1
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Sun C, Liu Q, Meng L, Li X. Small molecules (CO 2 , iPrNCO, and iPrNCNiPr) activation by the metallomimetics (μ-Hydrido) diborane anion: A DFT investigation on mechanism and chemoselectivity controlling. J Comput Chem 2024; 45:331-340. [PMID: 37846101 DOI: 10.1002/jcc.27240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/18/2023]
Abstract
Main-group metallomimetics provide a new way to replace transition metal complexes to activate inert small molecules under mild conditions. In this work, the activation mechanisms of CO2 , iPrNCO, and iPrNCNiPr by (μ-Hydrido) diborane anion ([1H]- ) have been investigated by density functional theory (DFT) calculations. Two different activation sites, BB versus BH bond of [1H]- , are investigated and compared. The results show that these inert molecules can be activated by [1H]- through cycloadditions under mild conditions. The reactions with iPrNCO and iPrNCNiPr are dynamic and thermodynamic controlling, the obtained products are related not only to the energy barrier but also to the stability of the products. Moreover, the competition for BB/BH bond site activation is directly related to the steric effect of small molecules. CO2 , which is without steric hindrance, can only be activated by the BB bond, whereas iPrNCNiPr can only be activated by the BH bond due to the large steric effect. The medium iPrNCO can be activated not only by the BB bond but also by the BH bond. Our study provides theoretical explanations for the reaction activity and chemoselectivity controlling of the title reaction, and displays the potential applications for compounds containing boron-boron bonds and inert small molecule activation.
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Affiliation(s)
- ChenFei Sun
- College of Chemistry and Material Science, Hebei Key Laboratory of Inorganic and Nano-Materials, Hebei Normal University, Shijiazhuang, China
| | - Qing Liu
- College of Chemistry and Material Science, Hebei Key Laboratory of Inorganic and Nano-Materials, Hebei Normal University, Shijiazhuang, China
| | - Lingpeng Meng
- College of Chemistry and Material Science, Hebei Key Laboratory of Inorganic and Nano-Materials, Hebei Normal University, Shijiazhuang, China
| | - Xiaoyan Li
- College of Chemistry and Material Science, Hebei Key Laboratory of Inorganic and Nano-Materials, Hebei Normal University, Shijiazhuang, China
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2
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Kozuch S. When, Where and Why Boron Prefers Boron to Nitrogen. Chemphyschem 2024; 25:e202300875. [PMID: 38146920 DOI: 10.1002/cphc.202300875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 12/27/2023]
Abstract
Boron is the archetypal Lewis acid, and therefore it is only natural that it prefers to bind nitrogen, its usual Lewis base counterpart. To challenge this assumption, we present a computationally designed bicyclopentane molecule akin to [1.1.1]propellane, but with pyramidal B and N inner atoms bonded by an "inverted" dative bond. Unexpectedly, the dimer of this system prefers to interact via an atypical boron-boron bond over the supposedly obvious boron-nitrogen bond. A molecular orbital analysis shows that the boron in this peculiar entity acts both as an electron donor and an electron acceptor, making the dimerization an amphoteric-amphoteric interaction process.
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Affiliation(s)
- Sebastian Kozuch
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel, 84105
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3
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Vishwakarma K, Ravi S, Mittal S. Ab initio Modeling of Hydrogen Bonding of Remdesivir and Adenosine with Uridine. Chemphyschem 2024; 25:e202300552. [PMID: 37983746 DOI: 10.1002/cphc.202300552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/18/2023] [Accepted: 11/19/2023] [Indexed: 11/22/2023]
Abstract
Remdesivir (RDV) emerged as an effective drug against the SARS-CoV-2 virus pandemic. One of the crucial steps in the mechanism of action of RDV is its incorporation into the growing RNA strand. RDV, an adenosine analogue, forms Watson-Crick (WC) type hydrogen bonds with uridine in the complementary strand and the strength of this interaction will control efficacy of RDV. While there is a plethora of structural and energetic information available about WC H-bonds in natural base pairs, the interaction of RDV with uridine has not been studied yet at the atomic level. In this article, we aim to bridge this gap, to understand RDV and its hydrogen bonding interactions, by employing density functional theory (DFT) at the M06-2X/cc-pVDZ level. The interaction energy, QTAIM analysis, NBO and SAPT2 are performed for RDV, adenosine, and their complex with uridine to gain insights into the nature of hydrogen bonding. The computations show that RDV has similar geometry, energetic, molecular orbitals, and aromaticity as adenosine, suggesting that RDV is an effective adenosine analogue. The important geometrical parameters, such as bond distances and red-shift in the stretching vibrational modes of adenosine, RDV and uridine identify two WC-type H-bonds. The relative strength of these two H-bonds is computed using QTAIM parameters and the computed hydrogen bond energy. Finally, the SAPT2 study is performed at the minima and at non-equilibrium base pair distances to understand the dominant intermolecular physical force. This study, based on a thorough analysis of a variety of computations, suggests that both adenosine and RDV have similar structure, energetic, and hydrogen bonding behaviour.
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Affiliation(s)
- Kamini Vishwakarma
- School of Advance Science and Languages, VIT Bhopal University, Kothrikalan, Sehore, Madhya, Pradesh, 466114, India
| | - Satyam Ravi
- School of Advance Science and Languages, VIT Bhopal University, Kothrikalan, Sehore, Madhya, Pradesh, 466114, India
| | - Sumit Mittal
- School of Advance Science and Languages, VIT Bhopal University, Kothrikalan, Sehore, Madhya, Pradesh, 466114, India
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4
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Tu YL, Zhang BB, Qiu BS, Wang ZX, Chen XY. Cross-Electrophile C-P III Coupling of Chlorophosphines with Organic Halides: Photoinduced P III and Aminoalkyl Radical Generation Enabled by Pnictogen Bonding. Angew Chem Int Ed Engl 2023; 62:e202310764. [PMID: 37668107 DOI: 10.1002/anie.202310764] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/06/2023]
Abstract
Pnictogen bonding (PnB) has gained recognition as an appealing strategy for constructing novel architectures and unlocking new properties. Within the synthetic community, the development of a straightforward and much simpler protocol for cross-electrophile C-PIII coupling remains an ongoing challenge with organic halides. In this study, we present a simple strategy for photoinduced PnB-enabled cross-electrophile C-PIII couplings using readily available chlorophosphines and organic halides via merging single electron transfer (SET) and halogen atom transfer (XAT) processes. In this photomediated transformation, the PnB formed between chlorophosphines and alkyl amines facilitates the photogeneration of PIII radicals and α-aminoalkyl radicals through SET. Subsequently, the resulting α-aminoalkyl radicals activate C-X bonds via XAT, leading to the formation of carbon radicals. This methodology offers operational simplicity and compatibility with both aliphatic and aromatic chlorophosphines and organic halides.
