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Monavari SM, Memarian N. Ab Initio investigation for DNA nucleotide bases sequencing using chiral carbon nanobelts and nanotubes. Sci Rep 2023; 13:18063. [PMID: 37872194 PMCID: PMC10593758 DOI: 10.1038/s41598-023-45361-3] [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: 09/13/2023] [Accepted: 10/18/2023] [Indexed: 10/25/2023] Open
Abstract
Understanding the interaction mechanism between DNA nucleotide bases and carbon nanomaterials is an important issue in the field of identifying nucleotide molecules sequencing. In this article, the adsorption behavior of DNA nucleotide bases on the external surface of chiral carbon nanobelts (CNBs) (6, 5), (7, 6) and (8, 6), was comprehensively investigated from electronic and optical perspectives. As a result, it was determined that the DNA nucleotide bases have optical absorption in the ultraviolet region. When bases are adsorbed on the surface of CNBs, the optical absorption peak of the new complex structure shifted to the visible region. The study of the optical properties of selected CNBs showed that CNB (6,5) performs better in detecting Cytosine and the red shift in the absorption spectrum of complex structure is noticeable. Also, the effect of infinite length for chiral CNTs in DNA nucleotide base sequencing was investigated using DFTB approach. Our investigations based on electronic properties showed that CNTs have better performance than CNBs in DNA nucleotide base sequencing.
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Affiliation(s)
| | - Nafiseh Memarian
- Faculty of Physics, Semnan University, P.O. Box: 35195-363, Semnan, Iran.
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2
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Liang Y, Ang WL, Lim RRX, Bonanni A. Exploring graphene oxide intrinsic electroactivity to elucidate the non-covalent interactions with DNA oligonucleotides. Chem Commun (Camb) 2022; 58:2662-2665. [PMID: 35107450 DOI: 10.1039/d1cc06657a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We show here how the electrochemical reduction signal of graphene oxide nanocolloids is inhibited upon the formation of non-covalent interactions with single stranded DNA oligonucleotides. The drop in the reduction current intensity is strongly influenced by the nucleobase sequence, and can therefore be directly correlated to the specific DNA homo-oligonucleotide.
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Affiliation(s)
- Yaquan Liang
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Wei Li Ang
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Rachel Rui Xia Lim
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Alessandra Bonanni
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
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3
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Giraud T, Bouguet-Bonnet S, Marchal P, Pickaert G, Averlant-Petit MC, Stefan L. Improving and fine-tuning the properties of peptide-based hydrogels via incorporation of peptide nucleic acids. NANOSCALE 2020; 12:19905-19917. [PMID: 32985645 DOI: 10.1039/d0nr03483e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Peptide self-assemblies have attracted intense research interest over the last few decades thanks to their implications in key biological processes (e.g., amyloid formation) and their use in biotechnological and (bio)material fields. In particular, peptide-based hydrogels have been highly considered as high potential supramolecular materials in the biomedical domain and open new horizons in terms of applications. To further understand their self-assembly mechanisms and to optimize their properties, several strategies have been proposed with the modification of the constituting amino acid chains via, per se, the introduction of d-amino acids, halogenated amino acids, pseudopeptide bonds, or other chemical moieties. In this context, we report herein on the incorporation of DNA-nucleobases into their peptide nucleic acid (PNA) forms to develop a new series of hybrid nucleopeptides. Thus, depending on the nature of the nucleobase (i.e., thymine, cytosine, adenine or guanine), the physicochemical and mechanical properties of the resulting hydrogels can be significantly improved and fine-tuned with, for instance, drastic enhancements of both the gel stiffness (up to 70-fold) and the gel resistance to external stress (up to 40-fold), and the generation of both thermo-reversible and uncommon red-edge excitation shift (REES) properties. To decipher the actual role of each PNA moiety in the self-assembly processes, the induced modifications from the molecular to the macroscopic scales are studied thanks to the multiscale approach based on a large panel of analytical techniques (i.e., rheology, NMR relaxometry, TEM, thioflavin T assays, FTIR, CD, fluorescence, NMR chemical shift index). Thus, such a strategy provides new opportunities to adapt and fit hydrogel properties to the intended ones and pushes back the limits of supramolecular materials.
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Affiliation(s)
- Tristan Giraud
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France.
