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Nano-Zirconium Dioxide Catalyzed Multicomponent Synthesis of Bioactive Pyranopyrazoles That Target Cyclin Dependent Kinase 1 in Human Breast Cancer Cells. Biomedicines 2023; 11:biomedicines11010172. [PMID: 36672680 PMCID: PMC9856062 DOI: 10.3390/biomedicines11010172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/05/2023] [Indexed: 01/12/2023] Open
Abstract
Small molecules are being used to inhibit cyclin dependent kinase (CDK) enzymes in cancer treatment. There is evidence that CDK is a drug-target for cancer therapy across many tumor types because it catalyzes the transfer of the terminal phosphate of ATP to a protein that acts as a substrate. Herein, the identification of pyranopyrazoles that were CDK inhibitors was attempted, whose synthesis was catalyzed by nano-zirconium dioxide via multicomponent reaction. Additionally, we performed an in-situ analysis of the intermediates of multicomponent reactions, for the first-time, which revealed that nano-zirconium dioxide stimulated the reaction, as estimated by Gibbs free energy calculations of spontaneity. Functionally, the novel pyranopyrazoles were tested for a loss of cell viability using human breast cancer cells (MCF-7). It was observed that compounds 5b and 5f effectively produced loss of viability of MCF-7 cells with IC50 values of 17.83 and 23.79 µM, respectively. In vitro and in silico mode-of-action studies showed that pyranopyrazoles target CDK1 in human breast cancer cells, with lead compounds 5b and 5f having potent IC50 values of 960 nM and 7.16 μM, respectively. Hence, the newly synthesized bioactive pyranopyrazoles could serve as better structures to develop CDK1 inhibitors against human breast cancer cells.
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Zheng Y, Han Y, Weight BM, Lin Z, Gifford BJ, Zheng M, Kilin D, Kilina S, Doorn SK, Htoon H, Tretiak S. Photochemical spin-state control of binding configuration for tailoring organic color center emission in carbon nanotubes. Nat Commun 2022; 13:4439. [PMID: 35915090 PMCID: PMC9343348 DOI: 10.1038/s41467-022-31921-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 07/04/2022] [Indexed: 12/04/2022] Open
Abstract
Incorporating fluorescent quantum defects in the sidewalls of semiconducting single-wall carbon nanotubes (SWCNTs) through chemical reaction is an emerging route to predictably modify nanotube electronic structures and develop advanced photonic functionality. Applications such as room-temperature single-photon emission and high-contrast bio-imaging have been advanced through aryl-functionalized SWCNTs, in which the binding configurations of the aryl group define the energies of the emitting states. However, the chemistry of binding with atomic precision at the single-bond level and tunable control over the binding configurations are yet to be achieved. Here, we explore recently reported photosynthetic protocol and find that it can control chemical binding configurations of quantum defects, which are often referred to as organic color centers, through the spin multiplicity of photoexcited intermediates. Specifically, photoexcited aromatics react with SWCNT sidewalls to undergo a singlet-state pathway in the presence of dissolved oxygen, leading to ortho binding configurations of the aryl group on the nanotube. In contrast, the oxygen-free photoreaction activates previously inaccessible para configurations through a triplet-state mechanism. These experimental results are corroborated by first principles simulations. Such spin-selective photochemistry diversifies SWCNT emission tunability by controlling the morphology of the emitting sites. Chemical functionalization of the sidewalls of single-wall carbon nanotubes (SWCNTs) is an emerging route to introduce fluorescent quantum defects and tailor the emission properties. Here, authors demonstrate that spin-selective photochemistry diversifies SWCNT emission tunability by controlling the morphology of the emitting sites.