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Affiliation(s)
- Yong-Liang Tu
- School of Chemical Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Bei-Bei Zhang
- School of Chemical Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing-Sheng Qiu
- School of Chemical Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Xiang Wang
- School of Chemical Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
- Binzhou Institute of Technology, Weiqiao-UCAS Science and Technology Park, Binzhou, Shandong Province, 256606, China
| | - Xiang-Yu Chen
- School of Chemical Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
- Binzhou Institute of Technology, Weiqiao-UCAS Science and Technology Park, Binzhou, Shandong Province, 256606, China
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5
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Karthikeyan S, Grishina M, Kandasamy S, Mangaiyarkarasi R, Ramamoorthi A, Chinnathambi S, Pandian GN, John Kennedy L. A review on medicinally important heterocyclic compounds and importance of biophysical approach of underlying the insight mechanism in biological environment. J Biomol Struct Dyn 2023; 41:14599-14619. [PMID: 36914255 DOI: 10.1080/07391102.2023.2187640] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/12/2023] [Indexed: 03/16/2023]
Abstract
Heterocyclic derivatives have more interesting biological properties which hold a remarkable place in pharmaceutical industries due to their unique physiochemical properties and ease of adaption in various biological environments. Of many, the above-said derivatives have been recently examined for their promising action against a few malignancies. Specifically, anti-cancer research has benefited from these derivatives' natural flexibility and dynamic core scaffold. In any case, concerning some other promising anti-cancer drugs, heterocyclic derivative doesn't come without deficiencies. To be a successful drug candidate it should poses Absorption, Distribution, Metabolism and Eliminations (ADME) parameter, and must also have good binding interaction towards carrier protein as well as DNA and less in toxic nature, economically feasible. In this review, we described the overview of biologically important heterocyclic derivatives and their main application in medicine. Further, we focus types of biophysical techniques to understand the binding interaction mechanism.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Subramani Karthikeyan
- Division of Physics, School of Advanced Sciences, Vellore Institute of Technology University, Chennai, India
- Centre for Healthcare Advancement, Innovation and Research, Vellore Institute of Technology University, Chennai, India
| | - Maria Grishina
- Laboratory of Computational Modelling of Drugs, South Ural State University, Chelyabinsk, Russia
| | | | | | - Anitha Ramamoorthi
- Department of Chemistry, Velammal Intitute of Technology, Velammal Knowledge Park, Panchetti, India
| | - Shanmugavel Chinnathambi
- Institute for Integrated Cell-Material Sciences, Institute for Advanced Study, Kyoto University, Kyoto, Japan
| | - Ganesh N Pandian
- Institute for Integrated Cell-Material Sciences, Institute for Advanced Study, Kyoto University, Kyoto, Japan
- Department of Molecular Engineering, Kyoto University, Kyoto, Japan
| | - L John Kennedy
- Division of Physics, School of Advanced Sciences, Vellore Institute of Technology University, Chennai, India
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6
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Waheed Kamran A, Zahoor M, Ali H, Khan S, Abu-farsakh H, Ali S. Chromate Ions Chemisorption over the Exterior Surface of Pristine Boron Nitride (B12N12) Nanocage: A Computational Study. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.110370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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7
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Mojica-Sánchez JP, Langarica-Rivera VM, Pineda-Urbina K, Nochebuena J, Jayaprakash GK, Sandoval ZG. Adsorption of glyphosate on graphene and functionalized graphenes: A DFT study. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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8
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Freindorf M, Delgado AAA, Kraka E. CO bonding in hexa‐ and pentacoordinate carboxy‐neuroglobin: A quantum mechanics/molecular mechanics and local vibrational mode study. J Comput Chem 2022. [DOI: 10.1002/jcc.26973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marek Freindorf
- Department of Chemistry Southern Methodist University Dallas Texas USA
| | | | - Elfi Kraka
- Department of Chemistry Southern Methodist University Dallas Texas USA
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9
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Jara-Cortés J, Matta CF, Hernández-Trujillo J. A fast approximate extension of the interacting quantum atoms energy decomposition to excited states. J Comput Chem 2022; 43:1068-1078. [PMID: 35470908 DOI: 10.1002/jcc.26863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/25/2022] [Accepted: 03/23/2022] [Indexed: 11/11/2022]
Abstract
An approach is developed for the fast calculation of the interacting quantum atoms energy decomposition (IQA) from the information contained in the first order reduced density matrix only. The proposed methodology utilizes an approximate exchange-correlation density from Density Matrix Functional Theory without the need to evaluate the correlation-exchange contribution directly. Instead, weight factors are estimated to decompose the exact Vxc into atomic and pairwise contributions. In this way, the sum of the IQA contributions recovers the energy obtained from the electronic structure calculation. This method can, hence, be applied to obtain atomic contributions in excited states on the same footing as in their ground states using any method that delivers the reduced first-order density matrix. In this way, one can locate chromophores from first principles quantum chemical calculations. Test calculations on the ground and excited states of a set of small molecules indicate that the scaled atomic contributions reproduce vertical electronic transition energies calculated exactly. This approach may be useful to extend the applicability of the IQA approach in the study of large photochemical systems especially when the calculations of the second order reduced density matrices is prohibitive or not possible.
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Affiliation(s)
- Jesús Jara-Cortés
- Unidad Académica de Ciencias Básicas e Ingenierías, Universidad Autónoma de Nayarit, Tepic, Mexico
| | - Chérif F Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, Canada
| | - Jesús Hernández-Trujillo
- Departamento de Física y Química Teórica, Facultad de Química, UNAM. Circuito Escolar, Ciudad Universitaria, Mexico City, Mexico
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10
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Lu Y, Liu Q, Wang ZX, Chen XY. Alkynyl Sulfonium Salts Can Be Employed as Chalcogen-Bonding Catalysts and Generate Alkynyl Radicals under Blue-Light Irradiation. Angew Chem Int Ed Engl 2022; 61:e202116071. [PMID: 35118784 DOI: 10.1002/anie.202116071] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Indexed: 12/14/2022]
Abstract
Chalcogen bonding (ChB) has emerged as a promising tool in organic synthesis. However, compared with the well-developed selenium- and tellurium-based salt catalysts, the ChB catalysis of sulfonium salts is still unknown. Here, we report a new type of alkynyl-sulfonium salt ChB catalysis for various ionic transformations, including transfer hydrogenation, bromination, bromolactonization, dimerization of 1,1-diphenylethylene, nitro-Michael addition reaction and Ritter reaction. More importantly, the photocapability of ChB was first demonstrated to generate alkynyl radicals for the synthesis of a variety of chalcogenoacetylenes. Mechanistic studies shed light on the mechanism of the photoinduced reactions and confirmed the involvement of alkynyl radicals which are difficult to generate otherwise.
