1
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Zgolli A, Fizer M, Mariychuk R, Dhaouadi H. Insights into the Adsorption Mechanism of Chlorpyrifos on Activated Carbon Derived from Prickly Pear Seeds Waste: An Experimental and DFT Modeling Study. ENVIRONMENTAL RESEARCH 2024:120221. [PMID: 39448016 DOI: 10.1016/j.envres.2024.120221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 10/18/2024] [Accepted: 10/21/2024] [Indexed: 10/26/2024]
Abstract
The removal of chlorpyrifos (CPF) from water was achieved using activated carbon (AC) derived from prickly pear seeds (PPS) wastes, developed through chemical activation with phosphoric acid. Several physico-chemical characterization methods were employed. The determination of surface functions using the Boehm assay indicated that the processed AC predominantly possesses acidic functions. The results obtained from the Boehm assay were corroborated by the pH value of the point of zero charge (pHpzc), which was equal to 2.5. Specific area calculation by the BET (Brunauer Emmett Teller) method revealed a large specific area (SBET) of 1077.66 m2 g⁻1. Adsorption experiments of CPF on AC demonstrated that the pseudo-second order (PSO) model and the Freundlich model were the most suitable for kinetic and isothermal modeling, respectively. The maximum CPF adsorption capacity of the PPS AC was found to be approximately 35 mg g⁻1. A theoretical study employing the density functional theory (DFT) was conducted using the B3LYP/6-311G (d, p) method. The most reliable adsorption energy (Eads) and Gibbs free energy (ΔGads) values between CPF and the functional groups on the AC surface were calculated. Results indicated a strong interaction between the lactone group of AC and CPF (ΔGads = -7.15 kcal mol⁻1, ΔEads = -21.55 kcal mol⁻1) and the hydroxyl group (ΔGads = -6.61 kcal mol⁻1, ΔEads = -20.66 kcal mol⁻1). This study demonstrates that activated carbon possesses significant adsorption power, making it highly effective for depolluting water contaminated by pesticides. The application of the theoretical DFT method enhances the understanding of the adsorption phenomenon of CPF on AC.
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Affiliation(s)
- Amira Zgolli
- University of Monastir, Faculty of Sciences, Laboratory of Environmental Chemistry and Clean Processes, LR21ES04, Monastir, Tunisia
| | - Maksym Fizer
- Department of Organic Chemistry, Educational and Scientific Institute of Chemistry and Ecology, Uzhhorod National University, Pidhirna 46, Uzhhorod 88000, Ukraine
| | - Ruslan Mariychuk
- Department of Ecology, Faculty of Humanity and Natural Sciences, University of Presov, 17(th) November str. 1, Presov, 08116, Slovakia
| | - Hatem Dhaouadi
- University of Monastir, Faculty of Sciences, Laboratory of Environmental Chemistry and Clean Processes, LR21ES04, Monastir, Tunisia.
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2
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Kikkawa Y, Tsuzuki S. Stability of n-alkanes and n-perfluoroalkanes against horizontal displacement on a graphite surface. Phys Chem Chem Phys 2024; 26:24314-24321. [PMID: 39257182 DOI: 10.1039/d4cp02418d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
The stability of adsorbed molecules on surfaces is fundamental and important for various applications, such as coating, lubrication, friction, and self-assembled structure formation. In this study, we investigated the structures and interaction energies (Eint) of propane, n-pentane, n-heptane, perfluoropropane, n-perfluoropentane, and n-perfluoroheptane adsorbed on the surface of C96H24 (a model surface of graphite). The changes in Eint (ΔEint = Eint - Eint(0)) associated with the horizontal displacement from the stable position were calculated using dispersion-corrected density functional theory (DFT; B3LYP-D3), where Eint(0) is the Eint at the stable position. The maximum value of ΔEint (ΔEint(max)) associated with the horizontal displacement increased as the chain length increased. The ΔEint(max) for the three n-alkanes were 1.10, 1.82, and 2.35 kcal mol-1, respectively. The values for n-perfluoroalkanes were 0.57, 0.83, and 1.04 kcal mol-1, respectively. The ΔEint(max) values for the n-alkanes were significantly larger than those for the corresponding n-perfluoroalkanes. The Eint(max) value per carbon atom of the n-alkanes (ca. 0.30 kcal mol-1) is approximately 2.5 times as large as that of n-perfluoroalkanes (ca. 0.12 kcal mol-1). The ΔEint associated with the horizontal displacement of propane and perfluoropropane on circumcoronene (C54H18) obtained by the B3LYP-D3 calculations are close to those obtained by the second order Møller-Plesset (MP2) and dispersion-corrected double hybrid DFT calculations, suggesting the sufficient accuracy of the ΔEint obtained by the B3LYP-D3. Thus, our quantitative analysis revealed the higher stability of n-alkanes against horizontal displacement on a graphite surface than that of n-perfluoroalkanes.
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Affiliation(s)
- Yoshihiro Kikkawa
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan.
| | - Seiji Tsuzuki
- Department of Applied Physics, The University of Tokyo, Tokyo 113-8656, Japan.
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3
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Laha RM, Aich S, Sarkar AK, Dutta T, Ghosh NN, Khamarui S, Maiti DK. New routes towards azomethine ylide generation from prolines to synthesize diverse N-heterocycles: a DFT supported endo-selective mechanism. Org Biomol Chem 2024; 22:7411-7424. [PMID: 39177485 DOI: 10.1039/d4ob01004c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Azomethine ylides are generated using either organocatalysts or metal catalysts via a ballet of decarboxylative C-N coupling choreographed by prolines. These strategies enable diastereoselective [3 + 2] cycloaddition, C-C coupling, and ring annulation, providing sustainable routes. The synthesized pyrrolizines and other heterocycles have potential applications in the development of crucial biomolecules and pharmaceuticals. The endoselectivity of the azomethine ylide is realized and supported through DFT calculations.
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Affiliation(s)
- Radha M Laha
- Department of Chemistry, University of Calcutta, 92 A. P. C. Road, Kolkata-700009, India.
- Department of Science & Humanities, Murshidabad Institute of Technology, West Bengal-742102, India
| | - Shobhon Aich
- Department of Chemistry, University of Calcutta, 92 A. P. C. Road, Kolkata-700009, India.
| | - Ankan Kumar Sarkar
- School of Material Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Tanmoy Dutta
- Department of Chemistry, JIS College of Engineering, Kalyani, West Bengal 741235, India
| | - Narendra Nath Ghosh
- Department of Chemistry, Pakuahat A.N.M. High School, Malda, West Bengal 732138, India
| | - Saikat Khamarui
- Department of Chemistry, Government General Degree College at Kalna-1, Purba Bardhhaman, 713405, India.
| | - Dilip K Maiti
- Department of Chemistry, University of Calcutta, 92 A. P. C. Road, Kolkata-700009, India.
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4
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Kahle L, Minisini B, Bui T, First JT, Buda C, Goldman T, Wimmer E. A dual-cutoff machine-learned potential for condensed organic systems obtained via uncertainty-guided active learning. Phys Chem Chem Phys 2024; 26:22665-22680. [PMID: 39158948 DOI: 10.1039/d4cp01980f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Machine-learned potentials (MLPs) trained on ab initio data combine the computational efficiency of classical interatomic potentials with the accuracy and generality of the first-principles method used in the creation of the respective training set. In this work, we implement and train a MLP to obtain an accurate description of the potential energy surface and property predictions for organic compounds, as both single molecules and in the condensed phase. We devise a dual descriptor, based on the atomic cluster expansion (ACE), that couples an information-rich short-range description with a coarser long-range description that captures weak intermolecular interactions. We employ uncertainty-guided active learning for the training set generation, creating a dataset that is comparatively small for the breadth of application and consists of alcohols, alkanes, and an adipate. Utilizing that MLP, we calculate densities of those systems of varying chain lengths as a function of temperature, obtaining a discrepancy of less than 4% compared with experiment. Vibrational frequencies calculated with the MLP have a root mean square error of less than 1 THz compared to DFT. The heat capacities of condensed systems are within 11% of experimental findings, which is strong evidence that the dual descriptor provides an accurate framework for the prediction of both short-range intramolecular and long-range intermolecular interactions.
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Affiliation(s)
- Leonid Kahle
- Materials Design SARL, 42 avenue Verdier, 92120 Montrouge, France.
| | - Benoit Minisini
- Materials Design SARL, 42 avenue Verdier, 92120 Montrouge, France.
| | - Tai Bui
- bp Exploration Operating Co. Ltd, Chertsey Road, Sunbury-on-Thames TW16 7LN, UK
| | - Jeremy T First
- bp, Center for High Performance Computing, 225 Westlake Park Blvd, Houston, TX 77079, USA
| | - Corneliu Buda
- bp Exploration Operating Co. Ltd, Chertsey Road, Sunbury-on-Thames TW16 7LN, UK
| | - Thomas Goldman
- bp Exploration Operating Co. Ltd, Chertsey Road, Sunbury-on-Thames TW16 7LN, UK
| | - Erich Wimmer
- Materials Design SARL, 42 avenue Verdier, 92120 Montrouge, France.
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5
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Griffrith C, Krul SE, Hoehn SJ, Phan T, Crespo-Hernández CE. Structural and Electronic Factors Controlling the Efficiency and Rate of Intersystem Crossing to the Triplet State in Thiophene Polycyclic Derivatives. Chemistry 2024:e202402721. [PMID: 39185738 DOI: 10.1002/chem.202402721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/21/2024] [Accepted: 08/26/2024] [Indexed: 08/27/2024]
Abstract
Thiophene polycyclic derivatives are widely used in organic light-emitting diodes, photovoltaics, and medicinal chemistry applications. Understanding the electronic and structural factors controlling their intersystem crossing rates is paramount for these applications to be successful. This study investigates the photophysical, electronic structure, and excited state dynamics of 1,2-benzodiphenylene sulfide, benzo[b]naphtho[1,2-d]thiophene, and benzo[b]naphtho[2,3-d]thiophene in polar aprotic and non-polar solvents. Steady-state absorption and emission spectroscopy, femtosecond transient absorption spectroscopy, and DFT and TD-DFT calculations are employed. Low fluorescence quantum yields of 1.2 to 2.7 % are measured in acetonitrile and cyclohexene, evidencing that the primary relaxation pathways in these thiophene derivatives are nonradiative. Linear interpolation of internal coordinates calculations predict that an S-C bond elongation reaction coordinate facilitates the efficient intersystem crossing to the T1 state. Excitation of 1,2-benzodiphenylene sulfide and benzo[b]naphtho[1,2-d]thiophene at 350 nm or benzo[b]naphtho[2,3-d]thiophene at 365 nm, populates the lowest-energy 1ππ* state, which relaxes to the 1ππ* minimum in tens of picoseconds or intersystem crosses to the triplet manifold in ca. 500 ps to 1.1 ns depending on the position at which the benzene rings are added. Excitation at 266 nm does not affect the intersystem crossing rates. Laser photodegradation experiments demonstrate that the thiophene polycyclic derivatives are highly photostable.
