong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P. R. China.
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, NC 27599-3420, USA. .,Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| |
Collapse
|
57
|
Integrated approach for studying bioactive compounds from Cladosporium spp. against estrogen receptor alpha as breast cancer drug target. Sci Rep 2022; 12:22446. [PMID: 36575224 PMCID: PMC9794773 DOI: 10.1038/s41598-022-22038-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 10/07/2022] [Indexed: 12/28/2022] Open
Abstract
Cladosporium spp. have been reported for their great diversity of secondary metabolites which represent as a prominent base material for verifying the biological activities. Several bioactive compounds which have antimicrobial, cytotoxic, quorum sensing inhibitory and phytotoxic activities have been isolated from Cladosporium species. Most of them are still needed to be explored for their anticancer properties. Therefore, the present study is focused on screening and identifying the bioactive compounds of Cladosporium spp. for their anticancer activity via the integrated approaches of Molecular Docking (MD), Molecular Dynamics Simulation (MDS) and Density Functional Theory (DFT) studies. A total of 123 bioactive compounds of Cladosporium spp. were explored for their binding affinity with the selected breast cancer drug target receptor such as estrogen receptor alpha (PDB:6CBZ). The Molecular Docking studies revealed that amongst the bioactive compounds screened, Altertoxin X and Cladosporol H showed a good binding affinity of - 10.5 kcal/mol and - 10.3 kcal/mol, respectively, with the estrogen receptor alpha when compared to the reference compound (17[Formula: see text]-Estradiol: - 10.2 kcal/mol). The MDS study indicated the stable binding patterns and conformation of the estrogen receptor alpha-Altertoxin X complex in a stimulating environment. In addition, in silico absorption, distribution, metabolism, excretion and toxicity (ADMET) study suggested that Altertoxin X has a good oral bioavailability with a high LD[Formula: see text] value of 2.375 mol/kg and did not cause any hepatotoxicity and skin sensitization. In summary, the integrated approaches revealed that Altertoxin X possesses a promising anticancer activity and could serve as a new therapeutic drug for breast cancer treatment.
Collapse
|
58
|
Rong C, Zhao D, He X, Liu S. Development and Applications of the Density-Based Theory of Chemical Reactivity. J Phys Chem Lett 2022; 13:11191-11200. [PMID: 36445239 DOI: 10.1021/acs.jpclett.2c03165] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Density functional theory, which is well-recognized for its accuracy and efficiency, has become the workhorse for modeling the electronic structure of molecules and extended materials in recent decades. Nevertheless, establishing a density-based conceptual framework to appreciate bonding, stability, function, reactivity, and other physicochemical properties is still an unaccomplished task. In this Perspective, we at first provide an overview of the four pathways currently available in the literature to tackle the matter, including orbital-free density functional theory, conceptual density functional theory, direct use of density-associated quantities, and the information-theoretic approach. Then, we highlight several recent advances of employing these approaches to realize new understandings for chemical concepts such as covalent bonding, noncovalent interactions, cooperation, frustration, homochirality, chirality hierarchy, electrophilicity, nucleophilicity, regioselectivity, and stereoselectivity. Finally, we provide a few possibilities for the future development of this relatively uncharted territory. Opportunities are abundant, and they are all ours for the taking.
Collapse
Affiliation(s)
- Chunying Rong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan410081, China
| | - Dongbo Zhao
- Institute of Biomedical Research, Yunnan University, Kunming650500, Yunnan, China
| | - Xin He
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong266237, China
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel HillNorth Carolina27599-3420, United States
- Department of Chemistry, University of North Carolina, Chapel HillNorth Carolina27599-3290, United States
| |
Collapse
|
59
|
Teale AM, Helgaker T, Savin A, Adamo C, Aradi B, Arbuznikov AV, Ayers PW, Baerends EJ, Barone V, Calaminici P, Cancès E, Carter EA, Chattaraj PK, Chermette H, Ciofini I, Crawford TD, De Proft F, Dobson JF, Draxl C, Frauenheim T, Fromager E, Fuentealba P, Gagliardi L, Galli G, Gao J, Geerlings P, Gidopoulos N, Gill PMW, Gori-Giorgi P, Görling A, Gould T, Grimme S, Gritsenko O, Jensen HJA, Johnson ER, Jones RO, Kaupp M, Köster AM, Kronik L, Krylov AI, Kvaal S, Laestadius A, Levy M, Lewin M, Liu S, Loos PF, Maitra NT, Neese F, Perdew JP, Pernal K, Pernot P, Piecuch P, Rebolini E, Reining L, Romaniello P, Ruzsinszky A, Salahub DR, Scheffler M, Schwerdtfeger P, Staroverov VN, Sun J, Tellgren E, Tozer DJ, Trickey SB, Ullrich CA, Vela A, Vignale G, Wesolowski TA, Xu X, Yang W. DFT exchange: sharing perspectives on the workhorse of quantum chemistry and materials science. Phys Chem Chem Phys 2022; 24:28700-28781. [PMID: 36269074 PMCID: PMC9728646 DOI: 10.1039/d2cp02827a] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/09/2022] [Indexed: 12/13/2022]
Abstract
In this paper, the history, present status, and future of density-functional theory (DFT) is informally reviewed and discussed by 70 workers in the field, including molecular scientists, materials scientists, method developers and practitioners. The format of the paper is that of a roundtable discussion, in which the participants express and exchange views on DFT in the form of 302 individual contributions, formulated as responses to a preset list of 26 questions. Supported by a bibliography of 777 entries, the paper represents a broad snapshot of DFT, anno 2022.
Collapse
Affiliation(s)
- Andrew M. Teale
- School of Chemistry, University of Nottingham, University ParkNottinghamNG7 2RDUK
| | - Trygve Helgaker
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway.
| | - Andreas Savin
- Laboratoire de Chimie Théorique, CNRS and Sorbonne University, 4 Place Jussieu, CEDEX 05, 75252 Paris, France.
| | - Carlo Adamo
- PSL University, CNRS, ChimieParisTech-PSL, Institute of Chemistry for Health and Life Sciences, i-CLeHS, 11 rue P. et M. Curie, 75005 Paris, France.
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, University of Bremen, P.O. Box 330440, D-28334 Bremen, Germany.
| | - Alexei V. Arbuznikov
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7Straße des 17. Juni 13510623Berlin
| | | | - Evert Jan Baerends
- Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands.
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy.
| | - Patrizia Calaminici
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), CDMX, 07360, Mexico.
| | - Eric Cancès
- CERMICS, Ecole des Ponts and Inria Paris, 6 Avenue Blaise Pascal, 77455 Marne-la-Vallée, France.
| | - Emily A. Carter
- Department of Mechanical and Aerospace Engineering and the Andlinger Center for Energy and the Environment, Princeton UniversityPrincetonNJ 08544-5263USA
| | | | - Henry Chermette
- Institut Sciences Analytiques, Université Claude Bernard Lyon1, CNRS UMR 5280, 69622 Villeurbanne, France.
| | - Ilaria Ciofini
- PSL University, CNRS, ChimieParisTech-PSL, Institute of Chemistry for Health and Life Sciences, i-CLeHS, 11 rue P. et M. Curie, 75005 Paris, France.
| | - T. Daniel Crawford
- Department of Chemistry, Virginia TechBlacksburgVA 24061USA,Molecular Sciences Software InstituteBlacksburgVA 24060USA
| | - Frank De Proft
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium.
| | | | - Claudia Draxl
- Institut für Physik and IRIS Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany. .,Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | - Thomas Frauenheim
- Bremen Center for Computational Materials Science, University of Bremen, P.O. Box 330440, D-28334 Bremen, Germany. .,Beijing Computational Science Research Center (CSRC), 100193 Beijing, China.,Shenzhen JL Computational Science and Applied Research Institute, 518110 Shenzhen, China
| | - Emmanuel Fromager
- Laboratoire de Chimie Quantique, Institut de Chimie, CNRS/Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France.
| | - Patricio Fuentealba
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile.
| | - Laura Gagliardi
- Department of Chemistry, Pritzker School of Molecular Engineering, The James Franck Institute, and Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.
| | - Giulia Galli
- Pritzker School of Molecular Engineering and Department of Chemistry, The University of Chicago, Chicago, IL, USA.
| | - Jiali Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China. .,Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paul Geerlings
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Nikitas Gidopoulos
- Department of Physics, Durham University, South Road, Durham DH1 3LE, UK.
| | - Peter M. W. Gill
- School of Chemistry, University of SydneyCamperdown NSW 2006Australia
| | - Paola Gori-Giorgi
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands.
| | - Andreas Görling
- Chair of Theoretical Chemistry, University of Erlangen-Nuremberg, Egerlandstrasse 3, 91058 Erlangen, Germany.
| | - Tim Gould
- Qld Micro- and Nanotechnology Centre, Griffith University, Gold Coast, Qld 4222, Australia.
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany.
| | - Oleg Gritsenko
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands.
| | - Hans Jørgen Aagaard Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark.
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie UniversityHalifaxNova ScotiaB3H 4R2Canada
| | - Robert O. Jones
- Peter Grünberg Institut PGI-1, Forschungszentrum Jülich52425 JülichGermany
| | - Martin Kaupp
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Straße des 17. Juni 135, 10623, Berlin.
| | - Andreas M. Köster
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav)CDMX07360Mexico
| | - Leeor Kronik
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovoth, 76100, Israel.
| | - Anna I. Krylov
- Department of Chemistry, University of Southern CaliforniaLos AngelesCalifornia 90089USA
| | - Simen Kvaal
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway.
| | - Andre Laestadius
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway.
| | - Mel Levy
- Department of Chemistry, Tulane University, New Orleans, Louisiana, 70118, USA.
| | - Mathieu Lewin
- CNRS & CEREMADE, Université Paris-Dauphine, PSL Research University, Place de Lattre de Tassigny, 75016 Paris, France.
