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Chávez BY, Paz JL, Gonzalez-Paz LA, Alvarado YJ, Contreras JS, Loroño-González MA. Theoretical Study of Cyanidin-Resveratrol Copigmentation by the Functional Density Theory. Molecules 2024; 29:2064. [PMID: 38731555 PMCID: PMC11085293 DOI: 10.3390/molecules29092064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 05/13/2024] Open
Abstract
Anthocyanins are colored water-soluble plant pigments. Upon consumption, anthocyanins are quickly absorbed and can penetrate the blood-brain barrier (BBB). Research based on population studies suggests that including anthocyanin-rich sources in the diet lowers the risk of neurodegenerative diseases. The copigmentation caused by copigments is considered an effective way to stabilize anthocyanins against adverse environmental conditions. This is attributed to the covalent and noncovalent interactions between colored forms of anthocyanins (flavylium ions and quinoidal bases) and colorless or pale-yellow organic molecules (copigments). The present work carried out a theoretical study of the copigmentation process between cyanidin and resveratrol (CINRES). We used three levels of density functional theory: M06-2x/6-31g+(d,p) (d3bj); ωB97X-D/6-31+(d,p); APFD/6-31+(d,p), implemented in the Gaussian16W package. In a vacuum, the CINRES was found at a copigmentation distance of 3.54 Å between cyanidin and resveratrol. In water, a binding free energy ∆G was calculated, rendering -3.31, -1.68, and -6.91 kcal/mol, at M06-2x/6-31g+(d,p) (d3bj), ωB97X-D/6-31+(d,p), and APFD/6-31+(d,p) levels of theory, respectively. A time-dependent density functional theory (TD-DFT) was used to calculate the UV spectra of the complexes and then compared to its parent molecules, resulting in a lower energy gap at forming complexes. Excited states' properties were analyzed with the ωB97X-D functional. Finally, Shannon aromaticity indices were calculated and isosurfaces of non-covalent interactions were evaluated.
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Affiliation(s)
- Breyson Yaranga Chávez
- Departamento Académico de Fisicoquímica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
| | - José L. Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
| | - Lenin A. Gonzalez-Paz
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Biomedicina Molecular (CBM), Laboratorio de Biocomputación (LB), Maracaibo 4001, Zulia, República Bolivariana de Venezuela
| | - Ysaias J. Alvarado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Biomedicina Molecular (CBM), Laboratorio de Biofísica Teórica y Experimental (LQBTE), Maracaibo 4001, Zulia, República Bolivariana de Venezuela
| | - Julio Santiago Contreras
- Departamento Académico de Química Orgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
| | - Marcos A. Loroño-González
- Departamento Académico de Fisicoquímica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
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Zgrabik JC, Bhuniya B, Branstad Phillips T, Barroso J, Vlaisavljevich B, Daly SR. Volatile lanthanide complexes with fluorinated heptadentate ligands. Dalton Trans 2024. [PMID: 38265072 DOI: 10.1039/d3dt04198k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Understanding factors that influence the volatility of lanthanide complexes remains an important goal for applications such as gas-phase f-metal separations and the synthesis of lanthanide-containing thin films. Lanthanide complexes often exhibit volatility differences that depend on the ability of ligands to saturate the lanthanide coordination sphere and attenuate intermolecular bonding in the solid state. This can make it difficult to assess how electronic factors associated with differing ligand substituents influence volatility. Here we describe the synthesis, structures, and thermal properties of a series of volatile lanthanide complexes (Ln = Nd, Er, and Yb) containing N4O3 ligands decorated with different alkyl and fluoroalkyl substituents (CF3, CF2CF2CF3, Me, and tBu). These ligands completely enveloped the tested lanthanides to form monomeric complexes with 7-coordinate distorted capped octahedral coordination geometries, as determined using single-crystal X-ray diffraction. Thermogravimetric analysis and bulk sublimation studies show how metal encapsulation affords complexes with the same volatility regardless of metal size, even with lanthanide ions with significantly different radii such as Nd3+ and Yb3+. Most notably, the results show that increasing ligand fluorination, a strategy often used to increase the volatility of metal complexes, is not always beneficial and can significantly attenuate the volatility of lanthanide complexes depending on location with respect to other substituents in the ligand framework. A pair-wise model based on density functional theory shows that the net intermolecular interactions in the unit cell can still be stronger when fluorination is present. In other words, even if individual interactions between neighboring molecules are weaker, the total number of interactions in the solid arising from the nature of crystal packing is equally important to consider.
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Affiliation(s)
- Joshua C Zgrabik
- Department of Chemistry, The University of Iowa, E331 Chemistry Building, Iowa City, Iowa 52242, USA.
| | - Balaka Bhuniya
- Department of Chemistry, The University of Iowa, E331 Chemistry Building, Iowa City, Iowa 52242, USA.
| | - Thomas Branstad Phillips
- Department of Chemistry, The University of Iowa, E331 Chemistry Building, Iowa City, Iowa 52242, USA.
| | - Jorge Barroso
- Department of Chemistry, The University of South Dakota, 414 E Clark St, Vermillion, SD, 57069, USA
| | - Bess Vlaisavljevich
- Department of Chemistry, The University of South Dakota, 414 E Clark St, Vermillion, SD, 57069, USA
| | - Scott R Daly
- Department of Chemistry, The University of Iowa, E331 Chemistry Building, Iowa City, Iowa 52242, USA.
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3
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Islam MS, Al-Majid AM, Haukka M, Parveen Z, Ravaiz N, Wadood A, Rehman AU, Ríos-Gutiérrez M, Domingo LR, Barakat A. A novel alpha-amylase inhibitor-based spirooxindole-pyrrolidine-clubbed thiochromene-pyrzaole pharmacophores: Unveiling the [3+2] cycloaddition reaction by molecular electron density theory. Chem Biol Drug Des 2023; 102:972-995. [PMID: 37563748 DOI: 10.1111/cbdd.14299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/29/2023] [Accepted: 07/14/2023] [Indexed: 08/12/2023]
Abstract
A novel spirooxindole-pyrrolidine clubbed thiochromene and pyrazole motifs were synthesized by [3+2] cycloaddition (32CA) reactions in one step process starting from the ethylene-based thiochromene and pyrazole scaffolds with the secondary amino-acids and substituted isatins in high yield. The 32CA reaction of AY 10 with ethylene derivative 6 has also been studied with Molecular Electron Density Theory. The high nucleophilic character of AY 10, N = 4.39 eV, allows explaining that the most favorable TS-on is 13.9 kcal mol-1 below the separated reagent. This 32CA, which takes place through a non-concerted one-step mechanism, presents a total ortho regio- and endo stereoselectivity, which is controlled by the formation of two intramolecular H… O hydrogen bonds. The design of spirooxindole-pyrrolidines engrafted thiochromene and pyrazole was tested for alpha-amylase inhibition and show a high efficacy in nanoscale range of reactivity. The key interaction between the most active hybrids and the receptor was studied by molecular docking. The physiochemical properties of the designed spirooxindole-pyrrolidines were carried out by in silico ADMET prediction. The newly synthesized most potent hybrid could be considered as a lead compound for drug discovery development for type 2 diabetes mellitus (T2DM).