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Affiliation(s)
- Cameron Griffrith
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, 44106, USA
| | - Sarah E Krul
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, 44106, USA
| | - Sean J Hoehn
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, 44106, USA
| | - Tram Phan
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, 44106, USA
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6
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Wang J, Wu XQ, Mo JS, Tan YF, Long HP, Zhou SQ, Liu S, Li J, Wang WX. Two pairs of new isobenzofuranone enantiomers from a soil-derived fungus Penicillium canescens DWS225. Nat Prod Res 2024; 38:2667-2675. [PMID: 37039464 DOI: 10.1080/14786419.2023.2198712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/27/2023] [Indexed: 04/12/2023]
Abstract
Two pairs of new isobenzofuranone derivative enantiomers, (±)-penicifurans E (1) and (±)-penicifurans F (2), together with four know compounds (3-6) were isolated from the solid fermentation of Penicillium canescens DWS225. The structures of these enantiomers were elucidated by extensive NMR spectroscopic data, and their absolute configurations were assigned by the experimental and calculated ECD data. The neuroprotective effects of all the isolates against oxygen-glucose deprivation/reperfusion injury in pheochromocytoma-12 cells (PC12) were investigated.
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Affiliation(s)
- Jing Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, PR China
- Hunan Key laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, PR China
| | - Xiao-Qian Wu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, PR China
- Hunan Key laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, PR China
| | - Ji-Song Mo
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, PR China
- Hunan Key laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, PR China
| | - Yu-Fen Tan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Hong-Ping Long
- The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, PR China
| | - Si-Qian Zhou
- The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, PR China
| | - Shao Liu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Jing Li
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, PR China
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Wen-Xuan Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, PR China
- Hunan Key laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, PR China
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7
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La Force H, Freindorf M, Kraka E. Ligand Characterization and DNA Intercalation of Ru(II) Polypyridyl Complexes: A Local Vibrational Mode Study. J Phys Chem A 2024; 128:5925-5940. [PMID: 38990174 DOI: 10.1021/acs.jpca.4c02954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
We investigated in this work ruthenium-ligand bonding across the RuN framework in 12 Ru(II) polypyridyl complexes in the gas phase and solution for both singlet and triplet states, in addition to their affinity for DNA binding through π-π stacking interactions with DNA nucleobases. As a tool to assess the intrinsic strength of the ruthenium-ligand bonds, we determined local vibrational force constants via our local vibrational mode analysis software. We introduced a novel local force constant that directly accounts for the intrinsic strength of the π-π stacking interaction between DNA and the intercalated Ru(II) complex. According to our findings, [Ru(phen)2(dppz)]2+ and [Ru(phen)2(11-CN-dppz)]2+ provide an intriguing trade-off between photoinduced complex excitation and the strength of the subsequent π-π stacking interaction with DNA. [Ru(phen)2(dppz)]2+ displays a small singlet-triplet splitting and a strong π-π stacking interaction in its singlet state, suggesting a favorable photoexcitation but potentially weaker interaction with DNA in the excited state. Conversely, [Ru(phen)2(11-CN-dppz)]2+ exhibits a larger singlet-triplet splitting and a stronger π-π stacking interaction with DNA in its triplet state, indicating a less favorable photoinduced transition but a stronger interaction with DNA postexcitation. We hope our study will inspire future experimental and computational work aimed at the design of novel Ru-polypyridyl drug candidates and that our new quantitative measure of π-π stacking interactions in DNA will find a general application in the field.
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Affiliation(s)
- Hunter La Force
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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8
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Watanabe K, Tsurumaki E, Hasegawa M, Toyota S. Structure and Chiroptical Properties of Anthra[1,2-a]anthracene-1-yl Dimers as New Biaryls. Chemistry 2024; 30:e202400929. [PMID: 38554080 DOI: 10.1002/chem.202400929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/23/2024] [Accepted: 03/30/2024] [Indexed: 04/01/2024]
Abstract
Dimers of anthra[1,2-a]anthracene-1-yl units and its mesityl derivative were synthesized by Ni(0)-mediated coupling of the corresponding chloro derivatives as new biaryls. The X-ray analysis and DFT calculations revealed that two polycyclic aromatic units with nonplanar deformations took a twisted conformation about the single bond as a chiral axis. Enantiomers of the nonsubstituted compound were resolved by chiral HPLC, and the enantiopure samples showed intense Cotton effects at 321 nm in the circular dichroism (CD) spectra and emission bands at 449 nm in the circularly polarized luminescence (CPL) spectra with dissymmetry factor of |glum| 3.6×10-3. The absolute stereochemistry of this biaryl was determined by the theoretical calculation of CD spectrum by the time-dependent DFT method. The barrier to enantiomerization was determined to be 108 kJ mol-1 at 298 K. The dynamic process proceeded via a stepwise mechanism involving the helical inversion of each aromatic unit and the rotation about the biaryl axis as analyzed by the DFT calculations.
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Affiliation(s)
- Kota Watanabe
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Eiji Tsurumaki
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Masashi Hasegawa
- Department of Chemistry, School of Science, Kitasato University, Sagamihara, Kanagawa, 252-0373, Japan
| | - Shinji Toyota
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
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9
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Xu L, Tan JB, Zheng YT, Sang ZH, Qin SY, Huang YT, Li MF, Zou ZX. New lignans from Phyllanthodendron dunnianum. Nat Prod Res 2024:1-9. [PMID: 38767208 DOI: 10.1080/14786419.2024.2356661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 05/11/2024] [Indexed: 05/22/2024]
Abstract
A new lignan phyllanins A (1) and a lignan phyllanins B (2) for which the absolute configuration was determined for the first time, along with four known lignans (3-6) were isolated from the branch and leaf extracts of Phyllanthodendron dunnianum. Their planar structures were mainly determined by a combination of 1D and 2D NMR, HRESIMS spectral analyses, and the absolute configurations of the compounds 1 and 2 were established by DFT GIAO 13C NMR and electronic circular dichroism (ECD) calculations. In addition, all these six lignans were firstly tested for the antibacterial activities against MRSA, Staphylococcus aureus, Enterococcus faecalis, Pseudomonas aeruginosa and Escherichia coli. Among these compounds, 2 and 5 showed potential antibacterial activities against MRSA and S. aureus with MIC values of 4 and 8 µg/mL, respectively.
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Affiliation(s)
- Li Xu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, China
| | - Jian-Bing Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, China
| | - Yu-Ting Zheng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, China
| | - Zi-Huan Sang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, China
| | - Si-Yu Qin
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, China
| | - Yuan-Tao Huang
- Affiliated Haikou Hospital of Xiangya School of Medicine, Central South University, Haikou, China
| | - Mei-Fang Li
- Affiliated Haikou Hospital of Xiangya School of Medicine, Central South University, Haikou, China
| | - Zhen-Xing Zou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, China
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10
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Zheng Y, Qin S, Xu L, Sang Z, Chen C, Tan J, Huang Y, Li M, Zou Z. Ochrolines A-C, three new indole diketopiperazines from cultures of endophytic fungi Bionectria ochroleuca SLJB-2. Fitoterapia 2024; 173:105809. [PMID: 38168565 DOI: 10.1016/j.fitote.2023.105809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/17/2023] [Accepted: 12/29/2023] [Indexed: 01/05/2024]
Abstract
Three new indole diketopiperazines, ochrolines A-C (1-3), along with three known compounds (4-6), were isolated and identified from the EtOAc extract of the solid fermentation of Bionectria ochroleuca SLJB-2. Notably, compound 1 featured a natural rarely-occurring caged skeleton with a 6/5/6/7 heterotetracyclic bridged ring system. The structures including absolute configurations of 1-3 were fully accomplished by extensive spectroscopic analyses, DFT GIAO 13C NMR and electronic circular dichroism (ECD) calculations. The plausible biogenetic pathways of these new indole diketopiperazines were also proposed. Moreover, the cytotoxic activity screening revealed that compound 2 exhibited moderate inhibitory effect against A549 with inhibition rate of 57.44% at the concentration of 50 μM and compound 1 exhibited mild inhibitory activities against A549, Hela and MCF-7.
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Affiliation(s)
- Yuting Zheng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Siyu Qin
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Li Xu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Zihuan Sang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Chen Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Jianbing Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Yuantao Huang
- Affiliated Haikou Hospital of Xiangya School of Medicine, Central South University, Haikou 570100, China
| | - Meifang Li
- Affiliated Haikou Hospital of Xiangya School of Medicine, Central South University, Haikou 570100, China
| | - Zhenxing Zou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China.
