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Muralidharan A, Subramani M, Subramani D, Ramasamy S. Inquest for the interaction of canonical and non-canonical DNA/RNA bases with ternary based 2D Si 2BN and doped Si 2BN for biosensing applications. J Biomol Struct Dyn 2023:1-32. [PMID: 37855316 DOI: 10.1080/07391102.2023.2270685] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/08/2023] [Indexed: 10/20/2023]
Abstract
Density functional theory (DFT) is invoked to investigate the interaction between the canonical (CN) and non-canonical (NC) bases with pristine Si2BN (Si2BN) and Phosphorous-doped Si2BN (P-dop-Si2BN) sheets. Inquest for the better sensing substrate is decided through the adsorption energy calculation which reveals that doping of phosphorous atom enhances the adsorption strength of AT (-83.74 kcal/mol) AU (-82.77 kcal/mol) and GC (-96.36 kcal/mol) base pairs. The CN and NC bases have higher adsorption energy than the previous reported values which concludes that the P-dop-Si2BN sheet will be optimal substrate to sense the bases. Meanwhile, the selected CN and NC (except hypoxanthine) bases interact with sheet in parallel manner which infers the π-π interaction with Si2BN and P-dop-Si2BN sheets. The energy gap variation (ΔEg%) of the P-dop-Si2BN complexes has a noticeable change, ranging from -24.75 to -197.28% which thrust the sensitivity of the P-dop-Si2BN sheet over the detection of CN and NC bases. The natural population analysis (NPA) and electron density difference map (EDDM) confirms that charges are transferred from CN and NC bases to Si2BN and P-dop-Si2BN sheet. The optical property of the P-dop-Si2BN complexes reveals that the noticeable red and blue shift in the visible and near-infrared regions (778 nm to 1143 nm) has been observed. Therefore, the above results conclude that the P-dop-Si2BN sheet plays a potential candidate to detect the CN and NC bases which contribute to the development of biosensors and DNA/RNA sequencing devices.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akilesh Muralidharan
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore, Tamilnadu, India
| | - Mohanapriya Subramani
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore, Tamilnadu, India
| | - Divyakaaviri Subramani
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore, Tamilnadu, India
| | - Shankar Ramasamy
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore, Tamilnadu, India
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2
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Li H, Lim JH, Lv Y, Li N, Kang B, Lee JY. Graphynes and Graphdiynes for Energy Storage and Catalytic Utilization: Theoretical Insights into Recent Advances. Chem Rev 2023; 123:4795-4854. [PMID: 36921251 DOI: 10.1021/acs.chemrev.2c00729] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Carbon allotropes have contributed to all aspects of people's lives throughout human history. As emerging carbon-based low-dimensional materials, graphyne family members (GYF), represented by graphdiyne, have a wide range potential applications due to their superior physical and chemical properties. In particular, graphdiyne (GDY), as the leader of the graphyne family, has been practically applied to various research fields since it was first successfully synthesized. GYF have a large surface area, both sp and sp2 hybridization, and a certain band gap, which was considered to originate from the overlap of carbon 2pz orbitals and the inhomogeneous π-bonds of carbon atoms in different hybridization forms. These properties mean GYF-based materials still have many potential applications to be developed, especially in energy storage and catalytic utilization. Since most of the GYF have yet to be synthesized and applications of successfully synthesized GYF have not been developed for a long time, theoretical results in various application fields should be shared to experimentalists to attract more intentions. In this Review, we summarized and discussed the synthesis, structural properties, and applications of GYF-based materials from the theoretical insights, hoping to provide different viewpoints and comments.