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Affiliation(s)
| | | | - Matti Haukka
- Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Zahida Parveen
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Nabeela Ravaiz
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Ashfaq Ur Rehman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Mar Ríos-Gutiérrez
- Department of Organic Chemistry, University of Valencia, Valencia, Spain
| | - Luis R Domingo
- Department of Organic Chemistry, University of Valencia, Valencia, Spain
| | - Assem Barakat
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
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Báez-Grez R, Pino-Rios R. On the Importance of Noncovalent Interactions in the Stabilization of Nonconventional Compounds Using Bulky Groups. ACS OMEGA 2023; 8:23168-23173. [PMID: 37396283 PMCID: PMC10308520 DOI: 10.1021/acsomega.3c02663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/01/2023] [Indexed: 07/04/2023]
Abstract
In this article, we studied the capability of bulky groups to contribute to the stabilization of a given compound in addition to the well-known steric effect related to substituents due to their composition (alkyl chains and aromatic groups, among others). For this purpose, the recently synthesized 1-bora-3-boratabenzene anion which contains large substituents was analyzed by means of the independent gradient model (IGM), natural population analysis (NPA) at the TPSS/def2-TZVP level, force field-based energy decomposition analysis (EDA-FF) applying the universal force field (UFF), and molecular dynamics calculations under the GFN2-xTB approach. The results indicate that the bulky groups should not only be considered for their steric effects but also for their ability to stabilize a system that could be very reactive.
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Affiliation(s)
- Rodrigo Báez-Grez
- Computational
and Theoretical Chemistry Group, Departamento de Ciencias Químicas,
Facultad de Ciencias Exactas, Universidad
Andres Bello, República 275, 8370146 Santiago, Chile
| | - Ricardo Pino-Rios
- Química
y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat., Casilla 121, Iquique 1100000, Chile
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Lefebvre C, Klein J, Khartabil H, Boisson JC, Hénon E. IGMPlot: A program to identify, characterize, and quantify molecular interactions. J Comput Chem 2023. [PMID: 37177853 DOI: 10.1002/jcc.27123] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 05/15/2023]
Abstract
We describe the development and features of a program called IGMPlot, which is based on the independent gradient model (IGM) and its local descriptor δ g $$ \delta g $$ . The IGM approach analyzes the gradient of the electron density (ED) in a molecular system to identify regions of space where chemical interactions take place. IGMPlot is intended for use by both experimental scientists and theoretical chemists. It is standalone software written in C++, with versions available for multiple platforms. Some key features are: probing and quantifying interactions between two given molecular fragments, determining bond strength (IBSI), estimating the atomic contributions to an intermolecular interaction and preparing data to build 2D and 3D representations of interaction regions. The software has been updated to include new features: critical point analysis of the ED, assessing ED asymmetry of a given bond (PDA) and a new descriptor called q g $$ qg $$ designed to enhance the IGM- δ g $$ \delta g $$ analysis. The program can be found at: http://igmplot.univ-reims.fr.
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Affiliation(s)
- C Lefebvre
- Laboratoire Lorrain de Chimie Moléculaire UMR CNRS 7053, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - J Klein
- Institut Charles Gerhardt Montpellier, UMR CNRS 5253, Université de Montpellier, Pôle Chimie Balard Recherche, Montpellier, France
| | - H Khartabil
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims, France
| | - J-C Boisson
- Laboratoire d'Informatique en Calcul Intensif et Image pour la Simulation (LICIIS), Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims, France
| | - E Hénon
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims, France
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6
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Wacha M, Helm DL, Smart MM, McMillen CD, Casabianca LB, Sachdeva R, Urick CR, Wilson LP, Thrasher JS. A New Motif in Halogen Bonding: Cooperative Intermolecular S-Br⋅⋅⋅O, O⋅⋅⋅F, and F⋅⋅⋅F Associations in the Crystal Packing of α,ω-Di(sulfonyl bromide) Perfluoroalkanes. Chem Asian J 2023; 18:e202300012. [PMID: 36735331 DOI: 10.1002/asia.202300012] [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: 01/05/2023] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/04/2023]
Abstract
We recently reported the first examples of S-Cl⋅⋅⋅O halogen bonding complemented by short F⋅⋅⋅F contacts between neighboring chains that resulted in stabilized crystals of ClSO2 (CF2 )4 SO2 Cl and ClSO2 (CF2 )6 SO2 Cl. More recently, other researchers studied our crystallographic data further using an Independent Gradient Model (IGM), and they suggested if one goes beyond IUPAC's proposed 'less than the sum of the van der Waals radii' criterion that even more noncovalent interactions between fluorine atoms on neighboring chains as well as Cl⋅⋅⋅Cl, Cl⋅⋅⋅S, O⋅⋅⋅F, and O⋅⋅⋅S attractive interactions can be found. With that said, we have prepared samples of the related BrSO2 (CF2 )n SO2 Br derivatives (where n=4, 6, 8, and others), which give rise to even stronger S-Br⋅⋅⋅O halogen bonding interactions complemented minimally by O⋅⋅⋅F and F⋅⋅⋅F intermolecular interactions as shown by X-ray crystallography and computational chemistry using IGM isosurface plots. Additional spectroscopic characterization (multinuclear NMR, FT-IR, and MS) of the disulfonyl bromide derivatives BrSO2 (CF2 )4 SO2 Br, BrSO2 (CF2 )6 SO2 Br, and BrSO2 (CF2 )8 SO2 Br has also been obtained as well as some preliminary spectroscopic evidence for BrSO2 (CF2 )2 SO2 Br and BrSO2 CF2 O(CF2 )2 OCF2 SO2 Br. The implication of these results toward the preparation of the corresponding disulfonyl iodides is discussed.