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11
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Ibáñez-Ibáñez L, Mollar-Cuni A, Apaloo-Messan E, Sharma AK, Mata JA, Maseras F, Vicent C. Ion mobility mass spectrometry uncovers regioselectivity in the carboxylate-assisted C-H activation of palladium N-heterocyclic carbene complexes. Dalton Trans 2024; 53:656-665. [PMID: 38073605 DOI: 10.1039/d3dt02793g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Carboxylate-assisted Pd-catalyzed C-H bond activation constitutes a mild and versatile synthetic tool to efficiently and selectively cleave inert C-H bonds. Herein, we demonstrate a simple method to experimentally evaluate both reactivity and selectivity in such systems using mass spectrometry (MS) methods. The N-heterocyclic carbene (NHC) cations [(NHC)PdX]+, bearing as X- ligand bases commonly used to promote the C-H activation (carboxylates and bicarbonate), are generated in the gas-phase by ESI-MS. Their C-H bond activation at the N-bound groups of the NHC is then studied using Collision Induced Dissociation (CID) experiments. Ion Mobility Spectrometry (IM)-MS is exploited to identify a number of regioisomers associated with the distinctive site selective C-H activations. It is demonstrated that such C-H activation concomitant with acetic acid release occurs from a mixture of activated [(NHC-H)Pd(CH3CO2H)]+ and non-activated [(NHC)Pd(CH3CO2)]+ complexes. The identity of the X-type ligands (X = Cl-, carboxylates and bicarbonate) has a significant impact on the regioisomer branching ratio upon CID conditions. IM-MS in conjunction with a DFT mechanistic study is presented for the acetate-assisted C-H activation of the [(NHC)Pd(CH3CO2)]+ cation featuring butyl and aryl as N-donor groups.
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Affiliation(s)
- Laura Ibáñez-Ibáñez
- Institute of Advanced Materials (INAM), Net of organometallic chemistry for sustainable solutions (OASIS), Universitat Jaume I, Avda. Sos Baynat s/n, 12071, Castellón, Spain.
| | - Andres Mollar-Cuni
- Institute of Advanced Materials (INAM), Net of organometallic chemistry for sustainable solutions (OASIS), Universitat Jaume I, Avda. Sos Baynat s/n, 12071, Castellón, Spain.
| | - Edmond Apaloo-Messan
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007 Tarragona, Spain.
| | - Akhilesh K Sharma
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007 Tarragona, Spain.
| | - Jose A Mata
- Institute of Advanced Materials (INAM), Net of organometallic chemistry for sustainable solutions (OASIS), Universitat Jaume I, Avda. Sos Baynat s/n, 12071, Castellón, Spain.
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, Avgda. Països Catalans, 16, 43007 Tarragona, Spain.
| | - Cristian Vicent
- Serveis Centrals d'Instrumentació Científica (SCIC). Universitat Jaume I, Avda. Sos Baynat s/n, 12071, Castellón, Spain.
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12
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Lorenzana-Vázquez G, Adams DG, Reyna LG, Meléndez E, Pavel IE. Experimental and Theoretical Screening of Core Gold Nanoparticles and Their Binding Mechanism to an Anticancer Drug, 2-Thiouracil. Molecules 2023; 29:121. [PMID: 38202703 PMCID: PMC10779594 DOI: 10.3390/molecules29010121] [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: 10/31/2023] [Revised: 12/16/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
This study demonstrated the capability of two readily available optical spectroscopy tools, namely UV-Vis absorption spectrophotometry and Raman/surface-enhanced Raman spectroscopy, to select in a rapid and noninvasive manner the most homogenous gold nanoparticle (AuNP) models and to identify their chemical binding mechanism to 2-thiouracil (2-TU). 2-TU is an anticancer drug of great promise in the antiproliferative and photothermal therapies of cancer. The citrate-capped AuNPs emerged as the most stable as well as time- and cost-effective AuNP model out of the three widely used colloidal nanocores (citrate-, borohydride-citrate-, and sodium dodecyl sulfate (SDS)-capped AuNPs) that were examined. 2-TU chemically attached to the relatively monodispersed AuNPs via a chemisorption mechanism. The 2-TU-AuNPs complex formed through the covalent bonding of the S atom of 2-TU to the nanosurface in a vertical orientation. The spectroscopic results were then confirmed with the help of density functional theory (DFT) calculations and other physicochemical characterization tools for nanomaterials such as transmission electron microscopy (TEM), dynamic light scattering (DLS), and zeta potential. Overall, the purified 2-TU-AuNPs were found to be spherical, had an average diameter of 25 ± 2 nm, a narrow size distribution (1-30 nm), a sharp localized surface plasmon resonance (LSPR) peak at 525 nm, and a negative surface charge (-14 mV).
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Affiliation(s)
| | - Daniel G. Adams
- Department of Physical and Environmental Sciences, Texas A&M University—Corpus Christi, Corpus Christi, TX 78412, USA (L.G.R.)
| | - Lauren G. Reyna
- Department of Physical and Environmental Sciences, Texas A&M University—Corpus Christi, Corpus Christi, TX 78412, USA (L.G.R.)
| | - Enrique Meléndez
- Department of Chemistry, University of Puerto Rico, Mayaguez Campus, Mayaguez, PR 00681, USA;
| | - Ioana E. Pavel
- Department of Physical and Environmental Sciences, Texas A&M University—Corpus Christi, Corpus Christi, TX 78412, USA (L.G.R.)
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13
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Ullah S, McKee ML, Samokhvalov A. A zinc-containing porphyrin aluminum MOF in sorption of diethyl sulfide vapor: mechanistic experimental and computational study. Phys Chem Chem Phys 2023; 25:31884-31897. [PMID: 37971379 DOI: 10.1039/d3cp03779g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
We report a mechanistic study of the interactions in the sorption of volatile organic sulfur compound (VOSC) diethyl sulfide (DES) by zinc porphyrin aluminum MOF (actAl-MOF-TCPPZn) compound 3. First, interactions were studied under dynamic conditions with the vapor of DES in flowing air, using in situ time-dependent ATR-FTIR spectroscopy in a controlled atmosphere with a new facile spectroscopic mini-chamber. The first binding site includes μ(O-H) and COO- groups as detected by characteristic peak shifts. Control experiments with a model compound, which lacks porosity and these groups, show no peak shifts. An additional insight was obtained by DFT computations using small clusters. The kinetics of sorption of DES by compound 3 is of the Langmuir adsorption model and pseudo-first order with rate constant robs = 0.442 ± 0.056 min-1. Sorption of DES under static conditions in saturated vapor results in stoichiometric adsorption complex [Al-MOF-TCPPZn]1(DES)4 characterized by spectroscopic, structural and gravimetric methods; the adsorbed amount is very high (381 mg g-1 sorbent). The repetitive sorption and desorption of DES are conducted, with facile regeneration. Finally, the mechanistic details were determined by Raman and photoluminescence (PL) spectroscopy using a confocal Raman microscope. Photoexcitation of compound 3 at 405 nm into the Soret band of the metalloporphyrin linker shows the characteristic PL peaks of Q-bands: the purely electronic Q(0-0) and first vibronic Q(0-1) bands. Upon interaction with DES, preferential quenching of PL from the Q(0-0) band occurs with a significant increase of the signal of the vibronic Q(0-1) band, reflecting bonding to the metalloporphyrin ring. Compound 3 is of interest to mechanistic studies of VOSCs, their removal from air, and optical chemo-sensing.
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Affiliation(s)
- Shaheed Ullah
- Department of Chemistry, Morgan State University, 1700 East Cold Spring Lane, Baltimore, MD 21251, USA.
| | - Michael L McKee
- Department of Chemistry and Biochemistry, 179 Chemistry Building, Auburn University, Auburn, AL 36849, USA
| | - Alexander Samokhvalov
- Department of Chemistry, Morgan State University, 1700 East Cold Spring Lane, Baltimore, MD 21251, USA.
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14
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Peng W, Tan J, Sang Z, Huang Y, Xu L, Zheng Y, Qin S, Tan H, Zou Z. Koninginins X-Z, Three New Polyketides from Trichoderma koningiopsis SC-5. Molecules 2023; 28:7848. [PMID: 38067579 PMCID: PMC10707852 DOI: 10.3390/molecules28237848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Koninginins X-Z (1-3), three novel polyketides, were isolated from the solid fermentation of the endophytic fungus Trichoderma koningiopsis SC-5. Their structures, including the absolute configurations, were comprehensively characterized by a combination of NMR spectroscopic methods, HRESIMS, 13C NMR, DFT GIAO 13C NMR, and electronic circular dichroism calculations as well as single crystal X-ray diffraction. In addition, all the compounds were evaluated for antifungal activity against Candida albicans.
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Affiliation(s)
- Weiwei Peng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (W.P.); (J.T.); (Z.S.); (L.X.); (Y.Z.); (S.Q.)
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, China
| | - Jianbing Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (W.P.); (J.T.); (Z.S.); (L.X.); (Y.Z.); (S.Q.)
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, China
| | - Zihuan Sang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (W.P.); (J.T.); (Z.S.); (L.X.); (Y.Z.); (S.Q.)
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510520, China
| | - Yuantao Huang
- Affiliated Haikou Hospital of Xiangya School of Medicine, Central South University, Haikou 570208, China;
| | - Li Xu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (W.P.); (J.T.); (Z.S.); (L.X.); (Y.Z.); (S.Q.)
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, China
| | - Yuting Zheng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (W.P.); (J.T.); (Z.S.); (L.X.); (Y.Z.); (S.Q.)
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, China
| | - Siyu Qin
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (W.P.); (J.T.); (Z.S.); (L.X.); (Y.Z.); (S.Q.)
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, China
| | - Haibo Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (W.P.); (J.T.); (Z.S.); (L.X.); (Y.Z.); (S.Q.)
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510520, China
| | - Zhenxing Zou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; (W.P.); (J.T.); (Z.S.); (L.X.); (Y.Z.); (S.Q.)
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha 410013, China
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15
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Parra RD. Hydrogen-Bond-Driven Peptide Nanotube Formation: A DFT Study. Molecules 2023; 28:6217. [PMID: 37687047 PMCID: PMC10488343 DOI: 10.3390/molecules28176217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
DFT calculations were carried out to examine geometries and binding energies of H-bond-driven peptide nanotubes. A bolaamphiphile molecule, consisting of two N-α amido glycylglycine head groups linked by either one CH2 group or seven CH2 groups, is used as a building block for nanotube self-assembly. In addition to hydrogen bonds between adjacent carboxy or amide groups, nanotube formation is also driven by weak C-H· · ·O hydrogen bonds between a methylene group and the carboxy OH group, and between a methylene group and an amide O=C group. The intratubular O-H· · ·O=C hydrogen bonds account for approximately a third of the binding energies. Binding energies calculated with the wB97XD/DGDZVP method show that the hydrocarbon chains play a stabilizing role in nanotube self-assembly. The shortest nanotube has the length of a single monomer and a diameter than increases with the number of monomers. Lengthening of the tubular structure occurs through intertubular O-H· · ·O=C hydrogen bonds. The average intertubular O-H· · ·O=C hydrogen bond binding energy is estimated to change with the size of the nanotubes, decreasing slightly towards some plateau value near 15 kcal/mol according to the wB97XD/DGDZVP method.
