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Eybek A, Kaya MO, Güleç Ö, Demirci T, Musatat AB, Özdemir O, Öner MNK, Kaya Y, Arslan M. Bovine carbonic anhydrase (bCA) inhibitors: Synthesis, molecular docking and theoretical studies of bisoxadiazole-substituted sulfonamide derivatives. Int J Biol Macromol 2024; 267:131489. [PMID: 38608980 DOI: 10.1016/j.ijbiomac.2024.131489] [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: 02/15/2024] [Revised: 03/28/2024] [Accepted: 04/07/2024] [Indexed: 04/14/2024]
Abstract
This paper describes the in vitro inhibition potential of bisoxadiazole-substituted sulfonamide derivatives (6a-t) against bovine carbonic anhydrase (bCA) after they were designed through computational analyses and evaluated the predicted interaction via molecular docking. First, in silico ADMET predictions and physicochemical property analysis of the compounds provided insights into solubility and permeability, then density functional theory (DFT) calculations were performed to analyse their ionization energies, nucleophilicity, in vitro electron affinity, dipole moments and molecular interactions under vacuum and dimethyl sulfoxide (DMSO) conditions. After calculating the theoretical inhibition constants, IC50 values determined from enzymatic inhibition were found between 12.93 and 45.77 μM. Molecular docking evaluation revealed favorable hydrogen bonding and π-interactions of the compounds within the bCA active site. The experimentally most active compound, 6p, exhibited the strongest inhibitory activity with a theoretical inhibition constant value of 9.41 nM and H-bonds with Gln91, Thr198, and Trp4 residues and His63 Pi-cation interactions with His63 residues. Overall, the study reveals promising bCA blocking potential for the synthesized derivatives, similar to acetazolamide.
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Affiliation(s)
- Abdulbaki Eybek
- Chemistry, Faculty of Arts and Science, Siirt University, 56100 Siirt, Turkey
| | - Mustafa Oğuzhan Kaya
- Basic Sciences, Faculty of Veterinary, Siirt University, 56100 Siirt, Turkey; Chemistry, Faculty of Arts and Science, Kocaeli University, 41001 Kocaeli, Turkey.
| | - Özcan Güleç
- Chemistry, Faculty of Sciences, Sakarya University, 54050, Sakarya, Turkey
| | - Tuna Demirci
- Scientific and Technological Research Laboratory, Düzce University, 81620 Düzce, Turkey
| | | | - Oğuzhan Özdemir
- Veterinary Science Department, Technical Sciences Vocational School, Batman University, 72000 Batman, Turkey
| | - Mine Nazan Kerimak Öner
- Medicinal and Aromatic Plants Program, İzmit Vocational School, Kocaeli University, 41285 Kocaeli, Turkey
| | - Yeşim Kaya
- Chemistry, Faculty of Arts and Science, Kocaeli University, 41001 Kocaeli, Turkey
| | - Mustafa Arslan
- Chemistry, Faculty of Sciences, Sakarya University, 54050, Sakarya, Turkey
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2
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Dakkouri M. A Theoretical Investigation of Novel Sila- and Germa-Spirocyclic Imines and Their Relevance for Electron-Transporting Materials and Drug Discovery. Molecules 2023; 28:6298. [PMID: 37687127 PMCID: PMC10489060 DOI: 10.3390/molecules28176298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
A new class of spirocyclic imines (SCIs) has been theoretically investigated by applying a variety of quantum chemical methods and basis sets. The uniqueness of these compounds is depicted by various peculiarities, e.g., the incidence of planar six-membered rings each with two imine groups (two π bonds) and the incorporation of the isosteres carbon, silicon, or germanium spiro centers. Additional peculiarities of these novel SCIs are mirrored by their three-dimensionality, the simultaneous occurrence of nucleophilic and electrophilic centers, and the cross-hyperconjugative (spiro-conjugation) interactions, which provoke charge mobility along the spirocyclic scaffold. Substitution of SCIs with strong electron-withdrawing substituents, like the cyano group or fluorine, enhances their docking capability and impacts their reactivity and charge mobility. To gain thorough knowledge about the molecular properties of these SCIs, their structures have been optimized and various quantum chemical concepts and models were applied, e.g., full NBO analysis and the frontier molecular orbitals (FMOs) theory (HOMO-LUMO energy gap) and the chemical reactivity descriptors derived from them. For the assessment of the charge density distribution along the SCI framework, additional complementary quantum chemical methods were used, e.g., molecular electrostatic potential (MESP) and Bader's QTAIM. Additionally, using the aromaticity index NICS (nuclear independent chemical shift) and other criteria, it could be shown that the investigated cross-hyperconjugated sila and germa SCIs are spiro-aromatics of the Heilbronner Craig-type Möbius aromaticity.
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Affiliation(s)
- Marwan Dakkouri
- Department of Electrochemistry, University of Ulm, D-89069 Ulm, Germany
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3
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Krishnapriya VU, Suresh CH. Imidazolin-2-imine and Imidazolin-2-methylidene Substitutions to Benzene, Pyridine, Phosphine, and N-Heterocyclic Carbene Predict Highly Electron-rich Ligands. Organometallics 2023. [DOI: 10.1021/acs.organomet.2c00666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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4
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da Fonseca AM, Soares NB, Colares RP, Macedo de Oliveira M, Santos Oliveira L, Marinho GS, Raya Paula de Lima M, da Rocha MN, Dos Santos HS, Marinho ES. Naphthoquinones biflorin and bis-biflorin ( Capraria biflora) as possible inhibitors of the fungus Candida auris polymerase: molecular docking, molecular dynamics, MM/GBSA calculations and in silico drug-likeness study. J Biomol Struct Dyn 2023; 41:11564-11577. [PMID: 36597918 DOI: 10.1080/07391102.2022.2163702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 12/24/2022] [Indexed: 01/05/2023]
Abstract
A new worldwide concern has emerged with the recent emergence of infections caused by Candida auris. This reflects its comparative ease of transmission, substantial mortality, and the increasing level of resistance seen in the three major classes of antifungal drugs. Efforts to create a better design for structure-based drugs that described numerous modifications and the search for secondary metabolic structures derived from plant species are likely to reduce the virulence of several fungal pathogens. In this context, the present work aimed to evaluate in silico two naphthoquinones isolated from the roots of Capraria biflora, biflorin, and its dimmer, bis-biflorin, as potential inhibitors of Candida auris polymerase. Based on the simulation performed with the two naphthoquinones, biflorin and bis-biflorin, it can be stated that bis-biflorin showed the best interactions with Candida auris polymerase. Still, biflorin also demonstrated favorable coupling energy. Predictive pharmacokinetic assays suggest that biflorin has high oral bioavailability and more excellent metabolic stability compared to the bis-biflorin analogue. constituting a promising pharmacological tool.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aluísio Marques da Fonseca
