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Zhang NX, Wang CZ, Lan JH, Wu QY, Shi WQ. Actinide endohedral inter-metalloid clusters of the group 15 elements. Phys Chem Chem Phys 2024; 26:25069-25075. [PMID: 39301705 DOI: 10.1039/d4cp02546f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Inter-metalloid clusters in Zintl chemistry have been extensively studied due to their unique electronic structures and potential applications. In this work, we explored a series of actinide endohedral inter-metalloid clusters of the group 15 elements [An@Bi12]4- (An = Th-U) and [An@Sb12]4- using density functional theory (DFT). [Th@Bi12]4- and [U@Bi12]4- exhibit Cs symmetry, while [Pa@Bi12]4- and [An@Sb12]4- (An = Th-U) have C1 structures. Bonding analyses such as bond order, molecular orbitals (MO) and quantum theory of atoms in molecules (QTAIM) show covalent An-Bi/An-Sb bonding in the clusters. All these clusters are highly stable according to the studied formation reactions and may be accessible experimentally. Compared with [An@Bi12]4-, [An@Sb12]4- possesses stronger bonding interactions, mainly arising from the higher electrostatic interaction energy. For clusters with the same group 15 elements, the bonding interactions increase gradually from Th to U, which is mainly determined by the covalent interactions of An-Bi/An-Sb bonding. This work is expected to provide potential avenues for the construction of robust inter-metalloid clusters of the group 15 elements.
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Affiliation(s)
- Nai-Xin Zhang
- Laboratory of Nuclear Energy Chemistry, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.
- College of Nuclear Science and Technology, Harbin Engineering University, Harbin 150001, China
| | - Cong-Zhi Wang
- Laboratory of Nuclear Energy Chemistry, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.
| | - Jian-Hui Lan
- Laboratory of Nuclear Energy Chemistry, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.
| | - Qun-Yan Wu
- Laboratory of Nuclear Energy Chemistry, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.
| | - Wei-Qun Shi
- Laboratory of Nuclear Energy Chemistry, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.
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2
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Ćeranić K, Milovanović B, Petković M. Density functional theory study of crown ether-magnesium complexes: from a solvated ion to an ion trap. Phys Chem Chem Phys 2023; 25:32656-32665. [PMID: 38010878 DOI: 10.1039/d3cp03991a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Metal ion detection rests on host-guest recognition. We propose a theoretical protocol for designing an optimal trap for a desired metal cation. A host for magnesium ions was sought for among derivatives of crown ethers 12-crown-4, 15-crown-5, and 18-crown-6. Mg-crown complexes and their hydrated counterparts with water molecules bound to the cation were optimized using density functional theory. Based on specific geometric criteria, Interacting quantum atoms analysis and density functional theory-based molecular dynamics of Mg-crown complexes immersed in water, crown ethers for optimal accommodation of Mg2+ in aqueous solution were identified. Selectivity of the chosen crowns towards Na+, K+, and Ca2+ ions is addressed.
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Affiliation(s)
- Katarina Ćeranić
- Innovative Centre of the Faculty of Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia
- University of Belgrade - Faculty of Physical Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia.
| | - Branislav Milovanović
- University of Belgrade - Faculty of Physical Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia.
| | - Milena Petković
- University of Belgrade - Faculty of Physical Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia.
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3
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Anisimov AA, Ananyev IV. Electron density-based protocol to recover the interacting quantum atoms components of intermolecular binding energy. J Chem Phys 2023; 159:124113. [PMID: 38127385 DOI: 10.1063/5.0167874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/11/2023] [Indexed: 12/23/2023] Open
Abstract
A new approach for obtaining interacting quantum atoms-defined components of binding energy of intermolecular interactions, which bypasses the use of standard six-dimensional integrals and two-particle reduced density matrix (2-RDM) reconstruction, is proposed. To examine this approach, three datasets calculated within the density functional theory framework using the def2-TZVP basis have been explored. The first two, containing 53 weakly bound bimolecular associates and 13 molecular clusters taken from the crystal, were used in protocol refinement, and the third one containing other 20 bimolecular and three cluster systems served as a validation reference. In addition, to verify the performance of the proposed approach on an exact 2-RDM, calculations within the coupled cluster formalism were performed for part of the first set systems using the cc-pVTZ basis set. The process of optimization of the proposed parametric model is considered, and the role of various energy contributions in the formation of non-covalent interactions is discussed with regard to the obtained trends.
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Affiliation(s)
- Aleksei A Anisimov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova Str. 28, GSP-1, Moscow 119334, Russian Federation
- National Research University Higher School of Economics, Myasnitskaya Str. 20, Moscow 101000, Russian Federation
| | - Ivan V Ananyev
- N.S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, GSP-1, Leninsky prospect 31, Moscow 119991, Russian Federation
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4
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Hercigonja M, Milovanović B, Etinski M, Petković M. Decorated crown ethers as selective ion traps: Solvent’s role in crown’s preference towards a specific ion. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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5
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The Ultrashort Spike-Ring Interaction in Substituted Iron Maiden Molecules. Molecules 2023; 28:molecules28052244. [PMID: 36903489 PMCID: PMC10004599 DOI: 10.3390/molecules28052244] [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: 02/06/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
The in forms of molecular iron maidens are known for their unique ultrashort interaction between the apical hydrogen atom or its small substituent and the surface of the benzene ring. It is generally believed that this forced ultrashort X⋯π contact is associated with high steric hindrance, which is responsible for specific properties of iron maiden molecules. The main aim of this article is to investigate the influence of significant charge enrichment or depletion of the benzene ring on the characteristics of the ultrashort C-X⋯π contact in iron maiden molecules. For this purpose, three strongly electron-donating (-NH2) or strongly electron-withdrawing (-CN) groups were inserted into the benzene ring of in-[34,10][7]metacyclophane and its halogenated (X = F, Cl, Br) derivatives. It is shown that, despite such extremely electron-donating or electron-accepting properties, the considered iron maiden molecules surprisingly reveal quite high resistance to changes in electronic properties.
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6
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Zhang NX, Wang CZ, Lan JH, Wu QY, Chai ZF, Shi WQ. Actinide-doped boron clusters: from borophenes to borospherenes. Phys Chem Chem Phys 2022; 24:29705-29711. [PMID: 36453525 DOI: 10.1039/d2cp04414e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Similar to graphene and fullerene, metal-doping has been considered to be an effective approach to the construction of highly stable boron clusters. In this work, a series of actinide metal-doped boron clusters AnB36 (An = Pa, Np, Pu, Am, Cm, Bk, and Cf) have been explored using extensive first-principles calculations. We found that the quasi-planar structure of B36 transforms to an endohedral borospherene An@B36 after actinide metal doping. Actinoborospherenes exhibit C2h symmetry with Pa, Np, and Pu dopants and for Am, Cm, Bk and Cf dopants with larger atomic radii, the symmetry of An@B36 is reduced to Ci. Bonding property analyses such as bond order, molecular orbital (MO) and quantum theory of atoms in molecules (QTAIM) analysis show that the covalency of the An-B bonds in C2h An@B36 (An = Pa, Np, and Pu) is higher than that in Ci An@B36 (An = Am, Cm, Bk, and Cf). These endohedral borospherenes are robust according to thermodynamic and dynamic analyses. As expected, the Ci An@B36 clusters are less stable compared to C2h An@B36, which is consistent with the stronger covalent bonds of the latter. These results indicate that the existence of the actinide-boron bonding is essential for the high stability of the An@B36 clusters, confirming that the fullerene-like boron cages can be stabilized by actinide encapsulation. This work is expected to provide potential routes for the construction of robust borospherenes.