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Affiliation(s)
- Hao Li
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Jong Hyeon Lim
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Yipin Lv
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, P. R. China
| | - Nannan Li
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Baotao Kang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, P. R. China
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
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3
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Slama M, Habli H, Laajimi M, Ghalla H, Ben El Hadj Rhouma M. Microsolvation of lithium cation in xenon clusters: An octahedral growth pattern. J Mol Graph Model 2022; 116:108229. [PMID: 35671571 DOI: 10.1016/j.jmgm.2022.108229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 05/09/2022] [Accepted: 05/19/2022] [Indexed: 01/18/2023]
Abstract
The structural and energetic proprieties for the Li + Xen (n = 1-18) clusters are investigated using both Basin-Hopping combined with Potential Model description (BH-PM) and DFT methods. A structural transition from tetrahedral (4 coordination) form to octahedral (6 coordination) one is observed for n = 6. Above this size, all structures have an octahedral core. The cubic-face-centered arrangement for xenon atoms is detected for Li + Xe14. To the best of our knowledge, the Li + Xen (n = 1-18) clusters are studied in the present work for the first time using the DFT theoretical approach. The M062X functional combined with aug-cc-pVDZ (for Li) and def2-TZVP (for Xe) basis sets reproduces accurately the CCSD(T) potential energy curve of Li + Xe system. Atom-Centered Density Matrix Propagation (ADMP) molecular dynamic calculations have been carried. Moreover, we investigate the larger sizes n = 31-35, 44, and 55 for the first time using the BH-PM theoretical approach. The closing of the first and second octahedron shells are proved for the n = 6 and 34 sizes, respectively. The relative stabilities of the Li + Xen molecules are also studied by computing the total energy, the binding energy per atoms for each size n. Then, the second energy difference between the size n and its two near neighbors allows identifying the magic number series. Our present data are analyzed, discussed and compared with the available theoretical and experimental data.
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Affiliation(s)
- Marwa Slama
- Université de Monastir, Institut Préparatoire aux Études des Ingénieurs de Monastir, Laboratoire d'Études des Milieux Ionisés et Réactifs (EMIR), 5000 Monastir, Tunisia.
| | - Hela Habli
- Université de Monastir, Faculté des Sciences de Monastir, Laboratoire de Physique Quantique et Statistique, Avenue de l'Environnement 5019 Monastir, Tunisia; Université de Sousse, Institut Supérieur des Sciences Appliquées et de Technologie de Sousse, Rue ibn Khaldun, Cité Taffala, 4003 Sousse, Tunisia
| | - Maha Laajimi
- Université de Monastir, Faculté des Sciences de Monastir, Laboratoire de Physique Quantique et Statistique, Avenue de l'Environnement 5019 Monastir, Tunisia
| | - Houcine Ghalla
- Université de Monastir, Faculté des Sciences de Monastir, Laboratoire de Physique Quantique et Statistique, Avenue de l'Environnement 5019 Monastir, Tunisia
| | - Mounir Ben El Hadj Rhouma
- Université de Monastir, Institut Préparatoire aux Études des Ingénieurs de Monastir, Laboratoire d'Études des Milieux Ionisés et Réactifs (EMIR), 5000 Monastir, Tunisia
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4
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Reina M, Celaya CA, Muñiz J. C
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and C
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E (E=N and B) Fullerenes as Potential Nanovehicles for Neuroprotective Drugs: A Comparative DFT Study. ChemistrySelect 2021. [DOI: 10.1002/slct.202101227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Miguel Reina
- Departamento de Química Inorgánica y Nuclear Facultad de Química Universidad Nacional Autónoma de México Circuito Exterior S.N. Ciudad Universitaria, P.O. Box 70–360 Coyoacán C.P. 04510 Ciudad de México México
| | - Christian A. Celaya
- Departamento de Química Inorgánica y Nuclear Facultad de Química Universidad Nacional Autónoma de México Circuito Exterior S.N. Ciudad Universitaria, P.O. Box 70–360 Coyoacán C.P. 04510 Ciudad de México México
- Instituto de Energías Renovables Universidad Nacional Autonoma de México Piv. Xochicalcos/n. Col. Centro Temixco, C.P. 62580 Morelos, México
| | - Jesús Muñiz
- Instituto de Energías Renovables Universidad Nacional Autonoma de México Piv. Xochicalcos/n. Col. Centro Temixco, C.P. 62580 Morelos, México
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Yuan Y, Wu S, Ai H, Lee JY, Kang B. γ-Graphyne nanotubes as defect-free catalysts of the oxygen reduction reaction: a DFT investigation. Phys Chem Chem Phys 2020; 22:8633-8638. [DOI: 10.1039/d0cp00644k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
γGyNTs as excellent metal-free ORR catalysts without any defects.