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4
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Ma H, Xu Z, Fang H, Lei X. Unexpected sequence adsorption features of polynucleotide ssDNA on graphene oxide. Phys Chem Chem Phys 2020; 22:11740-11746. [PMID: 32409813 DOI: 10.1039/d0cp01066a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The sequence features of single-stranded DNA (ssDNA) adsorbed on a graphene oxide (GO) surface are important for applications of the DNA/GO functional structure in biosensors, biomedicine, and materials science. In this study, molecular dynamics (MD) simulations were used to examine the adsorption of polynucleotide ssDNAs (A12, C12, G12, and T12) and single nucleotides (A, C, G, and T) on the GO surface. For the latter case, the nucleotide-GO interaction energy followed the trend G > A > C > T, even though it was influenced by specific adsorption sites. In the case of polynucleotides, unexpectedly polythymidine (T12) had the strongest interaction with the GO surface. The angle distributions of the adsorbed nucleobases indicated that T12 was more likely to form a quasi-parallel structure with GO compared to A12, C12, or G12. This was attributed to the weakest π-stacking interactions of thymine. Weaker intra-molecular base-stacking interactions made it easier to break the structures of pyrimidine bases relative to those of purine bases. Weaker inter-molecular base-stacking interactions between T12 and the GO surface enabled T12 to adjust its structure easily to a more stable one by slipping on the surface. This result provides a new understanding of polynucleotide ssDNA adsorption on GO surfaces, which will help in the design of functional DNA/GO structure-based platforms.
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Affiliation(s)
- Huishu Ma
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai, 201800, China
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5
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Hong T, Wang T, Xu YQ. Direct Measurement of π Coupling at the Single-Molecule Level using a Carbon Nanotube Force Sensor. NANO LETTERS 2018; 18:7883-7888. [PMID: 30457874 DOI: 10.1021/acs.nanolett.8b03690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We report a carbon nanotube (CNT) force sensor that combines a suspended CNT transistor with dual-trap optical tweezers to explore the interactions between two individual molecules in the near-equilibrium regime with sub-piconewton resolution. The directly measured equilibrium force (1.2 ± 0.5 pN) is likely related to the binding force between a CNT and a single DNA base, where two aromatic rings spontaneously attract to each other due to the noncovalent forces between them. On the basis of our force measurements, the binding free energy per base is calculated (∼0.34 eV), which is in good agreement with theoretical simulations. Moreover, three-dimensional scanning photocurrent microscopy enables us to simultaneously monitor the morphology changes of the CNT, leading to a comprehensive reconstruction of the CNT-DNA binding dynamics. These experimental results shed light on the fundamental understanding of the mechanical coupling between CNTs and DNA molecules and, more importantly, provide a new platform for direct observation of intermolecular interfaces at the single-molecule level.
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6
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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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Chehelamirani M, da Silva MC, Salahub DR. Electronic properties of carbon nanotubes complexed with a DNA nucleotide. Phys Chem Chem Phys 2018; 19:7333-7342. [PMID: 28239719 DOI: 10.1039/c6cp08376e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronic properties of carbon nanotubes (CNTs) play an important role in their interactions with nano-structured materials. In this work, interactions of adenosine monophosphate (AMP), a DNA nucleotide, with metallic and semi-conducting CNTs are studied using the density functional tight binding (DFTB) method. The electronic structure of semi-conducting CNTs was found to be changed as they turned to metallic CNTs in a vacuum upon interaction with the nucleotide while metallic CNTs remain metallic. Specifically, the band gap of semi-conducting CNTs was decreased by 0.79 eV on average while nearly no change was found in the metallic tubes. However, our investigations showed that the presence of explicit water molecules prevents the metallicity change and only small changes in the CNT band gap occur. According to our charge analysis, the average negative charge accumulated on CNTs upon interaction with the AMP was determined to be 0.77 e in a vacuum while it was 0.03 e in solution. Therefore, it is essential to include explicit water molecules in simulating complexes formed by DNA nucleotides and CNTs which were ignored in several past studies performed using quantum mechanical approaches.
