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Villani L, Mohire NR, Robertson EG. When Phenyl and Cyclopropyl Rings Meet: Spectroscopic Shifts and Conformational Questions. J Phys Chem A 2023; 127:7557-7567. [PMID: 37650854 DOI: 10.1021/acs.jpca.3c04314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The electronic and vibrational spectra of cyclopropylbenzene (CPB) and 1,3-bromocyclopropylbenzene (BrCPB) in the gas phase were investigated using quantum chemical calculations in combination with resonance-enhanced multi-photon ionization REMPI techniques including 1c-R2PI, UV-UV holeburning, and IR-UV ion depletion in the CH stretch region. The electronic spectra revealed the presence of a single conformer for both species, with the absence of any perpendicular conformer attributed to low computed barriers to conformer interconversion. Assignment of CPB to the bisected conformer was made through interpreting distinctive CH stretch bands in the IR-UV spectrum in conjunction with quantum chemical calculations. A local anharmonic model based on DFT calculations was adapted to reproduce the cyclopropyl CH stretch spectrum successfully. It was not feasible to definitively assign which bisected conformer of BrCPB was observed using vibrational information alone due to the close similarity of their predicted IR spectra. However, conformational sensitivity of the S1 ← S0 transition dipole moment (TDM) alignments leads to simulated rotational contours that display stark differences, which prompted assignment to the "B1" bisecting conformer with the cyclopropyl ring directed away from the bromine atom. The absence of the energetically comparable "B2" conformer is unexpected. The analysis of the convolution of aromatic and aliphatic modes serves as a basis for assignment in constrained aliphatic systems.
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Affiliation(s)
- Luigi Villani
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Nishit R Mohire
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Evan G Robertson
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
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Ahmed N, El-Nakib HE, Ramsis MM, Albably NO, Wober J, Weigand JJ, Schwedtmann K, Zierau O, Abadi AH. Structure-Activity Relationships of Triphenylethylene Derivatives and Their Evaluation as Anticancer and Antiviral Agents. ACS OMEGA 2023; 8:25903-25923. [PMID: 37521647 PMCID: PMC10373199 DOI: 10.1021/acsomega.3c01682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023]
Abstract
Tamoxifen (TAM) is a selective estrogen receptor modulator (SERM) that is used in the treatment of breast cancer, yet with the risk of developing uterine cancer. A perfect SERM would act as an estrogen activator on bones, the cardiovascular system, and the central nervous system while providing neutral or estrogen blocking effects on the breast and the uterus. Herein, we report on the design, synthesis, and evaluation of new rigid and flexible TAM analogues. Mainly, a chloro substituent is introduced at the para position of the TAM ring C blocking the CYP2D6 hydroxylation site. Most compounds showed estrogenic activity higher than TAM using the yeast estrogen screen assays, indicating the determinant role of the chloro substituent upon functional activity. Despite being estrogenic, compound 2B showed potent antiproliferative activity in the NCI 60 cell lines with mean GI50 = 3.67 μM, GI50 = 1.05 μM on MCF-7 cell lines, and GI50 = 1.30 μM on MDA-MB-231. The estrogenic activity of compound 2B was further confirmed by stimulating alkaline phosphatase in Ishikawa cells, and it showed no increase in relative uterine wet weight in ovariectomized rats. Compound 2F showed EC90 = 0.31 μg/mL and SI90 = 60 against Ebola virus; this is 200-fold more potent than the positive control favipiravir. This is the first time to report estrogenic triphenylethylenes as anti-EBOV agents. The anti-EBOV activity reported is a function of the substitution pattern of the scaffold rather than the functional activity. Moreover, compound 3D showed excellent PO pharmacokinetic properties in mice. In conclusion, for this class of TAM-like compounds, the blockage of the p-position of ring C is decisive for the functional activity; meanwhile, the triarylethylene substitution pattern is detrimental for the antiviral activity.
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Affiliation(s)
- Nermin
S. Ahmed
- Faculty
of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry, German University in Cairo, 11835 Cairo, Egypt
| | - Heba E. El-Nakib
- Faculty
of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry, German University in Cairo, 11835 Cairo, Egypt
| | - Marian M. Ramsis
- Faculty
of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry, German University in Cairo, 11835 Cairo, Egypt
| | - Nouran O. Albably
- Faculty
of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry, German University in Cairo, 11835 Cairo, Egypt
| | - Jannette Wober
- Faculty
of Biology, Institute of Zoology, Technische
Universität Dresden, 01062 Dresden, Germany
| | - Jan J. Weigand
- Faculty
of Chemistry and Food Chemistry, Institute of Inorganic Molecular
Chemistry, Technische Universität
Dresden, 01062 Dresden, Germany
| | - Kai Schwedtmann
- Faculty
of Chemistry and Food Chemistry, Institute of Inorganic Molecular
Chemistry, Technische Universität
Dresden, 01062 Dresden, Germany
| | - Oliver Zierau
- Faculty
of Biology, Institute of Zoology, Technische
Universität Dresden, 01062 Dresden, Germany
| | - Ashraf H. Abadi
- Faculty
of Pharmacy and Biotechnology, Department of Pharmaceutical Chemistry, German University in Cairo, 11835 Cairo, Egypt
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3
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Le X, Gao T, Wang L, Wei F, Chen C, Zhao Y. Self-Assembly of Short Amphiphilic Peptides and Their Biomedical Applications. Curr Pharm Des 2022; 28:3546-3562. [PMID: 36424793 DOI: 10.2174/1381612829666221124103526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 10/22/2022] [Accepted: 11/01/2022] [Indexed: 11/26/2022]
Abstract
A series of functional biomaterials with different sizes and morphologies can be constructed through self-assembly, among which amphiphilic peptide-based materials have received intense attention. One main possible reason is that the short amphiphilic peptides can facilitate the formation of versatile materials and promote their further applications in different fields. Another reason is that the simple structure of amphiphilic peptides can help establish the structure-function relationship. This review highlights the recent advances in the self-assembly of two typical peptide species, surfactant-like peptides (SLPs) and peptides amphiphiles (PAs). These peptides can self-assemble into diverse nanostructures. The formation of these different nanostructures resulted from the delicate balance of varied non-covalent interactions. This review embraced each non-covalent interaction and then listed the typical routes for regulating these non-covalent interactions, then realized the morphologies modulation of the self-assemblies. Finally, their applications in some biomedical fields, such as the stabilization of membrane proteins, templating for nanofabrication and biomineralization, acting as the antibacterial and antitumor agents, hemostasis, and synthesis of melanin have been summarized. Further advances in the self-assembly of SLPs and PAs may focus on the design of functional materials with targeted properties and exploring their improved properties.