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Affiliation(s)
- Yuan Yuan
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- P. R. China
| | - Si Wu
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- P. R. China
| | - Hongqi Ai
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- P. R. China
| | - Jin Yong Lee
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- P. R. China
- Department of Chemistry
| | - Baotao Kang
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- P. R. China
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6
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Kang B, Wu S, Ma J, Ai H, Lee JY. Synergy of sp-N and sp 2-N codoping endows graphdiyne with comparable oxygen reduction reaction performance to Pt. NANOSCALE 2019; 11:16599-16605. [PMID: 31460553 DOI: 10.1039/c9nr05363h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nitrogen doped graphdiyne (NGDY) has been reported to have comparable oxygen reduction reaction (ORR) performance to Pt-based catalysts. However, the source of this enhanced ORR performance is not clearly understood. Herein, density functional theory calculations were performed to study the detailed ORR process on NGDY. The theoretically predicted overpotential (η) of GDY materials was 0.442 V, which is comparable to that of Pt-based catalysts, suggesting that GDY is a candidate for non-expensive metal-free ORR catalyst. Our results revealed that the good ORR performance of NGDY originates from the synergy of sp-N and sp2-N, which rules out the experimental proposal that sp-N doping is the dominating factor. Our results further suggest that local positive charge is not a definite descriptor to predict the ORR performance of GDY; instead ΔGO shows a better correlation with performance. Furthermore, it was revealed that the adsorption site is crucial for determining ORR performance, which should not be ignored to fully understand the catalytic activity of GDY-based materials.
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Affiliation(s)
- Baotao Kang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, P. R. China.
| | - Si Wu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, P. R. China.
| | - Jiapeng Ma
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, P. R. China.
| | - Hongqi Ai
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, P. R. China.
| | - Jin Yong Lee
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, P. R. China. and Department of Chemistry, Sungkyunkwan University, Suwon, 440-746, R. Korea
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7
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Jung SW, Kim HS, Cho AE, Kim YH. Nitrogen Doping of Carbon Nanoelectrodes for Enhanced Control of DNA Translocation Dynamics. ACS APPLIED MATERIALS & INTERFACES 2018; 10:18227-18236. [PMID: 29741080 DOI: 10.1021/acsami.8b04453] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Controlling the dynamics of DNA translocation is a central issue in the emerging nanopore-based DNA sequencing. To address the potential of heteroatom doping of carbon nanostructures and for achieving this goal, herein, we carry out atomistic molecular dynamics simulations for single-stranded DNAs translocating between two pristine or doped carbon nanotube (CNT) electrodes. Specifically, we consider the substitutional nitrogen doping of capped CNT (capCNT) electrodes and perform two types of molecular dynamics simulations for the entrapped and translocating single-stranded DNAs. We find that the substitutional nitrogen doping of capCNTs facilitates and stabilizes the edge-on nucleobase configurations rather than the original face-on ones and slows down the DNA translocation speed by establishing hydrogen bonds between the N dopant atoms and nucleobases. Due to the enhanced interactions between DNAs and N-doped capCNTs, the duration time of nucleobases within the nanogap was extended by up to ∼300%. Given the possibility to be combined with the extrinsic light or gate voltage modulation methods, the current work demonstrates that the substitutional nitrogen doping is a promising direction for the control of DNA translocation dynamics through a nanopore or nanogap, based of carbon nanomaterials.