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Affiliation(s)
- Morteza Chehelamirani
- Department of Chemistry and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Maurício C da Silva
- Department of Chemistry and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Dennis R Salahub
- Department of Chemistry and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. and Institute for Quantum Science and Technology, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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8
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DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning. NANOMATERIALS 2016; 6:nano6110196. [PMID: 28335324 PMCID: PMC5245763 DOI: 10.3390/nano6110196] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/10/2016] [Accepted: 10/25/2016] [Indexed: 02/04/2023]
Abstract
Although there is a long history of the study of the interaction of DNA with carbon surfaces, limited information exists regarding the interaction of complex DNA-based nanostructures with the important material graphite, which is closely related to graphene. In view of the capacity of DNA to direct the assembly of proteins and optical and electronic nanoparticles, the potential for combining DNA-based materials with graphite, which is an ultra-flat, conductive carbon substrate, requires evaluation. A series of imaging studies utilizing Atomic Force Microscopy has been applied in order to provide a unified picture of this important interaction of structured DNA and graphite. For the test structure examined, we observe a rapid destabilization of the complex DNA origami structure, consistent with a strong interaction of single-stranded DNA with the carbon surface. This destabilizing interaction can be obscured by an intentional or unintentional primary intervening layer of single-stranded DNA. Because the interaction of origami with graphite is not completely dissociative, and because the frustrated, expanded structure is relatively stable over time in solution, it is demonstrated that organized structures of pairs of the model protein streptavidin can be produced on carbon surfaces using DNA origami as the directing material.
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9
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Basiuk VA, Andrade-Salas A. Noncovalent interactions of nucleic acid bases with fullerene C60 and short carbon nanotube models: a dispersion-corrected DFT study. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1246735] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Vladimir A. Basiuk
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, México, Mexico
| | - Arturo Andrade-Salas
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, México, Mexico
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10
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11
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Chehel Amirani M, Tang T. Electrostatics of DNA nucleotide-carbon nanotube hybrids evaluated from QM:MM simulations. NANOSCALE 2015; 7:19586-19595. [PMID: 26542447 DOI: 10.1039/c5nr03665h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Biomolecule-functionalized carbon nanotubes (CNTs) have been studied vastly in recent years due to their potential applications for instance in cancer detection, purification and separation of CNTs, and nanoelectronics. Studying the electrostatic potential generated by a biomolecule-CNT hybrid is important in predicting its interactions with the surrounding environment such as charged particles and surfaces. In this paper, we performed atomistic simulations using a QM:MM approach to evaluate the electrostatic potential and charge transfer for a hybrid structure formed by a DNA nucleotide and a CNT in solution. Four types of DNA nucleotides and two CNTs with chiralities of (4,4) and (7,0) were considered. The types of nucleotides and CNTs were both found to play important roles in the electrostatic potential and charge transfer of the hybrid. At the same distance from the CNT axis, the electrostatic potential for the nucleotide-(4,4) CNT hybrids was found to be stronger compared with that for the nucleotide-(7,0) CNT hybrids. Higher electric charge was also shown to be transferred from the DNA nucleotides to the (7,0) CNT compared with the (4,4) CNT. These results correlate with the previous finding that the nucleotides bound more tightly to the (7,0) CNT compared with the (4,4) CNT.
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Affiliation(s)
| | - Tian Tang
- Department of Mechanical Engineering, University of Alberta, Edmonton, AB, Canada.
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12
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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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Chehel Amirani M, Tang T. A QM:MM model for the interaction of DNA nucleotides with carbon nanotubes. Phys Chem Chem Phys 2015; 17:7564-75. [PMID: 25708519 DOI: 10.1039/c4cp05222f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Hybrid materials formed by DNA and carbon nanotubes (CNTs) have shown very interesting properties, but their simulation in solution using quantum mechanical approaches is still a challenge in the computational chemistry community. In this paper, we developed a QM:MM model to study the interactions between charged DNA nucleotides and carbon nanotubes in solution. All four types of DNA nucleotides were taken to interact with two CNTs of similar diameter but different chiralities: (4,4) and (7,0). The nucleotides and CNTs were treated at the QM level, while added water and neutralizing ions were modeled at the MM level. ONIOM simulations were performed at the (M06-2X/6-31G(d):Amber) level for the hybrids, as well as for individually solvated CNTs and nucleotides, which allowed us to evaluate the energy of binding. Our binding energy (BE) values range from 146.60 to 503.43 kJ mol(-1), indicating strong physisorption of nucleotides on CNTs. The relatively large BE, compared with past studies on nucleobase-CNT binding in a vacuum, could be due to the larger size of nucleotides compared with nucleobases, the charges on the nucleotides, and the inclusion of solution which causes the release of water molecules upon hybridization.
