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Gao Y, Wang Y. Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials. APPLIED PHYSICS REVIEWS 2024; 11:011306. [PMID: 38784221 PMCID: PMC11115426 DOI: 10.1063/5.0171364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.
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Affiliation(s)
- Yanjing Gao
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Yichun Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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2
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Kumar YB, Kumar N, John L, Mahanta HJ, Vaikundamani S, Nagamani S, Sastry GM, Sastry GN. Analyzing the cation-aromatic interactions in proteins: Cation-aromatic database V2.0. Proteins 2024; 92:179-191. [PMID: 37789571 DOI: 10.1002/prot.26600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/17/2023] [Accepted: 09/07/2023] [Indexed: 10/05/2023]
Abstract
The cation-aromatic database (CAD) is a comprehensive repository of cation-aromatic motifs found in experimentally determined protein structures, first reported in 2007 [Proteins, 2007, 67, 1179]. The present article is an update of CAD that contains information of approximately 27.26 million cation-aromatic motifs. CAD uses three distance parameters (r, d1, and d2) to determine the position of the cation relative to the centroid of the aromatic residue and classifies the motifs as cation-π or cation-σ interactions. As of June 2023, about 193 936 protein structures were retrieved from Protein Data Bank, and this resulted in the identification of an impressive number of 27 255 817 cation-aromatic motifs. Among these motifs, spherical motifs constituted 94.09%, while cylindrical motifs made up the remaining 5.91%. When considering the interaction of metal ions with aromatic residues, 965 564 motifs are identified. Remarkably, 82.08% of these motifs involved the binding of metal ions to the amino acid HIS. Moreover, the analysis of binding preferences between cations and aromatic residues revealed that the HIS-HIS, PHE-ARG, and TRP-ARG pairs exhibited a preferential geometry. The motif pair HIS-HIS was the most prevalent, accounting for 19.87% of the total, closely followed by TYR-LYS at 10.17%. Conversely, the motif pair TRP-HIS had the lowest occurrence, representing only 4.20% of the total. The data generated help in revealing the characteristics and biological functions of cation-aromatic interactions in biological molecules. The updated version of CAD (Cation-Aromatic Database V2.0) can be accessed at https://acds.neist.res.in/cadv2.
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Affiliation(s)
- Y Bhargav Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Nandan Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Lijo John
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Hridoy Jyoti Mahanta
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - S Vaikundamani
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Selvaraman Nagamani
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | | | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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Pandey A, Kumar N. Tracing the transition from covalent to non-covalent functionalization of pyrene through C-, N-, and O-based ionic and radical substrates using quantum mechanical calculations. RSC Adv 2023; 13:14119-14130. [PMID: 37188257 PMCID: PMC10177222 DOI: 10.1039/d3ra01457f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 04/13/2023] [Indexed: 05/17/2023] Open
Abstract
Pyrene is one of the widely investigated aromatic hydrocarbons given its unique optical and electronic properties. Modulating inherent characteristics of pyrene via covalent or non-covalent functionalization has been attractive for a wide variety of advanced biomedical and other device applications. In this study, we have reported the functionalization of pyrene via C, N, and O based ionic and radical substrates, and emphasized the transition of covalent to non-covalent functionalization through making the modulation in the substrate. As expected, strong interactions were observed for cationic substrates, however, anionic substrates also exhibited a competitive binding strength. For instance, methyl and phenyl substituted CH3 complexes exhibited IEs in the range of -17 kcal mol-1 to -127 kcal mol-1 and -14 kcal mol-1 to -95 kcal mol-1 and for cationic and anionic substrates, respectively. The analysis of topological parameters showed that un-substituted cationic, anionic, and radical substrates interact with pyrene via covalent interactions, and further become non-covalent upon methylation and phenylation of the substrates. In cationic complexes, the polarisation component is observed to be dominating the interactions, whereas highly competitive contributions from polarization and exchange components were observed in anionic and radical complexes. The contribution of the dispersion component increases with an increase in the degree of methylation and phenylation of the substrate, and starts dominating once the interactions become non-covalent in nature.