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Affiliation(s)
- Sang Won Jung
- Department of Bioinformatics , Korea University , Sejong Campus, 2511 Sejong-ro , Jochiwon-eup, Sejong 30019 , Korea
| | - Han Seul Kim
- Graduate School of Energy, Environment, Water, and Sustainability , Korean Advanced Institute of Science and Technology , 291 Deahak-ro , Yuseong-gu, Daejeon 34141 , Korea
| | - Art E Cho
- Department of Bioinformatics , Korea University , Sejong Campus, 2511 Sejong-ro , Jochiwon-eup, Sejong 30019 , Korea
| | - Yong-Hoon Kim
- Graduate School of Energy, Environment, Water, and Sustainability , Korean Advanced Institute of Science and Technology , 291 Deahak-ro , Yuseong-gu, Daejeon 34141 , Korea
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8
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Tawfik SA, Cui XY, Ringer SP, Stampfl C. TDDFT Study of the Optical Excitation of Nucleic Acid Bases-C 60 Complexes. J Phys Chem A 2017; 121:9058-9063. [PMID: 29111726 DOI: 10.1021/acs.jpca.7b07442] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The potential of C60 as a nucleic acid base (NAB) optical sensor is theoretically explored. We investigate the adsorption of four NABs, namely, adenine, cytosine, guanine, and thymine, on C60 in the gas phase. For the optimal NAB@C60 adsorption configurations, obtained using a dispersion-corrected density functional, we calculate the vis-near-ultraviolet optical response using time-dependent density functional theory. While the isolated C60 and NAB molecules do not exhibit visible optical excitation, we find that C60/NAB conjugation gives rise to distinct spectral features in the visible range. These results suggest that C60 conjugation can be applied for photodetection of individual NABs.
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Affiliation(s)
| | | | | | - C Stampfl
- School of Physics, The University of Sydney , Sydney, New South Wales 2006, Australia
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9
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Shakourian-Fard M, Kamath G. The effect of defect types on the electronic and optical properties of graphene nanoflakes physisorbed by ionic liquids. Phys Chem Chem Phys 2017; 19:4383-4395. [PMID: 28119976 DOI: 10.1039/c6cp07455c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Defect engineering and non-covalent interaction strategies allow for dramatically tuning the optoelectronic properties of graphene. Using ab initio density functional theory (M06-2X/cc-pVDZ), we find that the nature of defects on the graphene nanoflakes (GNFs) and the size of defective GNF (DGNF) surfaces affect the binding energy (ΔEb) of ionic liquids (ILs) and the UV-Vis absorption spectra of DGNFIL complexes. Further, our results indicate that increasing the size of DGNFs affects the geometrical structure of the surfaces and increases the binding energy of ILs by about 10%. Analysis based on AIM and EDA shows that the interactions between ILs and DGNFs are non-covalent in nature (dispersion energy being dominant) and associated with charge transfer between the IL and nanoflakes. A comparison between the ΔEb values of ILs on DGNFs, GNFs, and h-BN nanoflakes (h-BNNF) shows that the presence of defects on the GNF surfaces increases the binding energy values as follows: DGNFIL > pristine GNFIL > h-BNNFIL. Our calculations indicate that increasing the size of DGNF surfaces leads to a decrease in the HOMO-LUMO energy gap (Eg) of the DGNF surfaces. Orbital energy and density of state calculations show that the Eg of DV(SW)-GNFs decreases upon IL adsorption and their Fermi energy level is shifted depending on the type of IL, thus enabling better conductivity. Reactivity descriptors generally indicate that the chemical potential (μ) and chemical hardness (η) of nanoflakes decrease upon IL adsorption, whereas the electrophilicity index (ω) increases. The UV-Vis absorption spectrum of DV-GNF and SW-GNF shows four bands in the visible spectrum which correspond to π → π* transitions with the absorption bands of SW-GNF appearing at higher wavelengths than those of DV-GNF. The most intense absorption bands in DV-GNF (λ = 348 nm) and SW-GNF (λ = 375 nm) are associated with electronic transitions HOMO-1 → LUMO+2 and HOMO → LUMO+1, respectively. In addition, these absorption bands undergo a red-shift by both increasing the size of the DV(SW)-GNF surfaces and IL adsorption. We also observe that the energy gaps and absorption spectra can be altered by varying the defect types and the type of IL adsorbate, where the defect types affect the spectral shapes of the bands and adsorbates at the first absorption peak, thus having potential application for light-emitting devices.