- Mestrado Acadêmico em Sociobiodiversidades e Tecnologias Sustentáveis - MASTS, Instituto de Engenharias e Desenvolvimento Sustentável, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Acarape, CE, Brazil
| | - Neidelenio Baltazar Soares
- Instituto de Ciências Exatas e da Natureza, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Acarape, CE, Brazil
| | - Regilany Paulo Colares
- Instituto de Ciências Exatas e da Natureza, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Acarape, CE, Brazil
| | | | | | - Gabrielle Silva Marinho
- Grupo de Química Teórica e Eletroquímica - GQTE, Universidade Estadual de Ceará, Limoiro do Norte, CE, Brazil
| | - Mira Raya Paula de Lima
- Instituto Federal de Educação Ciência e Tecnologia do Ceará - Campus Juazeiro do Norte, Juazeiro do Norte, CE, Brazil
| | - Matheus Nunes da Rocha
- Grupo de Química Teórica e Eletroquímica - GQTE, Universidade Estadual de Ceará, Limoiro do Norte, CE, Brazil
| | | | - Emmanuel Silva Marinho
- Grupo de Química Teórica e Eletroquímica - GQTE, Universidade Estadual de Ceará, Limoiro do Norte, CE, Brazil
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Ravindranath L, Srishailam K, Venkatram Reddy B. Experimental and DFT Quantum Chemical Studies on Structural, Vibrational and Molecular Properties of Some Substituted 4-Phenylphenols. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2161584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- L. Ravindranath
- Department of Physics, Malla Reddy Engineering College(a), Hyderabad, India
- Department of Physics, Kakatiya University, Warangal, India
| | - K. Srishailam
- Department of Physics, SR University, Warangal, India
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A comparative study on the physicochemical properties of the nanostructured triazolium based ionic liquids composed of [5F-PhMTZ]+ cation and various anions with their non-fluorinated cation analogues. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Adhav VA, Pananghat B, Saikrishnan K. Probing the Directionality of S···O/N Chalcogen Bond and Its Interplay with Weak C-H···O/N/S Hydrogen Bond Using Molecular Electrostatic Potential. J Phys Chem B 2022; 126:7818-7832. [PMID: 36179131 DOI: 10.1021/acs.jpcb.2c03745] [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
The directionality of the chalcogen bond (Ch-bond) formed by S and its interplay with other weak interactions have important chemical and biological implications. Here, dimers made of CH3-S-X and O/N containing nucleophiles are studied and found to be stabilized by coexisting S···O/N and C-H···O/N interactions. Based on experimentally accessible electron density and molecular electrostatic potentials (MESPs), we showed that reciprocity between S···O/N and C-H···O/N interactions in the stability of cumulative molecular interaction (ΔE) was dependent on the strength of the σ-hole on S (Vs,max). Direct correlation between ΔE of dimers with Vs,max of S supports the electrostatic nature of the Ch-bond. Such interplay of the Ch-bond is necessary for its directionality in complex nucleophiles (carbonyl groups) with multiple electron-rich centers, which is explained using MESP. A correlation between the MESP minima in the π-region and the strength of the S-π interaction explains the directional selectivity of the Ch-bond.
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Affiliation(s)
- Vishal Annasaheb Adhav
- Department of Biology, Indian Institute of Science Education and Research, Pune411008, India
| | - Balanarayan Pananghat
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali140306, India
| | - Kayarat Saikrishnan
- Department of Biology, Indian Institute of Science Education and Research, Pune411008, India
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8
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Chen Q, Si Y, Guo W, Fu Y. A phenyl S-Te bond with unique redox activity in dilute electrolyte of a lithium battery. Chem Commun (Camb) 2022; 58:10993-10996. [PMID: 36093763 DOI: 10.1039/d2cc04184g] [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
Phenyl tellurosulfide (PhS-TePh) was used to study the redox activity of the S-Te bond in lithium batteries. PhS-TePh formed a dynamic covalent network during lithiation, which provided a balance between responsiveness and stability to facilitate ion and electron transfer, enabling Li/PhS-TePh cells to achieve stable cycling and excellent rate performance in dilute electrolyte.
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Affiliation(s)
- Qianhan Chen
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, P. R. China.
| | - Yubing Si
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, P. R. China.
| | - Wei Guo
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, P. R. China.
| | - Yongzhu Fu
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, P. R. China.
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9
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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]
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10
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Otero-de-la-Roza A. Finding critical points and reconstruction of electron densities on grids. J Chem Phys 2022; 156:224116. [PMID: 35705403 DOI: 10.1063/5.0090232] [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 quantum theory of atoms in molecules (QTAIM), developed by Bader and co-workers, is one of the most popular ways of extracting chemical insight from the results of quantum mechanical calculations. One of the basic tasks in QTAIM is to locate the critical points of the electron density and calculate various quantities (density, Laplacian, etc.) on them since these have been found to correlate with molecular properties of interest. If the electron density is given analytically, this process is relatively straightforward. However, locating the critical points is more challenging if the density is known only on a three-dimensional uniform grid. A density grid is common in periodic solids because it is the natural expression for the electron density in plane-wave calculations. In this article, we explore the reconstruction of the electron density from a grid and its use in critical point localization. The proposed reconstruction method employs polyharmonic spline interpolation combined with a smoothing function based on the promolecular density. The critical point search based on this reconstruction is accurate, trivially parallelizable, works for periodic and non-periodic systems, does not present directional lattice bias when the grid is non-orthogonal, and locates all critical points of the underlying electron density in all tests studied. The proposed method also provides an accurate reconstruction of the electron density over the space spanned by the grid, which may be useful in other contexts besides critical point localization.