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Affiliation(s)
- Rubén D Parra
- Department of Chemistry and Biochemistry, DePaul University, Chicago, IL 60614, USA
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16
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Parra RD. Bracelet-like Complexes of Lithium Fluoride with Aromatic Tetraamides, and Their Potential for LiF-Mediated Self-Assembly: A DFT Study. Molecules 2023; 28:4812. [PMID: 37375366 DOI: 10.3390/molecules28124812] [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: 05/25/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Geometries and binding energies of complexes between a LiF molecule and a model aromatic tetraamide are obtained using various DFT methods. The tetraamide consists of a benzene ring and four amides positioned so that the LiF molecule can bind via Li⋯O=C or N-H⋯F interactions. The complex with both interactions is the most stable one, followed by the complex with only N-H⋯F interactions. Doubling the size of the former resulted in a complex with a LiF dimer sandwiched between the model tetraamides. In turn, doubling the size of the latter resulted in a more stable tetramer with bracelet-like geometry having the two LiF molecules also sandwiched but far apart from each other. Additionally, all methods show that the energy barrier to transition to the more stable tetramer is small. The self-assembly of the bracelet-like complex mediated by the interactions of adjacent LiF molecules is demonstrated by all computational methods employed.
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Affiliation(s)
- Rubén D Parra
- Department of Chemistry and Biochemistry, DePaul University, Chicago, IL 60614, USA
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17
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Nwobodo I, Louis H, Unimuke TO, Ikenyirimba OJ, Iloanya AC, Mathias GE, Osabor VN, Ahuekwe EF, Adeyinka AS. Molecular Simulation of the Interaction of Diclofenac with Halogen (F, Cl, Br)-Encapsulated Ga 12As 12 Nanoclusters. ACS OMEGA 2023; 8:17538-17551. [PMID: 37251115 PMCID: PMC10210178 DOI: 10.1021/acsomega.2c06097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/05/2022] [Indexed: 05/31/2023]
Abstract
Diclofenac is one of the most frequently consumed over-the-counter anti-inflammatory agents globally, and several reports have confirmed its global ubiquity in several environmental compartments. Therefore, the need to develop more efficient monitoring/sensing devices with high detection limits is still needed. Herein, quantum mechanical simulations using density functional theory (DFT) computations have been utilized to evaluate the nanosensing efficacy and probe the applicability of Ga12As12 nanostructure and its engineered derivatives (halogen encapsulation F, Br, Cl) as efficient adsorbent/sensor materials for diclofenac. Based on the DFT computations, it was observed that diclofenac preferred to interact with the adsorbent material by assuming a flat orientation on the surface while interacting via its hydrogen atoms with the As atoms at the corner of the GaAs cage forming a polar covalent As-H bond. The adsorption energies were observed to be in the range of -17.26 to -24.79 kcal/mol and therefore suggested favorable adsorption with the surface. Nonetheless, considerable deformation was observed for the Br-encapsulated derivative, and therefore, its adsorption energy was observed to be positive. Additionally, encapsulation of the GaAs nanoclusters with halogens (F and Cl) enhanced the sensing attributes by causing a decrease in the energy gap of the nanocluster. And therefore, this suggests the feasibility of the studied materials as potentiometric sensor materials. These findings could offer some implications for the potential application of GaAs and their halogen-encapsulated derivatives for electronic technological applications.
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Affiliation(s)
- Ikechukwu
C. Nwobodo
- Computational
and Bio-Simulation Research Group, University
of Calabar, P.M.B. 1115, Calabar540221, Nigeria
- Department
of Pure and Applied Chemistry, University
of Calabar, P.M.B. 1115, Calabar540221, Nigeria
| | - Hitler Louis
- Computational
and Bio-Simulation Research Group, University
of Calabar, P.M.B. 1115, Calabar540221, Nigeria
- Department
of Pure and Applied Chemistry, University
of Calabar, P.M.B. 1115, Calabar540221, Nigeria
| | - Tomsmith O. Unimuke
- Computational
and Bio-Simulation Research Group, University
of Calabar, P.M.B. 1115, Calabar540221, Nigeria
- Department
of Pure and Applied Chemistry, University
of Calabar, P.M.B. 1115, Calabar540221, Nigeria
| | - Onyinye J. Ikenyirimba
- Department
of Chemistry Education, Alex Ekwueme Federal
University, P.M.B. 1010, Abakaliki, Ebonyi State010, Nigeria
| | - Anthony C. Iloanya
- Department
of Physics, Lehigh University, Bethlehem, Pennsylvania18015, United States
| | - Gideon E. Mathias
- Computational
and Bio-Simulation Research Group, University
of Calabar, P.M.B. 1115, Calabar540221, Nigeria
- Department
of Pure and Applied Chemistry, University
of Calabar, P.M.B. 1115, Calabar540221, Nigeria
| | - Vincent N. Osabor
- Department
of Pure and Applied Chemistry, University
of Calabar, P.M.B. 1115, Calabar540221, Nigeria
| | - Eze F. Ahuekwe
- Computational
and Bio-Simulation Research Group, University
of Calabar, P.M.B. 1115, Calabar540221, Nigeria
- Department
of Biological Sciences, Covenant University, Ota112104, Ogun State, Nigeria
| | - Adedapo S. Adeyinka
- Research
Centre for Synthesis and Catalysis, Department of Chemical Sciences, University of Johannesburg, Johannesburg2006, South Africa
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18
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Wu XQ, Li J, Zhou X, Wang J, Tan YF, Mo JS, Liu S, Xu KP, Tan GS, Zhang W, Wang WX. Liver-cell protective pyridones from the fungi Tolypocladium album dws120. PHYTOCHEMISTRY 2023; 212:113730. [PMID: 37220864 DOI: 10.1016/j.phytochem.2023.113730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/01/2023] [Accepted: 05/18/2023] [Indexed: 05/25/2023]
Abstract
Five previously undescribed pyridone derivatives, tolypyridones I-M, were identified from the solid rice medium fermented by Tolypocladium album dws120, along with two known compounds tolypyridone A (or trichodin A) and pyridoxatin. Their planar structures and partial relative configurations have been determined by careful interpretation of their spectroscopic data. The full assignment of the relative and absolute configurations of tolypyridones I-M was achieved by gauge-independent atomic orbital 13C NMR calculation, quantitative nuclear Overhauser effects based interatomic distance calculation, and electronic circular dichroism calculation. In addition, we have fully determined the configuration of tolypyridone A by X-ray diffraction analysis. In bioassay, tolypyridones I was able to restore cell viability and inhibit the release of alanine aminotransferase and aspartate aminotransferase for ethanol-induced LO2 cell, suggesting its potential as a liver protective agent.
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Affiliation(s)
- Xiao-Qian Wu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410008, PR China
| | - Jing Li
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410008, PR China; Department of Pharmacy, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China
| | - Xi Zhou
- School of Life Sciences, Central South University, Changsha, Hunan, 410008, PR China
| | - Jing Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410008, PR China
| | - Yu-Fen Tan
- Department of Pharmacy, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China
| | - Ji-Song Mo
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410008, PR China
| | - Shao Liu
- Department of Pharmacy, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China
| | - Kang-Ping Xu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410008, PR China
| | - Gui-Shan Tan
- Department of Pharmacy, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China
| | - Wei Zhang
- Hunan Institute for Drug Control, Changsha, Hunan, 410001, PR China
| | - Wen-Xuan Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410008, PR China.
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19
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Meng Y, Liu Q. New Insights into Adsorption Properties of the Tubular Au 26 from AIMD Simulations and Electronic Interactions. Molecules 2023; 28:molecules28072916. [PMID: 37049681 PMCID: PMC10096096 DOI: 10.3390/molecules28072916] [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: 03/02/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/14/2023] Open
Abstract
Recently, we revealed the electronic nature of the tubular Au26 based on spherical aromaticity. The peculiar structure of the Au26 could be an ideal catalyst model for studying the adsorptions of the Au nanotubes. However, through Google Scholar, we found that no one has reported connections between the structure and reactivity properties of Au26. Here, three kinds of molecules are selected to study the fundamental adsorption behaviors that occur on the surface of Au26. When one CO molecule is adsorbed on the Au26, the σ-hole adsorption structure is quickly identified as belonging to a ground state energy, and it still maintains integrity at a temperature of 500 K, where σ donations and π-back donations take place; however, two CO molecules make the structure of Au26 appear with distortions or collapse. When one H2 is adsorbed on the Au26, the H-H bond length is slightly elongated due to charge transfers to the anti-bonding σ* orbital of H2. The Au26-H2 can maintain integrity within 100 fs at 300 K and the H2 molecule starts moving away from the Au26 after 200 fs. Moreover, the Au26 can act as a Lewis base to stabilize the electron-deficient BH3 molecule, and frontier molecular orbitals overlap between the Au26 and BH3.
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Affiliation(s)
- Ying Meng
- School of Chemistry and Materials Engineering, Huainan Normal University, Huainan 232000, China
| | - Qiman Liu
- School of Chemistry and Materials Engineering, Huainan Normal University, Huainan 232000, China
- Anhui Province Key Laboratory of Low Temperature Co-Fired Materials, Huainan 232000, China
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20
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Olea Ulloa C, Muñoz-Castro A. Infinitene as two fused helicoidal trails of fused rings: evaluation of the magnetic behavior of [12]infinitene and anionic species displaying global aromaticity and antiaromaticity. Phys Chem Chem Phys 2023; 25:8190-8197. [PMID: 36880673 DOI: 10.1039/d2cp06039f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
The unique formation of an infinity-shaped carbon backbone made exclusively from fused benzene rings has recently been achieved. The structure of [12]infinitene can be viewed as two fused [6]helicene structures with a central crossover section, depicting a global aromatic behavior along with the overall structure, with deshielding regions along both helicoidal axes. In addition, the 13C-NMR characteristics are discussed. The formation of a cumulative region involving the shielding regions from the aromatic rings is depicted along with the overall aesthetically pleasant structural backbone, which is enhanced at the crossover section. For the evaluated dianionic counterpart, the structure shows a deshielding region above the fused-ring trail and a helicoidal shielding region, ascribed to a global antiaromatic counterpart. The aromaticity is recovered and enhanced at the tetranionic state. Thus, the neutral and tetranionic states are able to build up a long-ranged shielding region, given by the global aromatic behavior, with an enhanced shielding region at the center of the crossover section displaying π-π stacked rings.