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, NC 27599-3420, USA. .,Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, France.
| | - Neepa T. Maitra
- Department of Physics, Rutgers University at Newark101 Warren StreetNewarkNJ 07102USA
| | - Frank Neese
- Max Planck Institut für Kohlenforschung, Kaiser Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany.
| | - John P. Perdew
- Departments of Physics and Chemistry, Temple UniversityPhiladelphiaPA 19122USA
| | - Katarzyna Pernal
- Institute of Physics, Lodz University of Technology, ul. Wolczanska 219, 90-924 Lodz, Poland.
| | - Pascal Pernot
- Institut de Chimie Physique, UMR8000, CNRS and Université Paris-Saclay, Bât. 349, Campus d'Orsay, 91405 Orsay, France.
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA. .,Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - Elisa Rebolini
- Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France.
| | - Lucia Reining
- Laboratoire des Solides Irradiés, CNRS, CEA/DRF/IRAMIS, École Polytechnique, Institut Polytechnique de Paris, F-91120 Palaiseau, France. .,European Theoretical Spectroscopy Facility
| | - Pina Romaniello
- Laboratoire de Physique Théorique (UMR 5152), Université de Toulouse, CNRS, UPS, France.
| | - Adrienn Ruzsinszky
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA.
| | - Dennis R. Salahub
- Department of Chemistry, Department of Physics and Astronomy, CMS – Centre for Molecular Simulation, IQST – Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary2500 University Drive NWCalgaryAlbertaT2N 1N4Canada
| | - Matthias Scheffler
- The NOMAD Laboratory at the FHI of the Max-Planck-Gesellschaft and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Faradayweg 4-6, D-14195, Germany.
| | - Peter Schwerdtfeger
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study, Massey University Auckland, 0632 Auckland, New Zealand.
| | - Viktor N. Staroverov
- Department of Chemistry, The University of Western OntarioLondonOntario N6A 5B7Canada
| | - Jianwei Sun
- Department of Physics and Engineering Physics, Tulane University, New Orleans, LA 70118, USA.
| | - Erik Tellgren
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway.
| | - David J. Tozer
- Department of Chemistry, Durham UniversitySouth RoadDurhamDH1 3LEUK
| | - Samuel B. Trickey
- Quantum Theory Project, Deptartment of Physics, University of FloridaGainesvilleFL 32611USA
| | - Carsten A. Ullrich
- Department of Physics and Astronomy, University of MissouriColumbiaMO 65211USA
| | - Alberto Vela
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), CDMX, 07360, Mexico.
| | - Giovanni Vignale
- Department of Physics, University of Missouri, Columbia, MO 65203, USA.
| | - Tomasz A. Wesolowski
- Department of Physical Chemistry, Université de Genève30 Quai Ernest-Ansermet1211 GenèveSwitzerland
| | - Xin Xu
- Shanghai Key Laboratory of Molecular Catalysis and Innovation Materials, Collaborative Innovation Centre of Chemistry for Energy Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China.
| | - Weitao Yang
- Department of Chemistry and Physics, Duke University, Durham, NC 27516, USA.
| |
Collapse
|
60
|
Martínez JP, Trzaskowski B. Electrophilicity of Hoveyda-Grubbs Olefin Metathesis Catalysts as the Driving Force that Controls Initiation Rates. Chemphyschem 2022; 23:e202200580. [PMID: 36062870 DOI: 10.1002/cphc.202200580] [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: 08/03/2022] [Revised: 09/01/2022] [Indexed: 01/05/2023]
Abstract
The dissociative mechanism of initiation for a series of Hoveyda-Grubbs type metathesis catalysts modified at the para and meta positions in the isopropoxybenzylidene ligand is investigated by means of DFT calculations. The electron donating/withdrawing capacity of the ligand was screened through the incorporation of various substituents such as halogens, nitro, alkoxides, ketones, esters, amines, and amides. Variations in structural parameters, energy barriers for the Ru-O bond dissociation, and Ru-O bond strength were examined as a function of the Hammett constant. It was found that electronic properties of the catalysts such as chemical potential, hardness, and electrophilicity correlate linearly with the dissociative energy barriers. These findings enable a systematic rationalization and prediction of rate of precatalyst initiation through the calculation of only the HOMO-LUMO gap of catalysts, as the faster the initiation, the more electrophilic the catalyst.
Collapse
|
61
|
Murali M, Gowtham HG, Shilpa N, Krishnappa HKN, Ledesma AE, Jain AS, Shati AA, Alfaifi MY, Elbehairi SEI, Achar RR, Silina E, Stupin V, Ortega-Castro J, Frau J, Flores-Holguín N, Amruthesh KN, Shivamallu C, Kollur SP, Glossman-Mitnik D. Exploration of Anti-HIV Phytocompounds against SARS-CoV-2 Main Protease: Structure-Based Screening, Molecular Simulation, ADME Analysis and Conceptual DFT Studies. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238288. [PMID: 36500380 PMCID: PMC9736867 DOI: 10.3390/molecules27238288] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/21/2022] [Accepted: 11/14/2022] [Indexed: 11/29/2022]
Abstract
The ever-expanding pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has gained attention as COVID-19 and caused an emergency in public health to an unmatched level to date. However, the treatments used are the only options; currently, no effective and licensed medications are available to combat disease transmission, necessitating further research. In the present study, an in silico-based virtual screening of anti-HIV bioactive compounds from medicinal plants was carried out through molecular docking against the main protease (Mpro) (PDB: 6LU7) of SARS-CoV-2, which is a key enzyme responsible for virus replication. A total of 16 anti-HIV compounds were found to have a binding affinity greater than -8.9 kcal/mol out of 150 compounds screened. Pseudohypericin had a high affinity with the energy of -10.2 kcal/mol, demonstrating amino acid residual interactions with LEU141, GLU166, ARG188, and GLN192, followed by Hypericin (-10.1 kcal/mol). Moreover, the ADME (Absorption, Distribution, Metabolism and Excretion) analysis of Pseudohypericin and Hypericin recorded a low bioavailability (BA) score of 0.17 and violated Lipinski's rule of drug-likeness. The docking and molecular simulations indicated that the quinone compound, Pseudohypericin, could be tested in vitro and in vivo as potent molecules against COVID-19 disease prior to clinical trials.This was also supported by the theoretical and computational studies conducted. The global and local descriptors, which are the underpinnings of Conceptual Density FunctionalTheory (CDFT) have beenpredicted through successful model chemistry, hoping that they could be of help in the comprehension of the chemical reactivity properties of the molecular systems considered in this study.
Collapse
Affiliation(s)
| | | | | | | | - Ana E. Ledesma
- Centro de InvestigaciónenBiofísicaAplicada y Alimentos, Facultad de Ciencias Exactas y Tecnologías (FCEyN), Universidad Nacional de Santiago del Estero (CIBAAL-UNSE-CONICET), Santiago del Estero 4206, Argentina
| | - Anisha S. Jain
- Department of Microbiology, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Ali A. Shati
- Biology Department, Faculty of Science, King Khalid University, Abha 9004, Saudi Arabia
| | - Mohammad Y. Alfaifi
- Biology Department, Faculty of Science, King Khalid University, Abha 9004, Saudi Arabia
| | - Serag Eldin I. Elbehairi
- Biology Department, Faculty of Science, King Khalid University, Abha 9004, Saudi Arabia
- Cell Culture Lab, Egyptian Organization for Biological Products and Vaccines (VACSERA Holding Company), 51 Wezaret El-Zeraa St., Giza 12511, Egypt
| | - Raghu Ram Achar
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Ekaterina Silina
- Department of Hospital Surgery, N.I. Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Victor Stupin
- Department of Hospital Surgery, N.I. Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Joaquín Ortega-Castro
- Departament de Química, Facultat de Ciences, Universitat de les IllesBalears, E-07122 Palma de Malllorca, Spain
| | - Juan Frau
- Departament de Química, Facultat de Ciences, Universitat de les IllesBalears, E-07122 Palma de Malllorca, Spain
| | - Norma Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigaciónen Materiales Avanzados, Chihuahua 31136, Mexico
| | - Kestur Nagaraj Amruthesh
- Department of Studies in Botany, University of Mysore, Mysore 570006, India
- Correspondence: (K.N.A.); (C.S.); (S.P.K.)
| | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru 570015, India
- Correspondence: (K.N.A.); (C.S.); (S.P.K.)
| | - Shiva Prasad Kollur
- School of Physical Sciences, Amrita Vishwa Vidyapeetham, Mysuru Campus, Mysuru 570026, India
- Correspondence: (K.N.A.); (C.S.); (S.P.K.)
| | - Daniel Glossman-Mitnik
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigaciónen Materiales Avanzados, Chihuahua 31136, Mexico
| |
Collapse
|
62
|
Irons TJP, Huynh BC, Teale AM, De Proft F, Geerlings P. Molecular charge distributions in strong magnetic fields: a conceptual and current DFT study. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2145245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Tom J. P. Irons
- School of Chemistry, University of Nottingham, Nottingham, UK
| | - Bang C. Huynh
- School of Chemistry, University of Nottingham, Nottingham, UK
| | - Andrew M. Teale
- School of Chemistry, University of Nottingham, Nottingham, UK
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, Oslo, Norway
| | - Frank De Proft
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel, Brussels, Belgium
| | - Paul Geerlings
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel, Brussels, Belgium
| |
Collapse
|
63
|
Pal R, Patra SG, Chattaraj PK. Quantitative Structure-Toxicity Relationship in Bioactive Molecules from a Conceptual DFT Perspective. Pharmaceuticals (Basel) 2022; 15:1383. [PMID: 36355555 PMCID: PMC9695291 DOI: 10.3390/ph15111383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 10/29/2023] Open
Abstract
The preclinical drug discovery stage often requires a large amount of costly and time-consuming experiments using huge sets of chemical compounds. In the last few decades, this process has undergone significant improvements by the introduction of quantitative structure-activity relationship (QSAR) modelling that uses a certain percentage of experimental data to predict the biological activity/property of compounds with similar structural skeleton and/or containing a particular functional group(s). The use of machine learning tools along with it has made life even easier for pharmaceutical researchers. Here, we discuss the toxicity of certain sets of bioactive compounds towards Pimephales promelas and Tetrahymena pyriformis in terms of the global conceptual density functional theory (CDFT)-based descriptor, electrophilicity index (ω). We have compared the results with those obtained by using the commonly used hydrophobicity parameter, logP (where P is the n-octanol/water partition coefficient), considering the greater ease of computing the ω descriptor. The Human African trypanosomiasis (HAT) curing activity of 32 pyridyl benzamide derivatives is also studied against Tryphanosoma brucei. In this review article, we summarize these multiple linear regression (MLR)-based QSAR studies in terms of electrophilicity (ω, ω2) and hydrophobicity (logP, (logP)2) parameters.