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Affiliation(s)
- Alberto Otero-de-la-Roza
- Departamento de Química Física y Analítica and MALTA Consolider Team, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
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11
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da Fonseca AM, Soares NB, Meirú MIL, Colares RP, Neto MM, Sobrinho ACN, Dos Santos HS, Marinho ES. Combined study of docking and molecular dynamics against DNV-3 SN1 protein by bixinoids. J Biomol Struct Dyn 2022:1-11. [PMID: 35510585 DOI: 10.1080/07391102.2022.2070282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Dengue (DENV), Zica virus (ZIKV), and Chikungunya fever (CHIK) are tropical diseases that have caused a lot of problems in general worldwide. Transmitted by mosquitoes of the species Aedes aegypti and albopictus, they have not been completely eradicated in the country, and their proliferation has only increased in the Northeast region. Within the structure of the virus, it is possible to verify the presence of glycoprotein SN1, which is responsible for its replication. If this macromolecule is inhibited using a specific or complex linker, it can interrupt its replication activity. An alternative to this problem has been using structures derived from natural products that have pharmacological properties. A dynamic and molecular docking combined study used computational simulation in the four isomeric forms of bixin against the SN1 protein. The Z,E-bixin and E,E-bixin isomers, both with affinity energy -6.7 and -6.5 Kcal/mol, presented the best results. Thus, bixin and its isomers, found in annatto seeds, maybe an initial proposal in the search for prototype compounds to study to fight this lethal virus in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aluísio Marques da Fonseca
- Institute of Exact Sciences and Nature, University of International Integration of Afro-Brazilian Lusophony, Acarape, Brazil
| | - Neidelênio Baltazar Soares
- Institute of Exact Sciences and Nature, University of International Integration of Afro-Brazilian Lusophony, Acarape, Brazil
| | - Maria Imaculada Lourenço Meirú
- Academic Master in Sociobiodiversity and Sustainable Technologies, Institute of Engineering and Sustainable Development, University of International Integration of Afro-Brazilian Lusophony, Acarape, Brazil
| | - Regilany Paulo Colares
- Institute of Exact Sciences and Nature, University of International Integration of Afro-Brazilian Lusophony, Acarape, Brazil
| | | | | | | | - Emmanuel Silva Marinho
- Natural Sciences, Science and Technology Center, Ceará State University, Fortaleza, Brazil.,Theoretical and Electrochemical Chemistry Research Group/FAFIDAM, State University of Ceará, Limoeiro do Norte, Brazil
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12
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Synthesis Characterization and X-ray Structure of 2-(2,6-Dichlorophenylamino)-2-imidazoline Tetraphenylborate: Computational Study. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12073568] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The title compound tetraphenylborate salt of clonidine (Catapres®), 2-(2,6-dichlorophenylamino)-2-imidazoline tetraphenylborate (3), was prepared in 76 % yield by the reaction of 2-(2,6-dichlorophenylamino)-2-imidazoline hydrochloride (clonidine hydrochloride) (1) with sodium tetraphenylborate (2) in deionized water through anion exchange reaction at ambient temperature. The structure of the title borate salt was characterized by UV, thermal analysis, mass and NMR analyses. White crystals of (3) suitable for an X-ray structural analysis were obtained by slow growing from acetonitrile. The molecular structure of the titled compound (3) was crystallized in the acetonitrile, P21/c, a = 9.151 (3) Å, b = 12.522 (3) Å, c = 25.493 (6) Å, β = 105.161 (13)° V = 2819.5 (13) Å3, Z = 4. A DFT quantum chemistry calculation method was employed to investigate the interaction mechanism of clonidine with tetraphenylborate. The stable configurations of the complexes of clonidine with tetraphenylborate with electrostatic interactions were obtained. Finally, the interaction strength and type of the complexes were studied through the reduced density gradient (RDG) function. This study provides new theoretical insight into the interaction mechanism and a guide for screening and designing the optimal clonidine and tetraphenylborate reacting to form the complex.
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Shakourian-Fard M, Maryamdokht Taimoory S, Ghenaatian HR, Kamath G, Trant JF. Effect of mono-vacant defects on the adsorption properties of deep eutectic solvents onto hexagonal boron-nitride nanoflakes. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Suresh CH, Remya GS, Anjalikrishna PK. Molecular electrostatic potential analysis: A powerful tool to interpret and predict chemical reactivity. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1601] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Cherumuttathu H. Suresh
- Chemical Sciences and Technology Division CSIR‐National Institute for Interdisciplinary Science and Technology Thiruvananthapuram Kerala India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad India
| | - Geetha S. Remya
- Chemical Sciences and Technology Division CSIR‐National Institute for Interdisciplinary Science and Technology Thiruvananthapuram Kerala India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad India
| | - Puthannur K. Anjalikrishna
- Chemical Sciences and Technology Division CSIR‐National Institute for Interdisciplinary Science and Technology Thiruvananthapuram Kerala India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad India
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15
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Haritha M, Suresh CH. Hydration patterns of rings in drugs and relationship to lipophilicity: A DFT study. J Comput Chem 2022; 43:477-490. [PMID: 34978337 DOI: 10.1002/jcc.26808] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/09/2021] [Accepted: 12/22/2021] [Indexed: 11/11/2022]
Abstract
Rings are one of the major scaffold components of drugs in medicinal chemistry, due to their unique electronic distribution, scaffold rigidity, and three-dimensionality while lipophilicity is considered as a vital parameter of rings that can influence the reactivity, metabolic stability, and toxicity. We have analyzed the electronic features, hydration patterns, solvation effect and lipophilicity data for 51 most widely used ring systems in drugs. Molecular electrostatic potential (MESP) topology analysis has been used to assess the electronic distribution in rings which provided an easy interpretation of the most suitable hydration patterns of the ring with H2 O molecule. Further, the global minimum of ring…H2 O complex has been utilized to predict lipophilicity (logP) with the incorporation of implicit solvation effect. Classification of ring systems based on their molecular weight into four categories, viz. small ring 'sr', medium ring 'mr', large ring 'lr' and extra large ring 'xlr' systems has led to the finding of strong correlations between logP and hydration energy with R = 0.942, 0.933, 0.968 and 0.933, respectively. The micro solvation model is found to be useful for locating the hydrophobic-hydrophilic border for each category of rings in terms of hydration energy whereas the implicit solvation model used for two solvents, n-octanol and water on the most stable hydrated structure led to a global correlation between logP and solvation energy ratio. This correlation predicts a limiting logP value -7.03 for the most hydrophilic ring system and also suggests a clear partitioning of the ring molecules into hydrophobic and hydrophilic classes. The MESP topology-guided approach to understand the electronic features and hydration patterns of rings in drugs lead to powerful predictions on their lipophilicity behavior.
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Affiliation(s)
- Mambatta Haritha
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, Kerala, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Cherumuttathu H Suresh
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, Kerala, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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16
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Krishnapriya VU, Suresh CH. The use of electrostatic potential at nuclei in the analysis of halogen bonding. NEW J CHEM 2022. [DOI: 10.1039/d2nj00256f] [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
Molecular electrostatic potential data at interacting nuclei provide strong evidence of bond formation in many intermolecular halogen bonded complexes.
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Affiliation(s)
- Vilakkathala U. Krishnapriya
- Chemical Science and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram – 695019, Kerala, India
- Research Centre, University of Kerala, Thiruvananthapuram, 34, Kerala, India
| | - Cherumuttathu H. Suresh
- Chemical Science and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram – 695019, Kerala, India
- Research Centre, University of Kerala, Thiruvananthapuram, 34, Kerala, India
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17
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Li X, Li Y, Sun Y, Meng L, Zeng Y. BF 3 -Catalyzed Mukaiyama aldol reaction of acetaldehyde with 2-siloxy-1-propene. J Comput Chem 2021; 43:402-412. [PMID: 34931704 DOI: 10.1002/jcc.26800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/12/2021] [Accepted: 12/07/2021] [Indexed: 11/10/2022]
Abstract
The Mukaiyama aldol reaction is a powerful tool for the construction of the carbon-carbon bond and the formation of β-hydroxycarbonyl compounds. In this work, the mechanism of acetaldehyde and 2-siloxy-1-propene both in the absence and presence of the catalyst BF3 was investigated based on density functional theory. The mechanism includes two major steps: the formation of the carbon-carbon bond and the removal of SiH3 /BF2 by water. The energy barrier of the carbon-carbon bond formation process in the presence of BF3 is obviously lower, indicating that BF3 is a good catalyst for this reaction. In terms of molecular configuration, the different tensions between the five-membered-ring and six-membered-ring can be considered as the possible reason for the catalytic effect of BF3 . In terms of charge transfer, the charges of natural population analysis in the carbon atom of the carbonyl group in acetaldehyde becomes more positive, which is easier to attack by nucleophiles and promote the nucleophilic process.