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Affiliation(s)
- Max Wacha
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, GERMANY.,Department of Chemistry, Clemson University, Advanced Materials Research Laboratory, 91 Technology Drive, Anderson, South Carolina, 29625, USA
| | - David L Helm
- Department of Chemistry, Clemson University, Advanced Materials Research Laboratory, 91 Technology Drive, Anderson, South Carolina, 29625, USA.,Department of Chemistry, Clemson University, Hunter Laboratory, 211 S. Palmetto Blvd., Clemson, South Carolina, 29634, USA
| | - Megan M Smart
- Department of Chemistry, Clemson University, Hunter Laboratory, 211 S. Palmetto Blvd., Clemson, South Carolina, 29634, USA
| | - Colin D McMillen
- Department of Chemistry, Clemson University, Hunter Laboratory, 211 S. Palmetto Blvd., Clemson, South Carolina, 29634, USA
| | - Leah B Casabianca
- Department of Chemistry, Clemson University, Hunter Laboratory, 211 S. Palmetto Blvd., Clemson, South Carolina, 29634, USA
| | - Rakesh Sachdeva
- Department of Chemistry, Clemson University, Hunter Laboratory, 211 S. Palmetto Blvd., Clemson, South Carolina, 29634, USA
| | - Catherine R Urick
- Department of Chemistry, Clemson University, Advanced Materials Research Laboratory, 91 Technology Drive, Anderson, South Carolina, 29625, USA.,Department of Chemistry, Clemson University, Hunter Laboratory, 211 S. Palmetto Blvd., Clemson, South Carolina, 29634, USA
| | - London P Wilson
- Department of Chemistry, Clemson University, Advanced Materials Research Laboratory, 91 Technology Drive, Anderson, South Carolina, 29625, USA.,Department of Chemistry, Clemson University, Hunter Laboratory, 211 S. Palmetto Blvd., Clemson, South Carolina, 29634, USA
| | - Joseph S Thrasher
- Department of Chemistry, Clemson University, Advanced Materials Research Laboratory, 91 Technology Drive, Anderson, South Carolina, 29625, USA.,Department of Chemistry, Clemson University, Hunter Laboratory, 211 S. Palmetto Blvd., Clemson, South Carolina, 29634, USA
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7
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Wieduwilt EK, Boto RA, Macetti G, Laplaza R, Contreras-García J, Genoni A. Extracting Quantitative Information at Quantum Mechanical Level from Noncovalent Interaction Index Analyses. J Chem Theory Comput 2023; 19:1063-1079. [PMID: 36656682 DOI: 10.1021/acs.jctc.2c01092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The noncovalent interaction (NCI) index is nowadays a well-known strategy to detect NCIs in molecular systems. Even though it initially provided only qualitative descriptions, the technique has been recently extended to also extract quantitative information. To accomplish this task, integrals of powers of the electron distribution were considered, with the requirement that the overall electron density can be clearly decomposed as sum of distinct fragment contributions to enable the definition of the (noncovalent) integration region. So far, this was done by only exploiting approximate promolecular electron densities, which are given by the sum of spherically averaged atomic electron distributions and thus represent too crude approximations. Therefore, to obtain more quantum mechanically (QM) rigorous results from NCI index analyses, in this work, we propose to use electron densities obtained through the transfer of extremely localized molecular orbitals (ELMOs) or through the recently developed QM/ELMO embedding technique. Although still approximate, the electron distributions resulting from the abovementioned methods are fully QM and, above all, are again partitionable into subunit contributions, which makes them completely suitable for the NCI integral approach. Therefore, we benchmarked the integrals resulting from NCI index analyses (both those based on the promolecular densities and those based on ELMO electron distributions) against interaction energies computed at a high quantum chemical level (in particular, at the coupled cluster level). The performed test calculations have indicated that the NCI integrals based on ELMO electron densities outperform the promolecular ones. Furthermore, it was observed that the novel quantitative NCI-(QM/)ELMO approach can be also profitably exploited both to characterize and evaluate the strength of specific interactions between ligand subunits and protein residues in protein-ligand complexes and to follow the evolution of NCIs along trajectories of molecular dynamics simulations. Although further methodological improvements are still possible, the new quantitative ELMO-based technique could be already exploited in situations in which fast and reliable assessments of NCIs are crucial, such as in computational high-throughput screenings for drug discovery.
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Affiliation(s)
- Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Roberto A Boto
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Rubén Laplaza
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Julia Contreras-García
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
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Evangelista-Falcón W, Denhez C, Baena-Moncada A, Ponce-Vargas M. Revisiting the Sweet Taste Receptor T1R2-T1R3 through Molecular Dynamics Simulations Coupled with a Noncovalent Interactions Analysis. J Phys Chem B 2023; 127:1110-1119. [PMID: 36705604 DOI: 10.1021/acs.jpcb.2c07180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
It is nowadays widely accepted that sweet taste perception is elicited by the activation of the heterodimeric complex T1R2-T1R3, customarily known as sweet taste receptor (STR). However, the interplay between STR and sweeteners has not yet been fully clarified. Here through a methodology coupling molecular dynamics and the independent gradient model (igm) approach we determine the main interacting signatures of the closed (active) conformation of the T1R2 Venus flytrap domain (VFD) toward aspartame. The igm methodology provides a rapid and reliable quantification of noncovalent interactions through a score (Δginter) based on the attenuation of the electronic density gradient when two molecular fragments approach each other. Herein, this approach is coupled to a 100 ns molecular dynamics simulation (MD-igm) to explore the ligand-cavity contacts on a per-residue basis as well as a series of key inter-residue interactions that stabilize the closed form of VFD. We also apply an atomic decomposition scheme of noncovalent interactions to quantify the contribution of the ligand segments to the noncovalent interplay. Finally, a series of structural modification on aspartame are conducted in order to obtain guidelines for the rational design of novel sweeteners. Given that innovative methodologies to reliably quantify the extent of ligand-protein coupling are strongly demanded, this approach combining a noncovalent analysis and MD simulations represents a valuable contribution, that can be easily applied to other relevant biomolecular systems.