Collapse
Affiliation(s)
- Ranita Pal
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Shanti Gopal Patra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Pratim Kumar Chattaraj
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| |
Collapse
|
64
|
Pradeep S, Prabhuswaminath SC, Reddy P, Srinivasa SM, Shati AA, Alfaifi MY, Eldin I. Elbehairi S, Achar RR, Silina E, Stupin V, Manturova N, Glossman-Mitnik D, Shivamallu C, Kollur SP. Anticholinesterase activity of Areca Catechu: In Vitro and in silico green synthesis approach in search for therapeutic agents against Alzheimer's disease. Front Pharmacol 2022; 13:1044248. [PMID: 36408228 PMCID: PMC9672481 DOI: 10.3389/fphar.2022.1044248] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/17/2022] [Indexed: 08/29/2023] Open
Abstract
For many years, the primary focus has been on finding effective treatments for Alzheimer's disease (AD), which has led to the identification of promising therapeutic targets. The necessity for AD stage-dependent optimal settings necessitated a herbal therapy strategy. The plant species Areca Catechu L. (AC) was selected based on the traditional uses against CNS-related diseases. AC leaf extract were prepared using a Soxhlet extraction method and hydroxyapatite nanoparticles (HAp-NPs) were synthesized from the same (AC-HAp-NPs). Powder X-ray diffractometer (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), selected area electron diffraction (SAED) and fourier transform infrared spectroscopy (FTIR) were used to confirm the structure and morphology of the as-prepared AC-HAp-NPs. The crystalline character of the AC-HAp-NPs was visible in the XRD pattern. The synthesized material was found to be nanoflake, with an average diameter of 15-20 nm, according to SEM analysis. The TEM and SAED pictures also revealed the form and size of AC-HAp-NPs. In vitro anti-acetylcholinesterase and butyrylcholinesterase (AChE and BChE) activities of hydroxyapatite nanoparticles produced from an AC leaf extract was tested in this study. When compared to control, AC-HAp-NPs had higher anti-AChE and BChE activity. The anti-acetylcholinesterase action of phytoconstituents generated from AC leaf extract was mediated by 4AQD and 4EY7, according to a mechanistic study conducted utilizing in silico research. The global and local descriptors, which are the underpinnings of Conceptual Density Functional Theory (CDFT), have been predicted through the MN12SX/Def2TZVP/H2O model chemistry to help in the comprehension of the chemical reactivity properties of the five ligands considered in this study. The CDFT experiments are supplemented by the calculation of several useful calculated pharmacokinetics indices, their expected biological targets connected to the bioavailability of the five ligands in order to further the goal of studying their bioactivity.
Collapse
Affiliation(s)
- Sushma Pradeep
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Samudyata C. Prabhuswaminath
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Pruthvish Reddy
- Department of Biotechnology, Acharya Institute of Technology, Bengaluru, Karnataka, India
| | - Sudhanva M. Srinivasa
- Adichunchanagiri Institute for Molecular Medicine, Adichunchanagiri University, Mandya, Karnataka, India
| | - Ali A. Shati
- Biology Department, Faculty of Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Y. Alfaifi
- Biology Department, Faculty of Sciences, King Khalid University, Abha, Saudi Arabia
| | - Serag Eldin I. Elbehairi
- Biology Department, Faculty of Sciences, King Khalid University, Abha, Saudi Arabia
- Cell Culture Lab, Egyptian Organization for Biological Products and Vaccines (VACSERA Holding Company), Agouza, Giza, Egypt
| | - Raghu Ram Achar
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Ekaterina Silina
- Department of Surgery, Pirogov Russian National Research Medical University, Mascow, Russia
- Institute of Biodesign and Modeling of Complex Systems, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Victor Stupin
- Department of Surgery, Pirogov Russian National Research Medical University, Mascow, Russia
| | - Natalia Manturova
- Department of Surgery, Pirogov Russian National Research Medical University, Mascow, Russia
| | - Daniel Glossman-Mitnik
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Chih, Mexico
| | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Shiva Prasad Kollur
- School of Physical Sciences, Amrita Vishwa Vidyapeetham, Mysuru, Karnataka, India
| |
Collapse
|
65
|
Miranda-Quintana RA, Smiatek J. Application of Fundamental Chemical Principles for Solvation Effects: A Unified Perspective for Interaction Patterns in Solution. J Phys Chem B 2022; 126:8864-8872. [PMID: 36269164 DOI: 10.1021/acs.jpcb.2c06315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We demonstrate the utility of basic chemical principles like the "|Δμ| big is good" (DMB) rule for the study of solvation interactions between distinct solutes such as ions and solvents. The corresponding approach allows us to define relevant criteria for maximum solvation energies of ion pairs in different solvents in terms of electronegativities and chemical hardnesses. Our findings reveal that the DMB principle culminates into the strong and weak acids and bases concept as recently derived for specific ion effects in various solvents. The further application of the DMB approach highlights a similar condition for the chemical hardnesses with a reminiscence to the hard/soft acids and bases principle. Comparable conclusions can also be drawn with regard to the change of the solvent. We show that favorable solvent interactions are mainly driven by low chemical hardnesses as well as high electronegativity differences between the ions and the solvent. Our findings highlight that solvation interactions are governed by basic chemical principles, which demonstrates the close similarity between solvation mechanisms and chemical reactions.
Collapse
Affiliation(s)
- Ramón Alain Miranda-Quintana
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida32611, United States
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, StuttgartD-70569, Germany
| |
Collapse
|
66
|
Cador A, Hoffmann G, Tognetti V, Joubert L. A theoretical study on aza-Michael additions. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02921-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
67
|
Rong C, Heidar-Zadeh F, Miranda-Quintana RA, Liu S, Ayers PW. Ranking the energy minima of the 20 natural amino acids using conceptual tools. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02929-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
68
|
Gowtham HG, Murali M, Singh SB, Shivamallu C, Pradeep S, Shivakumar CS, Anandan S, Thampy A, Achar RR, Silina E, Stupin V, Ortega-Castro J, Frau J, Flores-Holguín N, Amruthesh KN, Kollur SP, Glossman-Mitnik D. Phytoconstituents of Withania somnifera unveiled Ashwagandhanolide as a potential drug targeting breast cancer: Investigations through computational, molecular docking and conceptual DFT studies. PLoS One 2022; 17:e0275432. [PMID: 36201520 PMCID: PMC9536605 DOI: 10.1371/journal.pone.0275432] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Breast cancer is the second most common malignancy in females worldwide and poses a great challenge that necessitates the identification of novel therapeutic agents from several sources. This research aimed to study the molecular docking and molecular dynamics simulations of four proteins (such as PDB: 6CBZ, 1FDW, 5GWK and 2WTT) with the selected phytochemicals from Withania somnifera to identify the potential inhibitors for breast cancer. The molecular docking result showed that among 44 compounds, two of them, Ashwagandhanolide and Withanolide sulfoxide have the potential to inhibit estrogen receptor alpha (ERα), 17-beta-hydroxysteroid -dehydrogenase type 1 (17β-HSD1), topoisomerase II alpha (TOP2A) and p73 tetramerization domain that are expressed during breast cancer. The molecular dynamics (MD) simulations results suggested that Ashwagandhanolide remained inside the binding cavity of four targeted proteins and contributed favorably towards forming a stable protein-ligand complex throughout the simulation. Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) properties confirmed that Ashwagandhanolide is hydrophobic and has moderate intestinal permeability, good intestinal absorption, and poor skin permeability. The compound has a relatively low VDss value (-1.652) and can be transported across ABC transporter and good central nervous system (CNS) permeability but did not easily cross the blood-brain barrier (BBB). This compound does not possess any mutagenicity, hepatotoxicity and skin sensitization. Based on the results obtained, the present study highlights the anticancer potential of Ashwagandhanolide, a compound from W. somnifera. Furthermore, in vitro and in vivo studies are necessary to perform before clinical trials to prove the potentiality of Ashwagandhanolide.