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Affiliation(s)
- Xiaosong Le
- State Key Laboratory of Heavy Oil Processing and the Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao266580, China
| | - Tianwen Gao
- State Key Laboratory of Heavy Oil Processing and the Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao266580, China
| | - Li Wang
- State Key Laboratory of Heavy Oil Processing and the Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao266580, China
| | - Feng Wei
- State Key Laboratory of Heavy Oil Processing and the Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao266580, China
| | - Cuixia Chen
- State Key Laboratory of Heavy Oil Processing and the Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao266580, China
| | - Yurong Zhao
- State Key Laboratory of Heavy Oil Processing and the Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao266580, China
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Bedeković N, Piteša T, Eraković M, Stilinović V, Cinčić D. Anticooperativity of Multiple Halogen Bonds and Its Effect on Stoichiometry of Cocrystals of Perfluorinated Iodobenzenes. CRYSTAL GROWTH & DESIGN 2022; 22:2644-2653. [PMID: 35401054 PMCID: PMC8991082 DOI: 10.1021/acs.cgd.2c00077] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/01/2022] [Indexed: 05/13/2023]
Abstract
To investigate influences on the topicity of perfluorinated halobenzenes as halogen bond (XB) donors in the solid state, we have conducted a database survey and prepared 18 novel cocrystals of potentially ditopic (13ditfb, 14ditfb) and tritopic (135titfb) XB donors with 15 monotopic pyridines. 135titfb shows high tendency to be mono- or ditopic, but with strong bases it can act as a tritopic XB donor. DFT calculations have shown that binding of a single acceptor molecule on one of the iodine atoms of the XB donor reduces the ESPmax on the remaining iodine atoms and dramatically decreases their potential for forming further halogen bonds, which explains both the high occurrence of crystal structures where the donors do not achieve their maximal topicity and the observed differences in halogen bond lengths. Despite the fact that this effect increases with the basicity of the acceptor, when the increase of halogen bond energy due to the basicity of the acceptor compensates its decrease due to the reduction of the acidity of the donor, it enables strong bases to form cocrystals in which a potentially polytopic XB donor achieves its maximal topicity.
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Affiliation(s)
- Nikola Bedeković
- University
of Zagreb, Faculty of Science,
Department of Chemistry, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Tomislav Piteša
- Ruđer
Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Mihael Eraković
- Ruđer
Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Vladimir Stilinović
- University
of Zagreb, Faculty of Science,
Department of Chemistry, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Dominik Cinčić
- University
of Zagreb, Faculty of Science,
Department of Chemistry, Horvatovac 102a, 10000 Zagreb, Croatia
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6
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Malloum A, Conradie J. Structures, binding energies and non-covalent interactions of furan clusters. J Mol Graph Model 2021; 111:108102. [PMID: 34915345 DOI: 10.1016/j.jmgm.2021.108102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 12/20/2022]
Abstract
Understanding of the furan solvent is subjected to the knowledge of the structures of the furan clusters and interactions taking place therein. Although, furan clusters can be very important to determine the dynamics and the properties of the furan solvent, there has been only a few investigations reported on furan dimer. In this work, we have explored the potential energy surfaces (PESs) of the furan clusters using two incremental levels of theory. Structures have been initially generated using classical molecular dynamics followed by full optimization at the MP2/aug-cc-pVDZ level of theory. The results show that the most stable structure of the furan dimer has a stacking configuration while that of the trimer has a cyclic configuration. We have noted that the structures of the furan tetramer have no definite configurations. In addition, we have performed a quantum theory of atoms in molecule (QTAIM) analysis to identify all possible non-covalent interactions of the furan clusters. The results show that six different types of non-covalent interactions can be identified in furan clusters. We have noted that the CH⋯C and CH⋯O hydrogen bondings are the strongest non-covalent interactions while the H⋯H bonding interaction is found to be the weakest. Furthermore, we have assessed the performance of ten DFT functionals in calculating the binding energies of the furan clusters. The ten DFT functionals (M05, M05-2X, M06, M06-2X, M08HX, PBE0, ωB97XD, PW6B95D3, APFD and MN15) have been benchmarked to DLPNO-CCSD(T)/CBS. The functionals M05-2X and M06 are recommended for further affordable investigations of the furan clusters.
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Affiliation(s)
- Alhadji Malloum
- Department of Chemistry, University of the Free State, PO BOX 339, Bloemfontein, 9300, South Africa; Department of Physics, Faculty of Science, University of Maroua, PO BOX 46, Maroua, Cameroon.
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, PO BOX 339, Bloemfontein, 9300, South Africa; Department of Chemistry, UiT - The Arctic University of Norway, N-9037 Tromsø, Norway
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Kundu A, Sen S, Patwari GN. Π-Stacking in Heterodimers of Propargylbenzene with (Fluoro)phenylacetylenes. ACS OMEGA 2021; 6:17720-17725. [PMID: 34278157 PMCID: PMC8280671 DOI: 10.1021/acsomega.1c02385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/17/2021] [Indexed: 06/13/2023]
Abstract
The heterodimers of propargylbenzene (PrBz) with phenylacetylene (PHA) and monosubstituted fluorophenylacetylenes (FPHAs) were investigated using electronic and vibrational spectroscopic methods. The vibrational spectra in the acetylenic C-H stretching region show a marginal shift (0-4 cm-1) upon dimer formation, which suggests minimal perturbation of the acetylenic group. The M06-2X/aug-cc-pVDZ calculations indicate that the π-stacked structures are the most stable, followed by other structures. In general, structures incorporating aromatic C-H···π interactions are much higher in energy. The appearance of the spectra and the energy considerations clearly indicate the preference for the π-stacked structures. Furthermore, the observed trend in the stabilization energies for heterodimers with the three FPHAs is inversely proportional to the dipole moments of FPHAs. On the other hand, the absence of any clear trends in the electrostatic component of the interaction energy is attributed to the presence of the methylene group in PrBz.