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Affiliation(s)
- Xuening Li
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China
| | - Ying Li
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China
| | - Yuanyuan Sun
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China
| | - Lingpeng Meng
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China
| | - Yanli Zeng
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China.,Hebei Key Laboratory of Inorganic Nano-materials, Hebei Normal University, Shijiazhuang, China
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18
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Force G, Perfetto A, Mayer RJ, Ciofini I, Lebœuf D. Macrolactonization Reactions Driven by a Pentafluorobenzoyl Group**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Guillaume Force
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) CNRS UMR 8182 Université Paris-Saclay Bâtiment 420 91405 Orsay France
| | - Anna Perfetto
- Chimie Paris-Tech PSL CNRS, Institute of Chemistry for Health and Life Science (I-CLeHS) Theoretical Chemistry and Modelling Group (CTM) 75005 Paris France
| | - Robert J. Mayer
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS) CNRS UMR 7006 Université de Strasbourg 8 allée Gaspard Monge 67000 Strasbourg France
| | - Ilaria Ciofini
- Chimie Paris-Tech PSL CNRS, Institute of Chemistry for Health and Life Science (I-CLeHS) Theoretical Chemistry and Modelling Group (CTM) 75005 Paris France
| | - David Lebœuf
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS) CNRS UMR 7006 Université de Strasbourg 8 allée Gaspard Monge 67000 Strasbourg France
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Force G, Perfetto A, Mayer RJ, Ciofini I, Lebœuf D. Macrolactonization Reactions Driven by a Pentafluorobenzoyl Group*. Angew Chem Int Ed Engl 2021; 60:19843-19851. [PMID: 34213811 DOI: 10.1002/anie.202105882] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/16/2021] [Indexed: 11/08/2022]
Abstract
Macrolactones constitute a privileged class of natural and synthetic products with a broad range of applications in the fine chemicals and pharmaceutical industry. Despite all the progress made towards their synthesis, notably from seco-acids, a macrolactonization promoter system that is effective, selective, flexible, readily available, and, insofar as possible, compatible with manifold functional groups is still lacking. Herein, we describe a strategy that relies on the formation of a mixed anhydride incorporating a pentafluorophenyl group which, due to its high electronic activation enables a convenient access to macrolactones, macrodiolides and esters with a broad versatility. Kinetic studies and DFT computations were performed to rationalize the reactivity of the pentafluorophenyl group in macrolactonization reactions.
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Affiliation(s)
- Guillaume Force
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS UMR 8182, Université Paris-Saclay, Bâtiment 420, 91405, Orsay, France
| | - Anna Perfetto
- Chimie Paris-Tech, PSL, CNRS, Institute of Chemistry for Health and Life Science (I-CLeHS), Theoretical Chemistry and Modelling Group (CTM), 75005, Paris, France
| | - Robert J Mayer
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Ilaria Ciofini
- Chimie Paris-Tech, PSL, CNRS, Institute of Chemistry for Health and Life Science (I-CLeHS), Theoretical Chemistry and Modelling Group (CTM), 75005, Paris, France
| | - David Lebœuf
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, 8 allée Gaspard Monge, 67000, Strasbourg, France
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20
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Fonseca AM, Silva LPD, Almeida-Neto FWDQ, Colares RP, Macedo de Oliveira M, Luthierre Gama Cavalcante A, Lemos TLG, Braz-Filho R, de Lima-Neto P, Marinho ES. Synthesis of a new quinine dimer biocatalysed by the coconut water. BIOCATAL BIOTRANSFOR 2021. [DOI: 10.1080/10242422.2021.1935897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Aluísio M. Fonseca
- Mestrado Acadêmico em Sociobiodiversidades e Tecnologias Sustentáveis – MASTS, Instituto de Engenharias e Desenvolvimento Sustentável, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Acarape, Brazil
- Instituto de Ciências Exatas e da Natureza, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Acarape, Brazil
| | - Leonardo Paes da Silva
- Grupo de Química Teórica, Departamento de Analítica e Físico-Química, Universidade Federal do Ceará, Fortaleza, Brasil
| | | | - Regilany Paulo Colares
- Instituto de Ciências Exatas e da Natureza, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Acarape, Brazil
| | - Mauro Macedo de Oliveira
- Mestrado Acadêmico em Sociobiodiversidades e Tecnologias Sustentáveis – MASTS, Instituto de Engenharias e Desenvolvimento Sustentável, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Acarape, Brazil
- Departamento de Química, Centro Universitário Paraíso – UNIFAP, Juazeiro do Norte, Brazil
| | | | - Telma L. G. Lemos
- Laboratório de Biocatálise e Produtos Naturais, Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Raimundo Braz-Filho
- Centro de Ciências e Tecnologias, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos Dos Goytacazes, Brazil
| | - Pedro de Lima-Neto
- Grupo de Química Teórica, Departamento de Analítica e Físico-Química, Universidade Federal do Ceará, Fortaleza, Brasil
| | - Emmanuel Silva Marinho
- Grupo de Química Teórica, Departamento de Analítica e Físico-Química, Universidade Federal do Ceará, Fortaleza, Brasil
- Faculdade de Filosofia Dom Aureliano Matos - FAFIDAM, Universidade Estadual do Ceará, Centro, Brazil
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21
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Electrostatic Potential Topology for Probing Molecular Structure, Bonding and Reactivity. Molecules 2021; 26:molecules26113289. [PMID: 34072507 PMCID: PMC8198923 DOI: 10.3390/molecules26113289] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/16/2021] [Accepted: 05/25/2021] [Indexed: 11/18/2022] Open
Abstract
Following the pioneering investigations of Bader on the topology of molecular electron density, the topology analysis of its sister field viz. molecular electrostatic potential (MESP) was taken up by the authors’ groups. Through these studies, MESP topology emerged as a powerful tool for exploring molecular bonding and reactivity patterns. The MESP topology features are mapped in terms of its critical points (CPs), such as bond critical points (BCPs), while the minima identify electron-rich locations, such as lone pairs and π-bonds. The gradient paths of MESP vividly bring out the atoms-in-molecule picture of neutral molecules and anions. The MESP-based characterization of a molecule in terms of electron-rich and -deficient regions provides a robust prediction about its interaction with other molecules. This leads to a clear picture of molecular aggregation, hydrogen bonding, lone pair–π interactions, π-conjugation, aromaticity and reaction mechanisms. This review summarizes the contributions of the authors’ groups over the last three decades and those of the other active groups towards understanding chemical bonding, molecular recognition, and reactivity through topology analysis of MESP.