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Affiliation(s)
- Anwesh Pandey
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology Jorhat 785006 Assam India
| | - Nandan Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology Jorhat 785006 Assam India
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4
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Crucial role of alkali metal ions and Si/Al ratio in selective adsorption of 1-octene using faujasite zeolites. Sep Purif Technol 2023. [DOI: 10.1016/j.seppur.2023.123531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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5
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Saha B, Bhattacharyya PK. Exploring alkali metal cation⋯hydrogen interaction in the formation half sandwich complexes with cycloalkanes: a DFT approach. PURE APPL CHEM 2023. [DOI: 10.1515/pac-2022-1111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Abstract
Gas and solvent phase stability of half sandwich complexes between cycloalkanes viz. cyclopropane, cyclobutane, cyclopentane, cyclohexane, bicyclo[2.2.2]octane and adamantane with alkali metal cations (Li+, Na+ and K+) are analysed using density functional theory (DFT). M06-2X/6-31++G(d,p) level is primarily used for the study. The studied half sandwich complexes are stable in gas phase (stabilization energy upto 26.55 kcal mol−1). Presence of solvent phase irrespective of its dielectric, imparts negative impact on the stability of the chosen complexes. The formation of the complexes is exothermic in nature. The process of complexation is both enthalpy (ΔH) and free energy (ΔG) driven. Variation in HOMO (highest occupied molecular orbital) energy also indicates towards the chemical stability of complexes. The interaction is non-covalent with primary contribution from induction component. NBO analysis indicates that C–H bond is the donor and antibonding metal orbital is the acceptor site in the process of complexation. Stability of the complexes depends on the size of the interacting monomers.
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Affiliation(s)
- Bapan Saha
- Department of Chemistry, Handique Girls’ College , Gauhati University , Guwahati 781001 , India
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Kumar YB, Pandey A, Kumar N, Sastry GN. Binding propensity and selectivity of cationic, anionic, and neutral guests with model hydrophobic hosts: A first principles study. J Comput Chem 2023; 44:432-441. [PMID: 36583416 DOI: 10.1002/jcc.26977] [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: 04/28/2022] [Revised: 06/23/2022] [Accepted: 07/21/2022] [Indexed: 01/03/2023]
Abstract
Computations play a critical role in deciphering the nature of host-guest interactions both at qualitative and quantitative levels. Reliable quantum chemical computations were employed to assess the nature, binding strength, and selectivity of ionic, and neutral guests with benzenoid hosts. Optimized complex structures reveal that alkali and ammonium ions are found to be in the hydrophobic cavity, while halide ions are outside, while both complexes elicit substantial binding energy. The origin of the selectivity of host toward the guest has been traced to the interaction and deformation energies, and the nature of associated interactions is quantified using energy decomposition and the Quantum Theory of Atoms in Molecules analyses. While the larger hosts lead to loosely bound complexes, as assessed by the longer intermolecular distances, the binding strengths are proportional to the size of the host systems. The binding of cationic complexes is electrostatic or polarization driven while exchange term dominates the anionic complexes. In contrast, dispersion contribution is a key in neutral complexes and plays a pivotal role in stabilizing the polyatomic complexes.
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Affiliation(s)
- Yenamareddy Bhargav Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Anwesh Pandey
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Nandan Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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Jin MY, Zhen Q, Xiao D, Tao G, Xing X, Yu P, Xu C. Engineered non-covalent π interactions as key elements for chiral recognition. Nat Commun 2022; 13:3276. [PMID: 35672365 PMCID: PMC9174283 DOI: 10.1038/s41467-022-31026-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/25/2022] [Indexed: 12/31/2022] Open
Abstract
Molecular recognition and self-assembly are often mediated by intermolecular forces involving aromatic π-systems. Despite the ubiquity of such interactions in biological systems and in the design of functional materials, the elusive nature of aromatic π interaction results in that they have been seldom used as a design element for promoting challenging chemical reactions. Described here is a well-engineered catalytic system into which non-covalent π interactions are directly incorporated. Enabled by a lone pair-π interaction and a π-π stacking interaction operating collectively, efficient chiral recognition is successfully achieved in the long-pursued dihydroxylation-based kinetic resolution. Density functional theory calculations shed light on the crucial role played by the lone pair-π interaction between the carbonyl oxygen of the cinchona alkaloid ligand and the electron-deficient phthalazine π moiety of the substrate in the stereoselectivity-determining transition states. This discovery serves as a proof-of-principle example showing how the weak non-covalent π interactions, if ingeniously designed, could be a powerful guide in attaining highly enantioselective catalysis.
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Affiliation(s)
- Ming Yu Jin
- Department of Chemistry and Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Qianqian Zhen
- Department of Chemistry and Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Dengmengfei Xiao
- Department of Chemistry and Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Guanyu Tao
- Department of Chemistry and Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Xiangyou Xing
- Department of Chemistry and Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Peiyuan Yu
- Department of Chemistry and Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Chen Xu
- Department of Chemistry and Shenzhen Grubbs Institute, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 518055, Shenzhen, China.