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Affiliation(s)
| | - Saumik Sen
- Department of Chemistry, Indian
Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - G. Naresh Patwari
- Department of Chemistry, Indian
Institute of Technology Bombay, Powai, Mumbai 400076, India
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8
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Filep T, Szabó L, Kondor AC, Jakab G, Szalai Z. Evaluation of the effect of the intrinsic chemical properties of pharmaceutically active compounds (PhACs) on sorption behaviour in soils and goethite. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 215:112120. [PMID: 33721665 DOI: 10.1016/j.ecoenv.2021.112120] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/22/2021] [Accepted: 02/27/2021] [Indexed: 06/12/2023]
Abstract
The role of the chemical properties of Pharmaceutically Active Compounds (PhACs) in their sorption behaviour and consequently in their fate and mobility is of major environmental interest, but a comprehensive evaluation is still lacking. The sorption of nine PhAC molecules with distinct physico-chemical properties on soils and goethite was described using linear, Freundlich and Langmuir models and the relationship between the chemical structures of the compounds and the parameters of the adsorption was evaluated using redundancy analysis (RDA). The latter showed that the sorption of the pharmaceuticals was determined by the intrinsic chemical characteristics of the molecules, as shown by the 35% value of constrained variability. For the hydrophobic estrogens, E1, E2 and EE2, the logD value and the number of hydrogen bond sites were found to be the main controlling factors for adsorption, indicating that hydrophobic interaction and hydrogen bonding are the dominant sorption mechanisms. The π energy of the molecules also proved a very important parameter, governing the retention of PhACs in soils, especially in the case of carbamazepine, oxazepam and lamotrigine. The main controlling factor for ionic compounds, such as diclofenac sodium, tramadol or lidocaine, is the fraction of PhACs present as charged species, revealing the importance of Coulomb forces. The results of this study will allow semi-quantitative predictions to be made on how the molecular structure governs the sorption of PhACs and which sorption mechanism could be involved.
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Affiliation(s)
- Tibor Filep
- Research Centre for Astronomy and Earth Sciences, Geographical Institute, Budapest, Hungary
| | - Lili Szabó
- Research Centre for Astronomy and Earth Sciences, Geographical Institute, Budapest, Hungary; Eötvös Loránd University, Faculty of Science, Environmental and Landscape Geography, Budapest, Hungary.
| | - Attila Csaba Kondor
- Research Centre for Astronomy and Earth Sciences, Geographical Institute, Budapest, Hungary
| | - Gergely Jakab
- Research Centre for Astronomy and Earth Sciences, Geographical Institute, Budapest, Hungary; Eötvös Loránd University, Faculty of Science, Environmental and Landscape Geography, Budapest, Hungary; Institute of Geography and Geoinformatics, University of Miskolc, Miskolc, Hungary
| | - Zoltán Szalai
- Research Centre for Astronomy and Earth Sciences, Geographical Institute, Budapest, Hungary; Eötvös Loránd University, Faculty of Science, Environmental and Landscape Geography, Budapest, Hungary
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9
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Singh S, Hsu PJ, Kuo JL, Patwari GN. Dipole moment enhanced π-π stacking in fluorophenylacetylenes is carried over from gas-phase dimers to crystal structures propagated through liquid like clusters. Phys Chem Chem Phys 2021; 23:9938-9947. [PMID: 33908511 DOI: 10.1039/d1cp00279a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The aggregates of monofluorinated phenylacetylenes in the gas-phase, investigated using the IR-UV double resonance spectroscopic method in combination with extensive structural search and electronic structure calculations, reveal the formation of liquid-like clusters with a π-stacked dimeric core. The structural assignment based on the IR spectra in the acetylenic and aromatic C-H stretching regions suggests that, unlike the parent non-fluorinated phenylacetylene, the substitution of a F atom on the phenyl ring increases the dipole moment, leading to robustness in the formation of a ππ stacked dimer, which propagates incorporating C-Hπ_{Ar/Ac} and C-HF interactions involving both acetylenic and aromatic C-H groups. The structural evolution of fluorophenylacetylene aggregates in the gas phase shows marginal effects due to fluorine atom position on the phenyl ring, with substitution in the para-position tending towards phenylacetylene. The present study signifies that the ππ stacked dimers act as a nucleus for the growth of higher clusters to which other molecular units are added predominantly via the {Ar}_C-Hπ_{Ar} type of interaction and the dominant interactions present in the crystal structures gradually emerge with increasing cluster size. Based on these features, gas-phase clusters of fluorophenylacetylene are hypothesized as "liquid-like clusters" acting as intermediates in the generation of various polymorphic forms starting from a ππ stacked dimer as the core molecular unit.
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Affiliation(s)
- Sumitra Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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10
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Loman JL, Makuvaza JT, Kokkin DL, Reid SA. Unraveling a trifecta of weak non-covalent interactions: The dissociation energy of the anisole-ammonia 1:1 complex. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2020.138106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Study on the halogen bond and π-π stacking interaction between fluoro substituted iodobenzene and pyrazine. J Mol Model 2020; 26:333. [DOI: 10.1007/s00894-020-04586-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/22/2020] [Indexed: 10/23/2022]
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Hasanzade Z, Raissi H. Molecular mechanism for the encapsulation of the doxorubicin in the cucurbit[n]urils cavity and the effects of diameter, protonation on loading and releasing of the anticancer drug:Mixed quantum mechanical/ molecular dynamics simulations. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 196:105563. [PMID: 32531653 DOI: 10.1016/j.cmpb.2020.105563] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/06/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND OBJECTIVES Doxorubicin is a common apoptotic chemotherapeutic which has shown an obvious inhibitory effect in cancer chemotherapy. Here, cucurbit[n]urils (n = 7,10) have been proposed as a doxorubicin carrier, and the effects of diameter, protonation on loading and releasing of the anticancer drug doxorubicin has been studied. METHODS The Density Functional Theory (DFT) calculation and Molecular Dynamics (MD) simulation are performed to study the adsorption process of the (guest) Doxorubicin molecule in the neutral and protonated states within the (host) cucurbit[n]urils (n = 7,10). RESULTS DFT results show that the adsorption process in water is thermodynamically favorable. It is found that the binding energies for protonated drug encapsulation in cucurbit[n]urils are weaker than those of the neutral drug, implying the protonation of doxorubicin can promote the drug release from the adsorption situation. The electron density values and their Laplacian are evaluated to identify the nature of the intermolecular interactions through the topological parameters using the Bader's theory of atoms in molecules. Furthermore, the natural bond orbital analysis shows that the electrons aretransferred from cucurbit[n]urils to drug in all complexes. MD simulation results indicate that value of drug diffusion coefficient is small, therefore, we expect DOX to be slowly released from the CB cavity. CONCLUSIONS Based on obtained results, cucurbit[n]urils may be a prominent nano-carrier to loading and release drug on to target cells.