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Affiliation(s)
- Yu Lu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Liu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Xiang Wang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang-Yu Chen
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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11
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Tahenti M, Issaoui N, Roisnel T, Marouani H. Synthesis, characterization, and computational survey of a novel material template o-xylylenediamine. J IRAN CHEM SOC 2022. [DOI: 10.1007/s13738-021-02392-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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12
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Sajjad MA, Schwerdtfeger P, Cai Y, Waters JM, Harrison JA, Nielson AJ. Bis‐anagostic structures in N,N’‐chelate ligand complexes of palladium(II). Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202200027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Peter Schwerdtfeger
- Massey University - Albany Campus: Massey University - Auckland Campus Chemistry NEW ZEALAND
| | - Yicao Cai
- Massey University - Albany Campus: Massey University - Auckland Campus Chemistry NEW ZEALAND
| | - Joyce M. Waters
- Massey University - Albany Campus: Massey University - Auckland Campus Chemistry NEW ZEALAND
| | - John A. Harrison
- Massey University - Albany Campus: Massey University - Auckland Campus Chemistry NEW ZEALAND
| | - Alastair James Nielson
- Massey University at Albany Chemistry. INS Albany CampusPrivate bag 102 904 NSMC Private Bag 102 904 Auckland NEW ZEALAND
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13
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Chen X, Lu Y, Liu Q, Wang ZX. Alkynyl Sulfonium Salts Can Be Employed as Chalcogen‐Bonding Catalysts and Generate Alkynyl Radicals under Blue‐Light Irradiation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xiangyu Chen
- University of Chinese Academy of Sciences School of Chemical Sciences Huaibei Town, 101408 Beijing 101408 Beijing CHINA
| | - Yu Lu
- University of the Chinese Academy of Sciences School of Chemical Sciiences CHINA
| | - Qiang Liu
- University of the Chinese Academy of Sciences Schoole of Chemical Sciences CHINA
| | - Zhi-Xiang Wang
- University of the Chinese Academy of Sciences School of Chemical Sciences CHINA
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14
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David J, Gómez S, Guerra D, Guerra D, Restrepo A. A Comprehensive Picture of the Structures, Energies, and Bonding in the Alanine Dimers. Chemphyschem 2021; 22:2401-2412. [PMID: 34554628 DOI: 10.1002/cphc.202100585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/22/2021] [Indexed: 12/14/2022]
Abstract
High level quantum mechanical computations and extensive stochastic searches of the potential energy surfaces of the Alanine dimers uncover rich and complex structural and interaction landscapes. A total of 416 strongly bound (up 13.4 kcal mol-1 binding energies at the DLPNO-CCSD(T)/6-311++G(d,p) level corrected by the basis set superposition error and by the zero point vibrational energies over B3LYP-D3 geometries), close energy equilibrium structures were located, bonded via 32 specific types of intermolecular contacts including Y⋅⋅⋅H-X primary and Y⋅⋅⋅H-C secondary hydrogen bonds, H⋅⋅⋅H dihydrogen contacts, and non conventional anti-electrostatic Y δ - ⋯ X δ - interactions. The putative global minimum is triply degenerate, corresponding to the structure of the common dimer of a carboxylic acid. All quantum descriptors of chemical bonding point to a multitude of weak individual interactions within each dimer, whose cumulative effect results in large binding energies and in an attractive fluxional wall of non-covalent interactions in the interstitial region between the monomers.
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Affiliation(s)
- Jorge David
- Escuela de Ciencias, Departamento de Ciencias Físicas, Universidad Eafit, AA 3300, Medellín, Colombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Doris Guerra
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Dario Guerra
- Departamento de Educación y Ciencias Básicas, Instituto Tecnológico Metropolitano, Calle 73 No. 76 A-354, Medellín, Colombia
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
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15
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Florez E, Acelas N, Gomez S, Hadad C, Restrepo A. To be or not to be? that is the entropic, enthalpic, and molecular interaction dilemma in the formation of (water)20 clusters and methane clathrate. Chemphyschem 2021; 23:e202100716. [PMID: 34761856 DOI: 10.1002/cphc.202100716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/08/2021] [Indexed: 11/09/2022]
Abstract
A detailed analysis under a comprehensive set of theoretical and computational tools of the thermodynamical factors and of the intermolecular interactions behind the stabilization of a well known set of (water)20 cavities and of the methane clathrate is offered in this work. Beyond the available reports of experimental characterization at extreme conditions of most of the systems studied here, all clusters should be amenable to experimental detection at 1 atm and moderate temperatures since 280 K marks the boundary at which, ignoring reaction paths, formation of all clusters is no longer spontaneous from the 20H2O → (H2O)20 and CH4 + 20H2O → CH4@512 processes. As a function of temperature, a complex interplay leading to the free energy of formation occurs between the destabilizing entropic contributions, mostly due to cluster vibrations, and the stabilizing enthalpic contributions, due to intermolecular interactions and the PV term, is best illustrated by the highly symmetric 512 cage consistently showing signs of stronger intermolecular bonding despite having smaller binding energy than the other clusters. A fluxional wall of attractive non-covalent interactions, arising because of the cumulative effect of a large number of tiny individual charge transfers to the interstitial region, plays a pivotal role stabilizing the CH4@512 clathrate.
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Affiliation(s)
- Elizabeth Florez
- Universidad de Medellín: Universidad de Medellin, Ciencias basicas, COLOMBIA
| | - Nancy Acelas
- Universidad de Medellín: Universidad de Medellin, Ciencias Basicas, COLOMBIA
| | - Sara Gomez
- Scuola Normale Superiore Classe di Scienze, Chemistry, ITALY
| | - Cacier Hadad
- Universidad de Antioquía: Universidad de Antioquia, Chemistry, COLOMBIA
| | - Albeiro Restrepo
- Universidad de Antioquia, Chemistry, AA 1226, 00000, Medellin, COLOMBIA
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16
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Duarte LJ, Richter WE, Bruns RE, Popelier PLA. Electrostatics Explains the Reverse Lewis Acidity of BH 3 and Boron Trihalides: Infrared Intensities and a Relative Energy Gradient (REG) Analysis of IQA Energies. J Phys Chem A 2021; 125:8615-8625. [PMID: 34549960 PMCID: PMC8503881 DOI: 10.1021/acs.jpca.1c05766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The reaction path
for the formation of BX3–NH3 (X = H,
F, Cl, Br) complexes was divided into two processes:
(i) rehybridization of the acid while adopting a pyramidal geometry,
and (ii) the complex formation from the pyramidal geometries of the
acid and base. The interacting quantum atom (IQA) method was used
to investigate the Lewis acidity trend of these compounds. This topological
analysis suggests that the boron–halogen bond exhibits a considerable
degree of ionicity. A relative energy gradient (REG) analysis on IQA
energies indicates that the acid–base complex formation is
highly dependent on electrostatic energy. With increasing halogen
electronegativity, a higher degree of ionicity of the B–X is
observed, causing an increase in the absolute value of X and B charges.
This increases not only the attractive electrostatic energy between
the acid and base but also enhances the repulsive energy. The latter
is the main factor behind the acidity trend exhibited by trihalides.
Changes in geometry are relevant only for complexes where BH3 acts as an acid, where lower steric hindrance facilitates the adoption
of the pyramidal geometry observed in the complex. The CCTDP analysis
shows that infrared intensities of BX3–NH3 are determined mostly by the atomic charges and not by the charge
transfer or polarization. The opposite is observed in covalent analogues.
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Affiliation(s)
- Leonardo J Duarte
- Chemistry Institute, University of Campinas, Campinas 13083-861, São Paulo, Brazil
| | - Wagner E Richter
- Department of Chemical Engineering, Federal University of Technology-Paraná, Ponta Grossa 84017-220, Paraná, Brazil
| | - Roy E Bruns
- Chemistry Institute, University of Campinas, Campinas 13083-861, São Paulo, Brazil
| | - Paul L A Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain.,Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain
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17
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Rojas-Valencia N, Gómez S, Núñez-Zarur F, Cappelli C, Hadad C, Restrepo A. Thermodynamics and Intermolecular Interactions during the Insertion of Anionic Naproxen into Model Cell Membranes. J Phys Chem B 2021; 125:10383-10391. [PMID: 34492187 DOI: 10.1021/acs.jpcb.1c06766] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The insertion process of Naproxen into model dimyristoylphosphatidylcholine (DMPC) membranes is studied by resorting to state-of-the-art classical and quantum mechanical atomistic computational approaches. Molecular dynamics simulations indicate that anionic Naproxen finds an equilibrium position right at the polar/nonpolar interphase when the process takes place in aqueous environments. With respect to the reference aqueous phase, the insertion process faces a small energy barrier of ≈5 kJ mol-1 and yields a net stabilization of also ≈5 kJ mol-1. Entropy changes along the insertion path, mainly due to a growing number of realizable microstates because of structural reorganization, are the main factors driving the insertion. An attractive fluxional wall of noncovalent interactions is characterized by all-quantum descriptors of chemical bonding (natural bond orbitals, quantum theory of atoms in molecules, noncovalent interaction, density differences, and natural charges). This attractive wall originates in the accumulation of tiny transfers of electron densities to the interstitial region between the fragments from a multitude of individual intermolecular contacts stabilizing the tertiary drug/water/membrane system.