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Vaňura P, Sýkora D, Böhm S, Uhlíková T. Cation–π interaction of thallium (I) with [7]helicene: an experimental and theoretical study. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2072784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Petr Vaňura
- University of Chemistry and Technology, Prague, Czech Republic
| | - David Sýkora
- University of Chemistry and Technology, Prague, Czech Republic
| | - Stanislav Böhm
- University of Chemistry and Technology, Prague, Czech Republic
| | - Tereza Uhlíková
- University of Chemistry and Technology, Prague, Czech Republic
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9
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Ali M, Song X, Ding D, Wang Q, Zhang Z, Tang Z. Bioremediation of PAHs and heavy metals co-contaminated soils: Challenges and enhancement strategies. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 295:118686. [PMID: 34920044 DOI: 10.1016/j.envpol.2021.118686] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/20/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
Systemic studies on the bioremediation of co-contaminated PAHs and heavy metals are lacking, and this paper provides an in-depth review on the topic. The released sources and transport of co-contaminated PAHs and heavy metals, including their co-occurrence through formation of cation-π interactions and their adsorption in soil are examined. Moreover, it is investigated that co-contamination of PAHs and heavy metals can drive a synergistic positive influence on bioremediation through enhanced secretion of extracellular polymeric substances (EPSs), production of biosynthetic genes, organic acid and enzymatic proliferation. However, PAHs molecular structure, PAHs-heavy metals bioavailability and their interactive cytotoxic effects on microorganisms can exert a challenging influence on the bioremediation under co-contaminated conditions. The fluctuations in bioavailability for microorganisms are associated with soil properties, chemical coordinative interactions, and biological activities under the co-contaminated PAHs-heavy metals conditions. The interactive cytotoxicity caused by the emergence of co-contaminants includes microbial cell disruption, denaturation of DNA and protein structure, and deregulation of antioxidant biological molecules. Finally, this paper presents the emerging strategies to overcome the bioavailability problems and recommends the use of biostimulation and bioaugmentation along with the microbial immobilization for enhanced bioremediation of PAHs-heavy metals co-contaminated sites. Better knowledge of the bioremediation potential is imperative to improve the use of these approaches for the sustainable and cost-effective remediation of PAHs and heavy metals co-contamination in the near future.
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Affiliation(s)
- Mukhtiar Ali
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Song
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Da Ding
- Nanjing Institute of Environmental Science, Ministry of Ecology and Environment of the People's Republic of China, Nanjing, 210042, China
| | - Qing Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zhuanxia Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiwen Tang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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10
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Structural Selectivity of PAH Removal Processes in Soil, and the Effect of Metal Co-Contaminants. ENVIRONMENTS 2022. [DOI: 10.3390/environments9020023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) form a convenient structural series of molecules with which to examine the selectivity exerted on their removal by soil microbiota. It is known that there is an inverse relationship between PAH molecular size and degradation rates in soil. In this paper, we look at how the magnitude of the slope for this relationship, m, can be used as an indicator of the effect of metal co-contaminants on degradation rates across a range of PAH molecular weights. The analysis utilises data collected from our previous microcosm study (Deary, M.E.; Ekumankama, C.C.; Cummings, S.P. Development of a novel kinetic model for the analysis of PAH biodegradation in the presence of lead and cadmium co-contaminants. Journal of Hazard Materials 2016, 307, 240–252) in which we followed the degradation of the 16 US EPA PAHs over 40 weeks in soil microcosms taken from a high organic matter content woodland soil. The soil was amended with a PAH mixture (total concentration of 2166 mg kg−1) and with a range of metal co-contaminant concentrations (lead, up to 782 mg kg−1; cadmium up to 620 mg kg−1; and mercury up to 1150 mg kg−1). It was found that the magnitude of m increases in relation to the applied concentration of metal co-contaminant, indicating a more adverse effect on microbial communities that participate in the removal of higher molecular weight PAHs. We conclude that m is a useful parameter by which we might measure the differential effects of environmental contaminants on the PAH removal. Such information will be useful in planning and implementing remediation strategies.
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11
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Simultaneous Interaction of Graphene Nanoflakes with Cations and Anions: A Cooperativity Study. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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Application of Innovative Analytical Modeling for the Physicochemical Analysis of Adsorption Isotherms of Silver Nitrate on Helicenes: Phenomenological Study of the Complexation Process. ADSORPT SCI TECHNOL 2021. [DOI: 10.1155/2021/6619389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The interaction between the silver ion and the cyclic aromatic molecules, namely, the helicenes, is the subject of this paper. In fact, a silver complexation system based on quartz crystal microbalance (QCM) sensor with a functional film of helicenes has been designed and developed at four temperatures. The developed system, in which the sensor response reflects the adsorption of the hexahelicene and the heptahelicene, was able to control the complexed mass of silver for each concentration. Experimental outcomes indicated that the quartz crystal coated with heptahelicene is the adequate material for silver adsorption. Then, a theoretical study has been performed through two statistical physics models (SMPG and SMRG) in order to analyze the experimental adsorption isotherms of the two helicenes at the ionic scale. The SMRG model was developed using the real gas law and was satisfactorily applied for the microscopic investigation of the hexahelicene isotherms indicating that the lateral interactions between the adsorbates are responsible of the decrease of the adsorbed quantity at saturation. The interpretation of the two models’ parameters indicated that the adsorption of the two helicenes is an endothermic phenomenon. Interestingly, the heptahelicene is recommended for silver complexation because it shows the highest adsorption energies involving chemical bonds during the complexation process. The SMPG model and the SMRG model also allow prediction of three thermodynamic functions (configurational entropy, Gibbs free enthalpy, and internal energy) which govern the adsorption mechanism of silver on the two helicenes.