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Affiliation(s)
| | - Heidar Raissi
- Chemistry Department, University of Birjand, Birjand, Iran.
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13
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Kundu A, Sen S, Patwari GN. Dipole Moment Propels π-Stacking of Heterodimers of Fluorophenylacetylenes. J Phys Chem A 2020; 124:7470-7477. [PMID: 32809828 DOI: 10.1021/acs.jpca.0c04005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electronic and vibrational spectroscopic investigations in combination with quantum chemical calculations were carried out to probe the formation of four sets of heterodimers of phenylacetylene with 2-fluorohenylacetylene, 3-fluorophenylacetylene, 4-fluorophenylacetylene, and 2,6-difluorophenylacetylene. The interaction of phenylacetylene with fluorophenylacetylenes leads to marginal (2-9 cm-1) red-shifts in the acetylenic C-H stretching frequencies of fluorophenylacetylenes, which suggests that constituent monomers are minimally perturbed in the heterodimer. On the other hand, the density-functional-theory-based calculations indicate that π-stacked structures outweigh other structures incorporating C-H···π and C-H···F interactions by about 8 kJ mol-1 or more. The IR spectra in the acetylenic C-H stretching region were interpreted based on the perturbed dipole model, which suggests formation of predominantly antiparallel π-stacked structures, propelled by dipole moment. However, the energy decomposition analysis suggests that among stabilizing components dispersion dominates, while electrostatics plays a pivotal role in the formation of the π-stacked structures. Interestingly, the ability of 2-fluorophenylacetylene and 2,6-difluorophenylacetylene to π-stack differs significantly, even though both of them have almost identical dipole moments and the dipole moment propels the formation of π-stack structures. These results suggest π-stacking transcends the classical electrostatic description in terms of dipole moment.
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Affiliation(s)
- Aniket Kundu
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Saumik Sen
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - G Naresh Patwari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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14
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Makuvaza JT, Loman JL, Kokkin DL, Reid SA. Probing cooperativity in C-H⋯N and C-H⋯π interactions: Dissociation energies of aniline⋯(CH 4) n (n = 1, 2) van der Waals complexes from resonant ionization and velocity mapped ion imaging measurements. J Chem Phys 2020; 153:044303. [PMID: 32752709 DOI: 10.1063/5.0015624] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recent studies of the weakly bound anisole⋯CH4 complex found a dual mode of binding, featuring both C/H⋯π and C/H⋯O noncovalent interactions. In this work, we examine the dissociation energies of related aniline⋯(CH4)n (n = 1, 2) van der Waals clusters, where both C/H⋯π and C/H⋯N interactions are possible. Using a combination of theory and experiments that include mass-selected two-color resonant two-photon ionization spectroscopy, two-color appearance potential (2CAP) measurements, and velocity-mapped ion imaging (VMI), we derive the dissociation energies of both complexes in the ground (S0), excited (S1), and cation radical (D0) states. As the amide group is non-planar in the ground state, the optimized ground state geometry of the aniline⋯CH4 1:1 complex shows two isomers, each with the methane positioned above the aniline ring. The observed redshift of the electronic origin from the aniline monomer is consistent with TDDFT calculations for the more stable isomer, where the methane sits on the same face as the amino hydrogens. The dissociation energies of the 1:1 complex, obtained from 2CAP measurements, are in good agreement with the calculated theoretical values from selected density functional theory methods. VMI data for the 1:1 complex gave a binding energy value overestimated by ∼179 cm-1 when compared to the 2CAP results, indicating that dissociative ionization selectively populates an excited vibrational level of the aniline cation radical. Given that the electron donating ability of aromatic substituents trends as -NH2 > -OCH3 > -CH3, it is noteworthy that the strength of methane binding also trends in this order, as found by experiment (dissociation energies in kJ/mol: 6.6 > 5.8 > 4.5) and predicted by theory (PBE0-D3/def2-QZVPPD, in kJ/mol: 6.9 > 6.0 > 5.0). For the 1:2 complex of aniline and methane, calculations predict that the more stable conformer is the one where the two methane molecules lie on opposite faces of the ring, consistent with the observed redshift of the electronic origin. Unlike the anisole-methane 1:2 complex, which shows an enhanced dissociation energy for the loss of one methane in comparison with the 1:1 complex, here, we find that the energy required to remove one methane from the ground state aniline-methane 1:2 complex is smaller than that of the 1:1 complex, consistent with theoretical expectations.
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Affiliation(s)
- James T Makuvaza
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, USA
| | - John L Loman
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, USA
| | - Damian L Kokkin
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, USA
| | - Scott A Reid
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53233, USA
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15
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Zhao Q, Gong GF, Yang HL, Zhang QP, Yao H, Zhang YM, Lin Q, Qu WJ, Wei TB. Pillar[5]arene-based supramolecular AIE hydrogel with white light emission for ultrasensitive detection and effective separation of multianalytes. Polym Chem 2020. [DOI: 10.1039/d0py00872a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A novel pillar[5]arene-based supramolecular AIE hydrogel (PDG) with white light emission was constructed. The PDG could be used for ultrasensitive detection and effective separation of multianalytes, and as fluorescent display materials.