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Affiliation(s)
- Natalia Rojas-Valencia
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, 050010Medellín, Colombia.,Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, 050026 Medellín, Colombia.,Escuela de Ciencias y Humanidades, Departamento de Ciencias Básicas, Universidad Eafit, AA 3300 Medellín, Colombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Francisco Núñez-Zarur
- Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, 050026 Medellín, Colombia
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Cacier Hadad
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, 050010Medellín, Colombia
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, 050010Medellín, Colombia
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18
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Affiliation(s)
| | - Alireza Fattahi
- Department of Chemistry Sharif University of Technology Tehran Iran
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19
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Abdolmaleki A, Gharibi H, Molavian MR, Norouzi M, Asefifeyzabadi N. Physicochemical modification of hydroxylated polymers to develop thermosensitive double network hydrogels. J Appl Polym Sci 2021. [DOI: 10.1002/app.50778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Amir Abdolmaleki
- Department of Chemistry, College of Sciences Shiraz University Shiraz Iran
- Department of Chemistry Isfahan University of Technology Isfahan Iran
| | - Hamidreza Gharibi
- Department of Chemistry Isfahan University of Technology Isfahan Iran
| | | | | | - Narges Asefifeyzabadi
- Department of Chemistry and Biochemistry Southern Illinois University Carbondale Illinois USA
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20
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Abstract
AbstractThe structural and bonding properties of Bi and Ac complexes with cyclen-based chelating ligands have been studied using relativistic DFT calculations in conjunction with TZ2P all-electron basis sets. Besides the parent cyclen ligand, the study has covered its extensions with pyridine-type (Lpy), carboxylate (DOTA, DOTPA), picolinate (MeDO2PA) and phosphonate (DOTMP) pendant arms. The effect of the cyclen ring size has been probed by increasing it from [12]aneN4 to [16]aneN4. Additional extensions in the DOTA complexes included the H2O ligand at the 9th coordination site as well as the p-SCN-Bn substituent (a popular linker to the targeting vector). The study focuses on the complex stability, the nature of bonding and the differences between Ac and Bi in the complexes. The metal–ligand interactions have been analysed by the Extended Transition State method combined with Natural Orbitals of Chemical Valence theory and Quantum Theory of Atoms in Molecules models.
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21
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Moaven S, Watson BT, Polaske TJ, Karl BM, Unruh DK, Bowling NP, Cozzolino AF. Self-Assembly of Complementary Components Using a Tripodal Bismuth Compound: Pnictogen Bonding or Coordination Chemistry? Inorg Chem 2021; 60:11242-11250. [DOI: 10.1021/acs.inorgchem.1c01232] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Shiva Moaven
- Department of Chemistry and Biochemistry, Texas Tech University, 1204 Boston Avenue, Lubbock, Texas 79409-1061, United States
| | - Brandon T. Watson
- Department of Chemistry and Biochemistry, Texas Tech University, 1204 Boston Avenue, Lubbock, Texas 79409-1061, United States
| | - Thomas J. Polaske
- Department of Chemistry, University of Wisconsin—Stevens Point, 2101 Fourth Avenue, Stevens Point, Wisconsin 54481, United States
| | - Brian M. Karl
- Department of Chemistry, University of Wisconsin—Stevens Point, 2101 Fourth Avenue, Stevens Point, Wisconsin 54481, United States
| | - Daniel K. Unruh
- Department of Chemistry and Biochemistry, Texas Tech University, 1204 Boston Avenue, Lubbock, Texas 79409-1061, United States
| | - Nathan P. Bowling
- Department of Chemistry, University of Wisconsin—Stevens Point, 2101 Fourth Avenue, Stevens Point, Wisconsin 54481, United States
| | - Anthony F. Cozzolino
- Department of Chemistry and Biochemistry, Texas Tech University, 1204 Boston Avenue, Lubbock, Texas 79409-1061, United States
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22
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Jin E, Yang Q, Ju CW, Chen Q, Landfester K, Bonn M, Müllen K, Liu X, Narita A. A Highly Luminescent Nitrogen-Doped Nanographene as an Acid- and Metal-Sensitive Fluorophore for Optical Imaging. J Am Chem Soc 2021; 143:10403-10412. [PMID: 34224242 PMCID: PMC8283754 DOI: 10.1021/jacs.1c04880] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Dibenzo[hi,st]ovalene (DBOV)
has excellent photophysical properties, including strong fluorescence
and high ambient stability. Moreover, the optical blinking properties
of DBOV have enabled optical super-resolution single-molecule localization
microscopy with an imaging resolution beyond the diffraction limit.
Various organic and inorganic fluorescent probes have been developed
for super-resolution imaging, but those sensitive to pH and/or metal
ions have remained elusive. Here, we report a diaza-derivative of
DBOV (N-DBOV), synthesized in eight steps with a total yield of 15%.
Nitrogen (N)-bearing zigzag edges were formed through oxidative cyclization
of amino groups in the last step. UV–vis and fluorescence spectroscopy
of N-DBOV revealed its promising optical properties comparable to
those of the parent DBOV, while cyclic voltammetry and density functional
theory calculations highlighted its lower orbital energy levels and
potential n-type semiconductor character. Notably,
in contrast to that of the parent DBOV, the strong luminescence of
N-DBOV is dependent on pH and the presence of heavy metal ions, indicating
the potential of N-DBOV in sensing applications. N-DBOV also exhibited
pH-responsive blinking, which enables pH-sensitive super-resolution
imaging. Therefore, N-DBOV appears to be a highly promising candidate
for fluorescence sensing in biology and environmental analytics.
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Affiliation(s)
- Enquan Jin
- Max Planck Institute for Polymer Research, Mainz 55128, Germany
| | - Qiqi Yang
- Max Planck Institute for Polymer Research, Mainz 55128, Germany
| | - Cheng-Wei Ju
- Max Planck Institute for Polymer Research, Mainz 55128, Germany.,College of Chemistry, Nankai University, Tianjin 300071, China
| | - Qiang Chen
- Max Planck Institute for Polymer Research, Mainz 55128, Germany
| | | | - Mischa Bonn
- Max Planck Institute for Polymer Research, Mainz 55128, Germany
| | - Klaus Müllen
- Max Planck Institute for Polymer Research, Mainz 55128, Germany.,Institute of Physical Chemistry, Johannes Gutenberg-University, Duesbergweg 10-14, Mainz 55128, Germany
| | - Xiaomin Liu
- Max Planck Institute for Polymer Research, Mainz 55128, Germany
| | - Akimitsu Narita
- Max Planck Institute for Polymer Research, Mainz 55128, Germany.,Organic and Carbon Nanomaterials Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa 904-0495, Japan
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23
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Majumdar D, Pal TK, Sakib SA, Das S, Bankura K, Mishra D. Synthesis, spectroscopic characterization, and SC-XRD study of one privileged heteronuclear Ni(II)/Hg(II)-Salen complex: An exclusive DFT outlook. INORG CHEM COMMUN 2021. [DOI: 10.1016/j.inoche.2021.108609] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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24
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Shen S, Jing X, Zhang X, Li X, Zeng Y. The competition and cooperativity of hydrogen/halogen bond and π-hole bond involving the heteronuclear ethylene analogues. J Comput Chem 2021; 42:908-916. [PMID: 33729600 DOI: 10.1002/jcc.26513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/07/2021] [Accepted: 03/01/2021] [Indexed: 11/08/2022]
Abstract
The noncovalent interactions involving heteronuclear ethylene analogues H2 CEH2 (E = Si, Ge and Sn) have been studied by the Møller-Plesset perturbation theory to investigate the competition and cooperativity between the hydrogen/halogen bond and π-hole bond. H2 CEH2 has a dual role of being a Lewis base and acid with the region of π-electron accumulation above the carbon atom and the region of π-electron depletion (π-hole) above the E atom to participate in the NCX···CE (X = H and Cl) hydrogen/halogen bond and CE···NCY (Y = H, Cl, Li and Na) π-hole bond, respectively. When HCN/ClCN interacts with H2 CEH2 by two sites, the strength of hydrogen bond/halogen bond is stronger than that of π-hole bond. The π-hole bond becomes obviously stronger when the metal substituent of YCN (Y = Li and Na) interacting with H2 CEH2 , showing the character of partial covalent, its strength is much greater than that of hydrogen/halogen bond. In the ternary complexes, both hydrogen/halogen bond and π-hole bond are simultaneously strengthened compared to those in the binary complexes, especially in the systems containing alkali metal.