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Affiliation(s)
- Wilfredo Evangelista-Falcón
- Laboratory of Biomolecules, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima15023, Perú
| | - Clément Denhez
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse 51687, ReimsCedex 02 BP39, France
| | - Angélica Baena-Moncada
- Laboratorio de Investigación de Electroquímica Aplicada, Facultad de Ciencias de la Universidad Nacional de Ingeniería, Av. Túpac Amaru 210, Rímac, Lima31-139, Perú
| | - Miguel Ponce-Vargas
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse 51687, ReimsCedex 02 BP39, France
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9
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Liu Q, Li G, Gui C, Lei Z. Solvents evaluation for extraction of polycyclic aromatics from FCC diesel: Experimental and computational thermodynamics. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.118205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Revealing Self-aggregation Mechanism of Asphaltenes during Oxidative Aging using Quantum Mechanical Calculations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.121063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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11
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Luo J, Dai H, Zeng C, Wu D, Cao M. A Theoretical Study of the Halogen Bond between Heteronuclear Halogen and Benzene. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27228078. [PMID: 36432179 PMCID: PMC9692316 DOI: 10.3390/molecules27228078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022]
Abstract
Halogen bonds play an important role in many fields, such as biological systems, drug design and crystal engineering. In this work, the structural characteristics of the halogen bond between heteronuclear halogen XD (ClF, BrCl, IBr, ICl, BrF and IF) and benzene were studied using density functional theory. The structures of the complexes between heteronuclear halogen and benzene have Cs symmetry. The interaction energies of the complexes between heteronuclear halogen XD (ClF, BrCl, IBr, ICl, BrF and IF) and benzene range from -27.80 to -37.18 kJ/mol, increasing with the increases in the polarity between the atoms of X and D, and are proportional to the angles of a between the Z axis and the covalent bond of heteronuclear halogen. The electron density (ρ) and corresponding Laplacian (∇2ρ) values indicate that the interaction of the heteronuclear halogen and benzene is a typical long-range weak interaction similar to a hydrogen bond. Independent gradient model analysis suggests that the van der Waals is the main interaction between the complexes of heteronuclear halogen and benzene. Symmetry-adapted perturbation theory analysis suggests that the electrostatic interaction is the dominant part in the complexes of C6H6⋯ClF, C6H6⋯ICl, C6H6⋯BrF and C6H6⋯IF, and the dispersion interaction is the main part in the complexes of C6H6⋯BrCl, C6H6⋯IBr.
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12
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A Molecular Electron Density Theory Study of the [3+2] Cycloaddition Reaction of an Azomethine Ylide with an Electrophilic Ethylene Linked to Triazole and Ferrocene Units. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196532. [PMID: 36235069 PMCID: PMC9571756 DOI: 10.3390/molecules27196532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022]
Abstract
The [3+2] cycloaddition (32CA) reaction of an azomethine ylide (AY) with an electrophilic ethylene linked to triazole and ferrocene units has been studied within the Molecular Electron Density Theory (MEDT) at the ωB97X-D/6-311G(d,p) level. The topology of the electron localization function (ELF) of this AY allows classifying it as a pseudo(mono)radical species characterized by the presence of two monosynaptic basins, integrating a total of 0.76 e, at the C1 carbon. While the ferrocene ethylene has a strong electrophilic character, the AY is a supernucleophile, suggesting that the corresponding 32CA reaction has a high polar character and a low activation energy. The most favorable ortho/endo reaction path presents an activation enthalpy of 8.7 kcal·mol-1, with the 32CA reaction being exergonic by -42.1 kcal·mol-1. This reaction presents a total endo stereoselectivity and a total ortho regioselectivity. Analysis of the global electron density transfer (GEDT) at the most favorable TS-on (0.23 e) accounts for the high polar character of this 32CA reaction, classified as forward electron density flux (FEDF). The formation of two intermolecular hydrogen bonds between the two interacting frameworks at the most favorable TS-on accounts for the unexpected ortho regioselectivity experimentally observed.
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13
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Al-Jabiri MH, Hazrah AS, Jäger W. Conformers of Vanillic Acid and Its Monohydrate: A Rotational Spectroscopic and Theoretical Study. J Phys Chem A 2022; 126:6686-6694. [DOI: 10.1021/acs.jpca.2c05120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mohamad H. Al-Jabiri
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Arsh S. Hazrah
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Wolfgang Jäger
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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14
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Quantitative surface and Hirshfeld surface analysis of nicorandil molecule and further insight into its solubility in several aqueous protic and aprotic cosolvent solutions. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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15
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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.
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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
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16
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Oliveros R. DA, Machado RA, Mora JR. Quantitative structure–property relationship analysis of the spectrochemical series by employing electronic descriptors from DFT calculations. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2040629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Deivi A. Oliveros R.
- Facultad de Ciencias, Universidad Central de Venezuela, Escuela de Química, Caracas, Venezuela
| | - Rubén A. Machado
- Centro de Química, Laboratorio de Química de Metales de Transición, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - José R. Mora
- Grupo de Química Computacional y Teórica, Departamento de Ingeniería Química, Universidad San Francisco de Quito, Instituto de Simulación Computacional, Quito, Ecuador
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17
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Hazrah AS, Nanayakkara S, Seifert NA, Kraka E, Jäger W. Structural study of 1- and 2-naphthol: new insights into the non-covalent H-H interaction in cis-1-naphthol. Phys Chem Chem Phys 2022; 24:3722-3732. [PMID: 35080568 DOI: 10.1039/d1cp05632h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Previous microwave studies of naphthol monomers were supplemented by measuring spectra of all 13C mono-substituted isotopologues of the cis- and trans-conformers of 1-naphthol and 2-naphthol in their natural abundances. The resulting data were utilized to determine substitution structures and so-called semi-experimental effective structures. Results from electronic structure calculations show that the OH group of cis-1-naphthol points ≈6° out of plane, which is consistent with the inertial defect data of cis- and trans-1-naphthol. The non-planarity of cis-1-naphthol is a result of a close-contact H-atom-H-atom interaction. This type of H-H interaction has been the subject of much controversy in the past and we provide here an in-depth theoretical analysis of it. The naphthol system is particularly well-suited for such analysis as it provides internal standards with its four different isomers. The methods used include quantum theory of atoms in molecules, non-covalent interactions, independent gradient model, local vibrational mode, charge model 5, and natural bond orbital analyses. We demonstrate that the close-contact H-H interaction is neither a purely attractive nor repulsive interaction, but rather a mixture of the two.