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Affiliation(s)
- Qi Zhao
- Key Laboratory of Eco-functional Polymer Materials of the Ministry of Education
- Key Laboratory of Eco-environmental Polymer Materials of Gansu Province
- College of Chemistry and Chemical Engineering
- Northwest Normal University
- Lanzhou
| | - Guan-Fei Gong
- Key Laboratory of Eco-functional Polymer Materials of the Ministry of Education
- Key Laboratory of Eco-environmental Polymer Materials of Gansu Province
- College of Chemistry and Chemical Engineering
- Northwest Normal University
- Lanzhou
| | - Hai-Long Yang
- Key Laboratory of Eco-functional Polymer Materials of the Ministry of Education
- Key Laboratory of Eco-environmental Polymer Materials of Gansu Province
- College of Chemistry and Chemical Engineering
- Northwest Normal University
- Lanzhou
| | - Qin-Peng Zhang
- Key Laboratory of Eco-functional Polymer Materials of the Ministry of Education
- Key Laboratory of Eco-environmental Polymer Materials of Gansu Province
- College of Chemistry and Chemical Engineering
- Northwest Normal University
- Lanzhou
| | - Hong Yao
- Key Laboratory of Eco-functional Polymer Materials of the Ministry of Education
- Key Laboratory of Eco-environmental Polymer Materials of Gansu Province
- College of Chemistry and Chemical Engineering
- Northwest Normal University
- Lanzhou
| | - You-Ming Zhang
- Key Laboratory of Eco-functional Polymer Materials of the Ministry of Education
- Key Laboratory of Eco-environmental Polymer Materials of Gansu Province
- College of Chemistry and Chemical Engineering
- Northwest Normal University
- Lanzhou
| | - Qi Lin
- Key Laboratory of Eco-functional Polymer Materials of the Ministry of Education
- Key Laboratory of Eco-environmental Polymer Materials of Gansu Province
- College of Chemistry and Chemical Engineering
- Northwest Normal University
- Lanzhou
| | - Wen-Juan Qu
- Key Laboratory of Eco-functional Polymer Materials of the Ministry of Education
- Key Laboratory of Eco-environmental Polymer Materials of Gansu Province
- College of Chemistry and Chemical Engineering
- Northwest Normal University
- Lanzhou
| | - Tai-Bao Wei
- Key Laboratory of Eco-functional Polymer Materials of the Ministry of Education
- Key Laboratory of Eco-environmental Polymer Materials of Gansu Province
- College of Chemistry and Chemical Engineering
- Northwest Normal University
- Lanzhou
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16
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Chatzimitakos TG, Karali KK, Stalikas CD. Magnetic graphene oxide as a convenient nanosorbent to streamline matrix solid-phase dispersion towards the extraction of pesticides from vegetables and their determination by GC–MS. Microchem J 2019. [DOI: 10.1016/j.microc.2019.104247] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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17
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Minovski N, Saçan MT, Eminoğlu EM, Erdem SS, Novič M. Revisiting fish toxicity of active pharmaceutical ingredients: Mechanistic insights from integrated ligand-/structure-based assessments on acetylcholinesterase. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 170:548-558. [PMID: 30572250 DOI: 10.1016/j.ecoenv.2018.11.099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 06/09/2023]
Abstract
The release of active pharmaceutical ingredients (APIs) into the environment is of great concern for aquatic ecosystem as many of these chemicals are designed to exert biological activity. Hence, their impact on non-target organisms like fish would not be surprising. In this respect, we revisited fish toxicity data of pharmaceuticals to generate linear and non-linear quantitative structure-toxicity relationships (QSTRs). We predicted fish lethality data from the validated QSTR models for 120 APIs with no experimental fish toxicity data. Toxicity of APIs on aquatic organisms is not fully characterized. Therefore, to provide a mechanistic insight for the assessment of API's toxicity to fish, the outcome of the derived QSTR models was integrated with structure-based toxicophore and molecular docking studies, utilizing the biomarker enzyme acetylcholinesterase originating from fish Torpedo californica (TcAChE). Toxicophore virtual screening of 60 chemicals with pT > 0 identified 23 hits as potential TcAChE binders with binding free energies ranging from -6.5 to -12.9 kcal/mol. The TcAChE-ligand interaction analysis revealed a good nesting of all 23 hits within TcAChE binding site through establishing strong lipophilic and hydrogen bonding interactions with the surrounding key amino acid residues. Among the chemicals passing the criteria of our integrated approach, majority of APIs belong noticeably to the Central Nervous System class. The screened chemicals displayed not only comprehensive toxicophore coverage, but also strong binding affinities according to the docking calculations, mainly due to interactions with TcAChE's key amino acid residues Tyr121, Tyr130, Tyr334, Trp84, Phe290, Phe330, Phe331, Ser122, and Ser200. Moreover, we propose here that binding of pharmaceuticals to AChE might have a potential in triggering molecular initiating events for adverse outcome pathways (AOPs), which in turn can play an important role for future screening of APIs lacking fish lethality data.
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Affiliation(s)
- Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
| | - Melek Türker Saçan
- Institute of Environmental Sciences, Bogazici University, 34342, Hisar Campus, Bebek, Istanbul, Turkey.
| | - Elif Merve Eminoğlu
- Faculty of Arts and Sciences, Department of Chemistry, Marmara University, 34722 Göztepe, Istanbul, Turkey
| | - Safiye Sağ Erdem
- Faculty of Arts and Sciences, Department of Chemistry, Marmara University, 34722 Göztepe, Istanbul, Turkey
| | - Marjana Novič
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
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18
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Mishra S, Sahoo DK, Hsu PJ, Matsuda Y, Kuo JL, Biswal HS, Patwari GN. A liquid crucible model for aggregation of phenylacetylene in the gas phase. Phys Chem Chem Phys 2019; 21:13623-13632. [DOI: 10.1039/c8cp07738j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural transformation from a π-stacked dimer to an aromatic C–H⋯π trimer and a tetramer.