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Affiliation(s)
- Shaojie Shen
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China
| | - Xinyue Jing
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China
| | - Xueying Zhang
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China.,Hebei Key Laboratory of Inorganic Nano-Materials, Hebei Normal University, Shijiazhuang, China
| | - Xiaoyan Li
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, China.,Hebei Key Laboratory of Inorganic Nano-Materials, 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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25
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Bavafa S, Nowroozi A, Ebrahimi A. The cooperativity and diminutive effects between the cation-π and aerogen bond in some complexes of heterocyclic rings. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1897172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Sadeghali Bavafa
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan (USB), Zahedan, Iran
| | - Alireza Nowroozi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan (USB), Zahedan, Iran
| | - Ali Ebrahimi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan (USB), Zahedan, Iran
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26
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Yuan Y, Fu S, Huo D, Su W, Zhang R, Wei J. Multipolar electrostatics for hairpin and pseudoknots in RNA: Improving the accuracy of force field potential energy function. J Comput Chem 2021; 42:771-786. [PMID: 33586809 DOI: 10.1002/jcc.26497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/17/2021] [Accepted: 01/24/2021] [Indexed: 12/19/2022]
Abstract
Molecular dynamics (MD) simulations that rely on force field methods has been widely used to explore the structure and function of RNAs. However, the current commonly used force fields are limited by the electrostatic description offered by atomic charge, dipole and at most quadrupole moments, failing to capture the anisotropic picture of electronic features. Actually, the distribution of electrons around atomic nuclei is not spherically symmetric but is geometry dependent. A multipolar electrostatic model based on high rank multipole moments is described in this work, which allows us to combine polarizability and anisotropy of electron density. RNA secondary structure was taken as a research system, and its substructures including stem, loops (hairpin loop, bulge loop, internal loop, and multi-branch loop), and pseudoknots (H-type and K-type) were investigated, respectively, as well as the hairpin. First, the atom-atom electrostatic properties derived from one chain of a duplex RNA 2MVY in our previous work (Ref. 58) were measured by the pilot RNA systems of hairpin, hairpin loop, stem, and H-type pseudoknot, respectively. The prediction results were not satisfactory. Consequently, to obtain a general set of electrostatic parameters for RNA force fields, the convergence behavior of the atom-atom electrostatic interactions in the pilot RNA systems was explored using high rank atomic multipole moments. The pilot RNA systems were cut into four types of different-sized molecular fragments, and the single nucleotide fragment and nucleotide-paired fragment proved to be the most reasonable systems for base-unpairing regions and base-pairing regions to investigate the convergence behavior of all types of atom-atom electrostatic interactions, respectively. Transferability of the electrostatic properties drawn from the pilot RNA systems to the corresponding test systems was also investigated. Furthermore, the convergence behavior of atomic electrostatic interactions in other substructures including bulge loop, internal loop, multi-branch loop, and K-type pseudoknot was expected to be modeled via the hairpin.
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Affiliation(s)
- Yongna Yuan
- School of Information Science & Engineering, Lanzhou University, Lanzhou, Gansu, China
| | - Shaowei Fu
- School of Information Science & Engineering, Lanzhou University, Lanzhou, Gansu, China
| | - Dongxu Huo
- School of Information Science & Engineering, Lanzhou University, Lanzhou, Gansu, China
| | - Wei Su
- School of Information Science & Engineering, Lanzhou University, Lanzhou, Gansu, China
| | - Ruisheng Zhang
- School of Information Science & Engineering, Lanzhou University, Lanzhou, Gansu, China
| | - Jiaxuan Wei
- School of Information Science & Engineering, Lanzhou University, Lanzhou, Gansu, China
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27
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Arokiyanathan AL, Lakshmipathi S. Theoretical perspective on the interaction of CO2 and H2O molecules with functionalized magnesium and scandium phthalocyanines. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02732-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Grineva AA, Filippov OA, Canac Y, Sortais JB, Nefedov SE, Lugan N, César V, Valyaev DA. Experimental and Theoretical Insights into the Electronic Properties of Anionic N-Heterocyclic Dicarbenes through the Rational Synthesis of Their Transition Metal Complexes. Inorg Chem 2021; 60:4015-4025. [DOI: 10.1021/acs.inorgchem.1c00073] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alina A. Grineva
- LCC-CNRS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31077 Toulouse Cedex 4, France
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 31 Leninsky Pr., Moscow 119991, Russia
| | - Oleg A. Filippov
- A. N. Nesmeyanov Institute of Organoelement Compounds (INEOS), Russian Academy of Sciences, 28 Vavilov str., GSP-1, B-334, Moscow 119991, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklay Str., Moscow 117997, Russia
| | - Yves Canac
- LCC-CNRS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31077 Toulouse Cedex 4, France
| | - Jean-Baptiste Sortais
- LCC-CNRS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31077 Toulouse Cedex 4, France
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris Cedex 05, France
| | - Sergei E. Nefedov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 31 Leninsky Pr., Moscow 119991, Russia
| | - Noël Lugan
- LCC-CNRS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31077 Toulouse Cedex 4, France
| | - Vincent César
- LCC-CNRS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31077 Toulouse Cedex 4, France
| | - Dmitry A. Valyaev
- LCC-CNRS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31077 Toulouse Cedex 4, France
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29
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30
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Li Y, Meng L, Zeng Y. Comparison of Anion‐Anion Halogen Bonds with Neutral‐Anion Halogen Bonds in the Gas Phase and Polar Solvents. Chempluschem 2021; 86:232-240. [DOI: 10.1002/cplu.202000734] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/25/2021] [Indexed: 01/23/2023]
Affiliation(s)
- Ying Li
- College of Chemistry and Materials Science Hebei Normal University Shijiazhuang 050024 P. R. China
| | - Lingpeng Meng
- College of Chemistry and Materials Science Hebei Normal University Shijiazhuang 050024 P. R. China
| | - Yanli Zeng
- College of Chemistry and Materials Science Hebei Normal University Shijiazhuang 050024 P. R. China
- National Experimental Chemistry Teaching Center Hebei Normal University) Shijiazhuang 050024 P. R. China
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31
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Zhang N, Huo S, Meng L, Li X. Nb(
i
PrNPMe
2
)
3
Fe–PMe
3
: A potential high reactivity heterobimetallic catalyst for acetylene cycloadditions. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.5966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Na Zhang
- College of Chemistry and Material Science Hebei Normal University Road East of 2nd Ring South Shijiazhuang 050024 China
| | - Suhong Huo
- College of Chemistry and Material Science Hebei Normal University Road East of 2nd Ring South Shijiazhuang 050024 China
| | - Lingpeng Meng
- National Demonstration Center for Experimental Chemistry Hebei Normal University Road East of 2nd Ring South Shijiazhuang 050024 China
| | - Xiaoyan Li
- College of Chemistry and Material Science Hebei Normal University Road East of 2nd Ring South Shijiazhuang 050024 China
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32