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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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15
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Zhou PP, Zhang RQ. Physisorption of benzene derivatives on graphene: critical roles of steric and stereoelectronic effects of the substituent. Phys Chem Chem Phys 2015; 17:12185-93. [DOI: 10.1039/c4cp05973e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The adsorption of benzene derivatives on the graphene surface is strongly dependent upon the substituent because of the critical roles of their steric and stereoelectronic effects.
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Affiliation(s)
- Pan-Pan Zhou
- Beijing Computational Science Research Center
- Beijing
- P. R. China
- Department of Chemistry
- Lanzhou University
| | - Rui-Qin Zhang
- Department of Physics and Materials Science
- City University of Hong Kong
- Hong Kong SAR
- P. R. China
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16
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Chehel Amirani M, Tang T. Binding of nucleobases with graphene and carbon nanotube: a review of computational studies. J Biomol Struct Dyn 2014; 33:1567-97. [DOI: 10.1080/07391102.2014.954315] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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17
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Interactions of the Watson–Crick nucleic acid base pairs with carbon nanotubes and graphene: DFT and MP2 study. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.07.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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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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19
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Singh P, Ménard-Moyon C, Battigelli A, Toma FM, Raya J, Kumar J, Nidamanuri N, Verma S, Bianco A. Double Functionalization of Carbon Nanotubes with Purine and Pyrimidine Derivatives. Chem Asian J 2013; 8:1472-81. [DOI: 10.1002/asia.201300116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 04/02/2013] [Indexed: 11/11/2022]
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20
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Boopathi S, Kolandaivel P. Molecular dynamics simulations and density functional theory studies of NALMA and NAGMA dipeptides. J Biomol Struct Dyn 2013; 31:158-73. [DOI: 10.1080/07391102.2012.698380] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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21
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Study of DNA base-Li doped SiC nanotubes in aqueous solutions: a computer simulation study. J Mol Model 2013; 19:1605-15. [DOI: 10.1007/s00894-012-1721-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 12/03/2012] [Indexed: 12/07/2022]
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22
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Gavrel G, Jousselme B, Filoramo A, Campidelli S. Supramolecular Chemistry of Carbon Nanotubes. MAKING AND EXPLOITING FULLERENES, GRAPHENE, AND CARBON NANOTUBES 2013; 348:95-126. [DOI: 10.1007/128_2013_450] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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23
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Neihsial S, Periyasamy G, Samanta PK, Pati SK. Understanding the Binding Mechanism of Various Chiral SWCNTs and ssDNA: A Computational Study. J Phys Chem B 2012. [DOI: 10.1021/jp305894c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Siamkhanthang Neihsial
- Theoretical
Sciences Unit and ‡New Chemistry Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur P.O., Bangalore
560064, India
| | - Ganga Periyasamy
- Theoretical
Sciences Unit and ‡New Chemistry Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur P.O., Bangalore
560064, India
| | - Pralok K. Samanta
- Theoretical
Sciences Unit and ‡New Chemistry Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur P.O., Bangalore
560064, India
| | - Swapan K. Pati
- Theoretical
Sciences Unit and ‡New Chemistry Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur P.O., Bangalore
560064, India
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24
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Wang C, Li S, Zhang R, Lin Z. Adsorption and properties of aromatic amino acids on single-walled carbon nanotubes. NANOSCALE 2012; 4:1146-1153. [PMID: 22095051 DOI: 10.1039/c1nr11073j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We investigated the adsorption of three aromatic amino acids-phenylalanine, tyrosine, and tryptophan-on the sidewalls of a number of representative single-walled carbon nanotubes (SWNTs) using density-functional tight-binding calculations, complemented by an empirical dispersion correction. The armchair (n, n) SWNTs (n = 3-12) and zigzag (n, 0) SWNTs (n = 4-12) were thoroughly examined. We found that the most stable amino acid/SWNT complexes for different SWNTs have similar local structures, and that the distance between the amino acid and SWNT is about 3 Å. Owing to the π-π and H-π stacking interactions, the benzene and indole rings are not exactly parallel to the SWNTs but instead lie at a small angle. We also investigated the diameter and chirality dependences of binding energies and found that SWNT (5, 0) has an especially large binding energy that can be used for SWNT identification or selection.