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Affiliation(s)
- Mehdi Shakourian-Fard
- Birjand University of Technology, Department of Chemical Engineering, Birjand, P.O. Box 97175/569, Iran.
| | - Ganesh Kamath
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
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10
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Wang Y, Xu Z. Interaction Mechanism of Doxorubicin and SWCNT: Protonation and Diameter Effects on the Drug Loading and Releasing. RSC Adv 2015; 6:314-322. [PMID: 26925231 PMCID: PMC4767018 DOI: 10.1039/c5ra20866a] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In the present work the adsorption of doxorubicin (DOX) on the surface of single-walled carbon nanotube (SWCNT) as well as its encapsulation in SWCNT, and their dependence on the protonation of NH2 group of DOX, solvent, and the diameter of armchair (n,n) SWCNT were systematically investigated using theoretical methods such as PM6-DH2 and M06-2X in the scheme of OMIOM. It was found that the two loadings, adsorption on the sidewall of CNT and the encapsulation in CNT, have distinct solvent, protonation and diameter dependences. The encapsulation is much stronger than the adsorption of DOX on the sidewall of CNT, and the former also has significantly higher solvent and protonation effects than the latter. The adsorption primarily occurs through π-π stacking and just becomes slightly stronger as the diameter of CNT increases, while besides π-π stacking the additional C-H/N-H/O-H…π and C=O…π also contribute to the encapsulation of DOX in CNT. It seems that (8,8) CNT (diameter ~ 11Å) energetically is an onset for the encapsulation since the encapsulation turns from endothermic to exothermic as the diameter is larger than approximately 11 Å, and the optimal diameter for the encapsulation is 14Å corresponding to (10,10) CNT. Thus for the thick CNT the encapsulation may also play an important role in the loading and releasing for the CNT-based drug delivery system of the DOX.
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Affiliation(s)
- Yixuan Wang
- Computational Chemistry Laboratory, Department of Natural and Forensic Sciences, Albany State University, Albany, Georgia 31705, United States
| | - Zhenfeng Xu
- Computational Chemistry Laboratory, Department of Natural and Forensic Sciences, Albany State University, Albany, Georgia 31705, United States
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11
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Tian G, Li H, Ma W, Wang Y. Substituent Effects in π-Stacking of Histidine on Functionalized-SWNT and Graphene. COMPUT THEOR CHEM 2015; 1062:44-49. [PMID: 25914869 DOI: 10.1016/j.comptc.2015.03.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adsorptions of histidine on the functionalized (10,0) single-walled carbon nanotube (SWNT) and graphene were investigated using density function theory methods, M05-2x and DFT-D. The results show that the binding of the histidine ring to the functionalized SWNT is weaker than that to the pristine SWNT for both singlet and triplet complexes, regardless of the electron-donating (-OH, -NH2) or electron-withdrawing (-COOH) character and their attached sites. The present decreased binding is opposite to the well-known enhanced binding in the substituted benzene dimers. Since the atoms of the histidine are distant from the substituent atoms by over 6Å, there would be no direct interaction between histidine and the substituent as in the case of the substituted benzene systems. The decreased binding can be mainly driven by the aromaticity of the functionalized SWNT. The nucleus-independent chemical shift (NICS) index analysis for the functionalized SWNTs in deed shows that local aromaticity of SWNT is decreased because of the electron redistribution induced by functional groups, and the π-π stacking between the histidine ring and functionalized-SWNT is therefore decreased as compared to the pristine SWNT. However, the above trend does not remain for the binding between the histidine and graphene. The binding of the histidine to the functionalized graphene with -OH and -NH2 is just slightly weaker than that to the pristine graphene, while its binding to COOH-SWNT becomes a little bit stronger.
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Affiliation(s)
- Ge Tian
- School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, Jinan, Shandong 250353, China ; Department of Natural Science, Albany State University, Albany, GA 31705, USA
| | - Huifang Li
- Department of Natural Science, Albany State University, Albany, GA 31705, USA ; Department of Chemistry, Gannan Normal University, GanZhou, JiangXi 341000, China
| | - Wanyong Ma
- School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, Jinan, Shandong 250353, China
| | - Yixuan Wang
- Department of Natural Science, Albany State University, Albany, GA 31705, USA
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12
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Halder A, Bhattacharya S, Datta A, Bhattacharyya D, Mitra A. The role of N7 protonation of guanine in determining the structure, stability and function of RNA base pairs. Phys Chem Chem Phys 2015; 17:26249-63. [DOI: 10.1039/c5cp04894j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ab initio computations and bioinformatics studies reveal that stabilization of some important RNA structural motifs might involve N7 protonation of guanine.