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Nanayakkara S, Freindorf M, Tao Y, Kraka E. Modeling Hydrogen Release from Water with Borane and Alane Catalysts: A Unified Reaction Valley Approach. J Phys Chem A 2020; 124:8978-8993. [PMID: 33064477 DOI: 10.1021/acs.jpca.0c07244] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The unified reaction valley approach combined with the local vibrational mode and ring puckering analysis is applied to investigate the hydrogen evolution from water in the presence of small hydrides such as BH3, metal hydrides as AlH3, and their derivatives. We studied a series of reactions involving BH3, AlH3, B2H6, Al2H6, and AlH3BH3 with one- and two-water molecules, considering multiple reaction paths. In addition, the influence of the aqueous medium was examined. A general reaction mechanism was identified for most of the reactions. Those that deviate could be associated with unusually high reaction barriers with no hydrogen release. The charge transfer along the reaction path suggests that a viable hydrogen release is achieved when the catalyst adopts the role of a charge donor during the chemical processes. The puckering analysis showed that twistboat and boat forms are the predominant configurations in the case of an intermediate six-membered ring formation, which influences the activation barrier. The local mode analysis was used as a tool to detect the H-H bond formation as well as to probe catalyst regenerability. Based on the correlation between the activation energy and the change in the charge separation for cleaving O-H and B(Al)-H bonds, two promising subsets of reactions could be identified along with prescriptions for lowering the reaction barrier individually with electron-donating/withdrawing substituents.
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Affiliation(s)
- Sadisha Nanayakkara
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Yunwen Tao
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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33
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Sadjadi S, Matta CF, Hamilton IP. Bonding and metastability for Group 12 dications. J Comput Chem 2020; 42:40-49. [PMID: 33063900 DOI: 10.1002/jcc.26431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 11/06/2022]
Abstract
Electronic structure and bonding properties of the Group 12 dications M2 2+ (M = Zn, Cd, Hg) are investigated and electron density-derived quantities are used to characterize the metastability of these species. Of particular interest are the complementary descriptions afforded by the Laplacian of the electron density ∇2 ρ(r) and the one-electron Bohm quantum potential (Q = ∇ 2 ρ r / 2 ρ r ) along the bond path. Further, properties derived from the pair density including the localization-delocalization matrices (LDMs) and the interacting quantum atoms (IQA) energies are analyzed within the framework of the quantum theory of atoms in molecules (QTAIM). From the crossing points of the singlet (ground) and triplet (excited) potential energy curves, the barriers for dissociation (BFD) are estimated to be 25.2 kcal/mol (1.09 eV) for Zn2 2+ , 22.8 kcal/mol (0.99 eV) for Cd2 2+ , and 26.4 kcal/mol (1.14 eV) for Hg2 2+ . For comparison and benchmarking purposes, the case of N2 2+ is considered as a texbook example of metastability. At the equilibrium geometries, LDMs, which are used here as an electronic fingerprinting tool, discriminate and group together Group 12 M2 2+ from its isoelectronic Group 11 M2 . While "classical" bonding indices are inconclusive in establishing regions of metastability in the bonding, it is shown that the one-electron Bohm quantum potential is promising in this regard.
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Affiliation(s)
- SeyedAbdolreza Sadjadi
- Department of Physics, Faculty of Science, Laboratory for Space Research, The University of Hong Kong, Hong Kong SAR, China
| | - Chérif F Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, Canada.,Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ian P Hamilton
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, Ontario, Canada
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34
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Lomas JS, Rosenberg RE, Brémond E. Cooperativity in a cycloalkane-1,2/1,3-polyol corona: Topological hydrogen bonding in 1,2-diol motifs. Magn Reson Chem 2020; 58:957-968. [PMID: 32529717 DOI: 10.1002/mrc.5065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/06/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
A corona, consisting of 18 carbon atoms bearing 12 hydroxy groups in a continuous hydrogen-bonded chain, is built up by alternating degenerate conformations of alternating alkane-1,2-diol and 1,3-diol motifs. Geometries, proton nuclear magnetic resonance shifts and interaction energies for the dodecahydroxycyclo-octadecane and selected fragments are determined by density functional calculations at the B3LYP/6-311+G(d,p) level. Cooperative effects of O-H⋯O-H bonding are evident from the simple juxtaposition of these two motifs with a common OH group in butane-1,2,4-triol conformers. Bracketing a 1,2-diol motif with two 1,3-diol motifs in hexane-1,3,4,6-tetrol leads to a structure in which the 1,2-diol motif displays a bond critical point for hydrogen bonding. This is associated with enhancement of the shift of the hydrogen-bonded OH proton and of the corresponding H⋯O interaction energy. The full corona has a complete outer ring of O-H⋯O-H bond paths, and an inner ring of bond paths, due to C-H⋯H-C hydrogen-hydrogen bonding, which result in a central ring critical point. The topological O-H⋯O-H hydrogen bond, never seen in simple alkane-1,2-diols, is associated with cooperative enhancement of the H⋯O interaction energy, but this is not a necessary condition for a bond path: values for topological C-H⋯H-C hydrogen-hydrogen bonds can be as low as -0.4 kcal mol-1 .
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Affiliation(s)
- John S Lomas
- ITODYS, CNRS, Université de Paris, Paris, France
| | | | - Eric Brémond
- ITODYS, CNRS, Université de Paris, Paris, France
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35
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Affiliation(s)
| | - Alireza Fattahi
- Department of Chemistry Sharif University of Technology Tehran Iran
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36
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Tanzifi M, Tavakkoli Yaraki M, Beiramzadeh Z, Heidarpoor Saremi L, Najafifard M, Moradi H, Mansouri M, Karami M, Bazgir H. Carboxymethyl cellulose improved adsorption capacity of polypyrrole/CMC composite nanoparticles for removal of reactive dyes: Experimental optimization and DFT calculation. Chemosphere 2020; 255:127052. [PMID: 32679636 DOI: 10.1016/j.chemosphere.2020.127052] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/07/2020] [Accepted: 05/10/2020] [Indexed: 06/11/2023]
Abstract
In this study, polypyrrole/carboxymethyl cellulose nanocomposite particles (PPy/CMC NPs) were synthesized and applied for removal of reactive red 56 (RR56)and reactive blue 160 (RB160) as highly toxic dyes. The amount of CMC was found significantly effective on the surface adsorption efficiency. Different optimization methods including the genetic programming, response surface methodology, and artificial neural network (ANN) were used to optimize the effect of different parameters including pH, adsorption time, initial dye concentration and adsorbent dose. The maximum adsorption of RR56 and RB160 were found under the following optimum conditions: pH of 4 and 5, adsorption time of 55 min and 52 min for RR56 and RB160, respectively, initial dye concentration of 100 mg/L and adsorbent dose of 0.09 g for both dyes. were obtained for RR56 and RB160, respectively. Also, the results indicated that ANN method could predict the experimental adsorption data with higher accuracy than other methods. The analysis of ANN results indicated that the adsorbent dose is the main factor in RR56 removal, followed by time, pH and initial concentration, respectively. However, initial concentration mostly determines the RB160 removal process. The isotherm data for both dyes followed the Langmuir isotherm model with a maximum adsorption capacity of 104.9 mg/g and 120.7 mg/g for RR56 and RB160, respectively. In addition, thermodynamic studies indicated the endothermic adsorption process for both studied dyes. Moreover, DFT calculations were carried out to obtain more insight into the interactions between the dyes and adsorbent. The results showed that the hydrogen bondings and Van der Waals interactions are dominant forces between the two studied dyes and PPy/CMC composite. Furthermore, the interaction energies calculated by DFT confirmed the experimental adsorption data, where PPy/CMC resulted in higher removal of both dyes compared to PPy. The developed nanocomposite showed considerable reusability up to 3 cylces of the batch adsorption process.