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Affiliation(s)
- Arsh S Hazrah
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
| | - Sadisha Nanayakkara
- Department of Chemistry, Southern Methodist University, Dallas, TX, 75275-0314, USA.
| | - Nathan A Seifert
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, Dallas, TX, 75275-0314, USA.
| | - Wolfgang Jäger
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
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18
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Lu T, Chen Q. Independent gradient model based on Hirshfeld partition: A new method for visual study of interactions in chemical systems. J Comput Chem 2022; 43:539-555. [PMID: 35108407 DOI: 10.1002/jcc.26812] [Citation(s) in RCA: 468] [Impact Index Per Article: 234.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/06/2022] [Accepted: 01/16/2022] [Indexed: 01/10/2023]
Abstract
The powerful independent gradient model (IGM) method has been increasingly popular in visual analysis of intramolecular and intermolecular interactions in recent years. However, we frequently observed that there is an evident shortcoming of IGM map in graphically studying weak interactions, that is its isosurfaces are usually too bulgy; in these cases, not only the graphical effect is poor, but also the color on some areas on the isosurfaces is inappropriate and may lead to erroneous analysis conclusions. In addition, the IGM method was originally proposed based on promolecular density, which is quite crude and does not take actual electronic structure into account. In this article, we propose an improvement version of IGM, namely IGM based on Hirshfeld partition of molecular density (IGMH), which replaces the free-state atomic densities involved in the IGM method with the atomic densities derived by Hirshfeld partition of actual molecular electron density. This change makes IGM have more rigorous physical background. A large number of application examples in this article, including molecular and periodic systems, weak and chemical bond interactions, fully demonstrate the important value of IGMH in intuitively understanding interactions in chemical systems. Comparisons also showed that the IGMH usually has markedly better graphical effect than IGM and overcomes known problems in IGM. Currently IGMH analysis has been supported in our wavefunction analysis code Multiwfn (http://sobereva.com/multiwfn). We hope that IGMH will become a new useful method among chemists for exploring interactions in wide variety of chemical systems.
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Affiliation(s)
- Tian Lu
- Beijing Kein Research Center for Natural Sciences, Beijing, China
| | - Qinxue Chen
- Beijing Kein Research Center for Natural Sciences, Beijing, China
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19
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Removal of nafcillin sodium monohydrate from aqueous solution by hydrogels containing nanocellulose: An experimental and theoretical study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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Mamane V, Weiss R, Cornaton Y, Khartabil H, Groslambert L, Hénon E, Pale P, Djukic JP. Deciphering the Role of Noncovalent Interactions in the Conformations of Dibenzo‐1,5‐dichalcogenocines. Chempluschem 2022; 87:e202100518. [DOI: 10.1002/cplu.202100518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/03/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Victor Mamane
- University of Strasbourg: Universite de Strasbourg Institut of Chemistry 1 Rue Blaise Pascal 67008 Strasbourg FRANCE
| | - Robin Weiss
- Université de Strasbourg: Universite de Strasbourg Institut de Chimie de Strasbourg FRANCE
| | - Yann Cornaton
- Université de Strasbourg: Universite de Strasbourg Institut de Chimie de Strasbroug FRANCE
| | - Hassan Khartabil
- Université de Reims Champagne-Ardenne: Universite de Reims Champagne-Ardenne Institut de Chimie Moléculaire FRANCE
| | - Loïc Groslambert
- Universite de Strasbourg Institut de Chimie de Strasbourg FRANCE
| | - Eric Hénon
- Universite de Reims Champagne-Ardenne Institut de Chimie Moléculaire FRANCE
| | - Patrick Pale
- Universite de Strasbourg Institut de Cimie de Strasbourg FRANCE
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21
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Lefebvre C, Van Gysel T, Michelin C, Rousset E, Djiré D, Allais F, Hoffmann N. Photocatalytic Radical Addition to Levoglucosenone. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Corentin Lefebvre
- ICMR, Equipe de Photochimie, CNRS Université de Reims Champagne-Ardenne UFR Sciences B.P. 1039 51687 Reims France
| | - Terence Van Gysel
- ICMR, Equipe de Photochimie, CNRS Université de Reims Champagne-Ardenne UFR Sciences B.P. 1039 51687 Reims France
| | - Clément Michelin
- ICMR, Equipe de Photochimie, CNRS Université de Reims Champagne-Ardenne UFR Sciences B.P. 1039 51687 Reims France
- Clermont Auvergne INP, ICCF Université Clermont Auvergne, CNRS 63000 Clermont-Ferrand France
| | - Elodie Rousset
- ICMR, Groupe chimie de coordination CNRS Université de Reims Champagne-Ardenne UFR Sciences B.P. 1039 51687 Reims France
| | - Djibril Djiré
- ICMR, Equipe de Photochimie, CNRS Université de Reims Champagne-Ardenne UFR Sciences B.P. 1039 51687 Reims France
- URD Agro-Biotechnologies Industrielles (ABI) CEBB AgroParisTech 51110 Pomacle France
| | - Florent Allais
- URD Agro-Biotechnologies Industrielles (ABI) CEBB AgroParisTech 51110 Pomacle France
| | - Norbert Hoffmann
- ICMR, Equipe de Photochimie, CNRS Université de Reims Champagne-Ardenne UFR Sciences B.P. 1039 51687 Reims France
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22
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Jiang Y, Lei Z, Yu G. Unraveling weak interactions between fluorinated gases and ionic liquids. Chem Eng Sci 2021. [DOI: 10.1016/j.ces.2021.116792] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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23
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Iribarren I, Sánchez‐Sanz G, Elguero J, Alkorta I, Trujillo C. Reactivity of Coinage Metal Hydrides for the Production of H 2 Molecules. ChemistryOpen 2021; 10:724-730. [PMID: 34319005 PMCID: PMC8340072 DOI: 10.1002/open.202100108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/30/2021] [Indexed: 12/03/2022] Open
Abstract
The formation of molecular hydrogen as well as the possibility of using coinage metal hydrides as a prospective complex to produce hydrogen was presented in this work. Therefore, the reactions involving the interaction between two coinage metal hydrides, MH (M=Cu, Ag and Au, homo and heterodimers), were studied. The free energy profiles corresponding to aforementioned complexation were analysed by means of ab initio methods of quantum chemistry. The characteristics of these intermediates, final complexes and the electron density properties of the established interactions were discussed.