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Saha B, Bhattacharyya PK. On the formation of sandwich complexes of aromatic inorganic linker: A DFT-D3 approach. Polyhedron 2021. [DOI: 10.1016/j.poly.2020.114911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Kumar N, Saha S, Sastry GN. Towards developing a criterion to characterize non-covalent bonds: a quantum mechanical study. Phys Chem Chem Phys 2021; 23:8478-8488. [DOI: 10.1039/d0cp05689h] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chemical bonds are central to chemistry, biology, and allied fields, but still, the criterion to characterize an interaction as a non-covalent bond has not been studied rigorously.
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Affiliation(s)
- Nandan Kumar
- Centre for Molecular Modeling
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Soumen Saha
- Centre for Molecular Modeling
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- Nagoya University
| | - G. Narahari Sastry
- Centre for Molecular Modeling
- CSIR-Indian Institute of Chemical Technology
- Hyderabad 500007
- India
- Academy of Scientific and Innovative Research (AcSIR)
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16
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Physico-chemical study of complexation of silver ion (Ag +) by macrocyclic molecules (hexa-Helicenes) based on statistical physics theory: new description of a cancer drug. Sci Rep 2020; 10:10328. [PMID: 32587284 PMCID: PMC7316866 DOI: 10.1038/s41598-020-67120-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/28/2020] [Indexed: 11/30/2022] Open
Abstract
In recent papers, it is found that the silver-[6]Helicene complex can be used as a cancer drug but the interaction silver-hexaHelicene has not yet proven. The idea of this paper is to investigate the complexation process of the [6]Helicene by the silver metal (Ag+) using three types of adsorbates. Indeed, the adsorption of silver chloride, silver nitrate and silver sulfide into the sensor films deposited on the QCM electrode are measured at three temperatures (293–333 K). Films of the [6]Helicene were deposited on the QCM resonators using spin coating method in order to obtain uniform and homogenous sensor surface. Experimental results indicated that the [6]Helicene can form a stable complex with the silver ion and that the AgCl is the appropriate adsorbate for the complexation achievement. Actually, an advanced modeling analysis by means of statistical physics adsorption models is applied to explore the new vision of the complextion system. The values of the models parameters are deduced from fitting the experimental data with the developed models. They result in confirming the experimental findings by comparing the complexation energies of the three examined systems. In particular, for the silver nitrate, the Van-der-Waals parameters explained the isotherms drop at high concentration through the lateral interactions between the adsorbates. The adsorption energies analysis showed the highest interaction AgCl-[6]Helicene. Density functional theory (DFT) simulations showed that chemical bonds take place during the adsorption of silver chloride on hexaHelicene which confirms that the [6]Helicene can function as a chiral molecular tweezer of the univalent cationic silver.
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Kim I, Lee Y, Kim SD. Cytotoxicity induced by the mixture components of nickel and poly aromatic hydrocarbons. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2019; 41:391-400. [PMID: 29934778 DOI: 10.1007/s10653-018-0139-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
Although particulate matter (PM) is composed of various chemicals, investigations regarding the toxicity that results from mixing the substances in PM are insufficient. In this study, the effects of low levels of three PAHs (benz[a]anthracene, benzo[a]pyrene, and dibenz[a,h]anthracene) on Ni toxicity were investigated to assess the combined effect of Ni-PAHs on the environment. We compared the difference in cell mortality and total glutathione (tGSH) reduction between single Ni and Ni-PAHs co-exposure using A549 (human alveolar carcinoma). In addition, we measured the change in Ni solubility in chloroform that was triggered by PAHs to confirm the existence of cation-π interactions between Ni and PAHs. In the single Ni exposure, the dose-response curve of cell mortality and tGSH reduction were very similar, indicating that cell death was mediated by the oxidative stress. However, 10 μM PAHs induced a depleted tGSH reduction compared to single Ni without a change in cell mortality. The solubility of Ni in chloroform was greatly enhanced by the addition of benz[a]anthracene, which demonstrates the cation-π interactions between Ni and PAHs. Ni-PAH complexes can change the toxicity mechanisms of Ni from oxidative stress to others due to the reduction of Ni2+ bioavailability and the accumulation of Ni-PAH complexes on cell membranes. The abundant PAHs contained in PM have strong potential to interact with metals, which can affect the toxicity of the metal. Therefore, the mixture toxicity and interactions between diverse metals and PAHs in PM should be investigated in the future.
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Affiliation(s)
- Injeong Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, South Korea
| | - Yeseul Lee
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, South Korea
| | - Sang Don Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, South Korea.