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Affiliation(s)
- Carolina Olea Ulloa
- Carrera de Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Pedro de Valdivia 425, Providencia, Santiago, Chile
| | - Alvaro Muñoz-Castro
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Bellavista 7, Santiago, 8420524, Chile.
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21
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Bueno OVM, San-Miguel MA, da Silva EZ. Ethanol Oxidation Reaction Mechanism on Gold Nanowires from Density Functional Theory. Chemphyschem 2023; 24:e202200723. [PMID: 36417575 DOI: 10.1002/cphc.202200723] [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: 09/29/2022] [Revised: 11/14/2022] [Accepted: 11/23/2022] [Indexed: 11/25/2022]
Abstract
Thin gold nanowires (NWs) are materials that could be used as support in different chemical reactions. Using density functional theory (DFT) it was shown that NWs that form linear atomic chains (LACs) are suitable for stimulating chemical reactions. To this end, the oxidation reaction of ethanol supported on the LACs of Au-NWs was investigated. Two types of LACs were used for the study, one pure and the other with an oxygen impurity. The results showed that the oxygen atom in the LAC fulfills important functions throughout the reaction pathway. Before the chemical reaction, it was observed that the LAC with impurity gains structural stability, that is, the oxygen acts as an anchor for the gold atoms in the LAC. In addition, the LAC was shown to be sensitive to disturbances in its vicinity, which modifies its nucleophilic character. During the chemical reaction, the oxidation of ethanol occurs through two different reaction paths and in two stages, both producing acetaldehyde (CH3 CHO). The different reaction pathways are a consequence of the presence of oxygen in the LAC (oxygen conditions the formation of reaction intermediates). In addition, the oxygen in the LAC also modifies the kinetic behavior in both reaction stages. It was observed that, by introducing an oxygen impurity in the LAC, the activation energy barriers decrease ∼69 % and ∼97 % in the first and second reaction stages, respectively.
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Affiliation(s)
- O V M Bueno
- Institute of Physics 'Gleb Wataghin', University of Campinas-Unicamp, 13083-859, Campinas, SP, Brazil
| | - M A San-Miguel
- Department of Physical Chemistry, Institute of Chemistry, University of Campinas-Unicamp, P. O. Box 6154, 13083-970, Campinas, SP, Brazil
| | - E Z da Silva
- Institute of Physics 'Gleb Wataghin', University of Campinas-Unicamp, 13083-859, Campinas, SP, Brazil
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22
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Tsuzuki S, Kaneko T, Sodeyama K. Accuracy of Intermolecular interaction Energies, Particularly Those of Hetero Atom Containing Molecules Obtained by van der Waals DFT Calculations. ChemistrySelect 2023. [DOI: 10.1002/slct.202203754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Seiji Tsuzuki
- Department of Applied Physics The University of Tokyo 7-3-1 Hongo Tokyo 113 8656 Japan
- Advanced Chemical Energy Research Centre (ACERC) Institute of Advanced Sciences Yokohama National University 79-5 Tokiwadai, Hodogaya-ku Yokohama 240-8501 Japan
| | - Tomoaki Kaneko
- Research and Services Division of Materials Data and Integrated System National Institute for Materials Science (NIMS) 1–1 Namiki Tsukuba Ibaraki 305-0044 Japan
| | - Keitaro Sodeyama
- Research and Services Division of Materials Data and Integrated System National Institute for Materials Science (NIMS) 1–1 Namiki Tsukuba Ibaraki 305-0044 Japan
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23
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Liu SC, Zhu XR, Liu DY, Fang DC. DFT calculations in solution systems: solvation energy, dispersion energy and entropy. Phys Chem Chem Phys 2023; 25:913-931. [PMID: 36519338 DOI: 10.1039/d2cp04720a] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
DFT calculations of reaction mechanisms in solution have always been a hot topic, especially for transition-metal-catalyzed reactions. The calculation of solvation energy is performed using either the polarizable continuum model (PCM) or the universal solvation model SMD. The PCM calculation is very sensitive to the choice of atomic radii to form a cavity, where the self-consistent isodensity PCM (SCI-PCM) has been recognized as the best choice and our IDSCRF radii can provide a similar cavity. Moving from a gas-phase case to a solution case, dispersion energy and entropy should be carefully treated. The solvent-solute dispersion is also important in solution systems, and it should be calculated together with the solute dispersion. Only half of the solvent-solute dispersion energy from the PCM calculation belongs to the solute molecules to maintain a thermal equilibrium between a solute molecule and its cavity, similar to the treatment of electrostatic energy. Relative solute dispersion energy should also be shared equally with the newly formed cavity. The entropy change from a gas phase to a liquid phase is quite large, but the modern quantum chemistry programs can only calculate the gas-phase translational entropy based on the idea-gas equation. In this review, we will provide an operable method to calculate the solution translational entropy, which has been coded in our THERMO program.
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Affiliation(s)
- Si-Cong Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Xin-Rui Zhu
- College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Dan-Yang Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - De-Cai Fang
- College of Chemistry, Beijing Normal University, Beijing 100875, China.
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24
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Pancani E, Veclani D, Agnes M, Mazza A, Venturini A, Malanga M, Manet I. Three-in-one: exploration of co-encapsulation of cabazitaxel, bicalutamide and chlorin e6 in new mixed cyclodextrin-crosslinked polymers. RSC Adv 2023; 13:10923-10939. [PMID: 37033421 PMCID: PMC10077339 DOI: 10.1039/d3ra01782f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 03/27/2023] [Indexed: 04/09/2023] Open
Abstract
Three-in-one: a single bCyD polymer easily prepared in water is used to co-encapsulate cabazitaxel and bicalutamide with chlorin e6 affording a nanoplatform to implement multimodal cancer therapy.
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Affiliation(s)
- Elisabetta Pancani
- Institute for Organic Synthesis and Photoreactivity (ISOF), National Research Council of Italy (CNR), Via P. Gobetti 101, I-40129 Bologna, Italy
| | - Daniele Veclani
- Institute for Organic Synthesis and Photoreactivity (ISOF), National Research Council of Italy (CNR), Via P. Gobetti 101, I-40129 Bologna, Italy
| | - Marco Agnes
- Institute for Organic Synthesis and Photoreactivity (ISOF), National Research Council of Italy (CNR), Via P. Gobetti 101, I-40129 Bologna, Italy
| | - Arianna Mazza
- Institute for Organic Synthesis and Photoreactivity (ISOF), National Research Council of Italy (CNR), Via P. Gobetti 101, I-40129 Bologna, Italy
| | - Alessandro Venturini
- Institute for Organic Synthesis and Photoreactivity (ISOF), National Research Council of Italy (CNR), Via P. Gobetti 101, I-40129 Bologna, Italy
| | - Milo Malanga
- CycloLab, Cyclodextrin R&D Ltd., Budapest, Hungary
| | - Ilse Manet
- Institute for Organic Synthesis and Photoreactivity (ISOF), National Research Council of Italy (CNR), Via P. Gobetti 101, I-40129 Bologna, Italy
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25
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Kojasoy V, Tantillo DJ. Impacts of noncovalent interactions involving sulfur atoms on protein stability, structure, folding, and bioactivity. Org Biomol Chem 2022; 21:11-23. [PMID: 36345987 DOI: 10.1039/d2ob01602h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This review discusses the various types of noncovalent interactions in which sulfur atoms participate and their effects on protein stability, structure, folding and bioactivity. Current approaches and recommendations for modelling these noncovalent interactions (in terms of both geometries and interaction energies) are highlighted.
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Affiliation(s)
- Volga Kojasoy
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
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26
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Louis H, Ekereke EE, Isang BB, Ikeuba AI, Amodu IO, Gber TE, Owen AE, Adeyinka AS, Agwamba EC. Assessing the Performance of Al 12N 12 and Al 12P 12 Nanostructured Materials for Alkali Metal Ion (Li, Na, K) Batteries. ACS OMEGA 2022; 7:46183-46202. [PMID: 36570229 PMCID: PMC9773795 DOI: 10.1021/acsomega.2c04319] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/26/2022] [Indexed: 06/17/2023]
Abstract
This study focused on the potential of aluminum nitride (Al12N12) and aluminum phosphide (Al12P12) nanomaterials as anode electrodes of lithium-ion (Li-ion), sodium-ion (Na-ion), and potassium-ion (K-ion) batteries as investigated via density functional theory (DFT) calculations at PBE0-D3, M062X-D3, and DSDPBEP86 as the reference method. The results show that the Li-ion battery has a higher cell voltage with a binding energy of -1.210 eV and higher reduction potential of -6.791 kcal/mol compared to the sodium and potassium ion batteries with binding energies of -0.749 and -0.935 eV and reduction potentials of -6.414 and -6.513 kcal/mol, respectively, using Al12N12 material. However, in Al12P12, increases in the binding energy and reduction potential were observed in the K-ion battery with values -1.485 eV and -7.535 kcal/mol higher than the Li and Na ion batteries with binding energy and reduction potential -1.483, -1.311 eV and -7.071, -7.184 eV, respectively. Finally, Al12N12 and Al12P12 were both proposed as novel anode electrodes in Li-ion and K-ion batteries with the highest performances.