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Affiliation(s)
- Saurabh Mishra
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400 076
- India
| | - Dipak Kumar Sahoo
- Homi Bhabha National Institute
- School of Chemical Sciences
- National Institute of Science Education and Research Bhubaneswar
- Khurda 752050
- India
| | - Po-Jen Hsu
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Yoshiyuki Matsuda
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 10617
- Taiwan
| | - Himansu S. Biswal
- Homi Bhabha National Institute
- School of Chemical Sciences
- National Institute of Science Education and Research Bhubaneswar
- Khurda 752050
- India
| | - G. Naresh Patwari
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai 400 076
- India
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19
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Hogan SWL, van Mourik T. Halogen bonding in mono- and dihydrated halobenzene. J Comput Chem 2018; 40:554-561. [PMID: 30549084 DOI: 10.1002/jcc.25733] [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: 07/31/2018] [Revised: 09/30/2018] [Accepted: 10/01/2018] [Indexed: 11/09/2022]
Abstract
Density functional theory calculations were performed on halogen-bonded and hydrogen-bonded systems consisting of a halobenzene (XPh; X = F, Cl, Br, I, and At) and one or two water molecules, using the M06-2X density functional with the 6-31+G(d) (for C, H, F, Cl, and Br) and aug-cc-pVDZ-PP (for I, At) basis sets. The counterpoise procedure was performed to counteract the effect of basis set superposition error. The results show halogen bonds form in the XPh-H2 O system when X > Cl. There is a trend toward stronger halogen bonding as the halogen group is descended, as assessed by interaction energy and X•••Ow internuclear separation (where Ow is the water oxygen). For all XPh-H2 O systems hydrogen-bonded systems exist, containing a combination of CH•••Ow and Ow Hw •••X hydrogen bonds. For all systems except X = At the X•••Hw hydrogen-bonding interaction is stronger than the X•••Ow halogen bond. In the XPh-(H2 O)2 system halogen bonds form only for X > Br. The two water molecules prefer to form a water dimer, either located around the CH bond (for X = Br, At, and I) or located above the benzene ring (for all halogens). Thus, even in the absence of competing strong interactions, halogen bonds may not form for the lighter halogens due to (1) competition from cooperative weak interactions such as CH•••O and OH•••X hydrogen bonds, or (2) if the formation of the halogen bond would preclude the formation of a water dimer. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Simon W L Hogan
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Scotland, United Kingdom
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Scotland, United Kingdom
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20
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Adam A, Mehrparvar S, Haberhauer G, Glüsenkamp KH, Wölper C. N-Aryl Imidazole Platforms - Synthesis and Structural Investigation. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Abdulselam Adam
- Institut für Organische Chemie; Universität Duisburg-Essen; Universitätsstr. 7 45117 Essen Germany
| | - Saber Mehrparvar
- Institut für Organische Chemie; Universität Duisburg-Essen; Universitätsstr. 7 45117 Essen Germany
| | - Gebhard Haberhauer
- Institut für Organische Chemie; Universität Duisburg-Essen; Universitätsstr. 7 45117 Essen Germany
| | | | - Christoph Wölper
- Institut für Organische Chemie; Universität Duisburg-Essen; Universitätsstr. 7 45117 Essen Germany
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21
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Lin Q, Fan YQ, Mao PP, Liu L, Liu J, Zhang YM, Yao H, Wei TB. Pillar[5]arene-Based Supramolecular Organic Framework with Multi-Guest Detection and Recyclable Separation Properties. Chemistry 2017; 24:777-783. [PMID: 29165843 DOI: 10.1002/chem.201705107] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Indexed: 12/20/2022]
Abstract
The selective detection and separation of target ions or molecules is an intriguing issue. Herein, a novel supramolecular organic framework (SOF-THBP) was constructed by bis-thioacetylhydrazine functionalized pillar[5]arenes. The SOF-THBP shows a fluorescent response for Fe3+ , Cr3+ , Hg2+ and Cu2+ ions. The xerogel of SOF-THBP shows excellent recyclable separation properties for these metal ions and the absorption rates were up to 99.29 %. More interestingly, by rationally introducing these metal ions into the SOF-THBP, a series of metal-ion-coordinated SOFs (MSOFs) such as MSOF-Fe, MSOF-Hg and MSOF-Cu were constructed. These metal ions coordinated MSOFs could selectively sense F- , Br- , and l-Cys, respectively. The detection limits of these MSOFs for F- , Br- and l-Cys were about 10-8 m.
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Affiliation(s)
- Qi Lin
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China, Key Laboratory of Polymer Materials of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, P. R. China
| | - Yan-Qing Fan
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China, Key Laboratory of Polymer Materials of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, P. R. China
| | - Peng-Peng Mao
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China, Key Laboratory of Polymer Materials of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, P. R. China
| | - Lu Liu
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China, Key Laboratory of Polymer Materials of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, P. R. China
| | - Juan Liu
- College of Chemical Engineering, Northwest University for Nationalities, Lanzhou, 730070, P. R. China
| | - You-Ming Zhang
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China, Key Laboratory of Polymer Materials of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, P. R. China
| | - Hong Yao
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China, Key Laboratory of Polymer Materials of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, P. R. China
| | - Tai-Bao Wei
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China, Key Laboratory of Polymer Materials of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, P. R. China
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22
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Karir G, Viswanathan KS. H−π Landscape of the Phenylacetylene–HCl System: Does This Provide the Gateway to the Markovnikov Addition? J Phys Chem A 2017; 121:5797-5808. [DOI: 10.1021/acs.jpca.7b04853] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ginny Karir
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Sector 81, Mohali 140306, Punjab India
| | - K. S. Viswanathan
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Sector 81, Mohali 140306, Punjab India
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23
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Mason KA, Pearcy AC, Attah IK, Platt SP, Aziz SG, El-Shall MS. Gas phase hydration of halogenated benzene cations. Is it hydrogen or halogen bonding? Phys Chem Chem Phys 2017; 19:18603-18611. [PMID: 28691724 DOI: 10.1039/c7cp03778c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Halogen bonding (XB) non-covalent interactions can be observed in compounds containing chlorine, bromine, or iodine which can form directed close contacts of the type R1-XY-R2, where the halogen X acts as a Lewis acid and Y can be any electron donor moiety including electron lone pairs on hetero atoms such as O and N, or π electrons in olefin double bonds and aromatic conjugated systems. In this work, we present the first evidence for the formation of ionic halogen bonds (IXBs) in the hydration of bromobenzene and iodobenzene radical cations in the gas phase. We present a combined thermochemical investigation using the mass-selected ion mobility (MSIM) technique and density functional theory (DFT) calculations of the stepwise hydration of the fluoro, chloro, bromo, and iodobenzene radical cations. The binding energy associated with the formation of an IXB in the hydration of the iodobenzene cation (11.2 kcal mol-1) is about 20% higher than the typical unconventional ionic hydrogen bond (IHB) of the CHδ+OH2 interaction. The formation of an IXB in the hydration of the iodobenzene cation involves a significant entropy loss (29 cal mol-1 K-1) resulting from the formation of a more ordered structure and a highly directional interaction between the oxygen lone pair of electrons of water and the electropositive region around the iodine atom of the iodobenzene cation. In comparison, the hydration of the fluorobenzene and chlorobenzene cations where IHBs are formed, -ΔS° = 18-21 cal mol-1 K-1 consistent with the formation of less ordered structures and loose interactions. The electrostatic potentials on the lowest energy structures of the hydrated halogenated benzene radical cations show clearly that the formation of an IXB is driven by a positively charged σ-hole on the external side of the halogen atom X along the C-X bond axis. The size of the σ-hole increases significantly in bromobenzene and iodobenzene radical cations which results in strong interaction potentials with the electron lone pairs of the oxygen atom of the water molecules and thus IXBs provide the most stable hydrated structures of the bromobenzene and iodobenzene radical cations. The results clearly distinguish the hydration behaviors resulting from the ionic hydrogen and halogen bonding interactions of fluorobenzene and iodobenzene cations, respectively, and establish the different bonding and structural features of the two interactions.
