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Lin S, Zhang X, Tian A, Wang P, Li Y, Shi C, Ma C, Fan Y. Boron nitride nanoplate-based strand exchange amplification with enhanced sensitivity and rapidity for quantitative detection of Staphylococcus aureus in food samples. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:892-898. [PMID: 38247331 DOI: 10.1039/d3ay02076b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Staphylococcus aureus is one of the most common foodborne pathogens that can cause serious food poisoning and infectious diseases in humans. Standard identification approaches include nucleic acid amplification, but current amplification tools suffer from low amplification efficiency, resulting in the risk of low sensitivity and long detection time. Herein, boron nitride nanoplates (BNNPs) were chosen as an additive for enhancing the sensitivity and rapidity of strand exchange amplification (SEA), thereby successfully expanding the application of nucleic acid detection for detecting Staphylococcus aureus in food samples. As a result, SEA based on boron nitride nanoplates (BNNP-SEA) was employed for sensitive and rapid detection of foodborne pathogen Staphylococcus aureus. Compared with classical SEA, the BNNP-based SEA assay was more than 10-fold sensitive, and the detection time was reduced by 15 minutes. The optimized BNNP-based SEA shows a wide linear range from 40 pg to 50 ng in a diluted solution of the target DNA with a low detection limit of 40 pg. Moreover, the BNNP-based SEA achieves the quantitative detection of Staphylococcus aureus in different food samples (pork, beef, mutton, duck, milk and shrimp). In contrast to the classical SEA, the BNNP-based SEA method enabled sensitive and rapid detection of Staphylococcus aureus in the above food samples at concentrations as low as 5 × 103 CFU mL-1. The BNNP-based SEA assay is specific, sensitive and reliable, offering a valuable diagnostic technology for routine analysis in food safety research.
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Affiliation(s)
- Shuo Lin
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Xin Zhang
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Anning Tian
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Pengyu Wang
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Yong Li
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Chao Shi
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, Department of the Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, China
| | - Cuiping Ma
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Yaofang Fan
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
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Kadhim MM, Alomar S, Hachim SK, Abdullaha SA, Zedan Taban T, Alnasoud N. BeO nanotube as a promising material for anticancer drugs delivery system. Comput Methods Biomech Biomed Engin 2023; 26:1889-1897. [PMID: 36580036 DOI: 10.1080/10255842.2022.2152679] [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: 08/18/2022] [Accepted: 11/22/2022] [Indexed: 12/30/2022]
Abstract
In this research, the application of BeO nanotube (BeONT) as a nanocarrier for Fluorouracil (5-FU) anticancer drug has been studied by density functional theory (DFT) approach. The method ωB97XD with 6-31 G** basis set were employed. A precise surface study, shows that there are two directions for 5-FU adsorption that did not deliver any of the imaginary frequency vibrational spectra, identifying that all relaxation structures are at the lowest energy level. Based on our calculations, the energy of adsorption for 5FU@BeONT structures are range -120 to -168 kJ/mol, in the gas phase and -395 to 4-00 kJ/mol in the aqueous phase. The highest and the lowest values of adsorption energy are both in strong physical adsorption. Due to receiving an electronic charge from 5-FU, BeONT exhibited a p-type semiconducting feature for all positions. In addition, based on natural bond orbital (NBO) analysis, the direction of charge transfer was from fluorine's σ orbitals of the drug to n* orbitals (O and Be atoms) of BeONT with a considerable amount of transferred energy. BeONT can be employed as a potential strong carrier for 5-FU drugs for practical purposes based on our findings.
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Affiliation(s)
- Mustafa M Kadhim
- Medical Laboratory Techniques Department, Al-Farahidi University, Baghdad, Iraq
| | | | - Safa K Hachim
- College of Technical Engineering, The Islamic University, Najaf, Iraq
- Medical Laboratory Techniques Department, Al-Turath University College, Baghdad, Iraq
| | | | - Taleeb Zedan Taban
- Laser and Optoelectronics Engineering Department, Kut University College, Kut, Wasit, Iraq
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Villanueva-Mejia F, Guevara-Martínez SJ, Arroyo-Albiter M, Alvarado-Flores JJ, Zamudio-Ojeda A. DFT Study of Adsorption Behavior of Nitro Species on Carbon-Doped Boron Nitride Nanoribbons for Toxic Gas Sensing. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:1410. [PMID: 37110995 PMCID: PMC10143892 DOI: 10.3390/nano13081410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 06/19/2023]
Abstract
The modifications of the electronic properties on carbon-doped boron nitride nanoribbons (BNNRs) as a response to the adsorption of different nitro species were investigated in the framework of the density functional theory within the generalized gradient approximation. Calculations were performed using the SIESTA code. We found that the main response involved tuning the original magnetic behavior to a non-magnetic system when the molecule was chemisorbed on the carbon-doped BNNR. It was also revealed that some species could be dissociated through the adsorption process. Furthermore, the nitro species preferred to interact over nanosurfaces where dopants substituted the B sublattice of the carbon-doped BNNRs. Most importantly, the switch on the magnetic behavior offers the opportunity to apply these systems to fit novel technological applications.