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Affiliation(s)
- Hitler Louis
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar540221, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar540221, Nigeria
| | - Ernest E. Ekereke
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar540221, Nigeria
- Department
of Mathematics, Faculty of Physical Sciences, University of Calabar, Calabar540221, Nigeria
| | - Bartholomew B. Isang
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar540221, Nigeria
- Department
of Mathematics, Faculty of Physical Sciences, University of Calabar, Calabar540221, Nigeria
| | - Alexander I. Ikeuba
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar540221, Nigeria
| | - Ismail O. Amodu
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar540221, Nigeria
- Department
of Mathematics, Faculty of Physical Sciences, University of Calabar, Calabar540221, Nigeria
| | - Terkumbur E. Gber
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar540221, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar540221, Nigeria
| | - Aniekan E. Owen
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar540221, Nigeria
- School
of Chemistry, University of St Andrews, St AndrewsKY16 9ST, United Kingdom
| | - Adedapo S. Adeyinka
- Department
of Chemical Sciences, University of Johannesburg, Auckland Park2006South Africa
| | - Ernest C. Agwamba
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar540221, Nigeria
- Department
of Chemistry, Covenant University, Ota50001, Nigeria
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27
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Gorges J, Bädorf B, Hansen A, Grimme S. Efficient Computation of the Interaction Energies of Very Large Non-covalently Bound Complexes. Synlett 2022. [DOI: 10.1055/s-0042-1753141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
AbstractWe present a new benchmark set consisting of 16 large non-covalently bound systems (LNCI16) ranging from 380 up to 1988 atoms and featuring diverse interaction motives. Gas-phase interaction energies are calculated with various composite DFT, semi-empirical quantum mechanical (SQM), and force field (FF) methods and are evaluated using accurate DFT reference values. Of the employed QM methods, PBEh-3c proves to be the most robust for large systems with a relative mean absolute deviation (relMAD) of 8.5% with respect to the reference interaction energies. r2SCAN-3c yields an even smaller relMAD, at least for the subset of complexes for which the calculation could be converged, but is less robust for systems with smaller HOMO–LUMO gaps. The inclusion of Fock-exchange is therefore important for the description of very large non-covalent interaction (NCI) complexes in the gas phase. GFN2-xTB was found to be the best performer of the SQM methods with an excellent result of only 11.1% deviation. From the assessed force fields, GFN-FF and GAFF achieve the best accuracy. Considering their low computational costs, both can be recommended for routine calculations of very large NCI complexes, with GFN-FF being clearly superior in terms of general applicability. Hence, GFN-FF may be routinely applied in supramolecular synthesis planning.1 Introduction2 The LNCI16 Benchmark Set3 Computational Details4 Generation of Reference Values5 Results and Discussion6 Conclusions
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Chen Y, Wang H, Ke X, Sang Z, Kuang M, Peng W, Tan J, Zheng Y, Zou Z, Tan H. Five new secondary metabolites from an endophytic fungus Phomopsis sp. SZSJ-7B. FRONTIERS IN PLANT SCIENCE 2022; 13:1049015. [PMID: 36452113 PMCID: PMC9702824 DOI: 10.3389/fpls.2022.1049015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/14/2022] [Indexed: 06/17/2023]
Abstract
Two previously undescribed lactones, phomolides A and B (1 and 2), and three new sesquiterpenoids, phomenes A-C (3-5), together with one known compound, colletotricholide A (6), were isolated from the endophytic fungus Phomopsis sp. SZSJ-7B. Their chemical structures, including the absolute configurations, were comprehensively established by extensive analyses of NMR, high-resolution electrospray ionization mass spectrometry, electronic circular dichroism powered by theoretical calculations, and X-ray diffractions. Moreover, the cytotoxic and antibacterial activities of compounds 1-6 were also evaluated, and the results demonstrated that compound 2 showed significant antibacterial effects towards methicillin-resistant Staphylococcus aureus and S. aureus strains with minimum inhibitory concentration as low as 6.25 μg/ml, which was comparable to that of the clinical drug vancomycin. Moreover, all compounds showed no cytotoxic activity.
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Affiliation(s)
- Yan Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Huan Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xin Ke
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Zihuan Sang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Min Kuang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, China
| | - Weiwei Peng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jianbing Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, China
| | - Yuting Zheng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, China
| | - Zhenxing Zou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, China
| | - Haibo Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Wang T, Shi H, Yu Z, Liu T. Theoretical insight into the mechanism of palladium-catalyzed oxidative cascade reaction of phenylacetylene and allenes with different assisting groups. J Organomet Chem 2022. [DOI: 10.1016/j.jorganchem.2022.122480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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30
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Testoff TT, Aikawa T, Tsung E, Lesko E, Wang L. DFT studies of aggregation induced energy splitting and excitonic diversification in benzene and anthracene multimers. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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31
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Orozco-Ic M, Sundholm D. Magnetic response properties of carbon nano-onions. Phys Chem Chem Phys 2022; 24:22487-22496. [PMID: 36106772 DOI: 10.1039/d2cp02718f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The magnetic response of a number of double- and triple-layer carbon nano-onions (CNOs) is analyzed by calculating the magnetically induced current density and the induced magnetic field using the pseudo-π model. Qualitatively the same magnetic response was obtained in calculations at the all-electron level. The calculations show that the CNOs exhibit strong net diatropic (paratropic) ring currents when the external magnetic field points perpendicularly to one of the six-membered (five-membered) rings. They are deshielded inside and shielded outside the CNO; the latter dominates for larger CNOs. The magnetic response originates from a combination of spherical paratropic current densities on the inside of each carbon layer and diatropic current densities on the outside of them. The quantitative differences in the aromaticity of the CNOs as compared to single fullerenes are discussed in terms of ring-current strengths. The magnetic response of some of the CNOs is approximately the sum of the magnetic response of the individual layers, whereas deviations are significant for CNOs containing C80. For the largest CNOs, the deviation from the sum of the fullerene contributions is larger, especially when the external magnetic field is perpendicular to a six-membered ring.
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Affiliation(s)
- Mesías Orozco-Ic
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, A. I. Virtasen aukio 1, FIN-00014 Helsinki, Finland.
| | - Dage Sundholm
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, A. I. Virtasen aukio 1, FIN-00014 Helsinki, Finland.
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Li J, Tan YF, Liu S, Wu XQ, Wang J, Xu KP, Tan GS, Zou ZX, Wang WX. Reassignment of the structures of pestalopyrones A-D. PHYTOCHEMISTRY 2022; 200:113205. [PMID: 35436477 DOI: 10.1016/j.phytochem.2022.113205] [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: 01/28/2022] [Revised: 03/10/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
Pestalopyrones A-D are four unusual tricyclic pyrone derivatives with flexible chiral structures, isolated from the endophytic fungus Pestalotiopsis neglecta S3. The full elucidation of their structures was a challenging task, and remained unsolved in the original article. Herein, the relative configurations of pestalopyrones A and pestalopyrones B were unambiguously assigned by detailed analyses on spectroscopic data and GIAO 13C NMR calculation method with sorted training sets (STS). The planar structures of pestalopyrones C and pestalopyrones D were revised by reinterpretation of their reported spectroscopic data, and then their relative configurations were deduced by STS GIAO 13C NMR calculation and NOE analysis. The absolute configurations of all the mentioned compounds were determined by the comparison of their experimental and calculated ECD curves.
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Affiliation(s)
- Jing Li
- Department of Pharmacy, Xiangya Hospital, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, PR China
| | - Yu-Fen Tan
- Department of Pharmacy, Xiangya Hospital, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, PR China
| | - Shao Liu
- Department of Pharmacy, Xiangya Hospital, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, PR China
| | - Xiao-Qian Wu
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China
| | - Jing Wang
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China
| | - Kang-Ping Xu
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China
| | - Gui-Shan Tan
- Department of Pharmacy, Xiangya Hospital, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, PR China
| | - Zhen-Xing Zou
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China
| | - Wen-Xuan Wang
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China.
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33
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Tupikina EY. Non-covalent interactions in the glutathione peroxidase active center and their influence on the enzyme activity. Org Biomol Chem 2022; 20:5551-5557. [PMID: 35791825 DOI: 10.1039/d2ob00890d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this computational work, the structure of the active center of the enzyme glutathione peroxidase (in three forms -SeH, -SeOH and -Se(O)OH) and the non-covalent interactions in it were investigated using modern quantum chemistry methods. The non-covalent interactions are described in detail. The presence of σ-hole interactions (chalcogen, tetrel and pnictogen bonds) formed mostly by a selenium atom as an electrophile in the glutathione peroxidase active center is confirmed for the first time. It is shown that a number of non-covalent interactions stabilize intermediates along the catalytic cycle and that modelling of the whole enzyme active center is necessary for accurate predictions of thermodynamic parameters, in particular, activation barriers.
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Affiliation(s)
- Elena Yu Tupikina
- Institute of Chemistry, St. Petersburg University, Universitetskaya emb. 7/9, St. Petersburg, Russia.
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34
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Li X, Wang Y, Lu H, Zhong S, Liu C, Song L, Tang S, Liang B. Phase Splitting Rules of the Primary/Secondary Amine–Tertiary Amine Systems: Experimental Rapid Screening and Corrected Quasi-Activity Coefficient Model. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.2c00533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xingyu Li
- Laboratory of Low-Carbon Technology and Chemical Reaction Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu 610207, China
| | - Yuheng Wang
- Laboratory of Low-Carbon Technology and Chemical Reaction Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Houfang Lu
- Laboratory of Low-Carbon Technology and Chemical Reaction Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu 610207, China
| | - Shan Zhong
- Laboratory of Low-Carbon Technology and Chemical Reaction Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Changjun Liu
- Laboratory of Low-Carbon Technology and Chemical Reaction Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Lei Song
- Laboratory of Low-Carbon Technology and Chemical Reaction Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Siyang Tang
- Laboratory of Low-Carbon Technology and Chemical Reaction Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Bin Liang
- Laboratory of Low-Carbon Technology and Chemical Reaction Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu 610207, China
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35
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Fully Bio-based Furyl-functionalized Bisphenols and Bio-based Cross-linking Poly(aryl ether ketone)s with High Biomass Content, Thermo-reversibility, Excellent Processing and Mechanical Properties. Polym Degrad Stab 2022. [DOI: 10.1016/j.polymdegradstab.2022.109961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Orozco-Ic M, Valiev RR, Sundholm D. Non-intersecting ring currents in [12]infinitene. Phys Chem Chem Phys 2022; 24:6404-6409. [PMID: 35262148 DOI: 10.1039/d2cp00637e] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The aromaticity of the newly synthesized [12]infinitene is addressed via analysis of the magnetically induced current density and the induced magnetic field. Our calculations reveal that [12]infinitene responds to an external magnetic field by creating two current-density pathways that flow diatropically along the edges of the molecule. The current-density pathways do not intersect. The entire structure is completely shielded suggesting that the infinitene molecule is aromatic, contrary to what the Möbius rule for twisted annulene structures predicts. We also studied the dication of [12]infinitene, which sustains two paratropic ring currents flowing along the edges. The space between the stacked rings at the crossing point is shorter for the dication as compared to the neutral molecule. Hence, a strong through-space current density appears at the crossing point of π-π stacked rings.