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Affiliation(s)
- Marjan Tanzifi
- Department of Chemical Engineering, Ilam University, Ilam, 69315-516, Iran; Nanotechnology Research Institute, Babol Noshirvani University of Technology, Shariati Ave., Babol, Iran.
| | - Mohammad Tavakkoli Yaraki
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore; Institute of Materials Research and Engineering (IMRE), The Agency for Science, Technology and Research (A∗STAR), 2 Fusionopolis Way, #08-03, Innovis, 138634, Singapore.
| | - Zahra Beiramzadeh
- Environmental Research Laboratory, School of Civil Engineering, Iran University of Science and Technology, Tehran, Iran
| | - Leily Heidarpoor Saremi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
| | | | - Hojatollah Moradi
- Surface Phenomenon and Liquid-Liquid Extraction Research Lab, School of Chemical Engineering, University College of Engineering, University of Tehran, Iran
| | - Mohsen Mansouri
- Department of Chemical Engineering, Ilam University, Ilam, 69315-516, Iran
| | - Mojtaba Karami
- Department of Computer and Information Technology, Ilam University, Ilam, Iran
| | - Hossein Bazgir
- Department of Chemical Engineering, Ilam University, Ilam, 69315-516, Iran
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Affiliation(s)
- Bruno Cuevas-Zuviría
- Centro de Biotecnologı́a y Genómica de Plantas (CBGP, UPM-INIA), Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Campus de Montegancedo-UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Luis F. Pacios
- Centro de Biotecnologı́a y Genómica de Plantas (CBGP, UPM-INIA), Instituto Nacional de Investigación y Tecnologı́a Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Campus de Montegancedo-UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
- Departamento de Biotecnologı́a-Biologı́a Vegetal, Escuela Técnica Superior de Ingenierı́a Agraria, Alimentaria y de Biosistemas (ETSIAAB), Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
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38
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Nielson AJ, Harrison JA, Sajjad MA, Schwerdtfeger P. Electronic and Steric Manipulation of the Agostic Interaction in benzo[ h ]quinoline Complexes of Pd(II) and Implications for the Formation of η 1 ‐Pd–C Bonds. Eur J Inorg Chem 2020; 2020:2639-2650. [DOI: 10.1002/ejic.202000348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Acke G, De Baerdemacker S, Martín Pendás Á, Bultinck P. Hierarchies of quantum chemical descriptors induced by statistical analyses of domain occupation number operators. WIREs Comput Mol Sci 2020. [DOI: 10.1002/wcms.1456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Stijn De Baerdemacker
- Department of Chemistry University of New Brunswick Fredericton New Brunswick Canada
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Lomas JS. Cooperativity in alkane-1,2- and 1,3-polyols: NMR, QTAIM, and IQA study of O─H … OH and C─H … OH bonding interactions. Magn Reson Chem 2020; 58:666-684. [PMID: 32201981 DOI: 10.1002/mrc.5014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/26/2020] [Accepted: 02/29/2020] [Indexed: 06/10/2023]
Abstract
Proton nuclear magnetic resonance chemical shifts and atom-atom interaction energies for alkanepolyols with 1,2-diol and 1,3-diol repeat units, and for their 1:1 pyridine complexes, are computed by density functional theory calculations. In the 1,3-polyols, based on a tG'Gg' repeat unit, the only important intramolecular hydrogen bonding interactions are O─H… OH. By quantum theory of atoms in molecules analysis of the electron density, unstable bond and ring critical points are found for such interactions in 1,2-polyols with tG'g repeat units, from butane-1,2,3,4-tetrol onwards and in their pyridine complexes from propane-1,2,3-triol onwards. Several features (OH proton shifts and charges, and interaction energies computed by the interacting quantum atoms approach) are used to monitor the dependence of cooperativity on chain length: This is much less regular in 1,2-polyols than in 1,3-polyols and by most criteria has a higher damping factor. Well defined C─H… OH interactions are found in butane-1,2,3,4-tetrol and higher members of the 1,2-polyol series, as well as in their pyridine complexes: There is no evidence for cooperativity with O─H… OH bonding. For the 1,2-polyols, there is a tenuous empirical relationship between the existence of a bond critical point for O─H… OH hydrogen bonding and the interaction energies of competing exchange channels, but the primary/secondary ratio is always less than unity.
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Affiliation(s)
- John S Lomas
- ITODYS (CNRS UMR-7086), Université de Paris, Paris, France
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Zhang XL, Zhang L, Chen JH, Li CY, Sun WM. On the Interaction between Superatom Al 12Be and DNA Nucleobases/Base Pairs: Bonding Nature and Potential Applications in O 2 Activation and CO Oxidation. ACS Omega 2020; 5:15325-15334. [PMID: 32637806 PMCID: PMC7331033 DOI: 10.1021/acsomega.0c01375] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
The interaction between quasi-chalcogen superatom Al12Be and DNA nucleobases/base pairs has been explored by searching for the most stable Al12Be-X (X = DNA bases and base pairs) complexes. Our results reveal that Al12Be prefers to combine with guanine by two Al-O and Al-N bonds rather than the other DNA bases, no matter in free state or base pair. The formed Al-N and Al-O bonds between Al12Be and DNA bases proved to be strong polar covalent bonds by the Wiberg bond index, nature bond orbitals, atoms in molecules theory, localized molecular orbitals, and electron localization functions analyses. More importantly, it is found that the formed global minimum of Al12Be-G has the ability to activate an oxygen molecule into a peroxide dianion 1O2 2-, which can further catalyze the CO oxidation via the Eley-Rideal mechanism with a small energy barrier of 7.78 kcal/mol. We hope that this study could not only provide an in-depth understanding on the intermolecular interaction between metallic superatoms and DNA at the molecular level but also attract more interest in designing and synthesizing superatom-based heterogeneous catalysts with DNA/nucleobases as basic building blocks.