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Affiliation(s)
- Nai-Xin Zhang
- Laboratory of Nuclear Energy Chemistry, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.
| | - Cong-Zhi Wang
- Laboratory of Nuclear Energy Chemistry, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.
| | - Jian-Hui Lan
- Laboratory of Nuclear Energy Chemistry, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.
| | - Qun-Yan Wu
- Laboratory of Nuclear Energy Chemistry, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhi-Fang Chai
- Laboratory of Nuclear Energy Chemistry, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.
| | - Wei-Qun Shi
- Laboratory of Nuclear Energy Chemistry, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.
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The IQA Energy Partition in a Drug Design Setting: A Hepatitis C Virus RNA-Dependent RNA Polymerase (NS5B) Case Study. Pharmaceuticals (Basel) 2022; 15:ph15101237. [PMID: 36297349 PMCID: PMC9609620 DOI: 10.3390/ph15101237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/30/2022] [Accepted: 10/01/2022] [Indexed: 11/05/2022] Open
Abstract
The interaction of the thumb site II of the NS5B protein of hepatitis C virus and a pair of drug candidates was studied using a topological energy decomposition method called interacting quantum atoms (IQA). The atomic energies were then processed by the relative energy gradient (REG) method, which extracts chemical insight by computation based on minimal assumptions. REG reveals the most important IQA energy contributions, by atom and energy type (electrostatics, sterics, and exchange–correlation), that are responsible for the behaviour of the whole system, systematically from a short-range ligand–pocket interaction until a distance of approximately 22 Å. The degree of covalency in various key interatomic interactions can be quantified. No exchange–correlation contribution is responsible for the changes in the energy profile of both pocket–ligand systems investigated in the ligand–pocket distances equal to or greater than that of the global minimum. Regarding the hydrogen bonds in the system, a “neighbour effect” was observed thanks to the REG method, which states that a carbon atom would rather not have its covalent neighbour oxygen form a hydrogen bond. The combination of IQA and REG enables the automatic identification of the pharmacophore in the ligands. The coarser Interacting Quantum Fragments (IQF) enables the determination of which amino acids of the pocket contribute most to the binding and the type of energy of said binding. This work is an example of the contribution topological energy decomposition methods can make to fragment-based drug design.
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Zapata-Acevedo CA, Guevara-Vela JM, Popelier PLA, Rocha Rinza T. Binding Energy Partition of Promising IRAK-4 Inhibitor (Zimlovisertib) for the Treatment of COVID-19 Pneumonia. Chemphyschem 2022; 23:e202200455. [PMID: 36044560 PMCID: PMC9538207 DOI: 10.1002/cphc.202200455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/19/2022] [Indexed: 01/05/2023]
Abstract
The technique of Fragment-Based Drug Design (FBDD) considers the interactions of different moieties of molecules with biological targets for the rational construction of potential drugs. One basic assumption of FBDD is that the different functional groups of a ligand interact with a biological target in an approximately additive, that is, independent manner. We investigated the interactions of different fragments of ligands and Interleukin-1 Receptor-Associated Kinase 4 (IRAK-4) throughout the FBDD design of Zimlovisertib, a promising anti-inflammatory, currently in trials to be used for the treatment of COVID-19 pneumonia. We utilised state-of-the-art methods of wave function analyses mainly the Interacting Quantum Atoms (IQA) energy partition for this purpose. By means of IQA, we assessed the suitability of every change to the ligand in the five stages of FBDD which led to Zimlovisertib on a quantitative basis. We determined the energetics of the interaction of different functional groups in the ligands with the IRAK-4 protein target and thereby demonstrated the adequacy (or lack thereof) of the changes made across the design of this drug. This analysis permits to verify whether a given alteration of a prospective drug leads to the intended tuning of non-covalent interactions with its protein objective. Overall, we expect that the methods exploited in this paper will prove valuable in the understanding and control of chemical modifications across FBDD processes.
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Affiliation(s)
- César Arturo Zapata-Acevedo
- Tecnologico de Monterrey: Instituto Tecnologico y de Estudios Superiores de MonterreyChemistryAv. Carlos Lazo 100Santa Fe, La Loma01389Álvaro ObregónMEXICO
| | | | - Paul L. A. Popelier
- UoM: The University of ManchesterChemistryOxford RoadM13 9PLManchesterUNITED KINGDOM
| | - Tomás Rocha Rinza
- Institute Of Chemistry, National Autonomous University of MexicoDepartment of Physical ChemistryCircuito Exterior, Ciudad Universitaria04510Mexico CityMEXICO
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9
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Jabłoński M. The physical nature of the ultrashort spike-ring interaction in iron maiden molecules. J Comput Chem 2022; 43:1206-1220. [PMID: 35593685 DOI: 10.1002/jcc.26879] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 11/08/2022]
Abstract
The so-called 'iron maiden' molecules belong to one of the most interesting subgroups of cyclophanes due to the presence of the ultrashort interaction between the CX apical bond and the benzene ring. This article presents an in-depth theoretical study of 16 'iron maiden' molecules, in which X = H, F, Cl or Br and the side chains are of various lengths and types: CSC, CSCC, CCC, and CCCC. It is shown that the H → F → Cl → Br substitution leads to a significant expansion of the 'iron maiden' molecule. Shorter chains lead to more pronounced effects, while insertion of sulfur atoms into the side chains lowers them. Structural changes are associated with an increase in energetic destabilization of X. Moreover, unlike for H, in the case of X = halogen, the out → in isomerization is energetically disadvantageous. The 'iron maiden' molecules are characterized by the presence of only three X⋯CAr bond paths. Particularly noteworthy are unusually large (even up to 32) values of the X⋯CAr bond ellipticity, which results from flat electron density distribution. The X⋯π interaction in each of the investigated 'iron maiden' molecule turned out to be multi-center, stabilizing and almost purely covalent in nature as indicated by the definitely dominant percentage (94.8%-101.6%) of the exchange-correlation energy. The spatial hindrance within the 'iron maiden' molecules appears to be not so much due to the X⋯π repulsion, but due to unfavorable steric interactions between X and the CC side bonds. It is also confirmed that some CH⋯HC interactions in aliphatic chains can be very weakly stabilizing.
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Affiliation(s)
- Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Toruń, Poland
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10
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Pavković N, Milovanović B, Stanojević A, Etinski M, Petković M. Proton leap: shuttling of protons onto benzonitrile. Phys Chem Chem Phys 2022; 24:3958-3969. [PMID: 35099492 DOI: 10.1039/d1cp04338b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The detailed description of chemical transformations in the interstellar medium allows deciphering the origin of a number of small and medium - sized organic molecules. We present density functional theory analysis of proton transfer from the trihydrogen cation and the ethenium cation to benzonitrile, a recently discovered species in the Taurus Molecular Cloud 1. Detailed energy transformations along the reaction paths were analyzed using the interacting quantum atoms methodology, which elucidated how the proton carrier influences the lightness to deliver the proton to benzonitrile's nitrogen atom. The proton carriers' deformation energy represents the largest destabilizing effect, whereas a proton's promotion energy, the benzonitrile-proton Coulomb attraction, as well as non-classical benzonitrile-proton and carrier-proton interaction are the dominant stabilizing energy components. As two ion-molecule reactions proceed without energy barriers, rate constants were estimated using the classical capture theory and were found to be an order of magnitude larger for the reaction with the trihydrogen cation compared to that with the ethenium cation (∼10-8 and 10-9 cm3 s-1, respectively). These results were obtained both with quantum chemical and ab initio molecular dynamics simulations (the latter performed at 10 K and 100 K), confirming that up to 100 K both systems choose energetically undemanding routes by tracking the corresponding minimum energy paths. A concept of a turning point is introduced, which is an equivalent to the transition state in barrierless reactions.