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Affiliation(s)
- Cuihong Wang
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, China
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25
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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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26
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Gholipour AR, Saydi H, Neiband MS, Neyband RS. Simultaneous interactions of pyridine with substituted benzene ring and H–F in X-ben⊥pyr···H–F complexes: a cooperative study. Struct Chem 2011. [DOI: 10.1007/s11224-011-9882-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Lu L, Chen W. Supramolecular self-assembly of biopolymers with carbon nanotubes for biomimetic and bio-inspired sensing and actuation. NANOSCALE 2011; 3:2412-2420. [PMID: 21523297 DOI: 10.1039/c1nr10113g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Biopolymers are important natural multifunctional macromolecules for biomimetic and bio-inspired advanced functional material design. They are not only simple dispersants for carbon nanotube stabilization as they have been found to have specific interactions with carbon nanotubes. Their molecular activity, orientation and crystallization are influenced by the CNTs, which endow their composites with a variety of novel sensing and actuation performances. This review focuses on the progress in supramolecular self-assembly of biopolymers with carbon nanotubes, and their advances in sensing and actuation. To promote the development of advanced biopolymer/CNT functional materials, new electromechanical characteristics of biopolymer/CNT composites are discussed in detail based on the relationship between the microscopic biopolymer structures and the macroscopic composite properties.
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Affiliation(s)
- Luhua Lu
- Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences, Suzhou, 215125, P. R. China
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28
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Singh P, Toma FM, Kumar J, Venkatesh V, Raya J, Prato M, Verma S, Bianco A. Carbon Nanotube-Nucleobase Hybrids: Nanorings from Uracil-Modified Single-Walled Carbon Nanotubes. Chemistry 2011; 17:6772-80. [DOI: 10.1002/chem.201100312] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Indexed: 11/11/2022]
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29
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Ai H, Zhang C, He W, Chan K, Li Q. Solvation counteracts coulombic repulsion in the binding of two cations to a model hexapeptide. J Mol Model 2011; 18:53-64. [DOI: 10.1007/s00894-011-1026-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 02/14/2011] [Indexed: 10/18/2022]
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Sun W, Bu Y, Wang Y. On the Binding Strength Sequence for Nucleic Acid Bases and C(60) with Density Functional and Dispersion-corrected Density Functional Theories: Whether C(60) could protect nucleic acid bases from radiation-induced damage? THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2011; 115:3220-3228. [PMID: 21625361 PMCID: PMC3101642 DOI: 10.1021/jp108812z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The major objective of this paper is to address a controversial binding sequence between nucleic acid bases (NABs) and C(60) by investigating adsorptions of NABs and their cations on C(60) fullerene with a variety of density functional theories including two novel hybrid meta-GGA functionals, M05-2x and M06-2x, as well as a dispersion-corrected density functional, PBE-D. The M05-2x/6-311++G** provides the same binding sequence as previously reported, guanine(G) > cytosine(C) > adenine (A) > thymine (T); however, M06-2x switches the binding strengths of A and C, and PBE-D eventually results in the following sequence, G>A>T>C, which is the same as the widely accepted hierarchy for the stacking of NABs on other carbon nanomaterials such as single-walled carbon nanotube and graphite. The results indicate that the questionable relative binding strength is due to insufficient electron correlation treatment with the M05-2x or even the M06-2x method. The binding energy of G@C(60) obtained with the M06-2x/6-311++G(d,p) and the PBE-D/cc-pVDZ is -7.10 and -8.07 kcal/mol, respectively, and the latter is only slightly weaker than that predicted by the MP2/6-31G(d,p) (-8.10kca/mol). Thus, the PDE-D performs better than the M06-2x for the observed NAB@C(60) π-stacked complexes. To discuss whether C(60) could prevent NABs from radiation-induced damage, ionization potentials of NABs and C(60), and frontier molecular orbitals of the complexes NABs@C(60) and (NABs@C(60))(+) are also extensively investigated. These results revealed that when an electron escapes from the complexes, a hole was preferentially created in C(60) for T and C complexes, while for G and A the hole delocalizes over the entire complex, rather than a localization on the C(60) moiety. The interesting finding might open a new strategy for protecting DNA from radiation-induced damage and offer a new idea for designing C(60)-based antiradiation drugs.