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Affiliation(s)
- Iñigo Iribarren
- Trinity Biomedical Sciences InstituteSchool of ChemistryThe University of DublinTrinity CollegeDublin 2Ireland
| | - Goar Sánchez‐Sanz
- Irish Centre of High-End ComputingGrand Canal QuayDublin 2 (Ireland)& School of ChemistryUniversity College Dublin BelfieldDublin 4Ireland
| | - José Elguero
- Instituto de Química Médica IQM-CSICJuan de la Cierva, 328006MadridSpain
| | - Ibon Alkorta
- Instituto de Química Médica IQM-CSICJuan de la Cierva, 328006MadridSpain
| | - Cristina Trujillo
- Trinity Biomedical Sciences InstituteSchool of ChemistryThe University of DublinTrinity CollegeDublin 2Ireland
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24
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Wei Y, Liu P. Analysis of the nature of interaction between AlN nanocage and ibuprofen using quantum chemical study. Struct Chem 2021. [DOI: 10.1007/s11224-021-01750-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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25
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Cuesta SA, Márquez EA, Loroño MA, Paz J, Mora JR. Theoretical study on the flash vacuum gas-phase pyrolysis reaction mechanism of 2-(2-benzylidenehydrazinyl)pyridine and analogous. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Iribarren I, Sánchez-Sanz G, Alkorta I, Elguero J, Trujillo C. Evaluation of Electron Density Shifts in Noncovalent Interactions. J Phys Chem A 2021; 125:4741-4749. [PMID: 34061527 PMCID: PMC8279648 DOI: 10.1021/acs.jpca.1c00830] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/26/2021] [Indexed: 12/12/2022]
Abstract
In the present paper, we report the quantitative evaluation of the electron density shift (EDS) maps within different complexes. Values associated with the total EDS maps exhibited good correlation with different quantities such as interaction energies, Eint, intermolecular distances, bond critical points, and LMOEDA energy decomposition terms. Besides, EDS maps at different cutoffs were also evaluated and related with the interaction energies values. Finally, EDS maps and their corresponding values are found to correlate with Eint within systems with cooperative effects. To our knowledge, this is the first time that the EDS has been quanitatively evaluated.
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Affiliation(s)
- Iñigo Iribarren
- Trinity
Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, Dublin, Dublin 2, Ireland
| | - Goar Sánchez-Sanz
- Irish
Centre For High-End Computing, 7 Floor, The Tower, Grand Canal Quay, Dublin 2 D02 HP83, Ireland
| | - Ibon Alkorta
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
| | - José Elguero
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
| | - Cristina Trujillo
- Trinity
Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, Dublin, Dublin 2, Ireland
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27
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Allart-Simon I, Moniot A, Bisi N, Ponce-Vargas M, Audonnet S, Laronze-Cochard M, Sapi J, Hénon E, Velard F, Gérard S. Pyridazinone derivatives as potential anti-inflammatory agents: synthesis and biological evaluation as PDE4 inhibitors. RSC Med Chem 2021; 12:584-592. [PMID: 34046629 PMCID: PMC8127987 DOI: 10.1039/d0md00423e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/10/2021] [Indexed: 11/21/2022] Open
Abstract
Cyclic nucleotide phosphodiesterase type 4 (PDE4), which controls the intracellular level of cyclic adenosine monophosphate (cAMP), has aroused scientific attention as a suitable target for anti-inflammatory therapy of respiratory diseases. This work describes the development and characterization of pyridazinone derivatives bearing an indole moiety as potential PDE4 inhibitors and their evaluation as anti-inflammatory agents. Among these derivatives, 4-(5-methoxy-1H-indol-3-yl)-6-methylpyridazin-3(2H)-one possesses promising activity, and selectivity towards PDE4B isoenzymes and is able to regulate potent pro-inflammatory cytokine and chemokine production by human primary macrophages.
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Affiliation(s)
- Ingrid Allart-Simon
- Université de Reims Champagne-Ardenne, Institut de Chimie Moléculaire de Reims (ICMR), UMR CNRS 7312, UFR Sciences, Moulin de la housse and UFR Pharmacie 51 rue Cognacq-Jay F-51096 Reims France
| | - Aurélie Moniot
- Université de Reims-Champagne-Ardenne, EA 4691 Biomatériaux & Inflammation en site OSseux (BIOS), UFR Pharmacie and UFR Odontologie 51 rue Cognacq-Jay F-51096 Reims France
| | - Nicolo Bisi
- Université de Reims Champagne-Ardenne, Institut de Chimie Moléculaire de Reims (ICMR), UMR CNRS 7312, UFR Sciences, Moulin de la housse and UFR Pharmacie 51 rue Cognacq-Jay F-51096 Reims France
| | - Miguel Ponce-Vargas
- Université de Reims Champagne-Ardenne, Institut de Chimie Moléculaire de Reims (ICMR), UMR CNRS 7312, UFR Sciences, Moulin de la housse and UFR Pharmacie 51 rue Cognacq-Jay F-51096 Reims France
| | - Sandra Audonnet
- Université de Reims-Champagne-Ardenne, URCACyt, UFR Pharmacie 51 rue Cognacq-Jay F-51096 Reims France
| | - Marie Laronze-Cochard
- Université de Reims Champagne-Ardenne, Institut de Chimie Moléculaire de Reims (ICMR), UMR CNRS 7312, UFR Sciences, Moulin de la housse and UFR Pharmacie 51 rue Cognacq-Jay F-51096 Reims France
| | - Janos Sapi
- Université de Reims Champagne-Ardenne, Institut de Chimie Moléculaire de Reims (ICMR), UMR CNRS 7312, UFR Sciences, Moulin de la housse and UFR Pharmacie 51 rue Cognacq-Jay F-51096 Reims France
| | - Eric Hénon
- Université de Reims Champagne-Ardenne, Institut de Chimie Moléculaire de Reims (ICMR), UMR CNRS 7312, UFR Sciences, Moulin de la housse and UFR Pharmacie 51 rue Cognacq-Jay F-51096 Reims France
| | - Frédéric Velard
- Université de Reims-Champagne-Ardenne, EA 4691 Biomatériaux & Inflammation en site OSseux (BIOS), UFR Pharmacie and UFR Odontologie 51 rue Cognacq-Jay F-51096 Reims France
| | - Stéphane Gérard
- Université de Reims Champagne-Ardenne, Institut de Chimie Moléculaire de Reims (ICMR), UMR CNRS 7312, UFR Sciences, Moulin de la housse and UFR Pharmacie 51 rue Cognacq-Jay F-51096 Reims France
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28
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Zhu S, Khan MA, Wang F, Bano Z, Xia M. Exploration of adsorption mechanism of 2-phosphonobutane-1,2,4-tricarboxylic acid onto kaolinite and montmorillonite via batch experiment and theoretical studies. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123810. [PMID: 33264909 DOI: 10.1016/j.jhazmat.2020.123810] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/11/2020] [Accepted: 08/29/2020] [Indexed: 06/12/2023]
Abstract
Two clay minerals, kaolinite (Kaol) and montmorillonite (Mt) with different crystal structures were chosen to investigate the comparative adsorption of 2-phosphonobutane-1,2,4-tricarboxylic acid (PBTC) through batch control experiments and theoretical studies. The systematical isotherm and kinetic studies agreed with Langmuir model and pseudo-second-order model, confirming a monolayer and chemisorption interaction process, respectively. The maximum removal capacities of Kaol and Mt for PBTC were 72.297 mg/g and 121.163 mg/g at pH=3.0 and T=298 K, respectively. Furthermore, the adsorption mechanisms were investigated by molecular dynamic (MD) simulations and density functional theory (DFT). The Interface force field (IFF) was firstly introduced into Materials Studio package to explore the microscopic mechanism of clay mineral interface. The dynamics behaviors verified that the oxygen (O) atom of carboxyl group has stronger affinity at the external surface of Mt, which consistent with the experimental data well. For DFT calculations, quantitative analysis around molecular van der Waals (vdW) surface was adopted to predict reactive sites for the electrophilic reaction. Independent Gradient Model (IGM) and Hirshfeld surface analyses in Multiwfn indicated that the high adsorption effect mainly attributes to hydrogen bond action. These findings improve our ability to explore the related properties occurring at the interface of different clay minerals.