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Affiliation(s)
- Francisco Villanueva-Mejia
- Instituto Tecnológico de Pabellón de Arteaga, Carretera a la estación de Rincón de Romos, km 1, Pabellón de Arteaga 20670, Aguascalientes, Mexico
| | - Santiago José Guevara-Martínez
- Department of Pharmacology, School of Exact Sciences and Engineering, University of Guadalajara, Boulevard Gral. Marcelino García Barragán 1421, Olímpica, Guadalajara 44840, Jalisco, Mexico;
| | - Manuel Arroyo-Albiter
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Michoacán, Mexico;
| | - José Juan Alvarado-Flores
- Facultad de Ingeniería en Tecnología de la Madera, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58040, Michoacán, Mexico;
| | - Adalberto Zamudio-Ojeda
- Department of Physics, School of Exact Sciences and Engineering, University of Guadalajara, Boulevard Gral. Marcelino García Barragán 1421, Olímpica, Guadalajara 44840, Jalisco, Mexico;
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Palomino-Asencio L, Chigo-Anota E, García-Hernández E. Insights on α-Glucose Biosensors/Carriers Based on Boron-Nitride Nanomaterials from an Atomistic and Electronic Point of View. Chemphyschem 2022; 23:e202200310. [PMID: 35945140 DOI: 10.1002/cphc.202200310] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/08/2022] [Indexed: 01/04/2023]
Abstract
The interaction of α-glucose with a BN-nanosheet, BN-nanotube, and BN-fullerene, was analyzed from an atomistic and electronic point of view, to evaluate such nanostructures as possible carriers and/or biosensors of the α-glucose molecule. Adsorption energies are in the range of physisorption (-0.79 eV to -0.91 eV) for the BN-nanosheet and -nanotube, and chemisorption (-2.24 eV to -2.35 eV), for the BN-fullerene. All systems, exhibit semiconductor-like behavior and great stability according to |LUMO-HOMO| energy gap [GapLH ] and chemical potential values, respectively. For the BN-nanosheet and -nanotube, the stabilization of the complexes is through hydrogen bonds, while for BN-fullerene is through a covalent bond and charge transfer. Furthermore, the BN-fullerene is able to dissociate the α-glucose molecule, which could help to decomposer such a compound, and be used for biological applications. The data taking into consideration solvent effects have no significant impact with respect to gas phase, except in the dipole moment (Md ) where we noticed an increase up to ∼45 %. Our results suggest that BN-nanosheet and -nanotube, may act as biosensors, while BN-fullerene, may serve as a carrier or degrader of the α-glucose molecule.
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Affiliation(s)
- Luz Palomino-Asencio
- Facultad de Ingeniería Química, Benemérita Universidad Autónoma de Puebla, 72570, Puebla, México
| | - Ernesto Chigo-Anota
- Facultad de Ingeniería Química, Benemérita Universidad Autónoma de Puebla, 72570, Puebla, México
| | - Erwin García-Hernández
- División de Mecatrónica, Subdirección de Posgrado e Investigación, Tecnológico Nacional de México Campus Zacapoaxtla, 73680, Zacapoaxtla, Puebla, México
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Paloncýová M, Pykal M, Kührová P, Banáš P, Šponer J, Otyepka M. Computer Aided Development of Nucleic Acid Applications in Nanotechnologies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204408. [PMID: 36216589 DOI: 10.1002/smll.202204408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.
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Affiliation(s)
- Markéta Paloncýová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Martin Pykal
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Petra Kührová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Pavel Banáš
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Jiří Šponer
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Michal Otyepka
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba, 708 00, Czech Republic
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6
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DNA nucleobase sequencing by aluminum nitride nanosheets in gas or water medium. J CLUST SCI 2022. [DOI: 10.1007/s10876-021-02117-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Guo K, Song Z, Wang G, Tang C. Detecting Redox Potentials Using Porous Boron Nitride/ATP-DNA Aptamer/Methylene Blue Biosensor to Monitor Microbial Activities. MICROMACHINES 2022; 13:mi13010083. [PMID: 35056248 PMCID: PMC8777636 DOI: 10.3390/mi13010083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 02/05/2023]
Abstract
Microbial activity has gained attention because of its impact on the environment and the quality of people’s lives. Most of today’s methods, which include genome sequencing and electrochemistry, are costly and difficult to manage. Our group proposed a method using the redox potential change to detect microbial activity, which is rooted in the concept that metabolic activity can change the redox potential of a microbial community. The redox potential change was captured by a biosensor consisting of porous boron nitride, ATP-DNA aptamer, and methylene blue as the fluorophore. This assembly can switch on or off when there is a redox potential change, and this change leads to a fluorescence change that can be examined using a multipurpose microplate reader. The results show that this biosensor can detect microbial community changes when its composition is changed or toxic metals are ingested.