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Affiliation(s)
- Nemanja Pavković
- University of Belgrade - Faculty of Physical Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia.
| | - Branislav Milovanović
- University of Belgrade - Faculty of Physical Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia.
| | - Ana Stanojević
- University of Belgrade - Faculty of Physical Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia.
| | - Mihajlo Etinski
- University of Belgrade - Faculty of Physical Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia.
| | - Milena Petković
- University of Belgrade - Faculty of Physical Chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia.
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11
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Zhang NX, Wang C, Wu Q, Lan J, Chai Z, Shi W. Highly stable actinide(III) complexes supported by doubly aromatic ligands. Phys Chem Chem Phys 2022; 24:5921-5928. [DOI: 10.1039/d1cp05058c] [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
Owing to the electron-deficient nature of boron atom, the structures and properties of boron clusters can be enriched by doping various metal atoms, including lanthanide metal atoms. Nevertheless, the viability...
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12
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Tarannam N, Shukla R, Kozuch S. Yet another perspective on hole interactions. Phys Chem Chem Phys 2021; 23:19948-19963. [PMID: 34514473 DOI: 10.1039/d1cp03533a] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hole interactions are known by different names depending on the key atom of the bond (halogen bond, chalcogen bond, hydrogen bond, etc.), and the geometry of the interaction (σ if in line, π if perpendicular to the Lewis acid plane). However, its origin starts with the creation of a Lewis acid by an underlying covalent bond, which forms an electrostatic depletion and a virtual antibonding orbital, which can create non-covalent interactions with Lewis bases. In this (maybe subjective) perspective, we will claim that hole interactions must be defined via the molecular orbital origin of the molecule. Under this premise we can better explore the richness of such bonding patterns. For that, we will study old, recent and new systems, trying to pinpoint some misinterpretations that are often associated with them. We will use as exemplars the triel bonds, a couple of metal complexes, a discussion on convergent σ-holes, and many cases of anti-electrostatic hole interactions.
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Affiliation(s)
- Naziha Tarannam
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| | - Rahul Shukla
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| | - Sebastian Kozuch
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
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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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14
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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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15
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Liu ZL, Bai Y, Li Y, He J, Lin QY, Zhang FQ, Wu HS, Jia JF. Competition between (18, 18) and (18, 16) configurations in Ni2(CO)5: An isomerization energy decomposition analysis. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2008144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Zhi-ling Liu
- School of Chemical and Material Science, Key Laboratory of Magnetic Molecules & Magnetic Information Materials, Ministry of Education, Shanxi Normal University, Linfen 041004, China
| | - Yan Bai
- School of Chemical and Material Science, Key Laboratory of Magnetic Molecules & Magnetic Information Materials, Ministry of Education, Shanxi Normal University, Linfen 041004, China
| | - Ya Li
- School of Chemical and Material Science, Key Laboratory of Magnetic Molecules & Magnetic Information Materials, Ministry of Education, Shanxi Normal University, Linfen 041004, China
| | - Jing He
- School of Chemical and Material Science, Key Laboratory of Magnetic Molecules & Magnetic Information Materials, Ministry of Education, Shanxi Normal University, Linfen 041004, China
| | - Qing-yang Lin
- School of Chemical and Material Science, Key Laboratory of Magnetic Molecules & Magnetic Information Materials, Ministry of Education, Shanxi Normal University, Linfen 041004, China
| | - Fu-qiang Zhang
- School of Chemical and Material Science, Key Laboratory of Magnetic Molecules & Magnetic Information Materials, Ministry of Education, Shanxi Normal University, Linfen 041004, China
| | - Hai-shun Wu
- School of Chemical and Material Science, Key Laboratory of Magnetic Molecules & Magnetic Information Materials, Ministry of Education, Shanxi Normal University, Linfen 041004, China
| | - Jian-feng Jia
- School of Chemical and Material Science, Key Laboratory of Magnetic Molecules & Magnetic Information Materials, Ministry of Education, Shanxi Normal University, Linfen 041004, China
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16
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Fernández-Alarcón A, Guevara-Vela JM, Casals-Sainz JL, Francisco E, Costales A, Martín Pendás Á, Rocha-Rinza T. The nature of the intermolecular interaction in (H 2X) 2 (X = O, S, Se). Phys Chem Chem Phys 2021; 23:10097-10107. [PMID: 33876160 DOI: 10.1039/d1cp00047k] [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
Hydrogen bonds (HBs) are crucial non-covalent interactions in chemistry. Recently, the occurrence of an HB in (H2S)2 has been reported (Arunan et al., Angew. Chem., Int. Ed., 2018, 57, 15199), challenging the textbook view of H2S dimers as mere van der Waals clusters. We herein try to shed light on the nature of the intermolecular interactions in the H2O, H2S, and H2Se dimers via correlated electronic structure calculations, Symmetry Adapted Perturbation Theory (SAPT) and Quantum Chemical Topology (QCT). Although (H2S)2 and (H2Se)2 meet some of the criteria for the occurrence of an HB, potential energy curves as well as SAPT and QCT analyses indicate that the nature of the interaction in (H2O)2 is substantially different (e.g. more anisotropic) from that in (H2S)2 and (H2Se)2. QCT reveals that the HB in (H2O)2 includes substantial covalent, dispersion and electrostatic contributions, while the last-mentioned component plays only a minor role in (H2S)2 and (H2Se)2. The major contributions to the interactions of the dimers of H2S and H2Se are covalency and dispersion as revealed by the exchange-correlation components of QCT energy partitions. The picture yielded by SAPT is somewhat different but compatible with that offered by QCT. Overall, our results indicate that neither (H2S)2 nor (H2Se)2 are hydrogen-bonded systems, showing how the nature of intermolecular contacts involving hydrogen atoms evolves in a group down the periodic table.
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Affiliation(s)
- Alberto Fernández-Alarcón
- Institute of Chemistry, National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán, C.P. 04510, Mexico City, Mexico.
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17
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Shteingolts SA, Stash AI, Tsirelson VG, Fayzullin RR. Orbital-Free Quantum Crystallographic View on Noncovalent Bonding: Insights into Hydrogen Bonds, π⋅⋅⋅π and Reverse Electron Lone Pair⋅⋅⋅π Interactions. Chemistry 2021; 27:7789-7809. [PMID: 33769620 DOI: 10.1002/chem.202005497] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Indexed: 01/16/2023]
Abstract
A detailed analysis of a complete set of the local potentials that appear in the Euler equation for electron density is carried out for noncovalent interactions in the crystal of a uracil derivative using experimental X-ray charge density. The interplay between the quantum theory of atoms in molecules and crystals and the local potentials and corresponding inner-crystal electronic forces of electrostatic and kinetic origin is explored. Partitioning of crystal space into atomic basins and atomic-like potential basins led us to the definite description of interatomic interaction and charge transfer. Novel physically grounded bonding descriptors derived within the orbital-free quantum crystallography provided the detailed examination of π-stacking and intricate C=O⋅⋅⋅π interactions and nonclassical hydrogen bonds present in the crystal. The donor-acceptor character of these interactions is revealed by analysis of Pauli and von Weizsäcker potentials together with well-known functions, e. g., deformation electron density and electron localization function. In this way, our analysis throws light on aspects of these closed-shell interactions hitherto hidden from the description.
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Affiliation(s)
- Sergey A Shteingolts
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
| | - Adam I Stash
- A.N. Nesmeyanov Institute of Organoelement Compounds Russian Academy of Sciences, 28 Vavilov Street, Moscow, 119991, Russian Federation
| | - Vladimir G Tsirelson
- D.I. Mendeleev University of Chemical Technology, 9 Miusskaya Square, Moscow, 125047, Russian Federation
| | - Robert R Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
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18
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Stanojević A, Milovanović B, Stanković I, Etinski M, Petković M. The significance of the metal cation in guanine-quartet – metalloporphyrin complexes. Phys Chem Chem Phys 2021; 23:574-584. [DOI: 10.1039/d0cp05798c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The distinct positions of the divalent metal ions with respect to the porphyrin ring are responsible for different interaction energies between metalloporphyrins and the guanine quartet.