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Rogachev AY, Liu S, Xu Q, Li J, Zhou Z, Spisak SN, Wei Z, Petrukhina MA. Placing Metal in the Bowl: Does Rim Alkylation Matter? Organometallics 2019. [DOI: 10.1021/acs.organomet.8b00837] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrey Yu. Rogachev
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Shuyang Liu
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Qi Xu
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Jingbai Li
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Zheng Zhou
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Sarah N. Spisak
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Zheng Wei
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Marina A. Petrukhina
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
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19
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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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20
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Cation–π Interaction of the Univalent Silver Cation with [2.2.2]Paracyclophane in the Gas Phase and in the Solid State: Experimental and Theoretical Study. J CLUST SCI 2018. [DOI: 10.1007/s10876-018-1461-8] [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]
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21
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Zhang Y, Chen S, Ying F, Su P, Wu W. Valence Bond Based Energy Decomposition Analysis Scheme and Its Application to Cation−π Interactions. J Phys Chem A 2018; 122:5886-5894. [DOI: 10.1021/acs.jpca.8b04201] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Yang Zhang
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, iChEM, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Sifeng Chen
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, iChEM, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Fuming Ying
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, iChEM, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Peifeng Su
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, iChEM, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, iChEM, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
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22
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Makrlík E, Sýkora D, Böhm S, Kvíčalová M, Vaňura P. Fascinating interaction of the ammonium cation with [2.2.2]paracyclophane: experimental and theoretical study. Mol Phys 2018. [DOI: 10.1080/00268976.2017.1418031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Emanuel Makrlík
- Faculty of Environmental Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - David Sýkora
- University of Chemistry and Technology, Prague, Czech Republic
| | - Stanislav Böhm
- University of Chemistry and Technology, Prague, Czech Republic
| | - Magdalena Kvíčalová
- Faculty of Environmental Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Petr Vaňura
- University of Chemistry and Technology, Prague, Czech Republic
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23
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Klepetářová B, Kvíčalová M, Sýkora D, Makrlík E, Vaňura P. Experimental and theoretical study on cation-π interaction of the univalent silver cation with pyrene in the gas phase and in the solid state. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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24
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Makrlík E, Sýkora D, Böhm S, Vaňura P. Cation-π interaction of the univalent sodium cation with [2.2.2]paracyclophane: Experimental and theoretical study. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.10.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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Makrlík E, Sýkora D, Böhm S, Vaňura P. Experimental and Theoretical Study on Cation–π Interaction of the Potassium Cation with [2.2.2]Paracyclophane. J CLUST SCI 2017. [DOI: 10.1007/s10876-017-1314-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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26
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Does alkali cation binding to aromatic ring retard the fluxional haptotropic migration? Evidences from density functional study. J CHEM SCI 2017. [DOI: 10.1007/s12039-017-1382-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Makrlík E, Sýkora D, Böhm S, Vaňura P. [2.2.2]Paracyclophane as a receptor for the cesium cation in the gas phase. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1334971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Emanuel Makrlík
- Faculty of Environmental Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - David Sýkora
- University of Chemistry and Technology, Prague, Czech Republic
| | - Stanislav Böhm
- University of Chemistry and Technology, Prague, Czech Republic
| | - Petr Vaňura
- University of Chemistry and Technology, Prague, Czech Republic
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28
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Zhao S, Jia H, Nulaji G, Gao H, Wang F, Wang C. Photolysis of polycyclic aromatic hydrocarbons (PAHs) on Fe 3+-montmorillonite surface under visible light: Degradation kinetics, mechanism, and toxicity assessments. CHEMOSPHERE 2017; 184:1346-1354. [PMID: 28687030 DOI: 10.1016/j.chemosphere.2017.06.106] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/22/2017] [Accepted: 06/25/2017] [Indexed: 06/07/2023]
Abstract
Photochemical behavior of various polycyclic aromatic hydrocarbons (PAHs) on Fe3+-modified montmorillonite was explored to determine their potential kinetics, pathways, and mechanism under visible light. Depending on the type of PAH molecules, the transformation rate follows the order of benzo[a]pyrene ≈ anthracene > benzo[a]anthracene > phenanthrene. Quantum simulation results confirm the crucial role of "cation-π" interaction between Fe3+ and PAHs on their transformation kinetics. Primary intermediates, including quinones, ring-opening products and benzene derivatives, were identified by gas chromatography-mass spectrometer (GC-MS), and the possible photodegradation pathway of benzo[a]pyrene was proposed. Meanwhile, radical intermediates, such as reactive oxygen species (ROS) and free organic radicals, were detected by electron paramagnetic resonance (EPR) technique. The photolysis of selected PAHs, such as anthracene and benzo[a]pyrene, on clay surface firstly occurs by electron transfer from PAHs to Fe3+-montmorillonite, followed by degradation involving photo-induced ROS such as ·OH and ·O2-. To investigate the acute toxicity of photolysis products, the Microtox® toxicity test was performed during the photodegradation processes of various PAHs. As a result, the photo-irradiation initially induces increased toxicity by generating reactive intermediates, such as free organic radicals, and then the toxicity gradually decreases with increasing of reaction time. Overall, the present study provides useful information to understand the fate and photo-transformation of PAHs in contaminated soils.