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Affiliation(s)
- Xiao-Ling Zhang
- Fujian
Key Laboratory of Drug Target Discovery and Structural and Functional
Research, The School of Pharmacy, Fujian Medical University, Fuzhou 350108, People’s Republic of China
| | - Li Zhang
- Fujian
Key Laboratory of Drug Target Discovery and Structural and Functional
Research, The School of Pharmacy, Fujian Medical University, Fuzhou 350108, People’s Republic of China
| | - Jing-Hua Chen
- Fujian
Key Laboratory of Drug Target Discovery and Structural and Functional
Research, The School of Pharmacy, Fujian Medical University, Fuzhou 350108, People’s Republic of China
| | - Chun-Yan Li
- The
School of Pharmacy, Fujian Medical University, Fuzhou 350108, People’s Republic of China
| | - Wei-Ming Sun
- Fujian
Key Laboratory of Drug Target Discovery and Structural and Functional
Research, The School of Pharmacy, Fujian Medical University, Fuzhou 350108, People’s Republic of China
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Zhao DX, Zhao J, Yang ZZ. Partitioning a Molecule into the Atomic Basins and the Resultant Atomic Charges from Quantum Chemical Topology Analysis of the Kohn-Sham Potential. J Phys Chem A 2020; 124:5023-5032. [PMID: 32423212 DOI: 10.1021/acs.jpca.0c01289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum chemical topology (QCT) solidifies the chemical basic concepts demonstrating how a molecular system is intrinsically partitioned into its components and what the interaction lines between them are. Here, QCT analysis using a Kohn-Sham one-electron potential (KSpot) in KS equation as a scalar function is initiated and explored, showing KSpot and its resultant electron force lines have novel spatial features which reveal that an atom in a molecule is a spatial basin governed by its nucleus as a 3D-attractor that terminates all the electron force lines defined by the negative gradient of KSpot and that a chemical bond line is just a minimum path of KSpot for the electron motion. Particularly, the atomic charges from this KSpot QCT analysis are moderate and good, having much lower dependence on basis sets chosen for computation. This may provide a platform for the study of molecular structures and properties, intra- and intermolecular electrostatic interaction, energy decomposition, and construction of force field.
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Affiliation(s)
- Dong-Xia Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, P. R. China
| | - Jian Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, P. R. China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, P. R. China
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Abstract
The reaction of laser-ablated iridium atoms with dinitrogen molecules and nitrogen atoms yield several neutral and ionic iridium dinitrogen complexes such as Ir(N2 ), Ir(N2 )+ , Ir(N2 )2 , Ir(N2 )2 - , IrNNIr, as well as the nitrido complexes IrN, Ir(N)2 and IrIrN. These reaction products were deposited in solid neon, argon and nitrogen matrices and characterized by their infrared spectra. Assignments of vibrational bands are supported by ab initio and first principle calculations as well as 14/15 N isotope substitution experiments. The structural and electronic properties of the new dinitrogen and nitrido iridium complexes are discussed. While the formation of the elusive dinitrido complex Ir(N)2 was observed in a subsequent reaction of IrN with N atoms within the cryogenic solid matrices, the threefold coordinated iridium trinitride Ir(N)3 could not be observed so far.
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Affiliation(s)
- Tony Stüker
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstr. 34/36, 14195, Berlin, Germany
| | - Helmut Beckers
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstr. 34/36, 14195, Berlin, Germany
| | - Sebastian Riedel
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstr. 34/36, 14195, Berlin, Germany
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44
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Mohammed K, Mohammed AA, Abdel Hakiem AF, Mahfouz RM. Computational evaluation on the molecular conformation, vibrational spectroscopy, NBO analysis and molecular docking of betaxolol and betaxolol-chlorthalidone cocrystals. J Mol Struct 2020; 1209:127744. [DOI: 10.1016/j.molstruc.2020.127744] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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45
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Le DTH, Tri NN, Man NTH, Trung NT. A theoretical study of X-H∙∙∙π and X∙∙∙π interactions in the complexes of furan, thiophene, pyrrole and hydrogen halides. VJCH 2020. [DOI: 10.1002/vjch.201900076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Do Thi Hong Le
- Laboratory of Computational Chemistry and Modeling, Department of Chemistry, Quy Nhon University; 170 An Duong Vuong, Quy Nhon, Binh Dinh 55000 Viet Nam
| | - Nguyen Ngoc Tri
- Laboratory of Computational Chemistry and Modeling, Department of Chemistry, Quy Nhon University; 170 An Duong Vuong, Quy Nhon, Binh Dinh 55000 Viet Nam
| | - Nguyen Thi Hong Man
- Laboratory of Computational Chemistry and Modeling, Department of Chemistry, Quy Nhon University; 170 An Duong Vuong, Quy Nhon, Binh Dinh 55000 Viet Nam
| | - Nguyen Tien Trung
- Laboratory of Computational Chemistry and Modeling, Department of Chemistry, Quy Nhon University; 170 An Duong Vuong, Quy Nhon, Binh Dinh 55000 Viet Nam
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46
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Kosti AA, Colreavy-donnelly S, Caraffini F, Anastassi ZA. Efficient Computation of the Nonlinear Schrödinger Equation with Time-Dependent Coefficients. Mathematics 2020; 8:374. [DOI: 10.3390/math8030374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Motivated by the limited work performed on the development of computational techniques for solving the nonlinear Schrödinger equation with time-dependent coefficients, we develop a modified Runge–Kutta pair with improved periodicity and stability characteristics. Additionally, we develop a modified step size control algorithm, which increases the efficiency of our pair and all other pairs included in the numerical experiments. The numerical results on the nonlinear Schrödinger equation with a periodic solution verified the superiority of the new algorithm in terms of efficiency. The new method also presents a good behaviour of the maximum absolute error and the global norm in time, even after a high number of oscillations.
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Affiliation(s)
- Juan F. Van der Maelen
- Departamento de Química Física y Analítica, Universidad de Oviedo, E-33006 Oviedo, Spain
- Centro de Investigación en Nanomateriales y Nanotecnología (CINN-CSIC), E-33940 El Entrego, Spain
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Previtali V, Sánchez-Sanz G, Trujillo C. Theoretical Investigation of Cyano-Chalcogen Dimers and Their Importance in Molecular Recognition. Chemphyschem 2019; 20:3186-3194. [PMID: 31608563 DOI: 10.1002/cphc.201900899] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/07/2019] [Indexed: 11/10/2022]
Abstract
In this manuscript the different noncovalent interactions established between (HYCN)2 dimers (Y=S, Se and Te) have been studied at the MP2 and CCSD(T) level of theory. Several homodimers have been taken into account, highlighting the capacity of these compounds to act both as electron donor and acceptor. The main properties studied were geometries, binding energy (Eb ), and molecular electrostatic potential (MEP). Given the wide application of chalcogen bonds, and more specifically of cyano-chalcogen moieties in molecular recognition, natural bond orbital (NBO), "atoms-in-molecules" (AIM), and electron density shift (EDS) analysis were also used to analyse the different noncovalent interactions upon complexation. The presence of hydrogen, chalcogen and dipole-dipole interactions was confirmed and their implications on molecular recognition were analysed.
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Affiliation(s)
- Viola Previtali
- Center for Nanomedicine & Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, Kongens Lyngby, DK, Denmark
| | - Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal Quay, Dublin 2, Ireland & School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cristina Trujillo
- School of Chemistry Trinity Biomedical Sciences Institute, Trinity College Dublini, 152-160 Pearse Street, Dublin 2, Ireland
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Rojas-Valencia N, Gómez S, Montillo S, Manrique-Moreno M, Cappelli C, Hadad C, Restrepo A. Evolution of Bonding during the Insertion of Anionic Ibuprofen into Model Cell Membranes. J Phys Chem B 2019; 124:79-90. [DOI: 10.1021/acs.jpcb.9b09705] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Natalia Rojas-Valencia
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Sebastian Montillo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | | | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Cacier Hadad
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
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