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Affiliation(s)
- Mesías Orozco-Ic
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, A. I. Virtasen aukio 1, FIN-00014 Helsinki, Finland.
| | - Rashid R Valiev
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, A. I. Virtasen aukio 1, FIN-00014 Helsinki, Finland. .,Research School of Chemistry and Applied Biomedical Sciences, National Research Tomsk Polytechnic University, Tomsk 634050, Russia
| | - Dage Sundholm
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, A. I. Virtasen aukio 1, FIN-00014 Helsinki, Finland.
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37
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Chalcogen···Chalcogen Bonding in Molybdenum Disulfide, Molybdenum Diselenide and Molybdenum Ditelluride Dimers as Prototypes for a Basic Understanding of the Local Interfacial Chemical Bonding Environment in 2D Layered Transition Metal Dichalcogenides. INORGANICS 2022. [DOI: 10.3390/inorganics10010011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
An attempt was made, using computational methods, to understand whether the intermolecular interactions in the dimers of molybdenum dichalcogenides MoCh2 (Ch = chalcogen, element of group 16, especially S, Se and Te) and similar mixed-chalcogenide derivatives resemble the room temperature experimentally observed interactions in the interfacial regions of molybdenites and their other mixed-chalcogen derivatives. To this end, MP2(Full)/def2-TVZPPD level electronic structure calculations on nine dimer systems, including (MoCh2)2 and (MoChCh′2)2 (Ch, Ch′ = S, Se and Te), were carried out not only to demonstrate the energetic stability of these systems in the gas phase, but also to reproduce the intermolecular geometrical properties that resemble the interfacial geometries of 2D layered MoCh2 systems reported in the crystalline phase. Among the six DFT functionals (single and double hybrids) benchmarked against MP2(full), it was found that the double hybrid functional B2PLYPD3 has some ability to reproduce the intermolecular geometries and binding energies. The intermolecular geometries and binding energies of all nine dimers are discussed, together with the charge density topological aspects of the chemical bonding interactions that emerge from the application of the quantum theory of atoms in molecules (QTAIM), the isosurface topology of the reduced density gradient noncovalent index, interaction region indicator and independent gradient model (IGM) approaches. While the electrostatic surface potential model fails to explain the origin of the S···S interaction in the (MoS2)2 dimer, we show that the intermolecular bonding interactions in all nine dimers examined are a result of hyperconjugative charge transfer delocalizations between the lone-pair on (Ch/Ch′) and/or the π-orbitals of a Mo–Ch/Ch′ bond of one monomer and the dπ* anti-bonding orbitals of the same Mo–Ch/Ch′ bond in the second monomer during dimer formation, and vice versa. The HOMO–LUMO gaps calculated with the MN12-L functional were 0.9, 1.0, and 1.1 eV for MoTe2, MoSe2 and MoS2, respectively, which match very well with the solid-state theoretical (SCAN-rVV10)/experimental band gaps of 0.75/0.88, 0.90/1.09 and 0.93/1.23 eV of the corresponding systems, respectively. We observed that the gas phase dimers examined are perhaps prototypical for a basic understanding of the interfacial/inter-layer interactions in molybdenum-based dichalcogenides and their derivatives.
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Avetisov VA, Frolkina MA, Markina AA, Muratov AD, Petrovskii VS. Short Pyridine-Furan Springs Exhibit Bistable Dynamics of Duffing Oscillators. NANOMATERIALS 2021; 11:nano11123264. [PMID: 34947612 PMCID: PMC8707925 DOI: 10.3390/nano11123264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/16/2022]
Abstract
The intensive development of nanodevices acting as two-state systems has motivated the search for nanoscale molecular structures whose dynamics are similar to those of bistable mechanical systems, such as Euler arches and Duffing oscillators. Of particular interest are the molecular structures capable of spontaneous vibrations and stochastic resonance. Recently, oligomeric molecules that were a few nanometers in size and exhibited the bistable dynamics of an Euler arch were identified through molecular dynamics simulations of short fragments of thermo-responsive polymers subject to force loading. In this article, we present molecular dynamics simulations of short pyridine-furan springs a few nanometers in size and demonstrate the bistable dynamics of a Duffing oscillator with thermally-activated spontaneous vibrations and stochastic resonance.
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Azide⋅⋅⋅Oxygen Interaction: A Crystal Engineering Tool for Conformational Locking. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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McKee NA, McKee ML. Evaluation of packing single and multiple atoms and molecules in the porous organic cage CC3- R. Phys Chem Chem Phys 2021; 23:19255-19268. [PMID: 34524296 DOI: 10.1039/d1cp01934a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The absorption of multiple atoms and molecules, including Kr, Xe, CH4, CO2, C2H2, H2O, and SF6, within CC3-R, a Porous Organic Cage (POC), was calculated and analyzed. The CC3-R molecule has one central cavity and four window sites. Most adsorbents were modeled with either one unit in the central cavity, four units in the window sites, or with five units in both sites. For Xe, the most favorable site was the central one. The CO2 molecule binds about 3 kcal mol-1 in free energy more strongly than CH4 in the central cavity of CC3-R at 300 K which may be enough to allow useful discrimination. Four C2H2 units and four CO2 units are calculated to bind similarly inside CC3-R (ΔH(298 K) = -8.6 and -7.7 kcal mol-1 per unit, respectively). Since H2O is smaller, more waters can easily fit inside. For twelve water molecules, the binding enthalpy per water is ΔH(298 K) = -16.4 kcal mol-1. For comparison, the binding enthalpy of (H2O)12 at the same level of theory (B3LYP/6-31G(d,p)-D3BJ//M06-2X/6-31G(d)) is predicted to be -12.3 kcal mol-1 per water. Finally, the dimerization of CC3-R and the association of CC3-R with CC3-S was studied as well as 3 to 9 iodine atoms enclosed in CC3-R.
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Affiliation(s)
- Nida A McKee
- Department of Chemistry and Biochemistry, Auburn, AL 36849, USA.
| | - Michael L McKee
- Department of Chemistry and Biochemistry, Auburn, AL 36849, USA.
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Thornton GL, Phelps R, Orr-Ewing AJ. Transient absorption spectroscopy of the electron transfer step in the photochemically activated polymerizations of N-ethylcarbazole and 9-phenylcarbazole. Phys Chem Chem Phys 2021; 23:18378-18392. [PMID: 34612379 PMCID: PMC9391922 DOI: 10.1039/d1cp03137f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/04/2021] [Indexed: 11/21/2022]
Abstract
The polymerization of photoexcited N-ethylcarbazole (N-EC) in the presence of an electron acceptor begins with an electron transfer (ET) step to generate a radical cation of N-EC (N-EC˙+). Here, the production of N-EC˙+ is studied on picosecond to nanosecond timescales after N-EC photoexcitation at a wavelength λex = 345 nm using transient electronic and vibrational absorption spectroscopy. The kinetics and mechanisms of ET to diphenyliodonium hexafluorophosphate (Ph2I+PF6-) or para-alkylated variants are examined in dichloromethane (DCM) and acetonitrile (ACN) solutions. The generation of N-EC˙+ is well described by a diffusional kinetic model based on Smoluchowski theory: with Ph2I+PF6-, the derived bimolecular rate coefficient for ET is kET = (1.8 ± 0.5) × 1010 M-1 s-1 in DCM, which is consistent with diffusion-limited kinetics. This ET occurs from the first excited singlet (S1) state of N-EC, in competition with intersystem crossing to populate the triplet (T1) state, from which ET may also arise. A faster component of the ET reaction suggests pre-formation of a ground-state complex between N-EC and the electron acceptor. In ACN, the contribution from pre-reaction complexes is smaller, and the derived ET rate coefficient is kET = (1.0 ± 0.3) × 1010 M-1 s-1. Corresponding measurements for solutions of photoexcited 9-phenylcarbazole (9-PC) and Ph2I+PF6- give kET = (5 ± 1) × 109 M-1 s-1 in DCM. Structural modifications of the electron acceptor to increase its steric bulk reduce the magnitude of kET: methyl and t-butyl additions to the para positions of the phenyl rings (para Me2Ph2I+PF6- and t-butyl-Ph2I+PF6-) respectively give kET = (1.2 ± 0.3) × 1010 M-1 s-1 and kET = (5.4 ± 1.5) × 109 M-1 s-1 for reaction with photoexcited N-EC in DCM. These reductions in kET are attributed to slower rates of diffusion or to steric constraints in the ET reaction.
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Affiliation(s)
- Georgia L Thornton
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Ryan Phelps
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Andrew J Orr-Ewing
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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Robust fluorogenic non-porphyrin interaction of Zn(II) and Hg(II) naphthadiaza-crown macrocyclic complexes with C60: Spectroscopic and dispersion-corrected DFT study. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2021.113414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Sureshan KM, Madhusudhanan MC, Balan H, Werz DB. Azide···Oxygen Interaction: A Crystal Engineering Tool for Conformational Locking. Angew Chem Int Ed Engl 2021; 60:22797-22803. [PMID: 34399025 DOI: 10.1002/anie.202106614] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/15/2021] [Indexed: 11/09/2022]
Abstract
We have designed, synthesized and crystallized 36 compounds, each containing an azide group and an oxygen atom separated by three bonds. Crystal structure analysis revealed that each of these molecules adopts a conformation in which the azide and oxygen groups orient syn to each other with a short O ··· N b contact. Geometry-optimized structures [using M06-2X/6-311G(d,p) level of theory ] also showed the syn conformation in all 36 of these cases, suggesting that this not merely a crystal packing effect. Quantum topological analysis using Bader's Atoms in Molecules (AIM) theory revealed bond paths and bond critical points (BCP) in these structures suggesting its nature and energetics to be similar to weak hydrogen bonding. The NCI-RDG plot clearly revealed the attractive interaction consisting of electrostatic or dispersive components in all the 36 systems. NBO analysis suggested a weak orbital-relaxation (charge-transfer) contribution of energy for a few (sp2) O-donor systems. Natural population analysis (NPA) and molecular electrostatic potential mapping (MESP) of these crystal structures further revealed the existence of favorable azide-oxygen interaction. A CSD search indicated the frequent and consistent occurrence of this interaction and its role dictating the syn conformation of azide and oxygen in molecules where these groups are separated by 2-4 bonds.