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Affiliation(s)
| | - Yuxiang Bu
- The corresponding authors: Yuxiang Bu,
; Yixuan Wang,
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31
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Rajarajeswari M, Iyakutti K, Kawazoe Y. Adsorption mechanism of single guanine and thymine on single-walled carbon nanotubes. J Mol Model 2011; 17:2773-80. [DOI: 10.1007/s00894-010-0946-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 12/27/2010] [Indexed: 11/29/2022]
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32
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Husale BS, Sahoo S, Radenovic A, Traversi F, Annibale P, Kis A. ssDNA binding reveals the atomic structure of graphene. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:18078-82. [PMID: 20977263 DOI: 10.1021/la102518t] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We used AFM to investigate the interaction of polyelectrolytes such as ssDNA and dsDNA molecules with graphene as a substrate. Graphene is an appropriate substrate due to its planarity, relatively large surfaces that are detectable via an optical microscope, and straightforward identification of the number of layers. We observe that in the absence of the screening ions deposited ssDNA will bind only to the graphene and not to the SiO(2) substrate, confirming that the binding energy is mainly due to the π-π stacking interaction. Furthermore, deposited ssDNA will map the graphene underlying structure. We also quantify the π-π stacking interaction by correlating the amount of deposited DNA with the graphene layer thickness. Our findings agree with reported electrostatic force microscopy (EFM) measurements. Finally, we inspected the suitability of using a graphene as a substrate for DNA origami-based nanostructures.
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Affiliation(s)
- By Sudhir Husale
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
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33
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Kumar RM, Elango M, Subramanian V. Carbohydrate-Aromatic Interactions: The Role of Curvature on XH···π Interactions. J Phys Chem A 2010; 114:4313-24. [DOI: 10.1021/jp907547f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. Mahesh Kumar
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - M. Elango
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
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34
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Morgado CA, Jurečka P, Svozil D, Hobza P, Šponer J. Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions. Phys Chem Chem Phys 2010; 12:3522-34. [DOI: 10.1039/b924461a] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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35
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Assessment of approximate quantum chemical methods for calculating the interaction energy of nucleic acid bases with graphene and carbon nanotubes. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2009.11.068] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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36
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Wang Y, Ai H. Theoretical insights into the interaction mechanism between proteins and SWCNTs: adsorptions of tripeptides GXG on SWCNTs. J Phys Chem B 2009; 113:9620-7. [PMID: 19548664 DOI: 10.1021/jp903315n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adsorptions of nine tripeptides GXG, ranging from negatively (D) and positively (K) charged, to hydrophilic (N and S), and to hydrophobic (G, V, F, W, and Y) residues, on the two cluster models (C(54)H(18) and C(54)) of (10,0) single-walled carbon nanotubes (SWCNTs) are systemically investigated with the MPWB1K and MP2 methods. The solvent effects are taken into account with the implicit CPCM model. The objective is to provide novel insights into the interaction mechanism between proteins and SWCNTs. Results reveal that the adsorption strength of two charged tripeptides is greatly affected by the solvent effect and the hydrogen saturability of the SWCNT models. In the gas phase, on the surface of C(54)H(18), GKG has the strongest adsorption (adsorption energy (AE): -29.3 kcal/mol at the MP2 level), whereas the adsorption of the negatively charged GDG is the strongest on C(54) (AE: -30.4 kcal/mol with MP2). However, because of strong solvation, the adsorptions of the charged residues (D and K) on both C(54)H(18) and C(54) surfaces in aqueous solution are either rather weak or even unbound. The two neutral hydrophilic residues (N and S) exhibit adsorptions on C(54)H(18) in the gas phase (AE: -3.3 and -4.2 kcal/mol), yet are unable to adsorb on SWCNTs in aqueous solution (AE: +0.3 kcal/mol at MP2+CPCM). The five hydrophobic residues present relatively strong adsorption on SWCNTs, especially for the three aromatic residues (GFG, GYG, and GWG), regardless of the CNT model and whether they are in the gas phase or solution. These results indicate that in general the aromatic groups of proteins would play a very important role on functionalizing CNTs, which basically supports the relevant experimental observations. In addition, the electron correlation is essential for adsorptions of GXG on pristine SWCNTs, and the three aromatic residues have the highest electron correlation effects. The present investigation provides strong evidence that for the functionalization of CNTs via proteins it is most likely that hydrophobic interaction and van der Waals are the dominant driving forces.