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Affiliation(s)
- Song Zhao
- Key Laboratory of Functional Materials and Devices for Special Environments, Xinjiang Technical Institute of Physics & Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
| | - Hanzhong Jia
- Key Laboratory of Functional Materials and Devices for Special Environments, Xinjiang Technical Institute of Physics & Chemistry, Chinese Academy of Sciences, Urumqi 830011, China.
| | - Gulimire Nulaji
- Key Laboratory of Functional Materials and Devices for Special Environments, Xinjiang Technical Institute of Physics & Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
| | - Hongwei Gao
- Key Laboratory of Functional Materials and Devices for Special Environments, Xinjiang Technical Institute of Physics & Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
| | - Fu Wang
- Key Laboratory of Functional Materials and Devices for Special Environments, Xinjiang Technical Institute of Physics & Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
| | - Chuanyi Wang
- Key Laboratory of Functional Materials and Devices for Special Environments, Xinjiang Technical Institute of Physics & Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
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29
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Demircan ÇA, Bozkaya U. Transition Metal Cation−π Interactions: Complexes Formed by Fe2+, Co2+, Ni2+, Cu2+, and Zn2+ Binding with Benzene Molecules. J Phys Chem A 2017; 121:6500-6509. [DOI: 10.1021/acs.jpca.7b05759] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Uğur Bozkaya
- Department of Chemistry, Hacettepe University, Ankara, 06800, Turkey
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30
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Bhattacharyya PK. Exploring Cation−π Interaction in the Complexes with B≡B Triple Bond: A DFT Study. J Phys Chem A 2017; 121:3287-3298. [DOI: 10.1021/acs.jpca.7b01326] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Shakourian-Fard M, Kamath G. The effect of defect types on the electronic and optical properties of graphene nanoflakes physisorbed by ionic liquids. Phys Chem Chem Phys 2017; 19:4383-4395. [PMID: 28119976 DOI: 10.1039/c6cp07455c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Defect engineering and non-covalent interaction strategies allow for dramatically tuning the optoelectronic properties of graphene. Using ab initio density functional theory (M06-2X/cc-pVDZ), we find that the nature of defects on the graphene nanoflakes (GNFs) and the size of defective GNF (DGNF) surfaces affect the binding energy (ΔEb) of ionic liquids (ILs) and the UV-Vis absorption spectra of DGNFIL complexes. Further, our results indicate that increasing the size of DGNFs affects the geometrical structure of the surfaces and increases the binding energy of ILs by about 10%. Analysis based on AIM and EDA shows that the interactions between ILs and DGNFs are non-covalent in nature (dispersion energy being dominant) and associated with charge transfer between the IL and nanoflakes. A comparison between the ΔEb values of ILs on DGNFs, GNFs, and h-BN nanoflakes (h-BNNF) shows that the presence of defects on the GNF surfaces increases the binding energy values as follows: DGNFIL > pristine GNFIL > h-BNNFIL. Our calculations indicate that increasing the size of DGNF surfaces leads to a decrease in the HOMO-LUMO energy gap (Eg) of the DGNF surfaces. Orbital energy and density of state calculations show that the Eg of DV(SW)-GNFs decreases upon IL adsorption and their Fermi energy level is shifted depending on the type of IL, thus enabling better conductivity. Reactivity descriptors generally indicate that the chemical potential (μ) and chemical hardness (η) of nanoflakes decrease upon IL adsorption, whereas the electrophilicity index (ω) increases. The UV-Vis absorption spectrum of DV-GNF and SW-GNF shows four bands in the visible spectrum which correspond to π → π* transitions with the absorption bands of SW-GNF appearing at higher wavelengths than those of DV-GNF. The most intense absorption bands in DV-GNF (λ = 348 nm) and SW-GNF (λ = 375 nm) are associated with electronic transitions HOMO-1 → LUMO+2 and HOMO → LUMO+1, respectively. In addition, these absorption bands undergo a red-shift by both increasing the size of the DV(SW)-GNF surfaces and IL adsorption. We also observe that the energy gaps and absorption spectra can be altered by varying the defect types and the type of IL adsorbate, where the defect types affect the spectral shapes of the bands and adsorbates at the first absorption peak, thus having potential application for light-emitting devices.