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Affiliation(s)
- Kana M Sureshan
- Indian Institute of Science Education and Research, School of Chemistry, Thiruvananthapuram, Maruthamala, 695551, Thiruvananthapuram, INDIA
| | - Mithun C Madhusudhanan
- IISER-TVM: Indian Institute of Science Education Research Thiruvananthapuram, School of Chemistry, Maruthamala, Vithura, 795551, Thiruvananthapuram, INDIA
| | - Haripriya Balan
- IISER-TVM: Indian Institute of Science Education Research Thiruvananthapuram, School of Chemistry, Maruthamala, Vithura, 695551, Thiruvananthapuram, INDIA
| | - Daniel B Werz
- TU Braunschweig: Technische Universitat Braunschweig, Institute fur Organic Chemie, Hagenring 30, Braunschweig, 38106, Braunschweig, GERMANY
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Delgado AAA, Humason A, Kalescky R, Freindorf M, Kraka E. Exceptionally Long Covalent CC Bonds-A Local Vibrational Mode Study. Molecules 2021; 26:molecules26040950. [PMID: 33670107 PMCID: PMC7916873 DOI: 10.3390/molecules26040950] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/04/2021] [Accepted: 02/07/2021] [Indexed: 01/29/2023] Open
Abstract
For decades one has strived to synthesize a compound with the longest covalent C−C bond applying predominantly steric hindrance and/or strain to achieve this goal. On the other hand electronic effects have been added to the repertoire, such as realized in the electron deficient ethane radical cation in its D3d form. Recently, negative hyperconjugation effects occurring in diamino-o-carborane analogs such as di-N,N-dimethylamino-o-carborane have been held responsible for their long C−C bonds. In this work we systematically analyzed CC bonding in a diverse set of 53 molecules including clamped bonds, highly sterically strained complexes such as diamondoid dimers, electron deficient species, and di-N,N-dimethylamino-o-carborane to cover the whole spectrum of possibilities for elongating a covalent C−C bond to the limit. As a quantitative intrinsic bond strength measure, we utilized local vibrational CC stretching force constants ka(CC) and related bond strength orders BSO n(CC), computed at the ωB97X-D/aug-cc-pVTZ level of theory. Our systematic study quantifies for the first time that whereas steric hindrance and/or strain definitely elongate a C−C bond, electronic effects can lead to even longer and weaker C−C bonds. Within our set of molecules the electron deficient ethane radical cation, in D3d symmetry, acquires the longest C−C bond with a length of 1.935 Å followed by di-N,N-dimethylamino-o-carborane with a bond length of 1.930 Å. However, the C−C bond in di-N,N-dimethylamino-o-carborane is the weakest with a BSO n value of 0.209 compared to 0.286 for the ethane radical cation; another example that the longer bond is not always the weaker bond. Based on our findings we provide new guidelines for the general characterization of CC bonds based on local vibrational CC stretching force constants and for future design of compounds with long C−C bonds.
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Belogolova EF, Shlykov SA, Eroshin AV, Doronina EP, Sidorkin VF. The hierarchy of ab initio and DFT methods for describing an intramolecular non-covalent SiN contact in the silicon compounds using electron diffraction geometries. Phys Chem Chem Phys 2021; 23:2762-2774. [PMID: 33496285 DOI: 10.1039/d0cp05872f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the series of silatranes XSi(OCH2CH2)3N, 1 (X = Me, 1a; H, 1b; F, 1c) with the known gas electron diffraction (GED) structures, the problematic geometry of 1-methylsilatrane 1a has been revised. In particular, the new value of the SiN distance (dSiN) in 1a turned out to be ∼0.06 Å longer than the generally accepted one. This dSiN resolves the long-standing contradiction between the data of the structural and spectral experiments regarding the sensitivity of 1 to the medium effect. We also performed the ab initio and DFT study of the combined series of silatranes 1a-c, silylalkylamines H3Si(CH2)3NMe2 (2a) and F3SiCH2NMe2 (2b), silylhydrazines F3SiN(Me)NMe2 (2c) and F3SiN(SiMe3)NMe2 (2d), and silyloxyamines ClH2SiONMe2 (2e,f), (F3C)F2SiONMe2 (2g,h) and F3SiONMe2 (2i), in which the GED dSiN values are in a wide range of 2-3 Å. None of the involved quantum chemical methods has succeeded in reproducing all the experimental gas-phase dSiN values in 1a-c, 2a-i with an acceptable accuracy (0.01-0.03 Å). The problems of the used methods, primarily CCSD with the Pople basis sets, are caused by four molecules with the geminal SiNN and SiON fragments (2d,f-i) and dSiN < 2.3 Å. A reasonable hierarchy of computationally accessible theory levels for studying the physicochemical manifestation of the non-covalent intramolecular SiN interactions can be constructed only at dSiN > 2.3 Å: MP2 < PBE0 ∼ B3PW91 ∼ SCS-MP2 < CCSD < CCSD(T).
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Affiliation(s)
- Elena F Belogolova
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, 1 Favorsky Street, 664033 Irkutsk, Russian Federation.
| | - Sergey A Shlykov
- Ivanovo State University of Chemistry and Technology, Sheremetievskiy ave. 7, 153000 Ivanovo, Russian Federation.
| | - Alexey V Eroshin
- Ivanovo State University of Chemistry and Technology, Sheremetievskiy ave. 7, 153000 Ivanovo, Russian Federation.
| | - Evgeniya P Doronina
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, 1 Favorsky Street, 664033 Irkutsk, Russian Federation.
| | - Valery F Sidorkin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, 1 Favorsky Street, 664033 Irkutsk, Russian Federation.
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Bönisch N, Maliuta M, Senkovska I, Bon V, Petkov P, Plätzer C, Müller P, Kaskel S. Linker Expansion and Its Impact on Switchability in Pillared-Layer MOFs. Inorg Chem 2021; 60:1726-1737. [PMID: 33439006 DOI: 10.1021/acs.inorgchem.0c03218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Linker elongation is an important method to systematically adjust porosity and pore size in isoreticular MOFs. In flexible structures, this approach opens the possibility for the systematic analysis of the building blocks and their contribution to the overall flexible behavior enabling tuning of the framework responsivity toward molecular stimuli. In this work, we report two new compounds isoreticular to the highly flexible pillared layer structure DUT-8(Ni) ([Ni2(2,6-ndc)2(dabco)]n, 2,6-ndc = 2,6-naphthalenedicarboxylate, dabco = 1,4-diazabicylo[2.2.2]octane). Aromatic linker 2,6-ndc was substituted by longer carboxylic linkers, namely, 4,4'-biphenyldicarboxylate (4,4'-bpdc) and 4,4'-stilbenedicarboxylate (4,4'-sdc), while the dabco pillar was retained. The structural response of the new compounds toward the desolvation and adsorption of various fluids was studied using advanced in situ PXRD techniques, demonstrating distinct differences in the flexible behavior of three compounds and disclosing the impact of linker structure on the framework response. Theoretical calculations provide mechanistic insights and an energetic rationale for the pronounced differences in switchability observed. The energetics of linker bending and linker-linker dispersion interactions govern the phase transitions in investigated MOFs.
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Affiliation(s)
- Nadine Bönisch
- Chair of Inorganic Chemistry I, Technische Universität Dresden, 01069 Dresden, Germany
| | - Mariia Maliuta
- Chair of Inorganic Chemistry I, Technische Universität Dresden, 01069 Dresden, Germany
| | - Irena Senkovska
- Chair of Inorganic Chemistry I, Technische Universität Dresden, 01069 Dresden, Germany
| | - Volodymyr Bon
- Chair of Inorganic Chemistry I, Technische Universität Dresden, 01069 Dresden, Germany
| | - Petko Petkov
- Department of Organic Chemistry and Pharmacognosy, Faculty of Chemistry and Pharmacy, Sofia University "St. Kl. Ohridski", 1164 Sofia, Bulgaria
| | - Christel Plätzer
- Chair of Inorganic Chemistry I, Technische Universität Dresden, 01069 Dresden, Germany
| | - Philipp Müller
- Chair of Inorganic Chemistry I, Technische Universität Dresden, 01069 Dresden, Germany
| | - Stefan Kaskel
- Chair of Inorganic Chemistry I, Technische Universität Dresden, 01069 Dresden, Germany
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Tcharkhetian AEG, Bruni AT, Rodrigues CHP. Combining experimental and theoretical approaches to study the structural and spectroscopic properties of Flakka (α-pyrrolidinopentiophenone). RESULTS IN CHEMISTRY 2021. [DOI: 10.1016/j.rechem.2021.100254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Wang F, Zhang D, Wu X, Deng S. Biodegradation of anionic polyacrylamide mediated by laccase and amidase: docking, virtual mutation based on affinity and DFT study. NEW J CHEM 2021. [DOI: 10.1039/d1nj02411f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The aim of this work was to document the elucidation of a mechanism as a reference.
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Affiliation(s)
- Fanglue Wang
- College of Material Science and Engineering Anhui University of Science and Technology
- Huainan 232001
- China
| | - Dongchen Zhang
- College of Material Science and Engineering Anhui University of Science and Technology
- Huainan 232001
- China
| | - Xuefeng Wu
- College of Food and Bioengineering Hefei University of Technology
- Hefei 230009
- China
| | - Shengsong Deng
- College of Food and Bioengineering Hefei University of Technology
- Hefei 230009
- China
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