Collapse
Affiliation(s)
| | - Mahadevamurthy Murali
- Applied Plant Pathology Laboratory, Department of Studies in Botany, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | | | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Sushma Pradeep
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - C. S. Shivakumar
- Department of Clinical Nutrition and Dietetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar, Karnataka, India
| | - Satish Anandan
- Department of Clinical Nutrition and Dietetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar, Karnataka, India
| | - Anjana Thampy
- Department of Clinical Nutrition and Dietetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar, Karnataka, India
| | - Raghu Ram Achar
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Ekaterina Silina
- Department of Human Pathology, I. M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Victor Stupin
- Department of Hospital Surgery, N.I. Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | | | - Juan Frau
- Departament de Química, Universitat de les Illes Balears, Palma de Malllorca, Spain
| | - Norma Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chih, México
| | - Kestur Nagaraj Amruthesh
- Applied Plant Pathology Laboratory, Department of Studies in Botany, University of Mysore, Manasagangotri, Mysore, Karnataka, India
| | - Shiva Prasad Kollur
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), University of the South Pacific, Laucala Campus, Suva, Fiji
- Department of Sciences, Amrita School of Arts and Sciences, Amrita Vishwa Vidyapeetham, Mysuru Campus, Mysore, Karnataka, India
| | - Daniel Glossman-Mitnik
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chih, México
| |
Collapse
|
69
|
Pal R, Poddar A, Chattaraj PK. On the Periodicity of the Information Theory and Conceptual DFT-Based Reactivity Descriptors. J Phys Chem A 2022; 126:6801-6813. [PMID: 36154006 DOI: 10.1021/acs.jpca.2c04106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The periodic trends in conceptual density functional and information theory-based reactivity descriptors are reported for the atoms H to Ba (Z = 1 to 56). Ionization potential, electron affinity, electronegativity, and hardness show periodic behavior following the Aufbau principle and popular electronic structure principles. They are in agreement with those reported in standard chemistry textbooks. The trend in the electrophilicity index, however, shows an interesting behavior, where it contradicts earlier reports. Our calculation reveals that the noble gas elements correspond to minimum ω values in each period which obey the minimum electrophilicity principle as well as reflect their low reactivity. Periodic trends in electroaccepting and electrodonating powers, along with that of net electrophilicity, are as expected. The behavior of information theory-based Shannon and GBP entropies, along with the Shannon entropy of shape function are also explored across the periodic table.
Collapse
Affiliation(s)
- Ranita Pal
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Arpita Poddar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Pratim Kumar Chattaraj
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| |
Collapse
|
70
|
Tsuneda T, Sumitomo H, Hasebe M, Tsutsumi T, Taketsugu T. Reactive orbital energy theory serving a theoretical foundation for the electronic theory of organic chemistry. J Comput Chem 2022; 44:93-104. [PMID: 36193762 DOI: 10.1002/jcc.27017] [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: 08/09/2022] [Revised: 09/11/2022] [Accepted: 09/14/2022] [Indexed: 11/07/2022]
Abstract
It is established that the reactive orbital energy theory (ROET) theoretically reproduces the rule-based electronic theory diagrams of organic chemistry by a comparative study on the charge transfer natures of typical organic carbon-carbon and carbon-heteroatom bond formation reactions: aldol, Mannich, α-aminooxylation, and isogyric reactions. The ROET, which is an expansion of the reaction electronic theories (e.g., the frontier orbital theory) in terms of orbital energies, elucidates the reactive orbitals driving reactions and the charge transferability indices of the reactions. Performing the ROET analyses of these reactions shows that the charge transfer directions given in the rule-based diagrams of the electronic theory are reproduced even for the functional groups of charge transfer destinations in all but only two processes for 38 reaction processes. The ROET analyses also make clear the detailed orbital-based pictures of these bond formation reactions: that is, the use of the out-of-plane antibonding π orbitals in acidic conditions (enol-mode) and in-plane antibonding π orbitals in basic conditions (enolate-mode), which explain the experimentally assumed mechanisms such as the π-bond formations in acidic conditions and σ-bond formations at α-carbons in basic conditions. Furthermore, the ROET analyses explicate that the methyl group initially accepts electrons and then donates them to the bond formations in the target reactions. It is, consequently, suggested that the ROET serves a theoretical foundation for the electronic theory of organic chemistry.
Collapse
Affiliation(s)
- Takao Tsuneda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan.,Graduate School of Science Technology and Innovation, Kobe University, Kobe, Japan
| | - Hiroki Sumitomo
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Masatoshi Hasebe
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Takuro Tsutsumi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan.,L-Station, Creative Research Institution (CRI), Hokkaido University, Sapporo, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| |
Collapse
|
71
|
In Vitro Anticancer Screening, Molecular Docking and Antimicrobial Studies of Triazole-Based Nickel(II) Metal Complexes. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196548. [PMID: 36235085 PMCID: PMC9570899 DOI: 10.3390/molecules27196548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
Herein we describe the synthesis of a series of nickel(II) complexes (C1–C3) with Schiff bases (HL1–HL3) derived from 4-amino-5-mercapto-3-methyl-1,2,4-triazole and ortho/meta/para-nitrobenzaldehyde having composition [Ni(L)2(H2O)2]. The obtained ligands and their complexes were characterized using physico-chemical techniques viz., elemental analysis, magnetic moment study, spectral (electronic, FT-IR, 1H-NMR) and thermal analysis. The elemental analysis and spectral analysis revealed that Schiff bases behave as monoanionic bidentate ligands towards the Ni(II) ion. Whereas, the magnetic moment study suggested the octahedral geometry of all the Ni(II) complexes. The thermal behavior of the complexes has been studied by thermogravimetric analysis and agrees well with the composition of complexes. Further, the biological activities such as antimicrobial and antifungal studies of the Schiff bases and Ni(II) complexes have been screened against bacterial species (Staphylococcus aureus and Pseudomonas aeruginosa) and fungal species (Aspergillus niger and Candida albicans) activity by MIC method, the results of which revealed that metal complexes exhibited significant antimicrobial activities than their respective ligands against the tested microbial species. Furthermore, the molecular docking technique was employed to investigate the active sites of the selected protein, which indeed helped us to screen the potential anticancer agents among the synthesized ligand and complexes. Further, these compounds have been screened for their in vitro anticancer activity using OVCAR-3 cell line. The results revealed that the complexes are more active than the ligands.
Collapse
|
72
|
Miranda-Quintana RA, Smiatek J. Electronic properties of amino acids and nucleobases: similarity classes and pairing principles from chemical reactivity indices. Phys Chem Chem Phys 2022; 24:22477-22486. [PMID: 36106477 DOI: 10.1039/d2cp02767d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a new classification scheme for amino acids and nucleobases based on the electronic properties of the individual molecules. Using chemical reactivity indices such as electronegativity, electrophilicity, and chemical hardness, we can identify similarities and differences between each class of amino acids and nucleobases. Notable differences emerge in particular with regard to high, neutral or low electronegativity as well as different combinations of chemical hardness. Our approach allows us to relate these insights to the properties of the side groups in terms of a unique reference scheme. We further show that hydrophobic differences between amino acids are rather negligible in the context of electronic properties. Our classification scheme also rationalizes the occurrence of distinct stable nucleobase pairs and clearly emphasizes certain differences between individual molecules. The stability and abundant occurrence of Watson-Crick nucleobase pairs is further discussed in the context of the minimum electrophilicity principle.
Collapse
Affiliation(s)
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany.
| |
Collapse
|
73
|
Fias S, Ayers PW, De Proft F, Geerlings P. Properties of the density functional response kernels and its implications on chemistry. J Chem Phys 2022; 157:114102. [PMID: 36137804 DOI: 10.1063/5.0094653] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An overview of mathematical properties of the non-local second order derivatives of the canonical, grand canonical, isomorphic, and grand isomorphic ensembles is given. The significance of their positive or negative semidefiniteness and the implications of these properties for atoms and molecules are discussed. Based on this property, many other interesting properties can be derived, such as the expansion in eigenfunctions, bounds on the diagonal and off-diagonal elements, and the eigenvalues of these kernels. We also prove Kato's theorem for the softness kernel and linear response and the dissociation limit of the linear responses as the sum of the linear responses of the individual fragments when dissociating a system into two non-interacting molecular fragments. Finally, strategies for the practical calculation of these kernels, their eigenfunctions, and their eigenvalues are discussed.
Collapse
Affiliation(s)
- Stijn Fias
- McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4L8, Canada
| | - Paul W Ayers
- McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4L8, Canada
| | - 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
| |
Collapse
|
74
|
Hernández-Mancera JP, Rojas-Valencia N, Núñez-Zarur F. Rationalizing the Substituent Effects in Diels-Alder Reactions of Triazolinediones with Anthracene. J Phys Chem A 2022; 126:6657-6667. [PMID: 36122186 DOI: 10.1021/acs.jpca.2c04970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work we tackle the problem of the substituent effects in the Diels-Alder cycloadditions between triazolinediones (TADs) and anthracene. Experiments showed that aryl TADs substituted with electron-withdrawing groups (EWG) are more reactive than those substituted with electron-donating (EDG) or alkyl groups. However, the molecular origin of this preference is not yet understood. By a combination of methods including the activation strain model (ASM), energy decomposition analysis (EDA), molecular orbital (MO) theory, and conceptual density functional theory (CDFT), we disclosed the substituent effects of TADs. First, ASM/EDA analysis revealed that the reactivity of alkyl and aryl-substituted TADs is controlled by interaction energies, ΔEint, which are ultimately defined by orbital interactions between frontier molecular orbitals. Moreover, alkyl-TADs are also controlled by the extent of strain at the transition state. The MO analysis suggested that the rate acceleration for EWG-substituted TADs is due to a more favorable orbital interaction between the HOMO of anthracene and the LUMO of the TADs, which is corroborated by calculations of charge transfer at the transition states. From CDFT, the chemical potential of anthracene is higher than those of TADs, indicating a flow of electron density from anthracene to TADs, in agreement with the results from the electrophilicity index.