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Affiliation(s)
- Mehdi Shakourian-Fard
- Birjand University of Technology, Department of Chemical Engineering, Birjand, P.O. Box 97175/569, Iran.
| | - Ganesh Kamath
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
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32
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Pinheiro S, Soteras I, Gelpí JL, Dehez F, Chipot C, Luque FJ, Curutchet C. Structural and energetic study of cation–π–cation interactions in proteins. Phys Chem Chem Phys 2017; 19:9849-9861. [DOI: 10.1039/c6cp08448f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Statistical and energetic analysis of cation–π–cation motifs in protein structures suggests a potential stabilizing role in the protein fold.
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Affiliation(s)
- Silvana Pinheiro
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Biomedicina (IBUB)
- Facultat de Farmàcia i Ciències de l'Alimentació
- Universitat de Barcelona
- Barcelona
- Spain
| | - Ignacio Soteras
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia and Institut de Biomedicina (IBUB)
- Facultat de Farmàcia i Ciències de l'Alimentació
- Universitat de Barcelona
- Santa Coloma de Gramenet
- Spain
| | - Josep Lluis Gelpí
- Departament de Bioquímica i Biomedicina Molecular
- Facultat de Biologia
- Universitat de Barcelona
- Spain
| | - François Dehez
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana – Champaign
- Unité Mixte de Recherche No. 7565
- Université de Lorraine
- Vandoeuvre-lès-Nancy cedex
- France
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana – Champaign
- Unité Mixte de Recherche No. 7565
- Université de Lorraine
- Vandoeuvre-lès-Nancy cedex
- France
| | - F. Javier Luque
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia and Institut de Biomedicina (IBUB)
- Facultat de Farmàcia i Ciències de l'Alimentació
- Universitat de Barcelona
- Santa Coloma de Gramenet
- Spain
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Biomedicina (IBUB)
- Facultat de Farmàcia i Ciències de l'Alimentació
- Universitat de Barcelona
- Barcelona
- Spain
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33
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Makrlík E, Sýkora D, Böhm S, Vaňura P. Cation-π interaction of Li+ with [6]helicene: Experimental and theoretical study. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.10.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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34
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Kennedy CR, Lin S, Jacobsen EN. The Cation-π Interaction in Small-Molecule Catalysis. Angew Chem Int Ed Engl 2016; 55:12596-624. [PMID: 27329991 PMCID: PMC5096794 DOI: 10.1002/anie.201600547] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Indexed: 11/11/2022]
Abstract
Catalysis by small molecules (≤1000 Da, 10(-9) m) that are capable of binding and activating substrates through attractive, noncovalent interactions has emerged as an important approach in organic and organometallic chemistry. While the canonical noncovalent interactions, including hydrogen bonding, ion pairing, and π stacking, have become mainstays of catalyst design, the cation-π interaction has been comparatively underutilized in this context since its discovery in the 1980s. However, like a hydrogen bond, the cation-π interaction exhibits a typical binding affinity of several kcal mol(-1) with substantial directionality. These properties render it attractive as a design element for the development of small-molecule catalysts, and in recent years, the catalysis community has begun to take advantage of these features, drawing inspiration from pioneering research in molecular recognition and structural biology. This Review surveys the burgeoning application of the cation-π interaction in catalysis.
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Affiliation(s)
- C Rose Kennedy
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA, 02138, USA
| | - Song Lin
- Department of Chemistry, University of California, Berkeley, 535 Latimer Hall, Berkeley, CA, 94720, USA
| | - Eric N Jacobsen
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA, 02138, USA.
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35
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Klepetářová B, Makrlík E, Sýkora D, Böhm S, Vaňura P. Cation–π interaction of the univalent silver cation with racemic [6]helicene in the gas phase and in the solid state. Polyhedron 2016. [DOI: 10.1016/j.poly.2016.05.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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36
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37
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Kennedy CR, Lin S, Jacobsen EN. Die Kation-π-Wechselwirkung in der Katalyse mit niedermolekularen Verbindungen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600547] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- C. Rose Kennedy
- Department of Chemistry and Chemical Biology; Harvard University; 12 Oxford St Cambridge MA 02138 USA
| | - Song Lin
- Department of Chemistry; University of California, Berkeley; 535 Latimer Hall Berkeley CA 94720 USA
| | - Eric N. Jacobsen
- Department of Chemistry and Chemical Biology; Harvard University; 12 Oxford St Cambridge MA 02138 USA
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38
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Janesko BG, Wiberg KB, Scalmani G, Frisch MJ. Electron Delocalization Range in Atoms and on Molecular Surfaces. J Chem Theory Comput 2016; 12:3185-94. [DOI: 10.1021/acs.jctc.6b00343] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Giovanni Scalmani
- Gaussian, Inc., 340
Quinnipiac St., Bldg. 40, Wallingford, Connecticut 06492, United States
| | - Michael J. Frisch
- Gaussian, Inc., 340
Quinnipiac St., Bldg. 40, Wallingford, Connecticut 06492, United States
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39
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Affiliation(s)
- A. Subha Mahadevi
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
| | - G. Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
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40
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Sharma B, Neela YI, Narahari Sastry G. Structures and energetics of complexation of metal ions with ammonia, water, and benzene: A computational study. J Comput Chem 2016; 37:992-1004. [PMID: 26833683 DOI: 10.1002/jcc.24288] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/26/2015] [Accepted: 12/01/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Bhaskar Sharma
- Center for Molecular Modelling; CSIR-Indian Institute of Chemical Technology; Tarnaka, Hyderabad Telangana 500 607 India
| | - Y. Indra Neela
- Center for Molecular Modelling; CSIR-Indian Institute of Chemical Technology; Tarnaka, Hyderabad Telangana 500 607 India
| | - G. Narahari Sastry
- Center for Molecular Modelling; CSIR-Indian Institute of Chemical Technology; Tarnaka, Hyderabad Telangana 500 607 India
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41
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Sarma D, Saha B, Chandra Deka B, Bhattacharyya PK. Unique cation–cyclohexane interactions in tri- and hexa-fluorocyclohexane multidecker complexes in the gas phase: a DFT study. RSC Adv 2016. [DOI: 10.1039/c6ra24508k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The formation of stable sandwich and multidecker complexes through electrostatic interaction in tri- and hexa-fluorocyclohexane has been analyzed in the light of density functional theory.