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Affiliation(s)
- Ana Stanojević
- University of Belgrade – Faculty of Physical Chemistry
- 11 158 Belgrade
- Serbia
| | | | - Ivana Stanković
- Institute of Chemistry
- Technology and Metallurgy
- 11 000 Belgrade
- Serbia
| | - Mihajlo Etinski
- University of Belgrade – Faculty of Physical Chemistry
- 11 158 Belgrade
- Serbia
| | - Milena Petković
- University of Belgrade – Faculty of Physical Chemistry
- 11 158 Belgrade
- Serbia
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19
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Zhang N, Li A, Wang C, Wu Q, Lan J, Chai Z, Zhao Y, Shi W. Theoretical prediction of chiral actinide endohedral borospherenes. NEW J CHEM 2021. [DOI: 10.1039/d1nj00211b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Actinide encapsulation can form chiral borospherenes, and the covalent character of An–B bonds dominates the formation of these actinoborospherenes.
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Affiliation(s)
- Naixin Zhang
- Laboratory of Nuclear Energy Chemistry
- Institute of High Energy Physics
- Chinese Academy of Sciences
- Beijing 100049
- China
| | - Ailin Li
- Laboratory of Nuclear Energy Chemistry
- Institute of High Energy Physics
- Chinese Academy of Sciences
- Beijing 100049
- China
| | - Congzhi Wang
- Laboratory of Nuclear Energy Chemistry
- Institute of High Energy Physics
- Chinese Academy of Sciences
- Beijing 100049
- China
| | - Qunyan Wu
- Laboratory of Nuclear Energy Chemistry
- Institute of High Energy Physics
- Chinese Academy of Sciences
- Beijing 100049
- China
| | - Jianhui Lan
- Laboratory of Nuclear Energy Chemistry
- Institute of High Energy Physics
- Chinese Academy of Sciences
- Beijing 100049
- China
| | - Zhifang Chai
- Laboratory of Nuclear Energy Chemistry
- Institute of High Energy Physics
- Chinese Academy of Sciences
- Beijing 100049
- China
| | - Yubao Zhao
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Weiqun Shi
- Laboratory of Nuclear Energy Chemistry
- Institute of High Energy Physics
- Chinese Academy of Sciences
- Beijing 100049
- China
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20
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Cuyacot BJR, Durník I, Foroutan-Nejad C, Marek R. Anatomy of Base Pairing in DNA by Interacting Quantum Atoms. J Chem Inf Model 2020; 61:211-222. [PMID: 33112145 DOI: 10.1021/acs.jcim.0c00642] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The formation of purine and pyrimidine base pairs (BPs), which contributes to shaping of the canonical and noncanonical 3D structures of nucleic acids, is one the most investigated phenomena in chemistry and life sciences. In this contribution, the anatomy of the bond energy (BDE) of the base-pairing interaction in 39 different arrangements found experimentally or predicted for DNA structures containing the four common nucleobases (A, C, G, T) in their neutral or protonated forms is described in light of the theory of interacting quantum atoms within the context of the quantum theory of atoms in molecules. The interplay of individual energy components involved in the three stages of the bond formation process (structural deformation, electron-density promotion, and intermolecular interaction) is studied. We recognized that for the neutral BPs, variations in the kinetic and electrostatic contributions to the BDE are rather negligible, leaving the exchange-correlation energy as the main stabilizing component. It is shown that the contribution of the exchange-correlation term can be recovered by including atoms that are formally assumed to be hydrogen bonded (primary interaction). In contrast, to recover the electrostatic component of interaction, one must consider both the primary and secondary (formally nonbonded atoms) interatomic interactions. The results of our study were employed to design new types of BPs with altered bonding anatomy. We demonstrate that improving the electrostatic characteristics of the BPs does not necessarily result in greater interaction energies if weak secondary hydrogen bonding is destroyed. However, the main tuning factor for systems with conserved interacting faces (primary interactions) is the electrostatic component of the interaction energy resulting from the secondary atom-atom electrostatics.
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Affiliation(s)
- Ben Joseph R Cuyacot
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Ivo Durník
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czechia.,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Cina Foroutan-Nejad
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czechia
| | - Radek Marek
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
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21
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Liu Z, Bai Y, Li Y, He J, Lin Q, Zhang F, Wu HS, Jia J. Triply Carbonyl-Bridged Ni 2(CO) 5 Featuring Triple Three-Center Two-Electron Ni—C–Ni Bonds Instead of Ni≡Ni Triple Bond. Inorg Chem 2020; 59:15365-15374. [DOI: 10.1021/acs.inorgchem.0c02334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhiling Liu
- School of Chemical and Material Science, Key Laboratory of Magnetic Molecules and Magnetic Information Materials, Ministry of Education, Shanxi Normal University, No. 1, Gongyuan Street, Linfen, Shanxi 041004, People’s Republic of China
| | - Yan Bai
- School of Chemical and Material Science, Key Laboratory of Magnetic Molecules and Magnetic Information Materials, Ministry of Education, Shanxi Normal University, No. 1, Gongyuan Street, Linfen, Shanxi 041004, People’s Republic of China
| | - Ya Li
- School of Chemical and Material Science, Key Laboratory of Magnetic Molecules and Magnetic Information Materials, Ministry of Education, Shanxi Normal University, No. 1, Gongyuan Street, Linfen, Shanxi 041004, People’s Republic of China
| | - Jing He
- School of Chemical and Material Science, Key Laboratory of Magnetic Molecules and Magnetic Information Materials, Ministry of Education, Shanxi Normal University, No. 1, Gongyuan Street, Linfen, Shanxi 041004, People’s Republic of China
| | - Qingyang Lin
- School of Chemical and Material Science, Key Laboratory of Magnetic Molecules and Magnetic Information Materials, Ministry of Education, Shanxi Normal University, No. 1, Gongyuan Street, Linfen, Shanxi 041004, People’s Republic of China
| | - Fuqiang Zhang
- School of Chemical and Material Science, Key Laboratory of Magnetic Molecules and Magnetic Information Materials, Ministry of Education, Shanxi Normal University, No. 1, Gongyuan Street, Linfen, Shanxi 041004, People’s Republic of China
| | - Hai-Shun Wu
- School of Chemical and Material Science, Key Laboratory of Magnetic Molecules and Magnetic Information Materials, Ministry of Education, Shanxi Normal University, No. 1, Gongyuan Street, Linfen, Shanxi 041004, People’s Republic of China
| | - Jianfeng Jia
- School of Chemical and Material Science, Key Laboratory of Magnetic Molecules and Magnetic Information Materials, Ministry of Education, Shanxi Normal University, No. 1, Gongyuan Street, Linfen, Shanxi 041004, People’s Republic of China
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22
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Guevara-Vela JM, Francisco E, Rocha-Rinza T, Martín Pendás Á. Interacting Quantum Atoms-A Review. Molecules 2020; 25:E4028. [PMID: 32899346 PMCID: PMC7504790 DOI: 10.3390/molecules25174028] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022] Open
Abstract
The aim of this review is threefold. On the one hand, we intend it to serve as a gentle introduction to the Interacting Quantum Atoms (IQA) methodology for those unfamiliar with it. Second, we expect it to act as an up-to-date reference of recent developments related to IQA. Finally, we want it to highlight a non-exhaustive, yet representative set of showcase examples about how to use IQA to shed light in different chemical problems. To accomplish this, we start by providing a brief context to justify the development of IQA as a real space alternative to other existent energy partition schemes of the non-relativistic energy of molecules. We then introduce a self-contained algebraic derivation of the methodological IQA ecosystem as well as an overview of how these formulations vary with the level of theory employed to obtain the molecular wavefunction upon which the IQA procedure relies. Finally, we review the several applications of IQA as examined by different research groups worldwide to investigate a wide variety of chemical problems.