Collapse
Affiliation(s)
| | - Natalia Rojas-Valencia
- Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 no. 30-65, 050026 Medellín, Colombia
| | - Francisco Núñez-Zarur
- Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 no. 30-65, 050026 Medellín, Colombia
| |
Collapse
|
75
|
Flores-Holguín N, Frau J, Glossman-Mitnik D. Editorial: Recent advances, new perspectives and applications of conceptual density functional theory. Front Chem 2022; 10:1003106. [PMID: 36157034 PMCID: PMC9507304 DOI: 10.3389/fchem.2022.1003106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- Norma Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Chih, Mexico
| | - Juan Frau
- Departament de Química, Universitat de Les Illes Balears, Palma de Mallorca, Spain
| | - Daniel Glossman-Mitnik
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Chih, Mexico
| |
Collapse
|
76
|
Geerlings P. From Density Functional Theory to Conceptual Density Functional Theory and Biosystems. Pharmaceuticals (Basel) 2022; 15:ph15091112. [PMID: 36145333 PMCID: PMC9505550 DOI: 10.3390/ph15091112] [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: 08/02/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 12/03/2022] Open
Abstract
The position of conceptual density functional theory (CDFT) in the history of density functional theory (DFT) is sketched followed by a chronological report on the introduction of the various DFT descriptors such as the electronegativity, hardness, softness, Fukui function, local version of softness and hardness, dual descriptor, linear response function, and softness kernel. Through a perturbational approach they can all be characterized as response functions, reflecting the intrinsic reactivity of an atom or molecule upon perturbation by a different system, including recent extensions by external fields. Derived descriptors such as the electrophilicity or generalized philicity, derived from the nature of the energy vs. N behavior, complete this picture. These descriptors can be used as such or in the context of principles such as Sanderson’s electronegativity equalization principle, Pearson’s hard and soft acids and bases principle, the maximum hardness, and more recently, the minimum electrophilicity principle. CDFT has known an ever-growing use in various subdisciplines of chemistry: from organic to inorganic chemistry, from polymer to materials chemistry, and from catalysis to nanotechnology. The increasing size of the systems under study has been coped with thanks to methodological evolutions but also through the impressive evolution in software and hardware. In this flow, biosystems entered the application portfolio in the past twenty years with studies varying (among others) from enzymatic catalysis to biological activity and/or the toxicity of organic molecules and to computational peptidology. On the basis of this evolution, one can expect that “the best is yet to come”.
Collapse
Affiliation(s)
- Paul Geerlings
- Research Group of General Chemistry (ALGC), Faculty of Science and Bio-Engineering Science, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| |
Collapse
|
77
|
Mo Y, Danovich D, Shaik S. The roles of charge transfer and polarization in non-covalent interactions: a perspective from ab initio valence bond methods. J Mol Model 2022; 28:274. [PMID: 36006511 DOI: 10.1007/s00894-022-05187-8] [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: 08/14/2021] [Accepted: 12/03/2021] [Indexed: 11/28/2022]
Abstract
Noncovalent interactions are ubiquitous and have been well recognized in chemistry, biology and material science. Yet, there are still recurring controversies over their natures, due to the wide range of noncovalent interaction terms. In this Essay, we employed the Valence Bond (VB) methods to address two types of interactions which recently have drawn intensive attention, i.e., the halogen bonding and the CH‧‧‧HC dihydrogen bonding. The VB methods have the advantage of interpreting molecular structures and properties in the term of electron-localized Lewis (resonance) states (structures), which thereby shed specific light on the alteration of the bonding patterns. Due to the electron localization nature of Lewis states, it is possible to define individually and measure both polarization and charge transfer effects which have different physical origins. We demonstrated that both the ab initio VB method and the block-localized wavefunction (BLW) method can provide consistent pictures for halogen bonding systems, where strong Lewis bases NH3, H2O and NMe3 partake as the halogen bond acceptors, and the halogen bond donors include dihalogen molecules and XNO2 (X = Cl, Br, I). Based on the structural, spectral, and energetic changes, we confirm the remarkable roles of charge transfer in these halogen bonding complexes. Although the weak C-H∙∙∙H-C interactions in alkane dimers and graphene sheets are thought to involve dispersion only, we show that this term embeds delicate yet important charge transfer, bond reorganization and polarization interactions.
Collapse
Affiliation(s)
- Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, NC, 27401, USA.
| | - David Danovich
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190407, Jerusalem, Israel
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190407, Jerusalem, Israel.
| |
Collapse
|
78
|
Carmona-Espindola J, Flores A, Gázquez JL, Vela A, Trickey S. Hardness of Molecules and Bandgap of Solids from a Generalized Gradient Approximation Exchange Energy Functional. J Chem Phys 2022; 157:114109. [DOI: 10.1063/5.0096678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The deviations from linearity of the energy as a function of the number of electrons that arise with current approximations to the exchange-correlation (XC) energy functional have important consequences for the frontier eigenvalues of molecules and the corresponding valence-band maxima for solids. In this work, we present an analysis of the exact theory that allows one to infer the effects of such approximations on the highest occupied and lowest unoccupied molecular orbital eigenvalues. Then we show the importance of the asymptotic behavior of the XC potential in the generalized gradient approximation (GGA) in the case of the NCAPR functional (nearly correct asymptotic potential revised) for determining the shift of the frontier orbital eigenvalues towards the exact values. Thereby we establish a procedure at the GGA level of refinement that allows one to make a single calculation to determine the ionization potential, the electron affinity, and the hardness of molecules (and its solid counterpart, the band gap) with an accuracy equivalent to that obtained for those properties through energy differences, a procedure which requires three calculations. For solids, the accuracy achieved for the band gap lies rather close to that which is obtained through hybrid XC energy functionals, but those also demand much greater computational effort than what is required with the simple NCAPR GGA calculation.
Collapse
Affiliation(s)
| | - Anaid Flores
- Chemistry, Universidad Autónoma Metropolitana Iztapalapa, Mexico
| | - José L. Gázquez
- Departamento de Quimica, Universidad Autonoma Metropolitana Iztapalapa, Mexico
| | | | - S.B. Trickey
- QTP, Department of Physics, University of Florida, United States of America
| |
Collapse
|
79
|
Liu S. Quantifying energetic information in density functional theory. J Chem Phys 2022; 157:101103. [DOI: 10.1063/5.0104919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Energy and information are two fundamental concepts in physics and chemistry. In density functional theory (DFT), all information pertaining to stability, reactivity, and other properties is encompassed in the ground state electron density. The basic theorems of DFT govern that energy is a universal functional of the density and thus it can be regarded as a special kind of information. In this work, we quantify the energetic information in terms of Shannon entropy and Fisher information for energetic distributions of atoms and molecules. Two identities are unveiled for an energetic density, its gradient and Laplacian to rigorously satisfy. A new partition scheme to decompose atoms in molecules has been proposed using the energetic distribution. We also show that our approach can simultaneously quantify both two-body and many-body interactions. This new framework should provide new analytical tools for us to appreciate electronic properties of molecular systems including stability and reactivity. More importantly, this work establishes the missing link in DFT between energy and information, the two most fundamental quantities in quantum theory.
Collapse
Affiliation(s)
- Shubin Liu
- Research Computing Ceter, University of North Carolina at Chapel Hill, United States of America
| |
Collapse
|
80
|
Eeckhoudt J, Bettens T, Geerlings P, Cammi R, Chen B, Alonso M, De Proft F. Conceptual density functional theory under pressure: Part I. XP-PCM method applied to atoms. Chem Sci 2022; 13:9329-9350. [PMID: 36093025 PMCID: PMC9384819 DOI: 10.1039/d2sc00641c] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022] Open
Abstract
High pressure chemistry offers the chemical community a range of possibilities to control chemical reactivity, develop new materials and fine-tune chemical properties. Despite the large changes that extreme pressure brings to the table, the field has mainly been restricted to the effects of volume changes and thermodynamics with less attention devoted to electronic effects at the molecular scale. This paper combines the conceptual DFT framework for analyzing chemical reactivity with the XP-PCM method for simulating pressures in the GPa range. Starting from the new derivatives of the energy with respect to external pressure, an electronic atomic volume and an atomic compressibility are found, comparable to their enthalpy analogues, respectively. The corresponding radii correlate well with major known sets of this quantity. The ionization potential and electron affinity are both found to decrease with pressure using two different methods. For the electronegativity and chemical hardness, a decreasing and increasing trend is obtained, respectively, and an electronic volume-based argument is proposed to rationalize the observed periodic trends. The cube of the softness is found to correlate well with the polarizability, both decreasing under pressure, while the interpretation of the electrophilicity becomes ambiguous at extreme pressures. Regarding the electron density, the radial distribution function shows a clear concentration of the electron density towards the inner region of the atom and periodic trends can be found in the density using the Carbó quantum similarity index and the Kullback-Leibler information deficiency. Overall, the extension of the CDFT framework with pressure yields clear periodic patterns.
Collapse
Affiliation(s)
- J Eeckhoudt
- General Chemistry Department (ALGC), Vrije Universiteit Brussel (VUB) Brussels Belgium
| | - T Bettens
- General Chemistry Department (ALGC), Vrije Universiteit Brussel (VUB) Brussels Belgium
| | - P Geerlings
- General Chemistry Department (ALGC), Vrije Universiteit Brussel (VUB) Brussels Belgium
| | - R Cammi
- Department of Chemical Science, Life Science and Environmental Sustainability, University of Parma Parma Italy
| | - B Chen
- Donostia International Physics Center Donostia-San Sebastian Spain
- IKERBASQUE, Basque Foundation for Science Plaza Euskadi 5 48009 Bilbao Spain
| | - M Alonso
- General Chemistry Department (ALGC), Vrije Universiteit Brussel (VUB) Brussels Belgium
| | - F De Proft
- General Chemistry Department (ALGC), Vrije Universiteit Brussel (VUB) Brussels Belgium
| |
Collapse
|
81
|
Experimental and theoretical approach for novel imidazolium ionic liquids as Smart Corrosion inhibitors for mild steel in 1.0 M hydrochloric acid. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.103967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
|
82
|
Cencer MM, Suslick BA, Moore JS. From skeptic to believer: The power of models. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
83
|
Khan SN, Griffith A, De Proft F, Miliordos E, Havenith RWA, Bykov D, Cunha AV. [Fe 4S 4] cubane in sulfite reductases: new insights into bonding properties and reactivity. Phys Chem Chem Phys 2022; 24:18543-18551. [PMID: 35904932 DOI: 10.1039/d2cp02124b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dissimilatory sulfite reductase enzyme has very characteristic active site where the substrate binds to an iron site, ligated by a siroheme macrocycle and a thiol directly connected to a [Fe4S4] cluster. This arrangement gives the enzyme remarkable efficiency in reducing sulfite and nitrite all the way to hydrogen sulfide and ammonia. For the first time we present a theoretical study where substrate binding modalities and activation are elucidated using active site models containing proton supply side chains and the [Fe4S4] cluster. Density functional theory (DFT) was deployed in conjunction with the energy decomposition scheme (as implemented in AMS), the quantum theory of atoms in molecules (QTAIM), and conceptual DFT (cDFT) descriptors. We quantified the role of the electrostatic interactions inside the active site created by the side chains as well as the influence of the [Fe4S4] cluster on the substrate binding. Furthermore, using conceptual DFT results we shed light of the activation process, thus, laying foundation for further mechanistic studies. We found that the bonding of the ligands to the iron complex is dominated by electrostatic interactions, but the presence of the [Fe4S4] cubane leads to substantial changes in electronic interaction. The spin state of the cubane, however, affects the binding energy only marginally. The conceptual DFT results show that the presence of the [Fe4S4] cubane affects the reactivity of the active site as it is involved in electron transfer. This is corroborated by an increase in the electrophilicity index, thus making the active site more prone to react with the ligands. The interaction energies between the ligand and the siroheme group are also increased upon the presence of the cubane group, thus, suggesting that the siroheme group is not an innocent spectator but plays an active role in the reactivity of the dSIR active site.