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22
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Ghenaatian HR, Shakourian-Fard M, Kamath G. Interaction of Cu n, Ag n and Au n (n = 1-4) nanoparticles with ChCl:Urea deep eutectic solvent. J Mol Graph Model 2021; 105:107866. [PMID: 33677361 DOI: 10.1016/j.jmgm.2021.107866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/19/2021] [Accepted: 02/08/2021] [Indexed: 11/28/2022]
Abstract
In this study, the interaction of noble metal nanoparticles (Mn, M = Cu, Ag, and Au; n = 1-4) with ChCl:Urea deep eutectic solvent was investigated using density functional theory (DFT) method. We find that ChCl:Urea mostly interact with the Mn nanoparticles through [Cl]- anion ([Cl]-…Mn) and nonconventional H-bonds of C-H⋯Mn and N-H⋯Mn. NBO, QTAIM, NCI and EDA analyses show that [Cl]-…Mn interactions are stronger than the nonconventional H-bonds interactions. Our results indicate that the nature of [Cl]-…Mn interactions is electrostatic, while the nonconventional H-bonds of C-H⋯Mn and N-H⋯Mn are van der Waals in nature. The negative values of enthalpy (ΔH) and free energy (ΔG) for the ChCl:Urea…Mn complexes reveal that the formation of ChCl:Urea…Mn complexes is exothermic and proceeds spontaneously. The calculation of binding energy (ΔEb) of Mn nanoparticles with ChCl:Urea shows that the strength of interaction of Aun nanoparticles with ChCl:Urea is more favorable than Cun and Agn, following the order ChCl:Urea…Aun > ChCl:Urea…Cun > ChCl:Urea…Agn. Furthermore, the ΔEb, ΔH and ΔG values enhance with increasing nanoparticle size from n = 1 to n = 4, ChCl:Urea…M4> ChCl:Urea…M3> ChCl:Urea…M2> ChCl:Urea…M1 (M = Cu, Ag, and Au).
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Affiliation(s)
| | - Mehdi Shakourian-Fard
- Department of Chemical Engineering, Birjand University of Technology, Birjand, P.O. Box 97175/569, Iran
| | - Ganesh Kamath
- Dalzierfiver LLC, 3500 Carlfied St, EL Sobrante, CA, 94803, USA
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23
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Roohi H, Safari A. The interplay between anion-π and H-bonding interactions in X −···s-Triazine···(HF) n(HCl) 3-n (X = F −, Cl − and CN −) complexes: DFT and DFT-D study. Mol Phys 2021. [DOI: 10.1080/00268976.2020.1827179] [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]
Affiliation(s)
- Hossein Roohi
- Quantum Chemistry Laboratory, Department of Chemistry, Faculty of Science, University of Guilan, Rasht, Iran
| | - Alireza Safari
- Quantum Chemistry Laboratory, Department of Chemistry, Faculty of Science, University of Guilan, Rasht, Iran
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24
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Ibrahim MAA, Ahmed OAM, El-Taher S, Al-Fahemi JH, Moussa NAM, Moustafa H. Cospatial σ-Hole and Lone Pair Interactions of Square-Pyramidal Pentavalent Halogen Compounds with π-Systems: A Quantum Mechanical Study. ACS OMEGA 2021; 6:3319-3329. [PMID: 33553949 PMCID: PMC7860235 DOI: 10.1021/acsomega.0c05795] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 01/13/2021] [Indexed: 05/08/2023]
Abstract
In the spirit of the mounting interest in noncovalent interactions, the present study was conducted to scrutinize a special type that simultaneously involved both σ-hole and lone pair (lp) interactions with aromatic π-systems. Square-pyramidal pentavalent halogen-containing molecules, including X-Cl-F4, F-Y-F4, and F-I-X4 compounds (where X = F, Cl, Br, and I and Y = Cl, Br, and I) were employed as σ-hole/lp donors. On the other hand, benzene (BZN) and hexafluorobenzene (HFB) were chosen as electron-rich and electron-deficient aromatic π-systems, respectively. The investigation relied upon a variety of quantum chemical calculations that complement each other. The results showed that (i) the binding energy of the X-Y-F4···BZN complexes increased (i.e., more negative) as the Y atom had a larger magnitude of σ-hole, contrary to the pattern of X-Y-F4···HFB complexes; (ii) the interaction energies of X-Y-F4···BZN complexes were dominated by both dispersion and electrostatic contributions, while dispersive interactions dominated X-Y-F4···HFB complexes; and (iii) the X4 atoms in F-I-X4···π-system complexes governed the interaction energy pattern: the larger the X4 atoms were, the greater the interaction energies were, for the same π-system. The results had illuminating facets in regard to the rarely addressed cases of the σ-hole/lp contradictory scene.
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Affiliation(s)
| | - Ossama A. M. Ahmed
- Chemistry
Department, Faculty of Science, Minia University, Minia 61519, Egypt
- Department
of Chemistry, Faculty of Science, Cairo
University, Giza 12613, Egypt
| | - Sabry El-Taher
- Department
of Chemistry, Faculty of Science, Cairo
University, Giza 12613, Egypt
| | - Jabir H. Al-Fahemi
- Chemistry
Department, Faculty of Applied Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Nayra A. M. Moussa
- Chemistry
Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Hussein Moustafa
- Department
of Chemistry, Faculty of Science, Cairo
University, Giza 12613, Egypt
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25
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Ismail TM, Mohan N, Sajith PK. Theoretical study of hydrogen bonding interactions in substituted nitroxide radicals. NEW J CHEM 2021. [DOI: 10.1039/d0nj05362g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Interaction energy (Eint) of hydrogen bonded complexes of nitroxide radicals can be assessed in terms of the deepest minimum of molecular electrostatic potential (Vmin).
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Affiliation(s)
| | - Neetha Mohan
- Department of Chemistry
- Christopher Ingold Building
- University College London (UCL)
- London WC1H 0AJ
- UK
| | - P. K. Sajith
- Department of Chemistry
- Farook College
- Kozhikode
- India
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26
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The conformational change of Plukenetia conophora oil derivatives and their acidic resistance, intra-fragment interactions, stability in different solvent media. J Mol Model 2020; 26:312. [PMID: 33089422 DOI: 10.1007/s00894-020-04574-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/15/2020] [Indexed: 10/23/2022]
Abstract
The synthesis of derivatives of bio-based lubricants from vegetable oil as an alternative to petroleum oil is significant due to the oil crisis, global warming, higher demand and serious environmental threat. In this study, the molecular properties of three derivatives of oil derived from Plukenetia conophora seeds, namely Plukenetia conophora oil (PK), rpoxidised Plukenetia conophora oil (EP) and poly(hydroxybutanethiol-ether) derivative of Plukenetia conophora oil (BP), were examined in acidic media and crystal form. The derivative BP has the highest resistance to acidic attack as evident from their poor interaction with acidic H3O+ from both HCl and HNO3. BP also has the best tendency of forming a crystal as evident from the lowest atomic diffusion in crystal model (L12). However, the result of the molecular electrostatic potential (MESP) analysis shows that BP has more electron-deficient surface compare to EP derivatives. The derivative BP is also found to have the lowest potential energy and higher root means square deviation (RMSD) of its atoms. Density clustering analysis further confirms that BP did not retain its most stable conformation for a longer period of simulation compared to PK and EP. The most visited conformation from the hierarchical and density clustering also corresponds to the minimum potential energy on the potential energy surface.Graphical abstract.