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Affiliation(s)
- José Manuel Guevara-Vela
- Institute of Chemistry, National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán C.P., Mexico City 04510, Mexico; (J.M.G.-V.); (T.R.-R.)
| | - Evelio Francisco
- Department of Analytical and Physical Chemistry, University of Oviedo, E-33006 Oviedo, Spain;
| | - Tomás Rocha-Rinza
- Institute of Chemistry, National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán C.P., Mexico City 04510, Mexico; (J.M.G.-V.); (T.R.-R.)
| | - Ángel Martín Pendás
- Department of Analytical and Physical Chemistry, University of Oviedo, E-33006 Oviedo, Spain;
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23
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Wang Y, Su P. Why Can Cationic Halogen Bond Donors Activate the Ritter-Type Solvolysis of Benzhydryl Bromide but Cationic Hydrogen Bond Donors Can Not? ACS OMEGA 2020; 5:21862-21872. [PMID: 32905280 PMCID: PMC7469379 DOI: 10.1021/acsomega.0c03000] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/13/2020] [Indexed: 05/27/2023]
Abstract
It is found by experiment that the cationic halogen bond donors (cationic iodoimidazolium compounds) can activate the Ritter-type solvolysis of benzhydryl bromide, while the cationic hydrogen bond donors (cationic imidazolium compounds) could not. To understand the activation mechanism, various noncovalent interactions between benzhydryl bromide and a series of activators in solution, including halogen bond, hydrogen bond, lone pair···π/π+, and C-H···π/π+, were explored theoretically. Our study revealed that the activation difference can be contributed by the variation of the noncovalent interactions. For halogen bond donors, the successful activation is attributed by halogen bond and lone pair···π. The halogen bonds mainly provide the stabilization energy of the ion-pair complex with the help of lone pair···π. For hydrogen-bond donors, the contribution of the hydrogen bond is unable to compensate the like-charge repulsion arising from the generation of the carbocation, leading to the unsuccessful activation. In general, lone pair···π makes a difference.
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Affiliation(s)
- Yueyan Wang
- The State Key Laboratory
of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory
of Theoretical and Computational Chemistry, and College of Chemistry
and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Peifeng Su
- The State Key Laboratory
of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory
of Theoretical and Computational Chemistry, and College of Chemistry
and Chemical Engineering, Xiamen University, Xiamen 361005, China
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24
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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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25
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Casals‐Sainz JL, Guevara‐Vela JM, Francisco E, Rocha‐Rinza T, Martín Pendás Á. Efficient implementation of the interacting quantum atoms energy partition of the second‐order Møller–Plesset energy. J Comput Chem 2020; 41:1234-1241. [DOI: 10.1002/jcc.26169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/30/2020] [Accepted: 01/30/2020] [Indexed: 12/19/2022]
Affiliation(s)
| | - José Manuel Guevara‐Vela
- Institute of Chemistry, National Autonomous University of Mexico, Circuito ExteriorCiudad Universitaria Mexico City Mexico
| | - Evelio Francisco
- Department of Analytical and Physical ChemistryUniversity of Oviedo Oviedo Spain
| | - Tomás Rocha‐Rinza
- Institute of Chemistry, National Autonomous University of Mexico, Circuito ExteriorCiudad Universitaria Mexico City Mexico
| | - Ángel Martín Pendás
- Department of Analytical and Physical ChemistryUniversity of Oviedo Oviedo Spain
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26
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Milovanović B, Stanojević A, Etinski M, Petković M. Intriguing Intermolecular Interplay in Guanine Quartet Complexes with Alkali and Alkaline Earth Cations. J Phys Chem B 2020; 124:3002-3014. [DOI: 10.1021/acs.jpcb.0c01165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Branislav Milovanović
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Ana Stanojević
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Milena Petković
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
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27
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Liu Z, Bai Y, Li Y, He J, Lin Q, Xie H, Tang Z. Unsaturated binuclear homoleptic nickel carbonyl anions Ni2(CO)n− (n = 4–6) featuring double three-center two-electron Ni–C–Ni bonds. Phys Chem Chem Phys 2020; 22:23773-23784. [DOI: 10.1039/d0cp03883k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The two nickel atoms in the Ni2(CO)n− (n = 4–6) complexes are joined by two bridging carbonyl ligands via the sharing three-center two-electron Ni–C–Ni bond in turn to achieve the (16,16), (16,18), and eventually the favored (18,18) configurations.
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Affiliation(s)
- Zhiling Liu
- School of Chemical and Material Science
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials
- Ministry of Education
- Shanxi Normal University
- Linfen
| | - Yan Bai
- School of Chemical and Material Science
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials
- Ministry of Education
- Shanxi Normal University
- Linfen
| | - Ya Li
- School of Chemical and Material Science
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials
- Ministry of Education
- Shanxi Normal University
- Linfen
| | - Jing He
- School of Chemical and Material Science
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials
- Ministry of Education
- Shanxi Normal University
- Linfen
| | - Qingyang Lin
- School of Chemical and Material Science
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials
- Ministry of Education
- Shanxi Normal University
- Linfen
| | - Hua Xie
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Zichao Tang
- Collaborative Innovation Center of Chemistry for Energy Materials
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- and Department of Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
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28
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Liu Z, Bai Y, Li Y, He J, Lin Q, Hou L, Wu HS, Zhang F, Jia J, Xie H, Tang Z. Multicenter electron-sharing σ-bonding in the AgFe(CO)4− complex. Dalton Trans 2020; 49:15256-15266. [DOI: 10.1039/d0dt02685a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
For the AgFe(CO)4− anion, the silver atom is covalently bonded to the anionic tetracarbonyl-iron, an isolobal analogue of the methyl radical, via a peculiar decentralized electron-sharing σ bond.
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29
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Sojka M, Tousek J, Badri Z, Foroutan-Nejad C, Necas M. Bifurcated hydrogen bonds in platinum(II) complexes with phosphinoamine ligands. Polyhedron 2019. [DOI: 10.1016/j.poly.2019.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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30
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Savastano M, García-Gallarín C, Giorgi C, Gratteri P, López de la Torre MD, Bazzicalupi C, Bianchi A, Melguizo M. Solid State and Solution Study on the Formation of Inorganic Anion Complexes with a Series of Tetrazine-Based Ligands. Molecules 2019; 24:E2247. [PMID: 31208109 PMCID: PMC6631435 DOI: 10.3390/molecules24122247] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 12/18/2022] Open
Abstract
Four molecules (L1-L4) constituted by an s-tetrazine ring appended with two identical aliphatic chains of increasing length bearing terminal morpholine groups were studied as anion receptors in water. The basicity properties of these molecules were also investigated. Speciation of the anion complexes formed in solution and determination of their stability constants were performed by means of potentiometric (pH-metric) titrations, while further information was obtained by NMR and isothermal titration calorimetry (ITC) measurements. The crystal structures of two neutral ligands (L3, L4) and of their H2L3(ClO4)2∙2H2O, H2L4(ClO4)2∙2H2O, H2L3(PF6)2, and H2L3(PF6)2∙2H2O anion complexes were determined by single crystal X-ray diffraction. The formation of anion-π interactions is the leitmotiv of these complexes, both in solution and in the solid state, although hydrogen bonding and/or formation of salt-bridges can contribute to their stability. Evidence of the ability of these ligands to form anion-π interactions is given by the observation that even the neutral (not-protonated) molecules bind anions in water to form complexes of significant stability, including elusive OH- anions.