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Affiliation(s)
- Kai Guo
- Correspondence: (K.G.); (C.T.)
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8
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Bhai S, Ganguly B. Exploiting the optical sensing of fluorophore-tagged DNA nucleobases on hexagonal BN and Al-doped BN sheets: a computational study. Phys Chem Chem Phys 2021; 24:829-841. [PMID: 34928284 DOI: 10.1039/d1cp04009j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hexagonal boron nitride (h-BN) sheets possess high fluorescence quenching ability and high affinity towards DNA/RNA, and they can be used as a sensing platform for rapid detection. We report the absorption and emission properties of DNA nucleobases such as adenine (A), cytosine (C), guanine (G), and thymine (T) tagged with benzoxazole on h-BN and aluminium-doped h-BN (Al_hBN) sheets. The binding affinity of studied nucleobases on h-BN sheets at the M062X/6-31G* level of theory showed the following adsorption trend: G ≥ T ≥ A > C, which is in good agreement with the previous results. The calculated stability trend of nucleobases on the Al_hBN sheet follows as C > G > A > T at the same level of theory. The physically adsorbed behavior of nucleobases to h-BN sheets was confirmed by the non-covalent interactions (NCIs) and the total density of states (TDOS) plots. The NCI results indicated that van der Waals interactions contribute significantly to the adsorption of nucleobases on h-BN sheets. Atoms in molecules (AIM) calculations revealed the electrostatic interactions between nucleobases and the Al_hBN sheet. The quenching phenomenon of nucleobase-tagged fluorophores on h-BN and Al_hBN sheets was investigated by TD-DFT calculations using the same level of theory. The thymine-tagged fluorophore upon adsorption to the pristine h-BN sheet was found to be blue-shifted (∼43 nm); however, the guanine-tagged fluorophore with Al_hBN showed a remarkable difference from other nucleobase-tagged fluorophores in the absorption and emission spectrum. Guanine-tagged fluorophores showed a smaller blue shift (∼7 nm) in the absorption spectrum; however, it showed a larger red shift (∼55 nm) than the other nucleobase-tagged fluorophores on Al_hBN sheets and can be useful in recognizing a sequence-specific phenomenon as a fluorescent biosensor of DNA and RNA to ascertain the presence of such nucleobases.
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Affiliation(s)
- Surjit Bhai
- Computational and Simulation Unit (Analytical and Environment Science Division and Centralized Instrument Facility) CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364002, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.,CSIR-CSMCRI, Bhavnagar-364002, Gujarat, India
| | - Bishwajit Ganguly
- Computational and Simulation Unit (Analytical and Environment Science Division and Centralized Instrument Facility) CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364002, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.,CSIR-CSMCRI, Bhavnagar-364002, Gujarat, India
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Miah MH, Hossain MR, Islam MS, Ferdous T, Ahmed F. A theoretical study of allopurinol drug sensing by carbon and boron nitride nanostructures: DFT, QTAIM, RDG, NBO and PCM insights. RSC Adv 2021; 11:38457-38472. [PMID: 35493251 PMCID: PMC9044057 DOI: 10.1039/d1ra06948a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/15/2021] [Indexed: 12/24/2022] Open
Abstract
The application of low-dimensional nanomaterials in clinical practice as efficient sensors has been increasing day by day due to progress in the field of nanoscience. In this research work, we have conducted a theoretical investigation to nominate a potential electrochemical sensor for the allopurinol (APN) drug molecule via studying the fundamental interactions of the drug molecule with two nanocages (carbon nanocage/CNC - C24 and boron nitride nanocage/BNNC - B12N12) and two nanosheets (graphene - C54H18 and boron nitride - B27N27H18) by means of the DFT B3LYP/6-31G(d,p) level of theory in both gas and water phases. The adsorption energies of APN-BNNC conjugated structures are in the range of -20.90 kcal mol-1 to -22.33 kcal mol-1, which indicates that weak chemisorption has occurred. This type of interaction happened due to charge transfer from the APN molecule to BNNC, which was validated and characterized based on the quantum theory of atoms in molecules, natural bond analysis, and reduced density gradient analysis. The highest decreases in energy gap (36.22% in gas and 26.79% in water) and maximum dipole moment (10.48 Debye in gas and 13.88 Debye in water) were perceived for the APN-BNNC conjugated structure, which was also verified via frontier molecular orbital (FMO) and MEP analysis. Also, the highest sensitivity (BNNC > BNNS > CNC > GNS) and favorable short recovery time (in the millisecond range) of BNNC can make it an efficient detector for the APN drug molecule.