Collapse
Affiliation(s)
- Shahriar N Khan
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849-5312, USA
| | - Alexa Griffith
- Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6373, USA.
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - Evangelos Miliordos
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849-5312, USA
| | - Remco W A Havenith
- Stratingh Institute for Chemistry and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Ghent Quantum Chemistry Group, Department of Chemistry, Ghent University, Krijgslaan 281 (S3), B-9000 Gent, Belgium
| | - Dmytro Bykov
- Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6373, USA.
| | - Ana V Cunha
- Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6373, USA. .,Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium.,Department of Chemistry of the University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| |
Collapse
|
84
|
Miranda-Quintana RA, Heidar-Zadeh F, Fias S, Chapman AEA, Liu S, Morell C, Gómez T, Cárdenas C, Ayers PW. Molecular interactions from the density functional theory for chemical reactivity: Interaction chemical potential, hardness, and reactivity principles. Front Chem 2022; 10:929464. [PMID: 35936089 PMCID: PMC9352952 DOI: 10.3389/fchem.2022.929464] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
In the first paper of this series, the authors derived an expression for the interaction energy between two reagents in terms of the chemical reactivity indicators that can be derived from density functional perturbation theory. While negative interaction energies can explain reactivity, reactivity is often more simply explained using the “|dμ| big is good” rule or the maximum hardness principle. Expressions for the change in chemical potential (μ) and hardness when two reagents interact are derived. A partial justification for the maximum hardness principle is that the terms that appear in the interaction energy expression often reappear in the expression for the interaction hardness, but with opposite sign.
Collapse
Affiliation(s)
- Ramón Alain Miranda-Quintana
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, United States
- *Correspondence: Ramón Alain Miranda-Quintana, ; Tatiana Gómez, Carlos Cárdenas, ; Paul W. Ayers,
| | | | - Stijn Fias
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Allison E. A. Chapman
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, NC, United states
| | - Christophe Morell
- Université de Lyon, Universit́e Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR CNRS 5280, Villeurbanne Cedex, France
| | - Tatiana Gómez
- Theoretical and Computational Chemistry Center, Institute of Applied Chemical Sciences, Faculty of Engineering, Universidad Autonoma de Chile, Santiago, Chile
- *Correspondence: Ramón Alain Miranda-Quintana, ; Tatiana Gómez, Carlos Cárdenas, ; Paul W. Ayers,
| | - Carlos Cárdenas
- Departamento de Fisica, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro para el desarrollo de la Nanociencias y Nanotecnologia, CEDENNA, Santiago, Chile
- *Correspondence: Ramón Alain Miranda-Quintana, ; Tatiana Gómez, Carlos Cárdenas, ; Paul W. Ayers,
| | - Paul W. Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
- *Correspondence: Ramón Alain Miranda-Quintana, ; Tatiana Gómez, Carlos Cárdenas, ; Paul W. Ayers,
| |
Collapse
|
85
|
An insight into reactivity and bioactivity properties of quorum sensing peptides against PDE10A: a computational peptidology approach. J Mol Model 2022; 28:209. [PMID: 35789297 DOI: 10.1007/s00894-022-05176-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/30/2022] [Indexed: 12/21/2022]
Abstract
Peptides are currently the most promising lead molecules. Quorum sensing peptides have a variety of structural features and are regularly exposed to post-translational modifications. Antiparkinsonian drugs lose their efficacy after a long period of use, and patients develop motor problems such as drug-induced dyskinesia (DIDs). The interaction between PDE10A and cAMP is necessary for dopamine neurotransmission and may play a role in Parkinson's disease pathogenesis. cAMP and cGMP are cyclic nucleotides that act as secondary messengers in the signal transduction pathway, influencing a range of CNS activities. PDE enzymes hydrolyze phosphodiester bonds to break down cAMP and cGMP, allowing them to control intracellular levels of these second messengers effectively. PDE expression, and hence cyclic nucleotide levels and their downstream targets, may change with age and in numerous age-related illnesses, including Parkinson's disease, according to mounting evidence. At the peak of dyskinesias, cyclic nucleotide levels were lower, and using phosphodiesterase inhibitors before antiparkinsonian medicines reduced the severity of dyskinesias. In a recent study, PapRIV was found to have the ability to activate BV-2 microglia cells, indicating that this quorum sensing peptide may play a role in gut-brain contact. As a result of the current in silico work, mainly focused on QSPs as a lead molecule for inhibiting PDE10A, the SRNAT QSP sequence has been a potent molecule in molecular docking and molecular dynamics simulations. Furthermore, we can test the efficiency of therapeutic components in vitro and in vivo utilizing this computational approach against PDE10A.
Collapse
|
86
|
Derbali I, Aroule O, Hoffmann G, Thissen R, Alcaraz C, Romanzin C, Zins EL. On the relevance of the electron density analysis for the study of micro-hydration and its impact on the formation of a peptide-like bond. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02893-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
87
|
Benomrane B, Hamza Reguig F, Krallafa AM. Effectiveness electronic density‐based descriptor to index hard–hard interaction. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Brahim Benomrane
- LCPM Laboratory, Faculty of Sciences, Chemistry Department University of Oran 1 Ahmed BenBella Oran Algeria
| | - Farouk Hamza Reguig
- LCPM Laboratory, Faculty of Sciences, Chemistry Department University of Oran 1 Ahmed BenBella Oran Algeria
| | - Abdelghani Mohamed Krallafa
- LCPM Laboratory, Faculty of Sciences, Chemistry Department University of Oran 1 Ahmed BenBella Oran Algeria
- SirMa CNRS UMR 7369, MEDyC University of Reims Champagne‐Ardenne Reims France
| |
Collapse
|
88
|
Ren M, Sun S, Wu Y, Shi Y, Wang ZJ, Cao H, Xie Y. The structure-activity relationship of aromatic compounds in advanced oxidation processes:a review. CHEMOSPHERE 2022; 296:134071. [PMID: 35216974 DOI: 10.1016/j.chemosphere.2022.134071] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 02/17/2022] [Accepted: 02/19/2022] [Indexed: 06/14/2023]
Abstract
Advanced oxidation processes (AOPs) are widely used as efficient technologies to treat highly toxic and harmful substances in wastewater. Taking the most representative aromatic compounds (monosubstituted benzenes, substituted phenols and heterocyclic compounds) as examples, this paper firstly introduces their structures and the structural descriptors studied in AOPs before, and the influence of structural differences in AOPs with different reactive oxygen species (ROS) on the degradation rate was discussed in detail. The structure-activity relationship of pollutants has been previously analyzed through quantitative structure-activity relationship (QSAR) model, in which ROS is a very important influencing factor. When electrophilic oxidative species attacks pollutants, aromatic compounds with electron donating groups are more favorable for degradation than aromatic compounds with electron donating groups. While nucleophilic oxidative species comes to the opposite conclusion. The choice of advanced oxidation processes, the synergistic effect of various active oxygen species and the used catalysts will also change the degradation mechanism. This makes the structure-dependent activity relationship uncertain, and different conclusions are obtained under the influence of various experimental factors.
Collapse
Affiliation(s)
- Mingzhu Ren
- Beijing Engineering Research Center of Process Pollution Control, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Energy Environmental Catalysis, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Sihan Sun
- Beijing Engineering Research Center of Process Pollution Control, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yiqiu Wu
- Beijing Engineering Research Center of Process Pollution Control, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yanchun Shi
- Beijing Engineering Research Center of Process Pollution Control, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; National Basic Public Science Data Center, Chinese Academy of Sciences, Beijing, 100190, China
| | - Zhou-Jun Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Energy Environmental Catalysis, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Hongbin Cao
- Beijing Engineering Research Center of Process Pollution Control, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; National Basic Public Science Data Center, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yongbing Xie
- Beijing Engineering Research Center of Process Pollution Control, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; National Basic Public Science Data Center, Chinese Academy of Sciences, Beijing, 100190, China.
| |
Collapse
|
89
|
Ćoćić D, Petrović B, Puchta R, Chrzanowska M, Katafias A, van Eldik R. Investigation of water substitution at Ru II complexes by conceptual density function theory approach. J Comput Chem 2022; 43:1161-1175. [PMID: 35484985 DOI: 10.1002/jcc.26878] [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: 12/31/2021] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 11/08/2022]
Abstract
In this paper, we investigated water exchange reactions and substitution of aqua RuII complexes of general formula [Ru(terpy)(N^N)(H2 O)]2+ (where N^N = ethylenediamine (en), 1,2-(aminomethyl)pyridine (ampy) and 2,2'-bipyridine (bipy)) by ammonia and thioformaldehyde. These reactions were studied in detail by applying conceptual density functional theory. This approach enabled us to gain further insight into the underlying reaction mechanism at the microscopic level (involving only direct participants of the reaction, without the influence of the solvent) and to put the concept of reaction mechanism on a quantitative basis. The course of the chemical reaction along the reaction coordinate ξ, is rationalized in terms of reaction energy, force, dipole moment, and reaction electronic flux (REF). The results yield and characterize the significant influence of an intermolecular hydrogen bond formed between the entering and the spectator ligand to the overall energy barrier of the reactions.