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Affiliation(s)
- Sidi Zhu
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Muhammad Asim Khan
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Fengyun Wang
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Zahira Bano
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Mingzhu Xia
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
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29
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Wieduwilt EK, Boisson JC, Terraneo G, Hénon E, Genoni A. A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach. J Chem Inf Model 2021; 61:795-809. [PMID: 33444021 DOI: 10.1021/acs.jcim.0c01188] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The independent gradient model (IGM) is a recent electron density-based computational method that enables to detect and quantify covalent and noncovalent interactions. When applied to large systems, the original version of the technique still relies on promolecular electron densities given by the sum of spherically averaged atomic electron distributions, which leads to approximate evaluations of the inter- and intramolecular interactions occurring in systems of biological interest. To overcome this drawback and perform IGM analyses based on quantum mechanically rigorous electron densities also for macromolecular systems, we coupled the IGM approach with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) that allow fast and reliable reconstructions of polypeptide and protein electron densities. The validation tests performed on small polypeptides and peptide dimers have shown that the novel IGM-ELMO strategy provides results that are systematically closer to the fully quantum mechanical ones and outperforms the IGM method based on the crude promolecular approximation, but still keeping a quite low computational cost. The results of the test calculations carried out on proteins have also confirmed the trends observed for the IGM analyses conducted on small systems. This makes us envisage the future application of the novel IGM-ELMO approach to unravel complicated noncovalent interaction networks (e.g., in protein-protein contacts) or to rationally design new drugs through molecular docking calculations and virtual high-throughput screenings.
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Affiliation(s)
- Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Jean-Charles Boisson
- CReSTIC EA 3804, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims Cedex 02 BP39, F-51687, France
| | - Giancarlo Terraneo
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, Milan I-20131, Italy
| | - Eric Hénon
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims Cedex 02 BP39, F-51687, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
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30
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Cantero-López P, Hidalgo-Rosa Y, Sandoval-Olivares Z, Santoyo-Flores J, Mella P, Arrué L, Zúñiga C, Arratia-Pérez R, Páez-Hernández D. The role of zero-field splitting and π-stacking interaction of different nitrogen-donor ligands on the optical properties of luminescent rhenium tricarbonyl complexes. NEW J CHEM 2021. [DOI: 10.1039/d1nj01544c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this work, a systematic evaluation of the role of zero-field splitting (ZFS), and the geometric arrangement of different nitrogen-donor ligands, including π-stacking interactions, in five selected rhenium luminescent complexes was performed.
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Affiliation(s)
- Plinio Cantero-López
- Center of Applied Nanoscience (CANS)
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Yoan Hidalgo-Rosa
- Doctorado en Fisicoquímica Molecular
- Universidad Andres Bello
- Santiago de Chile
- Chile
- ANID – Millennium Science Initiative Program- Millennium Nuclei on Catalytic Process towards Sustainable Chemistry (CSC)
| | | | | | - Pablo Mella
- Doctorado en Fisicoquímica Molecular
- Universidad Andres Bello
- Santiago de Chile
- Chile
- Universidad Andres Bello
| | - Lily Arrué
- Doctorado en Fisicoquímica Molecular
- Universidad Andres Bello
- Santiago de Chile
- Chile
| | - César Zúñiga
- Instituto de Ciencias Naturales
- Facultad de Medicina Veterinaria y Agronomía
- Universidad de Las Américas
- Sede Providencia
- 7500972 Santiago
| | - Ramiro Arratia-Pérez
- Center of Applied Nanoscience (CANS)
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
| | - Dayán Páez-Hernández
- Center of Applied Nanoscience (CANS)
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
- Chile
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Stability of spherical molecular complexes: a theoretical study of self-assembled M12L24 nanoballs. Struct Chem 2020. [DOI: 10.1007/s11224-020-01639-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Millan J, Lesarri A, Fernández JA, Martínez R. Exploring Epigenetic Marks by Analysis of Noncovalent Interactions. Chembiochem 2020; 22:408-415. [PMID: 32815664 DOI: 10.1002/cbic.202000380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/19/2020] [Indexed: 01/28/2023]
Abstract
Epigenetic marks are modest chemical modifications on DNA and histone proteins that regulate the activation or silencing of genes through modulation of the intermolecular interactions between the DNA strands and the protein machinery. The process is complex and not always well understood. One of the systems studied in greater detail is the epigenetic mark on H3K9: lysine 9 of histone 3. The degree of methylation or acetylation of this histone is linked to silencing or activation of the corresponding gene, but it is not clear which effect each mark has in gene expression. We shed light on this particular methylation process by using density functional theory (DFT) calculations. First, we built a model consisting of a DNA double strand containing three base pairs and a sequence of three amino acids of the histone's tail. Then, we computed the modulation introduced into the intermolecular interactions by each epigenetic modification: from mono- to trimethylation and acetylation. The calculations show that whereas acetylation and trimethylation result in a reduction of the DNA-peptide interaction; non-, mono-, and dimethylation increase the intermolecular interactions. Such observations compare well with the findings reported in the literature, and highlight the correlation between the balance of intermolecular forces and biological properties, simultaneously advancing quantum-mechanical studies of large biochemical systems at molecular level through the use of DFT methods.