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Affiliation(s)
- Antarip Halder
- Center for Computational Natural Sciences and Bioinformatics (CCNSB)
- International Institute of Information Technology (IIIT-H)
- Hyderabad 500032
- India
| | - Sohini Bhattacharya
- Center for Computational Natural Sciences and Bioinformatics (CCNSB)
- International Institute of Information Technology (IIIT-H)
- Hyderabad 500032
- India
| | - Ayan Datta
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | | | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics (CCNSB)
- International Institute of Information Technology (IIIT-H)
- Hyderabad 500032
- India
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13
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Kang B, Moon JH, Lee JY. Size dependent electronic band structures of β- and γ-graphyne nanotubes. RSC Adv 2015. [DOI: 10.1039/c5ra12188d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In the present paper, density functional theory calculations have been implemented by using Dmol3 to study the electronic band structures of β-graphyne nanotubes (βGyNTs) and γ-graphyne nanotubes (γGyNTs).
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Affiliation(s)
- Baotao Kang
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- People's Republic of China
| | - Jong Hun Moon
- Department of Chemistry
- Sungkyunkwan University
- Suwon
- Republic of Korea
| | - Jin Yong Lee
- Department of Chemistry
- Sungkyunkwan University
- Suwon
- Republic of Korea
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14
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Moreira da Costa L, Stoyanov SR, Gusarov S, Seidl PR, Walkimar de M. Carneiro J, Kovalenko A. Computational Study of the Effect of Dispersion Interactions on the Thermochemistry of Aggregation of Fused Polycyclic Aromatic Hydrocarbons as Model Asphaltene Compounds in Solution. J Phys Chem A 2014; 118:896-908. [DOI: 10.1021/jp408005h] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Leonardo Moreira da Costa
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Organic Processes, School of Chemistry, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil
- Institute
of Chemistry, Universidade Federal Fluminense, Niteroi, RJ 24220-900, Brazil
- Centro Universitário da Zona Oeste, Avenida Manuel Caldeira de Alvarenga 1203, Campo Grande, RJ 23070-200, Brazil
| | - Stanislav R. Stoyanov
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
| | - Sergey Gusarov
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
| | - Peter R. Seidl
- Department
of Organic Processes, School of Chemistry, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil
| | | | - Andriy Kovalenko
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Mechanical Engineering, University of Alberta, Edmonton, Alberta T6G 2G8, Canada
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15
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Insight into the interaction between DNA bases and defective graphenes: covalent or non-covalent. J Mol Graph Model 2013; 47:8-17. [PMID: 24215998 DOI: 10.1016/j.jmgm.2013.10.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/10/2013] [Accepted: 10/14/2013] [Indexed: 12/25/2022]
Abstract
Although some metal clusters and molecules were found to more significantly bind to defective graphenes than to pristine graphenes, exhibiting chemisorptions on defective graphenes, the present investigation shows that the adsorption of DNA bases on mono- and di-vacant defective graphenes does not show much difference from that on pristine graphene, and is still dominantly driven by noncovalent interactions. In the present study the adsorptions of the nucleobases, adenine (A), cytosine (C), guanine, (G), and thymine (T) on pristine and defective graphenes, are fully optimized using a hybrid-meta GGA density functional theory (DFT), M06-2X/6-31G*, and the adsorption energies are then refined with both M06-2X and B97-D/6-311++G**. Graphene is modeled as nano-clusters of C₇₂H₂₄, C₇₁H₂₄, and C₇₀H₂₄ for pristine, mono- and di-vacant defective graphenes, respectively, supplemented by a few larger ones. The result shows that guanine has the maximum adsorption energy in all of the three adsorption systems; and the sequence of the adsorption strength is G>A>T>C on the pristine and di-vacant graphene and G>T>A>C on the mono-vacant graphene. In addition, the binding energies of the DNA bases with the pristine graphene are less than the corresponding ones with di-vacant defective graphene; however, they are greater than those of mono-vacant graphene with guanine and adenine, while it is dramatic that the binding energies of mono-vacant graphene with thymine and cytosine appear larger than those of pristine graphene.