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Affiliation(s)
- Kyle A Mason
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA.
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24
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McClary B, Zinshteyn B, Meyer M, Jouanneau M, Pellegrino S, Yusupova G, Schuller A, Reyes JCP, Lu J, Guo Z, Ayinde S, Luo C, Dang Y, Romo D, Yusupov M, Green R, Liu JO. Inhibition of Eukaryotic Translation by the Antitumor Natural Product Agelastatin A. Cell Chem Biol 2017; 24:605-613.e5. [PMID: 28457705 PMCID: PMC5562292 DOI: 10.1016/j.chembiol.2017.04.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/09/2017] [Accepted: 04/06/2017] [Indexed: 01/10/2023]
Abstract
Protein synthesis plays an essential role in cell proliferation, differentiation, and survival. Inhibitors of eukaryotic translation have entered the clinic, establishing the translation machinery as a promising target for chemotherapy. A recently discovered, structurally unique marine sponge-derived brominated alkaloid, (-)-agelastatin A (AglA), possesses potent antitumor activity. Its underlying mechanism of action, however, has remained unknown. Using a systematic top-down approach, we show that AglA selectively inhibits protein synthesis. Using a high-throughput chemical footprinting method, we mapped the AglA-binding site to the ribosomal A site. A 3.5 Å crystal structure of the 80S eukaryotic ribosome from S. cerevisiae in complex with AglA was obtained, revealing multiple conformational changes of the nucleotide bases in the ribosome accompanying the binding of AglA. Together, these results have unraveled the mechanism of inhibition of eukaryotic translation by AglA at atomic level, paving the way for future structural modifications to develop AglA analogs into novel anticancer agents.
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Affiliation(s)
- Brandon McClary
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Boris Zinshteyn
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, and Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Mélanie Meyer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, Inserm U964, Illkirch 67404, France
| | - Morgan Jouanneau
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA
| | - Simone Pellegrino
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, Inserm U964, Illkirch 67404, France
| | - Gulnara Yusupova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, Inserm U964, Illkirch 67404, France
| | - Anthony Schuller
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, and Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | | | - Junyan Lu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zufeng Guo
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Safiat Ayinde
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yongjun Dang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Daniel Romo
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA.
| | - Marat Yusupov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, Inserm U964, Illkirch 67404, France.
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, and Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
| | - Jun O Liu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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25
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Kumar S, Singh SK, Vaishnav JK, Hill JG, Das A. Interplay among Electrostatic, Dispersion, and Steric Interactions: Spectroscopy and Quantum Chemical Calculations of π-Hydrogen Bonded Complexes. Chemphyschem 2017; 18:828-838. [PMID: 28124829 DOI: 10.1002/cphc.201601405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/24/2017] [Indexed: 11/07/2022]
Abstract
π-Hydrogen bonding interactions are ubiquitous in both materials and biology. Despite their relatively weak nature, great progress has been made in their investigation by experimental and theoretical methods, but this becomes significantly more complicated when secondary intermolecular interactions are present. In this study, the effect of successive methyl substitution on the supramolecular structure and interaction energy of indole⋅⋅⋅methylated benzene (ind⋅⋅⋅n-mb, n=1-6) complexes is probed through a combination of supersonic jet experiments and benchmark-quality quantum chemical calculations. It is demonstrated that additional secondary interactions introduce a subtle interplay among electrostatic and dispersion forces, as well as steric repulsion, which fine-tunes the overall structural motif. Resonant two-photon ionization and IR-UV double-resonance spectroscopy techniques are used to probe jet-cooled ind⋅⋅⋅n-mb (n=2, 3, 6) complexes, with redshifting of the N-H IR stretching frequency showing that increasing the degree of methyl substitution increases the strength of the primary N-H⋅⋅⋅π interaction. Ab initio harmonic frequency and binding energy calculations confirm this trend for all six complexes. Electronic spectra of the three dimers are broad and structureless, with quantum chemical calculations revealing that this is likely to be due to multiple tilted conformations of each dimer possessing similar stabilization energies.