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Affiliation(s)
- Yu Zheng
- Center for Integrated Nanotechnologies, Materials Physics and Applications Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
| | - Yulun Han
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
| | - Braden M Weight
- Center for Integrated Nanotechnologies, Materials Physics and Applications Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.,Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA.,Department of Physics, North Dakota State University, Fargo, ND, 58102, USA.,Department of Physics and Astronomy, University of Rochester, Rochester, NY, 14627, USA
| | - Zhiwei Lin
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Brendan J Gifford
- Center for Nonlinear Studies, and Theoretical Division Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Ming Zheng
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Dmitri Kilin
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
| | - Svetlana Kilina
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
| | - Stephen K Doorn
- Center for Integrated Nanotechnologies, Materials Physics and Applications Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Han Htoon
- Center for Integrated Nanotechnologies, Materials Physics and Applications Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
| | - Sergei Tretiak
- Center for Integrated Nanotechnologies, Materials Physics and Applications Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA. .,Center for Nonlinear Studies, and Theoretical Division Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
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Erickson M, Han Y, Rasulev B, Kilin D. Molecular Dynamics Study of the Photodegradation of Polymeric Chains. J Phys Chem Lett 2022; 13:4374-4380. [PMID: 35544382 DOI: 10.1021/acs.jpclett.2c00802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The development of reusable polymeric materials inspires an attempt to combine renewable biomass with upcycling to form a biorenewable closed system. It has been reported that 2,5-furandicarboxylic acid (FDCA) can be recovered for recycling when incorporated as monomers into photodegradable polymeric systems. Here, we conduct density functional theory (DFT) studies with periodic boundary conditions on microscopic structures involved in the photodegradation of polymeric chains incorporating FDCA and 2-nitro-1,3-benzenedimethanol. The photodegradation process of polymeric chains is studied using time-dependent excited-state molecular dynamics (TDESMD) in vacuum and aqueous environments. Changes in the photophysical properties for reaction intermediates are characterized by ground-state observables. The distribution of reaction intermediates and products is obtained from TDESMD trajectories using cheminformatics techniques. Results show that a higher degree of polymeric chain degradation is achieved in the vacuum environment. Additionally, one finds that the FDCA molecule is recoverable in the aqueous environment, in qualitative agreement with experimental findings.
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Affiliation(s)
- Meade Erickson
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Yulun Han
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Bakhtiyor Rasulev
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Dmitri Kilin
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
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Chen X, Liu M, Gao J. CARNOT: a Fragment-Based Direct Molecular Dynamics and Virtual-Reality Simulation Package for Reactive Systems. J Chem Theory Comput 2022; 18:1297-1313. [PMID: 35129348 DOI: 10.1021/acs.jctc.1c01032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Traditionally, the study of reaction mechanisms of complex reaction systems such as combustion has been performed on an individual basis by optimizations of transition structure and minimum energy path or by reaction dynamics trajectory calculations for one elementary reaction at a time. It is effective, but time-consuming, whereas important and unexpected processes could have been missed. In this article, we present a direct molecular dynamics (DMD) approach and a virtual-reality simulation program, CARNOT, in which plausible chemical reactions are simulated simultaneously at finite temperature and pressure conditions. A key concept of the present ab initio molecular dynamics method is to partition a large, chemically reactive system into molecular fragments that can be adjusted on the fly of a DMD simulation. The theory represents an extension of the explicit polarization method to reactive events, called ReX-Pol. We propose a highest-and-lowest adapted-spin approximation to define the local spins of individual fragments, rather than treating the entire system by a delocalized wave function. Consequently, the present ab initio DMD can be applied to reactive systems consisting of an arbitrarily varying number of closed and open-shell fragments such as free radicals, zwitterions, and separate ions found in combustion and other reactions. A graph-data structure algorithm was incorporated in CARNOT for the analysis of reaction networks, suitable for reaction mechanism reduction. Employing the PW91 density functional theory and the 6-31+G(d) basis set, the capabilities of the CARNOT program were illustrated by a combustion reaction, consisting of 28 650 atoms, and by reaction network analysis that revealed a range of mechanistic and dynamical events. The method may be useful for applications to other types of complex reactions.