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27
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Cala L, Villar P, de Lera ÁR, Fañanás FJ, Álvarez R, Rodríguez F. Multicomponent and multicatalytic asymmetric synthesis of furo[2,3- b]pyrrole derivatives: further insights into the mode of action of chiral phosphoric acid catalysts. Chem Sci 2020; 11:9181-9190. [PMID: 34094194 PMCID: PMC8161233 DOI: 10.1039/d0sc03342a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Multicomponent and multicatalytic reactions are those processes that try to imitate the way the enzymatic machinery transforms simple building blocks into complex products. The development of asymmetric versions of these reactions is a step forward in our dream of mirroring the exquisite selectivity of biological processes. In this context, the present work describes a new reaction for the asymmetric synthesis of furo[2,3-b]pyrrole derivatives from simple 3-butynamines, glyoxylic acid and anilines in the presence of a dual catalytic system, formed from a gold complex and a chiral phosphoric acid. Computations, aimed to understand the exceptional performance of 9-anthracenyl-substituted BINOL-derived phosphoric acid catalyst, suggest a fundamental role of non-covalent interactions being established between the catalyst and the reagents for the outcome of the multicomponent process. The linear geometry of the anthracenyl substituent along with the presence of an electron-withdrawing group in the aniline and an aromatic substituent in the 3-butynamine derivative seem to be key structural factors to explain the experimental results and, particularly, the high stereoselectivity.
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Affiliation(s)
- Lara Cala
- Instituto Universitario de Química Organometálica "Enrique Moles", Centro de Innovación en Química Avanzada (ORFEO-CINQA), Universidad de Oviedo Julián Clavería, 8 33006-Oviedo Spain
| | - Pedro Villar
- Departamento de Química Orgánica (CINBIO), Universidade de Vigo As Lagoas-Marcosende E-36310 Vigo Spain
| | - Ángel R de Lera
- Departamento de Química Orgánica (CINBIO), Universidade de Vigo As Lagoas-Marcosende E-36310 Vigo Spain
| | - Francisco J Fañanás
- Instituto Universitario de Química Organometálica "Enrique Moles", Centro de Innovación en Química Avanzada (ORFEO-CINQA), Universidad de Oviedo Julián Clavería, 8 33006-Oviedo Spain
| | - Rosana Álvarez
- Departamento de Química Orgánica (CINBIO), Universidade de Vigo As Lagoas-Marcosende E-36310 Vigo Spain
| | - Félix Rodríguez
- Instituto Universitario de Química Organometálica "Enrique Moles", Centro de Innovación en Química Avanzada (ORFEO-CINQA), Universidad de Oviedo Julián Clavería, 8 33006-Oviedo Spain
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28
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Kruse H, Mrazikova K, D'Ascenzo L, Sponer J, Auffinger P. Short but Weak: The Z‐DNA Lone‐Pair⋅⋅⋅π Conundrum Challenges Standard Carbon Van der Waals Radii. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Klaudia Mrazikova
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
- National Centre for Biomolecular ResearchFaculty of ScienceMasaryk University Kamenice 5 62500 Brno Czech Republic
| | - Luigi D'Ascenzo
- Department of Integrative Structural and Computational BiologyThe Scripps Research Institute La Jolla CA 92037 USA
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
- Regional Centre of Advanced Technologies and MaterialsFaculty of SciencePalacký University Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Pascal Auffinger
- Université de StrasbourgCNRS, Architecture et Réactivité de l'ARN, UPR9002 F-67000 Strasbourg France
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29
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Kruse H, Mrazikova K, D'Ascenzo L, Sponer J, Auffinger P. Short but Weak: The Z‐DNA Lone‐Pair⋅⋅⋅π Conundrum Challenges Standard Carbon Van der Waals Radii. Angew Chem Int Ed Engl 2020; 59:16553-16560. [DOI: 10.1002/anie.202004201] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Klaudia Mrazikova
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
- National Centre for Biomolecular Research Faculty of Science Masaryk University Kamenice 5 62500 Brno Czech Republic
| | - Luigi D'Ascenzo
- Department of Integrative Structural and Computational Biology The Scripps Research Institute La Jolla CA 92037 USA
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
- Regional Centre of Advanced Technologies and Materials Faculty of Science Palacký University Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Pascal Auffinger
- Université de Strasbourg CNRS, Architecture et Réactivité de l'ARN, UPR9002 F-67000 Strasbourg France
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30
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Sarkar S, Ramanathan N, Sruthi P, Sundararajan K. Computational and experimental evidence of N–H…π and cooperative πN…π∗ interactions in pyrrole…benzene and pyrrole…ethylene heterodimers at low temperatures. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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31
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Tupikina EY, Tokhadze KG, Denisov GS, Tolstoy PM. Lone pairs mapping by Laplacian of
3
He NMR chemical shift. J Comput Chem 2020; 41:1194-1199. [DOI: 10.1002/jcc.26166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 01/23/2020] [Accepted: 01/23/2020] [Indexed: 11/07/2022]
Affiliation(s)
- Elena Yu. Tupikina
- Institute of ChemistrySt. Petersburg State University St. Petersburg Russia
| | | | - Gleb S. Denisov
- Department of PhysicsSt. Petersburg State University St. Petersburg Russia
| | - Peter M. Tolstoy
- Institute of ChemistrySt. Petersburg State University St. Petersburg Russia
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32
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Chang CK, Lin ST. Improved Prediction of Phase Behaviors of Ionic Liquid Solutions with the Consideration of Directional Hydrogen Bonding Interactions. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.9b03741] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chun-Kai Chang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Shiang-Tai Lin
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
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33
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Zins EL. Microhydration of a Carbonyl Group: How does the Molecular Electrostatic Potential (MESP) Impact the Formation of (H 2O) n:(R 2C═O)Complexes? J Phys Chem A 2020; 124:1720-1734. [PMID: 32049521 DOI: 10.1021/acs.jpca.9b09992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The presence of a carbonyl group in a molecule usually leads to the identification of a π-hole on the molecular electrostatic potential (MESP) of the species. How does this electrophilic site influence the formation of microhydrated complexes? To address this point, a panel of R2CO solutes with various MESPs was selected, and we identified the structures and properties of several complexes containing one, two, three and six water molecules. The following solutes were considered in the present study: H2CO, F2CO, Cl2CO,(NC)2CO and H2C═CO. Geometry optimizations and frequency calculations were carried out at the LC-ωPBE/6-311++G(d,p) level, with the GD3BJ empirical correction for dispersion. For a number of n water molecules around the R2CO solute, the structure and the features of the most stable (H2O)n:(R2CO) complexes are highly dependent on the MESP of the isolated R2CO solute. The formation of pi-hole bondings appears to play a decisive role in the initiation of a three-dimensional organization of water molecules around the solute.