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Affiliation(s)
- Sumit Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India.,Present address: Department of Dynamics at Surfaces, Max Planck Institute of Biophysical Chemistry, Am Faßberg 11, 37077, Gottingen, Germany
| | - Santosh K Singh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
| | - Jamuna K Vaishnav
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India.,Present address: Indian Institute of Technology (IIT) Indore, Khandwa Rd, Simrol, Madhya, Pradesh, 452020, India
| | - J Grant Hill
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, 411008, Maharashtra, India
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26
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Zurro M, Mancheño OG. 1,2,3,-Triazole-Based Catalysts: From Metal- to Supramolecular Organic Catalysis. CHEM REC 2016; 17:485-498. [DOI: 10.1002/tcr.201600104] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 09/12/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Mercedes Zurro
- Institute for Organic Chemistry; University of Regensburg; Universitätsstrasse 31 93053 Regensburg Germany
| | - Olga García Mancheño
- Institute for Organic Chemistry; University of Regensburg; Universitätsstrasse 31 93053 Regensburg Germany
- Straubing Center of Science for Renewable Resources (WZS); Schulgasse 16 94315 Straubing Germany
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27
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Thurn HV, Grotemeyer J. Resonant Two-Photon Ionization Studies of Toluene with Anisole Cluster: A System with Competing Non-Covalent Interactions. ChemistrySelect 2016. [DOI: 10.1002/slct.201600442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Heinke V. Thurn
- Institute for Physical Chemistry; Christian-Albrechts-University at Kiel; Max-Eyth-Str. 1 24118 Kiel
| | - Jürgen Grotemeyer
- Institute for Physical Chemistry; Christian-Albrechts-University at Kiel; Max-Eyth-Str. 1 24118 Kiel
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28
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Rungnim C, Chanajaree R, Rungrotmongkol T, Hannongbua S, Kungwan N, Wolschann P, Karpfen A, Parasuk V. How strong is the edge effect in the adsorption of anticancer drugs on a graphene cluster? J Mol Model 2016; 22:85. [DOI: 10.1007/s00894-016-2937-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/22/2016] [Indexed: 10/22/2022]
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29
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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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30
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Zurro M, Asmus S, Bamberger J, Beckendorf S, García Mancheño O. Chiral Triazoles in Anion-Binding Catalysis: New Entry to Enantioselective Reissert-Type Reactions. Chemistry 2016; 22:3785-93. [PMID: 26743138 DOI: 10.1002/chem.201504094] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Indexed: 12/15/2022]
Abstract
Easily accessible and tunable chiral triazoles have been introduced as a novel class of C-H bond-based H-donors for anion-binding organocatalysis. They have proven to be effective catalysts for the dearomatization reaction of different N-heteroarenes. Although this dearomatization approach represents a powerful strategy to build chiral heterocycles, to date only a few catalytic methods to this end exist. In this work, the organocatalyzed enantioselective Reissert-type dearomatization of isoquinoline derivatives employing a number of structurally diverse chiral triazoles as anion-binding catalysts was realized. The here presented method was employed to synthesize a number of chiral 1,2-dihydroisoquinoline substrates with an enantioselectivity up to 86:14 e.r. Moreover, a thorough study of the determining parameters affecting the activity of this type of anion- binding catalysts was carried out.
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Affiliation(s)
- Mercedes Zurro
- Institute for Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany.,Straubing Center of Science for Renewable Resources (WZS), Schulgasse 16, 94315, Straubing, Germany
| | - Sören Asmus
- Institute for Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Julia Bamberger
- Institute for Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Stephan Beckendorf
- Institute of Organic Chemistry, University of Münster, Corrensstrasse 40, 48149, Münster, Germany
| | - Olga García Mancheño
- Institute for Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany. .,Straubing Center of Science for Renewable Resources (WZS), Schulgasse 16, 94315, Straubing, Germany.
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31
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Rosokha SV, Loboda EA. Interplay of Halogen and π–π Charge-Transfer Bondings in Intermolecular Associates of Bromo- or Iododinitrobenzene with Tetramethyl-p-phenylenediamine. J Phys Chem A 2015; 119:3833-42. [DOI: 10.1021/acs.jpca.5b01600] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sergiy V. Rosokha
- Department
of Biological,
Chemical and Physical Sciences, Roosevelt University, Chicago, Illinois 60605, United States
| | - Eric A. Loboda
- Department
of Biological,
Chemical and Physical Sciences, Roosevelt University, Chicago, Illinois 60605, United States
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32
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Pang Y, Xing P, Geng X, Zhu Y, Liu F, Wang L. Supramolecular assemblies of 2-hydroxy-3-naphthoic acid and N-heterocycles via various strong hydrogen bonds and weak X⋯π (X = C–H, π) interactions. RSC Adv 2015. [DOI: 10.1039/c5ra03837e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Hydrogen bonds and weak X⋯π (X = C–H, π) interactions in a series of multi-component molecules constructed from 2-hydroxy-3-naphthoic acid with N-heterocycles are discussed in context.
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Affiliation(s)
- Yanyan Pang
- Laboratory of Inorganic Synthesis and Applied Chemistry
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
- P. R. China
| | - Peiqi Xing
- Laboratory of Inorganic Synthesis and Applied Chemistry
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
- P. R. China
| | - Xiujuan Geng
- Laboratory of Inorganic Synthesis and Applied Chemistry
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
- P. R. China
| | - Yujing Zhu
- Laboratory of Inorganic Synthesis and Applied Chemistry
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
- P. R. China
| | - Faqian Liu
- Laboratory of Inorganic Synthesis and Applied Chemistry
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
- P. R. China
| | - Lei Wang
- Laboratory of Inorganic Synthesis and Applied Chemistry
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
- P. R. China
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33
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Lukášek J, Böhm S, Dvořáková H, Eigner V, Lhoták P. Regioselective Halogenation of Thiacalix[4]arenes in the Cone and 1,3-Alternate Conformations. Org Lett 2014; 16:5100-3. [DOI: 10.1021/ol5024536] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - Václav Eigner
- Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21 Prague 8, Czech Republic
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34
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Han N, Zeng Y, Sun C, Li X, Sun Z, Meng L. N···I Halogen Bonding Interactions: Influence of Lewis Bases on Their Strength and Characters. J Phys Chem A 2014; 118:7058-65. [DOI: 10.1021/jp502558p] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Na Han
- Institute
of Computational Quantum Chemistry, College of Chemistry and Material
Science, Hebei Normal University, Shijiazhuang 050024, PR China
| | - Yanli Zeng
- Institute
of Computational Quantum Chemistry, College of Chemistry and Material
Science, Hebei Normal University, Shijiazhuang 050024, PR China
| | - Cuihong Sun
- Institute
of Computational Quantum Chemistry, College of Chemistry and Material
Science, Hebei Normal University, Shijiazhuang 050024, PR China
- College
of Chemical Engineering, Shijiazhuang University, Shijiazhuang 050035, PR China
| | - Xiaoyan Li
- Institute
of Computational Quantum Chemistry, College of Chemistry and Material
Science, Hebei Normal University, Shijiazhuang 050024, PR China
| | - Zheng Sun
- Institute
of Computational Quantum Chemistry, College of Chemistry and Material
Science, Hebei Normal University, Shijiazhuang 050024, PR China
| | - Lingpeng Meng
- Institute
of Computational Quantum Chemistry, College of Chemistry and Material
Science, Hebei Normal University, Shijiazhuang 050024, PR China
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