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Affiliation(s)
| | - Bapan Saha
- Department of Chemistry
- Arya Vidyapeeth College
- Guwahati
- India
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42
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Experimental and theoretical study on cation–π interaction of the univalent thallium cation with [2.2.2]paracyclophane. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.10.074] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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43
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Makrlík E, Sýkora D, Böhm S, Vaňura P, Církva V, Storch J, Polášek M. Cation-π interaction of Tl+ with [6]helicene: Experimental and DFT study. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.06.080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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44
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Klepetářová B, Makrlík E, Vaňura P, Storch J. Contribution to cation–π interaction of the univalent silver cation with racemic [7]helicene in the solid state. Struct Chem 2015. [DOI: 10.1007/s11224-015-0679-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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45
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[6]Helicene as a novel molecular tweezer for the univalent silver cation: Experimental and theoretical study. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.04.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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46
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Interplay between π···π stacking and cation···π interaction: a theoretical NMR study. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2015. [DOI: 10.1007/s13738-015-0663-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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47
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Zaboli M, Raissi H. Structural, QTAIM, thermodynamic properties, bonding, aromaticity and NMR analyses of cation–π interactions of mono and divalent metal cations (Li+, Na+, K+, Be2+, Mg2+, and Ca2+) with substituted pyrazine derivatives. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1142/s0219633615500443] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Theoretical investigation of 42 cation-π complexes formed by the alkali metal ( Li +, Na +, K +), alkaline-earth cations ( Be 2+, Mg 2+, Ca 2+) and π-system of the pyrazine and its derivatives have been performed at density functional theory (DFT) (B3LYP functional) and MP2 methods with 6-311++G** basis set in the gas phase and the polarized continuum model (PCM)-water solvation. The following substituents have been taken into consideration: Br , Cl , CH 3, OH , OCH 3 and SH . The interactions present in these complexes have been investigated by means of the natural bond orbital (NBO) and the Bader's quantum theory of atoms in molecules (QTAIMs) approaches. The effects of the interactions on NMR data have been probed using the GIAO-based method to extend investigation of the studied compounds. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies show that charge transfer occurs within each complex. Vibrational frequencies and physical properties such as dipole moment, chemical potential, chemical hardness and chemical electrophilicity of these compounds have been systematically explored. The aromaticity of aromatic rings has been measured using several well-established indices of aromaticity such as nucleus-independent chemical shift, harmonic oscillator models of the aromaticity, para-delocalization index, average two-center indices, aromatic fluctuation index and π-fluctuation aromatic index.
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Affiliation(s)
- Maryam Zaboli
- Department of Chemistry, University of Birjand, Birjand, Iran
| | - Heidar Raissi
- Department of Chemistry, University of Birjand, Birjand, Iran
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Böhm S, Makrlík E, Vaňura P, Klepetářová B, Sýkora D. Theoretical study of cation–π interactions of Li+, Na+, and K+ with [6]helicene. MONATSHEFTE FUR CHEMIE 2015. [DOI: 10.1007/s00706-014-1393-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Makrlík E, Klepetářová B, Sýkora D, Böhm S, Vaňura P, Storch J. Experimental and theoretical study on cation-π interaction of the univalent silver cation with [7]helicene in the gas phase and in the solid state. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.06.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Makrlík E, Jaklová Dytrtová J, Vaňura P, Sýkora J, Vladimír Církva, Storch J. Cation–π interaction of Ag+ with [6]helicene: An experimental and theoretical study. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.04.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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