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Affiliation(s)
- Emilie-Laure Zins
- De la Molécule aux Nano-Objets: Réactivité, Interactions Spectroscopies, MONARIS, CNRS, Sorbonne Université, 75005, Paris, France
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34
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Bijina PV, Suresh CH. Molecular Electrostatic Potential Reorganization Theory to Describe Positive Cooperativity in Noncovalent Trimer Complexes. J Phys Chem A 2020; 124:2231-2241. [DOI: 10.1021/acs.jpca.9b11538] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Padinjare Veetil Bijina
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, Kerala695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Cherumuttathu H. Suresh
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, Kerala695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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35
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Ghasemi Gildeh SF, Roohi H, Mehrdad M, Rad-Moghadam K, Ghauri K. Experimental and theoretical probing of the physicochemical properties of ionic liquids composed of [Bn-DBU]+ cation and various anions. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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36
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Substituent effects on the halogen and pnictogen bonds characteristics in ternary complexes 4-YPhNH2···PH2F···ClX (Y = H, F, CN, CHO, NH2, CH3, NO2 and OCH3, and X = F, OH, CN, NC, FCC and NO2): A theoretical study. J CHEM SCI 2019. [DOI: 10.1007/s12039-019-1715-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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37
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Adeniyi AA, Akintayo CO, Akintayo ET, Conradie J. The conformational search, the stability, fragment interaction and resistance to acidic attack of epoxyl-polyurethanes in different solvent media. Struct Chem 2019. [DOI: 10.1007/s11224-019-01470-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Anjalikrishna PK, Suresh CH, Gadre SR. Electrostatic Topographical Viewpoint of π-Conjugation and Aromaticity of Hydrocarbons. J Phys Chem A 2019; 123:10139-10151. [PMID: 31647654 DOI: 10.1021/acs.jpca.9b09056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A molecular electrostatic potential (MESP) topographical study has been conducted for a variety of conjugated hydrocarbons at B3LYP/6-311+G(d,p) level of theory to understand their π-conjugation features and aromaticity. The value of MESP minimum (Vm) is related to the localized and delocalized distribution of π-electron density. The Vm values are located interior to the rings in polycyclic benzenoid hydrocarbons (PBHs), whereas they lie outside the boundary of the rings in antiaromatic and in fused systems consisting of aromatic and antiaromatic moieties. The Vm points lie on top and bottom of the π-regions in linear polyenes and annulenes, while a degenerate distribution of CPs around the midpoint region of triple bonds is observed in alkynes. The eigenvalues λ1, λ2, and λ3 of the Hessian matrix at Vm(MESP minima) are used to define the aromatic character of the cyclic structures. The eigenvalues follow the trend λ1 ≫ λ2 > λ3 ≅ 0 in PBHs, λ1 > λ2 > λ3 ≅ 0 in linear polyenes, and λ1 > λ2 > λ3 ≠ 0 in antiaromatic systems. The difference in the aromatic character of PBHs from that of benzene is related to the deviations Δλ1, Δλ2, and Δλ3. The total deviation ∑i=13Δλi is found to be ≤ 0.011 au for all aromatic systems and lies between 0.011 and 0.035 au for all nonaromatic systems. For antiaromatic systems, its value is found to be above 0.035 au. Further, ∑i=13Δλi gives a direct interpretation of Clar's aromatic sextet structures for PBHs. In summary, MESP topography mapping is a powerful technique to quantify the localized and delocalized π-electron distribution in a variety of unsaturated hydrocarbon systems.
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Affiliation(s)
- Puthannur K Anjalikrishna
- Chemical Sciences and Technology Division , CSIR-National Institute for Interdisciplinary Science and Technology , Thiruvananthapuram , Kerala 695019 , India.,Academy of Scientific and Innovative Research (AcSIR) , Ghaziabad 201002 , India
| | - Cherumuttathu H Suresh
- Chemical Sciences and Technology Division , CSIR-National Institute for Interdisciplinary Science and Technology , Thiruvananthapuram , Kerala 695019 , India.,Academy of Scientific and Innovative Research (AcSIR) , Ghaziabad 201002 , India
| | - Shridhar R Gadre
- Interdisciplinary School of Scientific Computing , Savitribai Phule Pune University , Pune 411007 , India
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Rohman SS, Sarmah B, Borthakur B, Remya GS, Suresh CH, Phukan AK. Extending the Library of Boron Bases: A Contribution from Theory. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00317] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Bikash Sarmah
- Department of Chemical Sciences, Tezpur University, Napaam 784028, Assam India
| | - Bitupon Borthakur
- Department of Chemical Sciences, Tezpur University, Napaam 784028, Assam India
| | - Geetha S. Remya
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, Kerala 695 019, India
| | - Cherumuttathu H. Suresh
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, Kerala 695 019, India
| | - Ashwini K. Phukan
- Department of Chemical Sciences, Tezpur University, Napaam 784028, Assam India
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Ibrahim MAA, Telb EMZ. A Computational Investigation of Unconventional Lone‐Pair Hole Interactions of Group V–VIII Elements. ChemistrySelect 2019. [DOI: 10.1002/slct.201900603] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational Chemistry LaboratoryChemistry DepartmentFaculty of ScienceMinia University Minia 61519 Egypt
| | - Ebtisam M. Z. Telb
- Computational Chemistry LaboratoryChemistry DepartmentFaculty of ScienceMinia University Minia 61519 Egypt
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41
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Liu M, Zeng Y, Sun Z, Meng L. Predicting the halogen-n
(n
= 3-6) synthons to form the “windmill” pattern bonding based on the halogen-bonded interactions. J Comput Chem 2019; 40:1219-1226. [DOI: 10.1002/jcc.25781] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/29/2018] [Accepted: 01/02/2019] [Indexed: 01/18/2023]
Affiliation(s)
- Mengyu Liu
- Institute of Computational Quantum Chemistry, College of Chemistry and Material Science; Hebei Normal University; Shijiazhuang 050024 People's Republic of China
| | - Yanli Zeng
- Institute of Computational Quantum Chemistry, College of Chemistry and Material Science; Hebei Normal University; Shijiazhuang 050024 People's Republic of China
- National Demonstration Center for Experimental Chemistry Education; Hebei Normal University; Shijiazhuang 050024 People's Republic of China
| | - Zheng Sun
- Institute of Computational Quantum Chemistry, College of Chemistry and Material Science; Hebei Normal University; Shijiazhuang 050024 People's Republic of China
| | - Lingpeng Meng
- Institute of Computational Quantum Chemistry, College of Chemistry and Material Science; Hebei Normal University; Shijiazhuang 050024 People's Republic of China
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42
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Tupikina EY, Efimova AA, Denisov GS, Tolstoy PM. Outer electronic shell visualization by NMR chemical shift laplacian of a helium probe. J Comput Chem 2018; 39:2459-2462. [DOI: 10.1002/jcc.25585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/15/2018] [Accepted: 08/16/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Elena Yu. Tupikina
- Department of Physics; St. Petersburg State University; Uljanovskaja 1, St. Petersburg 198504 Russia
| | - Alexandra A. Efimova
- Department of Physics; St. Petersburg State University; Uljanovskaja 1, St. Petersburg 198504 Russia
| | - Gleb S. Denisov
- Department of Physics; St. Petersburg State University; Uljanovskaja 1, St. Petersburg 198504 Russia
| | - Peter M. Tolstoy
- Center for Magnetic Resonance; St. Petersburg State University; Universitetsky pr. 26, 198504 Russia
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43
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Kalai C, Alikhani ME, Zins EL. The molecular electrostatic potential analysis of solutes and water clusters: a straightforward tool to predict the geometry of the most stable micro-hydrated complexes of β-propiolactone and formamide. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2345-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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44
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Suresh CH, Bijina PV. Hidden Dicarbene Nature of Acetylenes and Captodative Bonding on Carbon. Chemphyschem 2018; 19:3266-3272. [PMID: 30192059 DOI: 10.1002/cphc.201800726] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/03/2018] [Accepted: 09/06/2018] [Indexed: 11/09/2022]
Abstract
DFT derived molecular electrostatic potential (MESP), ¹³C NMR chemical shift (δ), bond order and coordination reactions show that alkynes (RCCR) attain 1,2-dicarbene nature during CCR angle bending. Alkyne carbon atoms of bent structures exhibit MESP features unique to lone-pair bearing atoms, δ around 200 ppm typical for carbene centers and large reduction in CC triple bond character. Lone pair bearing atoms of R substituents enhance the carbene character. The bent alkynes can be trapped with Lewis acids (BH₃, BF₃, AlF₃ and AlCl₃) as the lone pairs developed on carbon centers provide strong donor type dative bonding. The dative bond gives a formal valence electron count six on carbon and suggests the for-mation of acceptor type dative bonding to carbon from Lewis base (NH₃). Reaction of alkynes with (Lewis acid-Lewis base) systems yield (Lewis acid)₂-Alkyne-Lewis base)₂ complexes which are exothermic and exergonic for many cases. These complexes are examples of captodative carbon(II) compounds.