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Affiliation(s)
- Yixuan Wang
- Department of Natural Science, Albany State University, Albany, GA 31705, USA.
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37
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Singh P, Kumar J, Toma FM, Raya J, Prato M, Fabre B, Verma S, Bianco A. Synthesis and Characterization of Nucleobase−Carbon Nanotube Hybrids. J Am Chem Soc 2009; 131:13555-62. [DOI: 10.1021/ja905041b] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Prabhpreet Singh
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Laboratoire d’Immunologie et Chimie Thérapeutiques, 67000 Strasbourg, France, Department of Chemistry, Indian Institute of Technology, Kanpur-208016 UP, India, Dipartimento di Scienze Farmaceutiche, Università di Trieste, 34127 Trieste, Italy, SISSA, Via Beirut 2−4, 34151 Trieste, Italy, Laboratoire de RMN et de biophysique des membranes, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, 67000 Strasbourg, France, Matière Condensée et
| | - Jitendra Kumar
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Laboratoire d’Immunologie et Chimie Thérapeutiques, 67000 Strasbourg, France, Department of Chemistry, Indian Institute of Technology, Kanpur-208016 UP, India, Dipartimento di Scienze Farmaceutiche, Università di Trieste, 34127 Trieste, Italy, SISSA, Via Beirut 2−4, 34151 Trieste, Italy, Laboratoire de RMN et de biophysique des membranes, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, 67000 Strasbourg, France, Matière Condensée et
| | - Francesca Maria Toma
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Laboratoire d’Immunologie et Chimie Thérapeutiques, 67000 Strasbourg, France, Department of Chemistry, Indian Institute of Technology, Kanpur-208016 UP, India, Dipartimento di Scienze Farmaceutiche, Università di Trieste, 34127 Trieste, Italy, SISSA, Via Beirut 2−4, 34151 Trieste, Italy, Laboratoire de RMN et de biophysique des membranes, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, 67000 Strasbourg, France, Matière Condensée et
| | - Jesus Raya
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Laboratoire d’Immunologie et Chimie Thérapeutiques, 67000 Strasbourg, France, Department of Chemistry, Indian Institute of Technology, Kanpur-208016 UP, India, Dipartimento di Scienze Farmaceutiche, Università di Trieste, 34127 Trieste, Italy, SISSA, Via Beirut 2−4, 34151 Trieste, Italy, Laboratoire de RMN et de biophysique des membranes, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, 67000 Strasbourg, France, Matière Condensée et
| | - Maurizio Prato
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Laboratoire d’Immunologie et Chimie Thérapeutiques, 67000 Strasbourg, France, Department of Chemistry, Indian Institute of Technology, Kanpur-208016 UP, India, Dipartimento di Scienze Farmaceutiche, Università di Trieste, 34127 Trieste, Italy, SISSA, Via Beirut 2−4, 34151 Trieste, Italy, Laboratoire de RMN et de biophysique des membranes, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, 67000 Strasbourg, France, Matière Condensée et
| | - Bruno Fabre
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Laboratoire d’Immunologie et Chimie Thérapeutiques, 67000 Strasbourg, France, Department of Chemistry, Indian Institute of Technology, Kanpur-208016 UP, India, Dipartimento di Scienze Farmaceutiche, Università di Trieste, 34127 Trieste, Italy, SISSA, Via Beirut 2−4, 34151 Trieste, Italy, Laboratoire de RMN et de biophysique des membranes, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, 67000 Strasbourg, France, Matière Condensée et
| | - Sandeep Verma
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Laboratoire d’Immunologie et Chimie Thérapeutiques, 67000 Strasbourg, France, Department of Chemistry, Indian Institute of Technology, Kanpur-208016 UP, India, Dipartimento di Scienze Farmaceutiche, Università di Trieste, 34127 Trieste, Italy, SISSA, Via Beirut 2−4, 34151 Trieste, Italy, Laboratoire de RMN et de biophysique des membranes, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, 67000 Strasbourg, France, Matière Condensée et
| | - Alberto Bianco