Collapse
Affiliation(s)
- Dušan Ćoćić
- Department of Chemistry, Faculty of Science, University of Kragujevac, Kragujevac
| | - Biljana Petrović
- Department of Chemistry, Faculty of Science, University of Kragujevac, Kragujevac
| | - Ralph Puchta
- Inorganic Chemistry, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany.,Central Institute for Scientific Computing (CISC), University of Erlangen-Nuremberg, Erlangen, Germany.,Computer Chemistry Center, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Marta Chrzanowska
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Toruń
| | - Anna Katafias
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Toruń
| | - Rudi van Eldik
- Inorganic Chemistry, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany.,Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Toruń
| |
Collapse
|
90
|
Unimuke T, Louis H, Eno EA, Agwamba EC, Adeyinka AS. Meta-Hybrid Density Functional Theory Prediction of the Reactivity, Stability, and IGM of Azepane, Oxepane, Thiepane, and Halogenated Cycloheptane. ACS OMEGA 2022; 7:13704-13720. [PMID: 35559178 PMCID: PMC9088921 DOI: 10.1021/acsomega.1c07361] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/31/2022] [Indexed: 05/09/2023]
Abstract
The application of plain cycloalkanes and heterocyclic derivatives in the synthesis of valuable natural products and pharmacologically active intermediates has increased tremendously in recent times with much attention being paid to the lower cycloalkane members. The structural and molecular properties of higher seven-membered and nonaromatic heterocyclic derivatives are less known despite their stable nature and vast application; thus, an insight into their structural and electronic properties is still needed. Appropriate quantum chemical calculations utilizing the ab initio (MP2) method, meta-hybrid (M06-2X) functional, and long-range-separated functionals (ωB97XD) have been utilized in this work to investigate the structural reactivity, stability, and behavior of substituents on cycloheptane (CHP) and its derivatives: azepane, oxepane, thiepane, fluorocycloheptane (FCHP), bromocycloheptane (BrCHP), and chlorocycloheptane (ClCHP). Molecular global reactivity descriptors such as Fukui function, frontier molecular orbitals (FMOs), and molecular electrostatic potential were computed and compared with lower members. The results of two population methods CHELPG and Atomic Dipole Corrected Hirshfeld Charges (ADCH) were equally compared to scrutinize the charge distribution in the molecules. The susceptibility of intramolecular interactions between the substituents and cycloalkane ring is revealed by natural bond orbital analysis and intramolecular weak interactions by the independent gradient model (IGM). Other properties such as atomic density of states, intrinsic bond strength index (IBSI), and dipole moments are considered. It is acclaimed that the strain effect is a major determinant effect in the energy balance of cyclic molecules; thus, the ring strain energies and validation of spectroscopic specificities with reference to the X-ray crystallographic data are also considered.
Collapse
Affiliation(s)
- Tomsmith
O. Unimuke
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540004, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar 540004, Nigeria
| | - Hitler Louis
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540004, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar 540004, Nigeria
| | - Ededet A. Eno
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540004, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar 540004, Nigeria
| | - Ernest C. Agwamba
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar 540004, Nigeria
- Department
of Chemical Sciences, Clifford University
Owerrinta, Abia State 440001, Nigeria
| | - Adedapo S. Adeyinka
- Research
Centre for Synthesis and Catalysis, Department of Chemical Sciences, University of Johannesburg, Johannesburg 2006, South Africa
| |
Collapse
|
91
|
Flores-Holguín N, Frau J, Glossman-Mitnik D. Virtual Prospection of Marine Cyclopeptides as Therapeutics by Means of Conceptual DFT and Computational ADMET. Pharmaceuticals (Basel) 2022; 15:509. [PMID: 35631336 PMCID: PMC9144238 DOI: 10.3390/ph15050509] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 02/04/2023] Open
Abstract
Bioactive peptides are chemical compounds created through the covalent bonding of amino acids, known as amide or peptide bonds. Due to their unusual chemistry and various biological effects, marine bioactive peptides have garnered considerable research. The effectiveness of a bioactive marine peptide is attributed to its structural features, such as amino acid content and sequence, which vary depending on the degree of action. Cyclic peptides combine several favorable properties such as good binding affinity, target selectivity and low toxicity that render them an attractive modality for the development of therapeutics. The apratoxins are a class of molecules formed by a series of cyclic depsipeptides with potent cytotoxic activities. The objective of this research is to pursue a computational prospection of the molecular structures and properties of several cylopeptides of marine origin with potential therapeutic applications. The methodology will be based on the determination of the chemical reactivity descriptors of the studied molecules through the consideration of the Conceptual DFT model and validation of a particular model chemistry, MN12SX/Def2TZVP/H2O. These studies will be complemented by a determination of the pharmacokinetics and ADMET parameters by resorting to certain cheminformatics tools.
Collapse
Affiliation(s)
- Norma Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
| | - Juan Frau
- Departament de Química, Facultat de Ciènces, Universitat de les Illes Balears, E-07122 Palma de Malllorca, Spain;
| | - Daniel Glossman-Mitnik
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
| |
Collapse
|
92
|
Gingrich PW, Siegel JB, Tantillo DJ. Assessing Alkene Reactivity toward Cytochrome P450-Mediated Epoxidation through Localized Descriptors and Regression Modeling. J Chem Inf Model 2022; 62:1979-1987. [PMID: 35421306 DOI: 10.1021/acs.jcim.1c01567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The prediction of sites of epoxidation by cytochrome P450s during metabolism is particularly important in drug design, as epoxides are capable of alkylating biological macromolecules. Reliable methods are needed to quantitatively predict P450-mediated epoxidation barriers for inclusion in high-throughput screening campaigns alongside protein-ligand docking. Utilizing the fractional occupation number weighted density (FOD) and orbital-weighted Fukui index (fw+) as descriptors of local reactivity and a data set of 36 alkene epoxidation barriers computed with density functional theory (DFT), we developed and validated a multiple linear regression model for the reliable estimation of epoxidation barriers using only substrate structures as input. Using our recommended level of theory (GFN2-xTB//GFN-FF), mean absolute errors in the training and test sets were found to be 0.66 and 0.70 kcal/mol, respectively, with coefficients of determination of ca. 0.80. We demonstrate the utility of this approach on three known substrates of CYP101A1 and further show that this approach is inappropriate for particularly electron-rich alkenes. By employing a modern semiempirical method on force-field-generated geometries, the required descriptors can be calculated on the millisecond timescale per structure, making the approach well suited for incorporation into high-throughput methodologies alongside docking.
Collapse
Affiliation(s)
- Phillip W Gingrich
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Justin B Siegel
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| |
Collapse
|
93
|
Flores-Holguín N, Frau J, Glossman-Mitnik D. Computational Chemistry Study of Natural Apocarotenoids and Their Synthetic Glycopeptide Conjugates as Therapeutic Drugs. Physiology (Bethesda) 2022. [DOI: 10.5772/intechopen.103130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The objective of the research to be presented in the chapter is the determination of the chemical reactivity properties of some natural apocarotenoids and their synthetic glycopeptide conjugates that could have the ability to inhibit SARS-CoV-2 replication. The study will be based on the consideration of the Conceptual DFT branch of Density Functional Theory (DFT) through the consideration of particular successful model chemistry which has been demonstrated as satisfying the Janak and Ionization Energy theorems within Generalized Gradient Approximation (GGA) theory. The research will be complemented by a report of the ADMET and pharmacokinetic properties hoping that this information could be of help in the development of new pharmaceutical drugs for fighting COVID-19.
Collapse
|
94
|
Chakraborty D, Hase WL. Direct dynamics simulation of the thermal O(
3
P) + dimethylamine reaction in the triplet surface. I. Rate constant and product branching. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Debdutta Chakraborty
- Department of Chemistry and Biochemistry Texas Tech University Lubbock Texas USA
- Department of Chemistry Birla Institute of Technology Mesra Ranchi India
| | - William L. Hase
- Department of Chemistry and Biochemistry Texas Tech University Lubbock Texas USA
| |
Collapse
|
95
|
Zaklika J, Hładyszowski J, Ordon P, Komorowski L. From the Electron Density Gradient to the Quantitative Reactivity Indicators: Local Softness and the Fukui Function. ACS OMEGA 2022; 7:7745-7758. [PMID: 35284764 PMCID: PMC8908489 DOI: 10.1021/acsomega.1c06540] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Important reactivity measures such as the local softness, the Fukui function, and the global hardness have been calculated directly from first principles with the use of the electron density function, beyond the finite difference approximation. Our recently derived density gradient theorem and the principle of nearsightedness of the electronic matter have been instrumental in obtaining the original, albeit approximate, result on the local softness of an atom. By integration of the local softness s(r), we obtain the global softness S and the Fukui function f(r) = s(r)/S. Local and global softness values have also been calculated analytically for the basic hydrogenic orbitals; the general relation to the atomic number S = σZ -2 has been demonstrated, with constants σ characteristic for each orbital type. Global hardness η = 1/S calculated for atoms and ions has been favorably tested against its conventional measure given by the finite difference approximation: (I - A). Calculated test results for atoms and ions in rows 1-4 of the periodic table have been presented.