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Affiliation(s)
- Matteo Savastano
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia, 3-13, 50019 Sesto Fiorentino, Italy.
| | | | - Claudia Giorgi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia, 3-13, 50019 Sesto Fiorentino, Italy.
| | - Paola Gratteri
- Department of NEUROFARBA-Pharmaceutical and Nutraceutical Section, and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy.
| | | | - Carla Bazzicalupi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia, 3-13, 50019 Sesto Fiorentino, Italy.
| | - Antonio Bianchi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia, 3-13, 50019 Sesto Fiorentino, Italy.
| | - Manuel Melguizo
- Department of Inorganic and Organic Chemistry, University of Jaén, 23071 Jaén, Spain.
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31
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Wang Y, Pigeon P, Top S, Sanz García J, Troufflard C, Ciofini I, McGlinchey MJ, Jaouen G. Atypical Lone Pair–π Interaction with Quinone Methides in a Series of Imido‐Ferrociphenol Anticancer Drug Candidates. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902456] [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)
- Yong Wang
- PSL, Chimie ParisTech 11 rue Pierre et Marie Curie F-75005 Paris France
- Sorbonne Université, UPMC Univ Paris 6, UMR 8232 CNRS, IPCM place Jussieu F-75005 Paris France
| | - Pascal Pigeon
- PSL, Chimie ParisTech 11 rue Pierre et Marie Curie F-75005 Paris France
- Sorbonne Université, UPMC Univ Paris 6, UMR 8232 CNRS, IPCM place Jussieu F-75005 Paris France
| | - Siden Top
- Sorbonne Université, UPMC Univ Paris 6, UMR 8232 CNRS, IPCM place Jussieu F-75005 Paris France
| | - Juan Sanz García
- PSL, Chimie ParisTech 11 rue Pierre et Marie Curie F-75005 Paris France
| | - Claire Troufflard
- Sorbonne Université, UPMC Univ Paris 6, UMR 8232 CNRS, IPCM place Jussieu F-75005 Paris France
| | - Ilaria Ciofini
- PSL, Chimie ParisTech 11 rue Pierre et Marie Curie F-75005 Paris France
| | | | - Gérard Jaouen
- PSL, Chimie ParisTech 11 rue Pierre et Marie Curie F-75005 Paris France
- Sorbonne Université, UPMC Univ Paris 6, UMR 8232 CNRS, IPCM place Jussieu F-75005 Paris France
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32
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Wang Y, Pigeon P, Top S, Sanz García J, Troufflard C, Ciofini I, McGlinchey MJ, Jaouen G. Atypical Lone Pair-π Interaction with Quinone Methides in a Series of Imido-Ferrociphenol Anticancer Drug Candidates. Angew Chem Int Ed Engl 2019; 58:8421-8425. [PMID: 30977944 DOI: 10.1002/anie.201902456] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/29/2019] [Indexed: 11/10/2022]
Abstract
Ferrociphenols, especially those possessing a heterocycle at the terminus of an aliphatic chain, display strong anticancer activity through a novel redox mechanism that generates active metabolites such as quinone methides (QMs). X-ray crystallography and UV/Vis spectroscopy reveal that the specific lone pair (lp)-π interaction between a carbonyl group of the imide and the quinone motif of the QM plays an important role in the exceptional cytotoxic behaviour of their imido-ferrociphenol precursors. This intramolecular lp-π interaction markedly enhanced the stability of the QMs and lowered the pKa values of the corresponding phenol/phenolate couples. As the first example of such a non-covalent interaction that stabilizes QMs remotely, it not only expands the scope of the lp-π interaction in supramolecular chemistry, but also represents a new mode of stabilization of a QM. This unprecedented application of lp-π interactions in imido-ferrociphenol anticancer drug candidates may also have great potential in drug discovery and organocatalyst design.
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Affiliation(s)
- Yong Wang
- PSL, Chimie ParisTech, 11 rue Pierre et Marie Curie, F-75005, Paris, France.,Sorbonne Université, UPMC Univ Paris 6, UMR 8232 CNRS, IPCM, place Jussieu, F-75005, Paris, France
| | - Pascal Pigeon
- PSL, Chimie ParisTech, 11 rue Pierre et Marie Curie, F-75005, Paris, France.,Sorbonne Université, UPMC Univ Paris 6, UMR 8232 CNRS, IPCM, place Jussieu, F-75005, Paris, France
| | - Siden Top
- Sorbonne Université, UPMC Univ Paris 6, UMR 8232 CNRS, IPCM, place Jussieu, F-75005, Paris, France
| | - Juan Sanz García
- PSL, Chimie ParisTech, 11 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Claire Troufflard
- Sorbonne Université, UPMC Univ Paris 6, UMR 8232 CNRS, IPCM, place Jussieu, F-75005, Paris, France
| | - Ilaria Ciofini
- PSL, Chimie ParisTech, 11 rue Pierre et Marie Curie, F-75005, Paris, France
| | | | - Gérard Jaouen
- PSL, Chimie ParisTech, 11 rue Pierre et Marie Curie, F-75005, Paris, France.,Sorbonne Université, UPMC Univ Paris 6, UMR 8232 CNRS, IPCM, place Jussieu, F-75005, Paris, France
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33
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Sadeghi S, Amani M. Co-doped triel-pnicogen graphene as metal-free catalyst for CO oxidation: Role of multi-center covalency. J Mol Model 2019; 25:77. [PMID: 30806794 DOI: 10.1007/s00894-019-3960-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/07/2019] [Indexed: 11/24/2022]
Abstract
Third and fifth group atoms, named triel and pnicogen, respectively, were used for graphene doping. AlP and AlN structures were selected as co-doped graphene-based catalysts. The electronic structure and catalytic properties of binary AlN, AlP co-doped graphene were investigated through density functional theory (DFT). Results show that the AlP co-doped graphene strictly enhances the oxygen reactivity compared to AlN one. The CO oxidation on AlP and AlN co-doped graphene sheets is mainly done through Eley-Rideal mechanism as follows: CO + O2➔CO2 + Oads and CO + Oads➔ CO2. The CO oxidation reaction paths over the AlN and AlP-co-doped graphene have revealed that they can be regarded as the competent catalyst for CO oxidation in the presence of O2. Mechanistically, both AlP and AlN co-doped graphene catalysts are appropriately active in the first step while the second step is too hard to do regarding the multi-center covalency character between O2 and AlP co-doped graphene and hence its catalytic efficiency is significantly lower compared to AlN co-doped graphene sheet. Thus, the substitution of a C-C bond with Al-N is an effective way to design the graphene-based catalysts for CO oxidation.
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Affiliation(s)
- Sadegh Sadeghi
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, PO Box 14115-175, Tehran, Iran
| | - Mitra Amani
- Chemical engineering department, Islamic Azad University, Robatkarim Branch, Robatkarim, Iran.