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Affiliation(s)
- Cherumuttathu H Suresh
- National Institute for Interdisciplinary Science and Technology, Chemical Sciences and Technology Division, Pappanamcode, 695019, Trivandrum, INDIA
| | - Padinjare Veetil Bijina
- National Institute for Interdisciplinary Science and Technology CSIR, 695019, Trivandrum, INDIA
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45
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Panneer SVK, Ravva MK, Mishra BK, Subramanian V, Sathyamurthy N. Co-operativity in non-covalent interactions in ternary complexes: a comprehensive electronic structure theory based investigation. J Mol Model 2018; 24:258. [PMID: 30159795 DOI: 10.1007/s00894-018-3796-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 08/14/2018] [Indexed: 11/24/2022]
Abstract
The structure and stability of various ternary complexes in which an extended aromatic system such as coronene interacts with ions/atoms/molecules on opposite faces of the π-electron cloud were investigated using ab initio calculations. By characterizing the nature of the intermolecular interactions using an energy decomposition analysis, it was shown that there is an interplay between various types of interactions and that there are co-operativity effects, particularly when different types of interactions coexist in the same system. Graphical abstract Weak OH-π, π-π and van der Waals-π ternary systems are stabilized through dispersion interactions. Cation-π ternary systems are stabilized by through-space electrostatic interactions.
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Affiliation(s)
| | | | | | - Venkatesan Subramanian
- Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai, 600020, India.
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46
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Chang CK, Chen WL, Wu DT, Lin ST. Improved Directional Hydrogen Bonding Interactions for the Prediction of Activity Coefficients with COSMO-SAC. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.8b02493] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chun-Kai Chang
- Department of Chemical Engineering, National Taiwan University, Taipei City 10617, Taiwan
| | - Wei-Lin Chen
- Department of Chemical Engineering, National Taiwan University, Taipei City 10617, Taiwan
| | - David T. Wu
- Departments of Chemistry and of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Shiang-Tai Lin
- Department of Chemical Engineering, National Taiwan University, Taipei City 10617, Taiwan
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Durán-Solares G, Fugarolas-Gómez W, Ortíz-Pastrana N, López-Sandoval H, Villaseñor-Granados TO, Flores-Parra A, Altmann PJ, Barba-Behrens N. Lone pair···π interactions on the stabilization of intra and intermolecular arrangements of coordination compounds with 2-methyl imidazole and benzimidazole derivatives. J COORD CHEM 2018. [DOI: 10.1080/00958972.2018.1494269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Guillermo Durán-Solares
- Departamento de Química Inorgánica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Walter Fugarolas-Gómez
- Departamento de Química Inorgánica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Naytzé Ortíz-Pastrana
- Departamento de Química Inorgánica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
- Department of Chemistry Cinvestav, Ciudad de Mexico, Mexico
| | - Horacio López-Sandoval
- Departamento de Química Inorgánica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | | | | | - Philipp J. Altmann
- Catalysis Research Center, Technische Universität München, Garching, Germany
| | - Norah Barba-Behrens
- Departamento de Química Inorgánica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
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Kakekhani A, Roling LT, Kulkarni A, Latimer AA, Abroshan H, Schumann J, AlJama H, Siahrostami S, Ismail-Beigi S, Abild-Pedersen F, Nørskov JK. Nature of Lone-Pair–Surface Bonds and Their Scaling Relations. Inorg Chem 2018; 57:7222-7238. [DOI: 10.1021/acs.inorgchem.8b00902] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arvin Kakekhani
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Luke T. Roling
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Ambarish Kulkarni
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Allegra A. Latimer
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Hadi Abroshan
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Julia Schumann
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Hassan AlJama
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Samira Siahrostami
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Sohrab Ismail-Beigi
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, United States
| | - Frank Abild-Pedersen
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Jens K. Nørskov
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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Kashyap C, Ullah SS, Mazumder LJ, Kanti Guha A. Non-covalent interaction in benzene and substituted benzene: A theoretical study. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.03.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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50
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Saraswat M, Venkataramani S. Through bond and through space interactions in dehydro-diazine radicals: a case study of 3c-5e interactions. Phys Chem Chem Phys 2018; 20:4386-4395. [PMID: 29369313 DOI: 10.1039/c7cp07579k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Owing to the 3c-5e (3-centred-5-electrons) interactions between two nitrogen lone pairs and a radical electron, the dehydrodiazine radical isomers are very interesting from the fundamental point of view. Among them, pyrimidine has three (1a-1c), pyridazine has two (2a and 2b) and pyrazine has only one (3a) radical isomer. Based on quantum chemical calculations at the (U)B3LYP, (U)M06-2X, (U)BLYP, CBS-QB3 and (U)CCSD(T) levels with cc-pVTZ as the basis set, we found the 4-dehydropyrimidine (1b) radical to be the most stable isomer among the three pyrimidine radicals, followed by the 2-dehydropyrimidine (1a) and 5-dehydropyrimidine (1c) radical isomers. In the case of pyridazine, 3-dehydro radical isomer (2a) is more stable than 4-dehydropyridazine (2b). Bond dissociation energy (BDE) calculations and estimation of radical stabilization energies (RSE) using isodesmic reactions revealed the stability order among the six isomeric diazine radicals as 1c < 2b < 2a < 1a < 3a < 1b. Spin densities at each radical centre and non-zero values at nitrogen centres provided information about the extent of delocalization of radical electrons, which was consistent with the relative stability order of all the isomers. The multiconfigurational CASSCF and natural bond orbital (NBO) calculations suggested the presence of direct through space interactions (between lone pairs and a radical, TS) that play a dominant role over the through bond (through intervening bonds, TB) interactions in deciding the stability order. To confirm these results, we have also estimated the proton affinities (PAs) for each nitrogen atom and compared them with their respective parent diazines, where lowering of the PA values convincingly envisaged the extent and strength of interactions between the nitrogen and radical centre. Atoms-in-molecules (AIM) analysis and estimation of hyperfine coupling constants have also been performed to verify these results. All these results showed that the through space interaction between the lone pair and the radical electron is very important for the electronic structural and stability aspects in dehydrodiazine radicals.
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Affiliation(s)
- Mayank Saraswat
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector-81, Knowledge City, SAS Nagar, Mohali, Punjab - 140306, India.
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