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Gajewicz A, Rasulev B, Dinadayalane TC, Urbaszek P, Puzyn T, Leszczynska D, Leszczynski J. Advancing risk assessment of engineered nanomaterials: application of computational approaches. Adv Drug Deliv Rev 2012; 64:1663-93. [PMID: 22664229 DOI: 10.1016/j.addr.2012.05.014] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 05/20/2012] [Accepted: 05/25/2012] [Indexed: 02/06/2023]
Abstract
Nanotechnology that develops novel materials at size of 100nm or less has become one of the most promising areas of human endeavor. Because of their intrinsic properties, nanoparticles are commonly employed in electronics, photovoltaic, catalysis, environmental and space engineering, cosmetic industry and - finally - in medicine and pharmacy. In that sense, nanotechnology creates great opportunities for the progress of modern medicine. However, recent studies have shown evident toxicity of some nanoparticles to living organisms (toxicity), and their potentially negative impact on environmental ecosystems (ecotoxicity). Lack of available data and low adequacy of experimental protocols prevent comprehensive risk assessment. The purpose of this review is to present the current state of knowledge related to the risks of the engineered nanoparticles and to assess the potential of efficient expansion and development of new approaches, which are offered by application of theoretical and computational methods, applicable for evaluation of nanomaterials.
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Affiliation(s)
- Agnieszka Gajewicz
- Laboratory of Environmental Chemometrics, Institute for Environmental and Human Health Protection, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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Choi TH, Han YK. Assessment of the Performance of B2PLYP-D for Describing Intramolecular π-π and σ-π Interactions. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.12.4195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Sun W, Bu Y, Wang Y. Interaction and protection mechanism between Li@C(60) and nucleic acid bases (NABs): performance of PM6-DH2 on noncovalent interaction of NABs-Li@C60. J Comput Chem 2011; 33:490-501. [PMID: 22170247 DOI: 10.1002/jcc.22881] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 09/27/2011] [Accepted: 10/23/2011] [Indexed: 12/17/2022]
Abstract
To discuss the protection mechanism of DNA from radiation as well as assess the performance of PM6-DH2 on noncovalent interactions, the interaction of four nucleic acid bases (NABs) such as adenine (A), cytosine (C), guanine (G), and thymine (T), with Li@C(60) was extensively investigated with the-state-of-art theoretical methods describing noncovalent systems, like M06-2x, PBE-D, and PM6-DH2 methods. In the gas phase, the binding strength of NABs to Li@C(60) from M06-2x decreases in the sequence, G>C>A>T. As dispersion was explicitly included, PBE-D relatively enhances the binding of A and T and corrects the sequence to, G>A>C∼T. PM6-DH2 predicted similar binding energies to those from PBE-D within 0.5 kcal/mol and the same binding sequence, suggesting that the PM6-DH2 method is promising for nano-scale systems. In the aqueous solution, binding of NABs-Li@C(60) is considerably decreased, and the M06-2X and PM6-D methods yield a different sequence from the gas phase, G>A>T>C. The encapsulation of Li atom results in a lower IP for Li@C(60) than those of NABs, and the dominant localization of single-occupied molecular orbital on Li@C(60) moiety of the complexes NABs-Li@C(60) further indicates that an electron would be ejected from Li@C(60) upon radiation and Li@C(60) is therefore able to protect DNA bases from radiation. In addition, it was revealed that Li prefers coordination with the hexagonal ring at Li@C(60) , which clarifies the existing controversy in this respect. Finally, Yang's reduced density gradient approach clearly shows that the weak and strong noncovalent interaction regions in the complexes, NABs-Li@C(60) and (NABs-Li@C(60) )(+).
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Affiliation(s)
- Wenming Sun
- The Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, People's Republic of China
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