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Affiliation(s)
- Judith Millan
- Departamento de Química, Facultad de Ciencia y Tecnología, Universidad de La Rioja, Madre de Dios, 53, Logroño, 26006, Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica, I.U. CINQUIMA, Universidad de Valladolid, Valladolid, 47011, Spain
| | - José A Fernández
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco-UPV/EHU, Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Rodrigo Martínez
- Departamento de Química, Facultad de Ciencia y Tecnología, Universidad de La Rioja, Madre de Dios, 53, Logroño, 26006, Spain
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34
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Wang Y, Zhang C, Zhao YL, Zhao R, Houk KN. Understand the Specific Regio- and Enantioselectivity of Fluostatin Conjugation in the Post-Biosynthesis. Biomolecules 2020; 10:E815. [PMID: 32466453 PMCID: PMC7355926 DOI: 10.3390/biom10060815] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/22/2022] Open
Abstract
Fluostatins, benzofluorene-containing aromatic polyketides in the atypical angucycline family, conjugate into dimeric and even trimeric compounds in the post-biosynthesis. The formation of the C-C bond involves a non-enzymatic stereospecific coupling reaction. In this work, the unusual regio- and enantioselectivities were rationalized by density functional theory calculations with the M06-2X (SMD, water)/6-311 + G(d,p)//6-31G(d) method. These DFT calculations reproduce the lowest energy C1-(R)-C10'-(S) coupling pathway observed in a nonenzymatic reaction. Bonding of the reactive carbon atoms (C1 and C10') of the two reactant molecules maximizes the HOMO-LUMO interactions and Fukui function involving the highest occupied molecular orbital (HOMO) of nucleophile p-QM and lowest unoccupied molecular orbital (LUMO) of electrophile FST2- anion. In particular, the significant π-π stacking interactions of the low-energy pre-reaction state are retained in the lowest energy pathway for C-C coupling. The distortion/interaction-activation strain analysis indicates that the transition state (TScp-I) of the lowest energy pathway involves the highest stabilizing interactions and small distortion among all possible C-C coupling reactions. One of the two chiral centers generated in this step is lost upon aromatization of the phenol ring in the final difluostatin products. Thus, the π-π stacking interactions between the fluostatin 6-5-6 aromatic ring system play a critical role in the stereoselectivity of the nonenzymatic fluostatin conjugation.
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Affiliation(s)
- Yuanqi Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China;
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resource and Ecology, Guangdong Key Laboratory of Marine Materia, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China;
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China;
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; (R.Z.); (K.N.H.)
| | - Rosalinda Zhao
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; (R.Z.); (K.N.H.)
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; (R.Z.); (K.N.H.)
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35
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Klein J, Khartabil H, Boisson JC, Contreras-García J, Piquemal JP, Hénon E. New Way for Probing Bond Strength. J Phys Chem A 2020; 124:1850-1860. [PMID: 32039597 DOI: 10.1021/acs.jpca.9b09845] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The covalent chemical bond is intimately linked to electron sharing between atoms. The recent independent gradient model (IGM) and its δg descriptor provide a way to quantify locally this electron density interpenetration from wavefunction calculations. Each bond has its own IGM-δgpair signature. The present work establishes for the first time a strong link between this bond signature and the physically grounded bond force constant concept. Analyzing a large set of compounds and bonds, the intrinsic bond strength index (IBSI) emerges from the IGM formulation. Our study shows that the IBSI does not belong to the class of conventional bond orders (like Mulliken, Wiberg, Mayer, delocalization index, or electron localization function-ELF), but is rather a new complementary index, related to the bond strength. A fundamental outcome of this research is a novel index allowing to range all two-center chemical bonds by their intrinsic strength in molecular situation. We believe that the IBSI is a powerful and robust tool for interpretation accessible to a wide community of chemists (organic, inorganic chemistry, including transition-metal complexes and reaction mechanisms).
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Affiliation(s)
- Johanna Klein
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, 51687 Reims Cedex 02 BP39, France
| | - Hassan Khartabil
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, 51687 Reims Cedex 02 BP39, France
| | - Jean-Charles Boisson
- CReSTIC EA 3804, Université de Reims Champagne-Ardenne, Moulin de la Housse, 51687 Reims Cedex 02 BP39, France
| | - Julia Contreras-García
- Laboratoire de Chimie Théorique and UMR CNRS 7616, Sorbonne Université, 4 Pl Jussieu, 75252 Paris Cedex 05, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique and UMR CNRS 7616, Sorbonne Université, 4 Pl Jussieu, 75252 Paris Cedex 05, France.,Institut Universitaire de France, 75005 Paris, France
| | - Eric Hénon
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, 51687 Reims Cedex 02 BP39, France
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36
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Caramori GF, Østrøm I, Ortolan AO, Nagurniak GR, Besen VM, Muñoz-Castro A, Orenha RP, Parreira RLT, Galembeck SE. The usefulness of energy decomposition schemes to rationalize host–guest interactions. Dalton Trans 2020; 49:17457-17471. [DOI: 10.1039/d0dt03518a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The findings reported here reveal the robustness and practical application of EDA-NOCV in rationalizing molecular recognition situations in host–guest systems.
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Affiliation(s)
| | - Ina Østrøm
- Department of Chemistry
- Federal University of Santa Catarina
- Florianópolis
- Brazil
| | | | | | - Vitor M. Besen
- Department of Chemistry
- Federal University of Santa Catarina
- Florianópolis
- Brazil
| | - Alvaro Muñoz-Castro
- Laboratorio de Química Inorgánica y Materiales Moleculares
- Facultad de Ingeniería
- Universidad Autonoma de Chile
- Santiago
- Chile
| | - Renato P. Orenha
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas
- Universidade de Franca
- Franca
- Brazil
| | - Renato L. T. Parreira
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas
- Universidade de Franca
- Franca
- Brazil
| | - Sérgio E. Galembeck
- Departamento de Química
- Faculdade de Filosofia
- Ciências e Letras de Ribeirão Preto
- Universidade de São Paulo
- Ribeirão Preto
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