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34
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Yourdkhani S, Chojecki M, Korona T. Interaction of Non-polarizable Cations with Azaborine Isomers and Their Mono-Substituted Derivatives: Position, Induction, and Non-Classical Effects Matter. Chemphyschem 2018; 19:3092-3106. [DOI: 10.1002/cphc.201800691] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Sirous Yourdkhani
- Department of Chemical Physics and Optics; Faculty of Mathematics and Physics; Charles University; Ke Karlovu 3, CZ- 12116 Prague 2 Czech Republic
- Faculty of Chemistry; University of Warsaw; ul. Pasteura 1 02-093 Warsaw Poland
| | - Michał Chojecki
- Faculty of Chemistry; University of Warsaw; ul. Pasteura 1 02-093 Warsaw Poland
| | - Tatiana Korona
- Faculty of Chemistry; University of Warsaw; ul. Pasteura 1 02-093 Warsaw Poland
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35
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Foroutan‐Nejad C, Straka M, Fernández I, Frenking G. Buckyball Difluoride F 2−@C 60+—A Single‐Molecule Crystal. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Cina Foroutan‐Nejad
- Department of ChemistryFaculty of ScienceMasaryk University Kamenice 5 62500 Brno Czech Republic
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2. 16610 Prague Czech Republic
| | - Israel Fernández
- Departamento de Química Orgánica I and Centro de Innovación en Química Avanzada (ORFEO-CINQA)Facultad de Ciencias QuímicasUniversidad Complutense de Madrid 28040 Madrid Spain
| | - Gernot Frenking
- Fachbereich ChemiePhilipps-Universität Marburg Hans-Meerwein-Strasse 4 35043 Marburg Germany
- Institute of Advanced SynthesisSchool of Chemistry and Molecular EngineeringJiangsu National Synergetic Innovation Center for Advanced MaterialsNanjing Tech University Nanjing 211816 China
- Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia Euskadi Spain
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36
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Buckyball Difluoride F
2
−
@C
60
+
—A Single‐Molecule Crystal. Angew Chem Int Ed Engl 2018; 57:13931-13934. [DOI: 10.1002/anie.201809699] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Indexed: 11/07/2022]
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37
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Petković M, Nakarada Đ, Etinski M. When hydroquinone meets methoxy radical: Hydrogen abstraction reaction from the viewpoint of interacting quantum atoms. J Comput Chem 2018; 39:1868-1877. [PMID: 29799128 DOI: 10.1002/jcc.25359] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 04/16/2018] [Accepted: 04/27/2018] [Indexed: 01/01/2023]
Abstract
Interacting Quantum Atoms methodology is used for a detailed analysis of hydrogen abstraction reaction from hydroquinone by methoxy radical. Two pathways are analyzed, which differ in the orientation of the reactants at the corresponding transition states. Although the discrepancy between the two barriers amounts to only 2 kJ/mol, which implies that the two pathways are of comparable probability, the extent of intra-atomic and inter-atomic energy changes differs considerably. We thus demonstrated that Interacting Quantum Atoms procedure can be applied to unravel distinct energy transfer routes in seemingly similar mechanisms. Identification of energy components with the greatest contribution to the variation of the overall energy (intra-atomic and inter-atomic terms that involve hydroquinone's oxygen and the carbon atom covalently bound to it, the transferring hydrogen and methoxy radical's oxygen), is performed using the Relative energy gradient method. Additionally, the Interacting Quantum Fragments approach shed light on the nature of dominant interactions among selected fragments: both Coulomb and exchange-correlation contributions are of comparable importance when considering interactions of the transferring hydrogen atom with all other atoms, whereas the exchange-correlation term dominates interaction between methoxy radical's methyl group and hydroquinone's aromatic ring. This study represents one of the first applications of Interacting Quantum Fragments approach on first order saddle points. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Milena Petković
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, 11 158, Serbia
| | - Đura Nakarada
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, 11 158, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, 11 158, Serbia
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38
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Singh SK, Joshi PR, Shaw RA, Hill JG, Das A. Interplay between hydrogen bonding and n→π* interaction in an analgesic drug salicin. Phys Chem Chem Phys 2018; 20:18361-18373. [PMID: 29942975 DOI: 10.1039/c8cp00655e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The competition and cooperation between weak intermolecular interactions are important in determining the conformational preferences of molecules. Understanding the relative strengths of these effects in the context of potential drug candidates is therefore essential. We use a combination of gas-phase spectroscopy and quantum-chemical calculations to elucidate the nature of such interactions for the analgesic salicin [2-(hydroxymethyl)phenyl β-d-glucopyranoside], an analog of aspirin found in willow bark. Of several possible conformers, only three are observed experimentally, and these are found to correspond with the three lowest energy conformers obtained from density functional theory calculations and simulated Franck-Condon spectra. Natural bond orbital analyses show that these are characterized by a subtle interplay between weak n→π* interaction and conventional strong hydrogen bond, with additional insights into this interaction provided by analysis of quantum theory of atoms in molecules and symmetry-adapted perturbation theory calculations. In contrast, the higher energy conformers, which are not observed experimentally, are mostly stabilized by the hydrogen bond with negligible contribution of n→π* interaction. The n→π* interaction results in a preference for the benzyl alcohol group of salicin to adopt a gauche conformation, a characteristic also found when salicin is bound to the β-glucosidase enzyme. As such, understanding the interplay between these weak interactions has significance in the rationalization of protein structures.
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Affiliation(s)
- Santosh K Singh
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune-411008, Maharashtra, India.
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39
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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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40
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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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41
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Racioppi S, Della Pergola R, Colombo V, Sironi A, Macchi P. Electron Density Analysis of Metal Clusters with Semi-Interstitial Main Group Atoms. Chemical Bonding in [Co 6X(CO) 16] - Species. J Phys Chem A 2018; 122:5004-5015. [PMID: 29733600 DOI: 10.1021/acs.jpca.8b02690] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In this work, we propose a careful and thorough analysis of the chemical bond nature in high nuclearity metal carbonyl clusters having semi-interstitial main group atoms. We investigated the species [Co6X(CO)16]- (X = As, P), known for a rather interesting conformational flexibility of the cluster (leading to open or closed cages) and a corresponding polymorphism in the solid state (observed at least for X = As). The factors that trigger the molecular isomerism and the nature of X-Co and Co-Co interactions emerge from theoretical calculations and high resolution X-ray diffraction. Both energy and charge density atomic partitioning (QTAIM, EDA, IQA) are employed for this analysis, with the aim of revealing the stabilizing/destabilizing factors of the interaction between the cage and the semi-interstitial atoms in the various conformations.
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Affiliation(s)
- S Racioppi
- Dipartimento di Chimica , Università degli Studi di Milano , Via Golgi, 19 , 20133 Milano , Italy.,Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - R Della Pergola
- Dipartimento di Scienze Ambientali e della Terra , Università di Milano-Bicocca , Piazza della Scienza 1 , 20126 Milano , Italy
| | - V Colombo
- Dipartimento di Chimica , Università degli Studi di Milano , Via Golgi, 19 , 20133 Milano , Italy
| | - A Sironi
- Dipartimento di Chimica , Università degli Studi di Milano , Via Golgi, 19 , 20133 Milano , Italy
| | - P Macchi
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland
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42
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Jaroš A, Badri Z, Bora PL, Bonab EF, Marek R, Straka M, Foroutan-Nejad C. How Does a Container Affect Acidity of its Content: Charge-Depletion Bonding Inside Fullerenes. Chemistry 2018; 24:4245-4249. [DOI: 10.1002/chem.201706017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Adam Jaroš
- Institute of Organic Chemistry and Biochemistry, of the; Czech Academy of Sciences; Flemingovo nám. 2. 16610 Prague Czech Republic
| | - Zahra Badri
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5/A4 62500 Brno Czech Republic
| | - Pankaj Lochan Bora
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5/A4 62500 Brno Czech Republic
- Department of Chemistry, Faculty of Science; Masaryk University; 62500 Brno Czech Republic
| | - Esmaeil Farajpour Bonab
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5/A4 62500 Brno Czech Republic
- Department of Chemistry, Faculty of Science; Masaryk University; 62500 Brno Czech Republic
| | - Radek Marek
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5/A4 62500 Brno Czech Republic
- Department of Chemistry, Faculty of Science; Masaryk University; 62500 Brno Czech Republic
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry, of the; Czech Academy of Sciences; Flemingovo nám. 2. 16610 Prague Czech Republic
| | - Cina Foroutan-Nejad
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5/A4 62500 Brno Czech Republic
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43
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Durec M, Marek R, Kozelka J. Water-Tryptophan Interactions: Lone-pair⋅⋅⋅π or O−H⋅⋅⋅π? Molecular Dynamics Simulations of β-Galactosidase Suggest that Both Modes Can Co-exist. Chemistry 2018; 24:5849-5859. [DOI: 10.1002/chem.201705364] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Matúš Durec
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5/A4 625 00 Brno Czech Republic
- Department of Condensed Matter Physics, Faculty of Science; Masaryk University; Kotlářská 2 611 37 Brno Czech Republic
| | - Radek Marek
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5/A4 625 00 Brno Czech Republic
- National Center for Biomolecular Research, Faculty of Science; Masaryk University; Kamenice 5/A4 625 00 Brno Czech Republic
| | - Jiří Kozelka
- Department of Condensed Matter Physics, Faculty of Science; Masaryk University; Kotlářská 2 611 37 Brno Czech Republic
- Biologie Intégrée du Globule Rouge, UMR S1134, Inserm; Université Paris Diderot, Sorbonne Paris Cité, Université de la Réunion, Université des Antilles; 75739 Paris France
- Institut National de la Transfusion Sanguine (INTS); 75739 Paris France
- Laboratoire d'Excellence GR-Ex; 75739 Paris France
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44
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Špačková N, Trošanová Z, Šebesta F, Jansen S, Burda JV, Srb P, Zachrdla M, Žídek L, Kozelka J. Protein environment affects the water–tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants. Phys Chem Chem Phys 2018; 20:12664-12677. [DOI: 10.1039/c7cp08623g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water molecules can interact with the π-face of tryptophan either forming an O–H⋯π hydrogen bond or by a lone-pair⋯π interaction. Surrounding amino acids can favor the one or the other interaction type.