Collapse
Affiliation(s)
- Jarosław Zaklika
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jerzy Hładyszowski
- Department of Physical Chemistry and Biophysics, Wrocław Medical University, ul. Borowska 211 A, 50-556 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
| |
Collapse
|
96
|
Redjem N, Lakehal S, Lakehal A, Morell C, Merzoud L, Chermette H. Reactivity and a Charge-Transfer Model Analysis in Aminopolycarboxylic-Metal Complexes. Inorg Chem 2022; 61:4673-4680. [PMID: 35254062 DOI: 10.1021/acs.inorgchem.1c03860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the present work, we have calculated several density functional theory (DFT) reactivity descriptors for the aminopolycarboxylate (APC) acids at the B3LYP/6311++G (d,p) levels of theory, aiming to analyze their reactivity. Reactivity descriptors such as ionization energy, molecular hardness, electrophilicity, and condensed Fukui function local indices have been determined to predict the reactivity of APCs. The influence of the solvent was taken into account by employing the CPCM model. The results indicate that the solvation slightly modifies the tendency of the reactivity of the APCs studied. On the other hand, we applied a global and local charge-transfer partitioning model, which introduces two charge-transfer channels [one for accepting electrons (electrophilic) and another for donating one (nucleophilic)] to the complexation reaction of a set of APC acids with transition metals (Mn, Co, and Ni targets enlarged by Fe, Cu, and Zn). The correlation between the charges obtained for the interaction between APC acids and transition metal stability constants provides support for their interpretation as measures of the electrophilicity and nucleophilicity of a chemical species and, at the same time, allows one to describe the donation and back-donation processes in terms of the DFT of chemical reactivity. Also, the application of dual descriptors for these acids provides valuable information concerning the atoms in the reactants playing the most important roles in the reaction, thus helping to improve our understanding of the reaction under study.
Collapse
Affiliation(s)
- Nawel Redjem
- Laboratoire de Chimie Appliquée et Technologie des Matériaux, Université Larbi Ben M'hidi Oum el Bouaghi, 04000 Oum El Bouaghi, Algeria
| | - Salima Lakehal
- Laboratoire de Chimie des Matériaux et des Vivants: Activité & Réactivité, Université Batna 1, 05000 Batna, Algeria.,Institut des Sciences de la Terre et de l'univers, Université de Batna 2, 05001 Batna, Algeria
| | - Aicha Lakehal
- Faculté des Sciences Techniques, Université de Batna 2, 05000 Batna, Algeria
| | - Christophe Morell
- Université de Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5280, Institut des Sciences Analytiques, 69622 Villeurbanne Cedex, France
| | - Lynda Merzoud
- Université de Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5280, Institut des Sciences Analytiques, 69622 Villeurbanne Cedex, France
| | - Henry Chermette
- Université de Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5280, Institut des Sciences Analytiques, 69622 Villeurbanne Cedex, France
| |
Collapse
|
97
|
Barrera Y, Anderson JS. Predicting the reactivity of unsaturated molecules to methyl radical addition using a radical two-parameter general-purpose reactivity indicator. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2021.139333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
98
|
Halabi A, Rincón E, Chamorro E. Machine learning predictive classification models for the carcinogenic activity of activated metabolites derived from aromatic amines and nitroaromatics. Toxicol In Vitro 2022; 81:105347. [DOI: 10.1016/j.tiv.2022.105347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/08/2022] [Indexed: 11/29/2022]
|
99
|
Mariwamy VH, Kollur SP, Shivananda B, Begum M, Shivamallu C, Dharmashekara C, Pradeep S, Jain AS, Prasad SK, Syed A, Elgorban AM, Al-Rejaie S, Ortega-Castro J, Frau J, Flores-Holguín N, Glossman-Mitnik D. N-((1 H-Pyrrol-2-yl)methylene)-6-methoxypyridin-3-amine and Its Co(II) and Cu(II) Complexes as Antimicrobial Agents: Chemical Preparation, In Vitro Antimicrobial Evaluation, In Silico Analysis and Computational and Theoretical Chemistry Investigations. Molecules 2022; 27:1436. [PMID: 35209226 PMCID: PMC8880514 DOI: 10.3390/molecules27041436] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Researchers are interested in Schiff bases and their metal complexes because they offer a wide range of applications. The chemistry of Schiff bases of heterocompounds has got a lot of attention because of the metal's ability to coordinate with Schiff base ligands. In the current study, a new bidentate Schiff base ligand, N-((1H-pyrrol-2-yl)methylene)-6-methoxypyridin-3-amine (MPM) has been synthesized by condensing 6-methoxypyridine-3-amine with pyrrole-2-carbaldehyde. Further, MPM is used to prepare Cu(II) and Co(II) metal complexes. Analytical and spectroscopic techniques are used for the structural elucidation of the synthesized compounds. Both MPM and its metal complexes were screened against Escherichia coli, Bacillus subtilis, Staphylococcus aureus and Klebsiella pneumoniae species for antimicrobial studies. Furthermore, these compounds were subjected to in silico studies against bacterial proteins to comprehend their best non-bonded interactions. The results confirmed that the Schiff base ligand show considerably higher binding affinity with good hydrogen bonding and hydrophobic interactions against various tested microbial species. These results were complemented with a report of the Conceptual DFT global reactivity descriptors of the studied compounds together with their biological scores and their ADMET computed parameters.
Collapse
Affiliation(s)
- Vinusha H. Mariwamy
- Department of Chemistry, Sri Jayachamarajendra College of Enegineering, JSS Science and Technology University, Mysuru 570 006, Karnataka, India; (V.H.M.); (B.S.); (M.B.)
| | - Shiva Prasad Kollur
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), Laucala Campus, The University of the South Pacific, Suva, Fiji
- Department of Sciences, Amrita School of Arts and Sciences, Mysuru Campus, Amrita Vishwa Vidyapeetham, Mysore 570 026, Karnataka, India
| | - Bindya Shivananda
- Department of Chemistry, Sri Jayachamarajendra College of Enegineering, JSS Science and Technology University, Mysuru 570 006, Karnataka, India; (V.H.M.); (B.S.); (M.B.)
| | - Muneera Begum
- Department of Chemistry, Sri Jayachamarajendra College of Enegineering, JSS Science and Technology University, Mysuru 570 006, Karnataka, India; (V.H.M.); (B.S.); (M.B.)
| | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570 026, Karnataka, India; (C.D.); (S.P.); (A.S.J.); (S.K.P.)
| | - Chandan Dharmashekara
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570 026, Karnataka, India; (C.D.); (S.P.); (A.S.J.); (S.K.P.)
| | - Sushma Pradeep
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570 026, Karnataka, India; (C.D.); (S.P.); (A.S.J.); (S.K.P.)
| | - Anisha S. Jain
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570 026, Karnataka, India; (C.D.); (S.P.); (A.S.J.); (S.K.P.)
| | - Shashanka K. Prasad
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570 026, Karnataka, India; (C.D.); (S.P.); (A.S.J.); (S.K.P.)
| | - Asad Syed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.S.); (A.M.E.)
| | - Abdallah M. Elgorban
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.S.); (A.M.E.)
| | - Salim Al-Rejaie
- Department of Pharmacology and Toxicology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
| | - Joaquín Ortega-Castro
- Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain; (J.O.-C.); (J.F.)
| | - Juan Frau
- Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain; (J.O.-C.); (J.F.)
| | - Norma Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
| | - Daniel Glossman-Mitnik
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
| |
Collapse
|
100
|
Ma Y, Tao Y, Qu H, Wang C, Yan F, Gao X, Zhang M. Exploration of plant-derived natural polyphenols toward COVID-19 main protease inhibitors: DFT, molecular docking approach, and molecular dynamics simulations. RSC Adv 2022; 12:5357-5368. [PMID: 35425531 PMCID: PMC8981245 DOI: 10.1039/d1ra07364h] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 01/19/2022] [Indexed: 12/18/2022] Open
Abstract
Recent outbreaks of coronavirus have brought serious challenges to public health around the world, and it is essential to find effective treatments. In this study, the 3C-like proteinase (3CLpro) of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has been considered as an important drug target because of its role in viral replication. We initially optimized 251 compounds at the PM7 level of theory for docking with 3CLpro, and then we selected the top 12 compounds for further optimization with the B3LYP-D3/6-311G** method and obtained the top four compounds by further molecular docking. Quantum chemistry calculations were performed to predict molecular properties, such as the electrostatic potential and some CDFT descriptors. We also performed molecular dynamics simulations and free energy calculations to determine the relative stability of the selected four potential compounds. We have identified key residues controlling the 3CLpro/ligand binding from per-residue based decomposition of the binding free energy. Convincingly, the comprehensive results support the conclusion that the compounds have the potential to become a candidate for anti-coronavirus treatment.
Collapse
Affiliation(s)
- Yufei Ma
- School of Biomedical Engineering and Technology, Tianjin Medical University 22 Qixiangtai Road Tianjin 300070 China
| | - Yulian Tao
- School of Biomedical Engineering and Technology, Tianjin Medical University 22 Qixiangtai Road Tianjin 300070 China
| | - Hanyang Qu
- School of Biomedical Engineering and Technology, Tianjin Medical University 22 Qixiangtai Road Tianjin 300070 China
| | - Cuihong Wang
- School of Science, Tianjin Chengjian University 26 Jinjing Road Tianjin 300384 China
| | - Fei Yan
- School of Biomedical Engineering and Technology, Tianjin Medical University 22 Qixiangtai Road Tianjin 300070 China
| | - Xiujun Gao
- School of Biomedical Engineering and Technology, Tianjin Medical University 22 Qixiangtai Road Tianjin 300070 China
| | - Meiling Zhang
- School of Biomedical Engineering and Technology, Tianjin Medical University 22 Qixiangtai Road Tianjin 300070 China
| |
Collapse
|