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Affiliation(s)
- Xin Chen
- Peking University Shenzhen Graduate School, Shenzhen, Guangdong 581055, China.,Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 581055, China
| | - Meiyi Liu
- Peking University Shenzhen Graduate School, Shenzhen, Guangdong 581055, China.,Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 581055, China
| | - Jiali Gao
- Peking University Shenzhen Graduate School, Shenzhen, Guangdong 581055, China.,Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 581055, China.,Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Han Y, Iduoku K, Grant G, Rasulev B, Leontyev A, Hobbie EK, Tretiak S, Kilina SV, Kilin DS. Hot Carrier Dynamics at Ligated Silicon(111) Surfaces: A Computational Study. J Phys Chem Lett 2021; 12:7504-7511. [PMID: 34342460 DOI: 10.1021/acs.jpclett.1c02084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We provide a case-study for thermal grafting of benzenediazonium bromide onto a hydrogenated Si(111) surface using ab initio molecular dynamics (AIMD) calculations. A sequence of reaction steps is identified in the AIMD trajectory, including the loss of N2 from the diazonium salt, proton transfer from the surface to the bromide ion that eliminates HBr, and deposition of the phenyl group onto the surface. We next assess the influence of the phenyl groups on photophysics of hydrogen-terminated Si(111) slabs. The nonadiabatic couplings necessary for a description of the excited-state dynamics are calculated by combining ab initio electronic structures and reduced density matrix formalism with Redfield theory. The phenyl-terminated slab shows reduced nonradiative relaxation and recombination rates of hot charge carriers in comparison with the hydrogen-terminated slab. Altogether, our results provide atomistic insights revealing that (i) the diazonium salt thermally decomposes at the surface allowing the formation of covalently bonded phenyl group, and (ii) the coverage of phenyl groups on the surface slows down charge carrier cooling driven by electron-phonon interactions, which increases photoluminescence efficiency at the near-infrared spectral region.
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Affiliation(s)
- Yulun Han
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Kweeni Iduoku
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Gena Grant
- Turtle Mountain Community College, 10145 BIA Road 7, PO Box 340, Belcourt, North Dakota 58316, United States
| | - Bakhtiyor Rasulev
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Alexey Leontyev
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Erik K Hobbie
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Sergei Tretiak
- Theoretical Division and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Svetlana V Kilina
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Dmitri S Kilin
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
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Guo H, Yang X, Zwier T. Virtual Issue on Combustion Chemistry. J Phys Chem A 2020; 124:5995-5996. [PMID: 32698590 DOI: 10.1021/acs.jpca.0c05674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Yamaoka S, Hyeon-Deuk K. Decelerated Liquid Dynamics Induced by Component-Dependent Supercooling in Hydrogen and Deuterium Quantum Mixtures. J Phys Chem Lett 2020; 11:4186-4192. [PMID: 32375000 DOI: 10.1021/acs.jpclett.0c00801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Isotopic mixtures of p-H2 and o-D2 molecules have been an attractive binary system because they include two kinds of purely isotopic molecules which possess the same electronic potential but the twice different mass inducing differently pronounced nuclear quantum effects (NQEs). Accessing details of structures and dynamics in such quantum mixtures combining complex molecular dynamics with NQEs of different strengths remains a challenging problem. Taking advantage of the nonempirical molecular dynamics method which describes p-H2 and o-D2 molecules, we found that the liquid dynamics slows down at a specific mixing ratio, which can be connected to the observed anomalous slowdown of crystallization in the quantum mixtures. We attributed the decelerated dynamics to the component-dependent supercooling of p-H2 taking place in the mixtures, demonstrating that there is an optimal mixing ratio to hinder crystallization. The obtained physical insights will help in experimentally controlling and achieving unknown quantum mixtures including superfluid.
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Affiliation(s)
- Shutaro Yamaoka
- Department of Chemistry, Kyoto University, Kyoto 606-8502, Japan
| | - Kim Hyeon-Deuk
- Department of Chemistry, Kyoto University, Kyoto 606-8502, Japan
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