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Affiliation(s)
- Nad'a Špačková
- Department of Condensed Matter Physics
- Faculty of Science
- Masaryk University
- 61137 Brno
- Czech Republic
| | - Zuzana Trošanová
- Department of Condensed Matter Physics
- Faculty of Science
- Masaryk University
- 61137 Brno
- Czech Republic
| | - Filip Šebesta
- Department of Chemical Physics and Optics
- Faculty of Mathematics and Physics
- Charles University
- 12116 Praha
- Czech Republic
| | - Séverine Jansen
- Department of Condensed Matter Physics
- Faculty of Science
- Masaryk University
- 61137 Brno
- Czech Republic
| | - Jaroslav V. Burda
- Department of Chemical Physics and Optics
- Faculty of Mathematics and Physics
- Charles University
- 12116 Praha
- Czech Republic
| | - Pavel Srb
- National Centre for Biomolecular Research
- Faculty of Science
- Masaryk University
- 62500 Brno
- Czech Republic
| | - Milan Zachrdla
- National Centre for Biomolecular Research
- Faculty of Science
- Masaryk University
- 62500 Brno
- Czech Republic
| | - Lukáš Žídek
- National Centre for Biomolecular Research
- Faculty of Science
- Masaryk University
- 62500 Brno
- Czech Republic
| | - Jiří Kozelka
- Department of Condensed Matter Physics
- Faculty of Science
- Masaryk University
- 61137 Brno
- Czech Republic
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45
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Casademont-Reig I, Woller T, Contreras-García J, Alonso M, Torrent-Sucarrat M, Matito E. New electron delocalization tools to describe the aromaticity in porphyrinoids. Phys Chem Chem Phys 2018; 20:2787-2796. [DOI: 10.1039/c7cp07581b] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
There are several possible pathways in the macrocycle of large porphyrinoids and, among aromaticity indices, only AVminis capable of recognizing the most aromatic one.
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Affiliation(s)
- Irene Casademont-Reig
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU)
- and Donostia International Physics Center (DIPC)
- P.K. 1072
- 20080 Donostia
| | - Tatiana Woller
- Eenheid Algemene Chemie (ALGC). Vrije Universiteit Brussel (VUB)
- Pleinlaan 2
- 1050 Brussels
- Belgium
| | - Julia Contreras-García
- Sorbonne Universités, UPMC Univ. Paris
- UMR 7616 Laboratoire de Chimie Théorique
- CNRS
- UMR 7616
- Paris
| | - Mercedes Alonso
- Eenheid Algemene Chemie (ALGC). Vrije Universiteit Brussel (VUB)
- Pleinlaan 2
- 1050 Brussels
- Belgium
| | - Miquel Torrent-Sucarrat
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU)
- and Donostia International Physics Center (DIPC)
- P.K. 1072
- 20080 Donostia
| | - Eduard Matito
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU)
- and Donostia International Physics Center (DIPC)
- P.K. 1072
- 20080 Donostia
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46
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Affiliation(s)
- Rundong Zhao
- Materials and Energy Division, Beijing Computational Science Research Center, Beijing, China
| | - Rui-Qin Zhang
- Materials and Energy Division, Beijing Computational Science Research Center, Beijing, China
- Department of Physics, City University of Hong Kong, Hong Kong SAR, China
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47
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Casalz-Sainz JL, Guevara-Vela JM, Francisco E, Rocha-Rinza T, Martín Pendás Á. Where Does Electron Correlation Lie? Some Answers from a Real Space Partition. Chemphyschem 2017; 18:3553-3561. [DOI: 10.1002/cphc.201700940] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/04/2017] [Indexed: 11/09/2022]
Affiliation(s)
- José Luis Casalz-Sainz
- Departament of Analytical and Physical Chemistry; University of Oviedo; E-33006 Oviedo Spain
| | | | - Evelio Francisco
- Departament of Analytical and Physical Chemistry; University of Oviedo; E-33006 Oviedo Spain
| | - Tomás Rocha-Rinza
- Institute of Chemistry; National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán C.P.; 04510 Mexico City Mexico
| | - Ángel Martín Pendás
- Departament of Analytical and Physical Chemistry; University of Oviedo; E-33006 Oviedo Spain
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48
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Novák M, Marek R, Foroutan-Nejad C. Anti-Electrostatic CH-Ion Bonding in Decorated Graphanes. Chemistry 2017; 23:14931-14936. [DOI: 10.1002/chem.201703459] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Martin Novák
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Radek Marek
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
- Department of Chemistry, Faculty of Science; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Cina Foroutan-Nejad
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
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49
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Lone pair-π interactions in biological systems: occurrence, function, and physical origin. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 46:729-737. [PMID: 28466098 DOI: 10.1007/s00249-017-1210-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/13/2017] [Accepted: 04/13/2017] [Indexed: 01/13/2023]
Abstract
Lone pair-π interactions are now recognized as a supramolecular bond whose existence in biological systems is documented by a growing number of examples. They are commonly attributed to electrostatic forces. This review attempts to highlight some recent discoveries evidencing the important role which lone pair-π interactions, and anion-π interactions in particular, play in stabilizing the structure and affecting the function of biomolecules. Special attention is paid to studies exploring the physical origin of these at first glance counterintuitive interactions between a lone pair of electrons of one residue and the π-cloud of another. Recent theoretical work went beyond the popular electrostatic model and inquired the extent to which orbital interactions have to be taken into account. In at least one biologically relevant case-that of anion-flavin interactions-a substantial charge-transfer component has been shown to operate.
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50
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Neel AJ, Hilton MJ, Sigman MS, Toste FD. Exploiting non-covalent π interactions for catalyst design. Nature 2017; 543:637-646. [PMID: 28358089 PMCID: PMC5907483 DOI: 10.1038/nature21701] [Citation(s) in RCA: 514] [Impact Index Per Article: 73.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 01/27/2017] [Indexed: 12/18/2022]
Abstract
Molecular recognition, binding and catalysis are often mediated by non-covalent interactions involving aromatic functional groups. Although the relative complexity of these so-called π interactions has made them challenging to study, theory and modelling have now reached the stage at which we can explain their physical origins and obtain reliable insight into their effects on molecular binding and chemical transformations. This offers opportunities for the rational manipulation of these complex non-covalent interactions and their direct incorporation into the design of small-molecule catalysts and enzymes.
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Affiliation(s)
- Andrew J Neel
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Margaret J Hilton
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, USA
| | - Matthew S Sigman
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, USA
| | - F Dean Toste
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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