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Laboratoire d’Immunologie et Chimie Thérapeutiques, 67000 Strasbourg, France, Department of Chemistry, Indian Institute of Technology, Kanpur-208016 UP, India, Dipartimento di Scienze Farmaceutiche, Università di Trieste, 34127 Trieste, Italy, SISSA, Via Beirut 2−4, 34151 Trieste, Italy, Laboratoire de RMN et de biophysique des membranes, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, 67000 Strasbourg, France, Matière Condensée et
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38
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Liu H, Bu Y, Mi Y, Wang Y. Interaction Site Preference between Carbon Nanotube and Nifedipine: A Combined Density Functional Theory and Classical Molecular Dynamics Study. THEOCHEM 2009; 901:163-168. [PMID: 19680462 PMCID: PMC2725364 DOI: 10.1016/j.theochem.2009.01.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A novel hybrid density functional theory, MPWB1K, was firstly employed to investigate static adsorptions of a nifedipine on a (10,10) type of single-walled carbon nanotube (SWCNT), which was modeled by C(200)H(40) and C(280) respectively. For both SWCNT models the internal adsorption is more stable than the external adsorption in a range of 5.3-7.8 kcal/mol, which indicates that a nifedipine has a preference to internally adsorb on the (10,10) SWCNT. Molecular dynamic simulations were then used to predict the dynamic behaviors of a nifedipine and the (10, 10) SWCNT system in both gas phase and aqueous solution. The classical MD simulations show that for both cases a nifedipine could spontaneously encapsulate into the SWCNT and migrate in a surprising oscillation behavior inside the SWCNT, however, both phenomena are significantly delayed in the presence of water molecules. The present study suggests that the nanotube network may be used as an efficient tool for transporting this kind of calcium channel antagonists.
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Affiliation(s)
- Huichun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Yunjie Mi
- Department of Natural Science, Albany State University, Albany, GA 31705, USA
| | - Yixuan Wang
- Department of Natural Science, Albany State University, Albany, GA 31705, USA
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39
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Stepanian SG, Karachevtsev MV, Glamazda AY, Karachevtsev VA, Adamowicz L. Raman Spectroscopy Study and First-Principles Calculations of the Interaction between Nucleic Acid Bases and Carbon Nanotubes. J Phys Chem A 2009; 113:3621-9. [DOI: 10.1021/jp810205a] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stepan G. Stepanian
- B. Verkin Institute for Low Temperature Physics and Engineering, NAS of Ukraine, 47, Lenin Avenue, 61103 Kharkov, Ukraine, and Department of Chemistry, University of Arizona, Tucson, Arizona 85721
| | - Maksym V. Karachevtsev
- B. Verkin Institute for Low Temperature Physics and Engineering, NAS of Ukraine, 47, Lenin Avenue, 61103 Kharkov, Ukraine, and Department of Chemistry, University of Arizona, Tucson, Arizona 85721
| | - Alexander Yu. Glamazda
- B. Verkin Institute for Low Temperature Physics and Engineering, NAS of Ukraine, 47, Lenin Avenue, 61103 Kharkov, Ukraine, and Department of Chemistry, University of Arizona, Tucson, Arizona 85721
| | - Victor A. Karachevtsev
- B. Verkin Institute for Low Temperature Physics and Engineering, NAS of Ukraine, 47, Lenin Avenue, 61103 Kharkov, Ukraine, and Department of Chemistry, University of Arizona, Tucson, Arizona 85721
| | - L. Adamowicz
- B. Verkin Institute for Low Temperature Physics and Engineering, NAS of Ukraine, 47, Lenin Avenue, 61103 Kharkov, Ukraine, and Department of Chemistry, University of Arizona, Tucson, Arizona 85721
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40
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Lipparini F, Scalmani G, Mennucci B. Non covalent interactions in RNA and DNA base pairs: a quantum-mechanical study of the coupling between solvent and electronic density. Phys Chem Chem Phys 2009; 11:11617-23. [DOI: 10.1039/b915898g] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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