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Affiliation(s)
- Md Helal Miah
- Department of Physics, Bangabandhu Sheikh Mujibur Rahman Science and Technology University Gopalganj-8100 Bangladesh
| | - Md Rakib Hossain
- Department of Physics, Bangabandhu Sheikh Mujibur Rahman Science and Technology University Gopalganj-8100 Bangladesh
| | - Md Saiful Islam
- Department of Physics, Bangabandhu Sheikh Mujibur Rahman Science and Technology University Gopalganj-8100 Bangladesh
| | - Tahmina Ferdous
- Department of Physics, Jahangirnagar University Savar Dhaka-1342 Bangladesh
| | - Farid Ahmed
- Department of Physics, Jahangirnagar University Savar Dhaka-1342 Bangladesh
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Adsorption behavior of uracil on external surface of MgO nanotubes: A new class of hybrid nano-bio materials. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Maleki PA, Nemati‐Kande E, Saray AA. Using Quantum Density Functional Theory Methods to Study the Adsorption of Fluorouracil Drug on Pristine and Al, Ga, P and As Doped Boron Nitride Nanosheets. ChemistrySelect 2021. [DOI: 10.1002/slct.202101333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Ebrahim Nemati‐Kande
- Department of Physical Chemistry Faculty of Chemistry Urmia University Urmia Iran
| | - Akbar Abdi Saray
- Department of Physics Basic Science Faculty Urmia University Urmia Iran
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Verma A, Zhang W, van Duin ACT. ReaxFF reactive molecular dynamics simulations to study the interfacial dynamics between defective h-BN nanosheets and water nanodroplets. Phys Chem Chem Phys 2021; 23:10822-10834. [PMID: 33908500 DOI: 10.1039/d1cp00546d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this work, the authors have developed a reactive force field (ReaxFF) to investigate the effect of water molecules on the interfacial interactions with vacancy defective hexagonal boron nitride (h-BN) nanosheets by introducing parameters suitable for the B/N/O/H chemistry. Initially, molecular dynamics simulations were performed to validate the structural stability and hydrophobic nature of h-BN nanosheets. The water molecule dissociation mechanism in the vicinity of vacancy defective h-BN nanosheets was investigated, and it was shown that the terminal nitrogen and boron atoms bond with a hydrogen atom and hydroxyl group, respectively. Furthermore, it is predicted that the water molecules arrange themselves in layers when compressed in between two h-BN nanosheets, and the h-BN nanosheet fracture nucleates from the vacancy defect site. Simulations at elevated temperatures were carried out to explore the water molecule trajectory near the functionalized h-BN pores, and it was observed that the intermolecular hydrogen bonds lead to agglomeration of water molecules near these pores when the temperature was lowered to room temperature. The study was extended to observe the effect of pore sizes and temperatures on the contact angle made by a water nanodroplet on h-BN nanosheets, and it was concluded that the contact angle would be less at higher temperatures and larger pore sizes. This study provides important information for the use of h-BN nanosheets in nanodevices for water desalination and underwater applications, as these h-BN nanosheets possess the desired adsorption capability and structural stability.
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Affiliation(s)
- Akarsh Verma
- Department of Mechanical Engineering, The Pennsylvania State University, University Park, PA-16802, USA. and Department of Mechanical and Industrial Engineering, Indian Institute of Technology, Roorkee-247667, India and Department of Mechanical Engineering, University of Petroleum and Energy Studies, Dehradun-248007, India
| | - Weiwei Zhang
- Department of Mechanical Engineering, The Pennsylvania State University, University Park, PA-16802, USA.
| | - Adri C T van Duin
- Department of Mechanical Engineering, The Pennsylvania State University, University Park, PA-16802, USA.
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Understanding structural and molecular properties of complexes of nucleobases and Au13 golden nanocluster by DFT calculations and DFT-MD simulation. Sci Rep 2021; 11:435. [PMID: 33432001 PMCID: PMC7801688 DOI: 10.1038/s41598-020-80161-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/10/2020] [Indexed: 01/29/2023] Open
Abstract
The characterization of the complexes of biomolecules and nanostructures is highly interesting and benefits the rational development and design of nano-materials and nano-devices in nano-biotechnology. In this work, we have used dispersion corrected density functional theory (DFT-D) as well as DFT based molecular dynamics simulations to provide an atomistic understanding of interaction properties of DNA nucleobases and Au13 nanocluster. Various active sites of interacting molecules considering their relative orientation and distance are explored. Our goal is to stimulate the binding characteristics between two entities and evaluate this through the interaction energy, the charge transfer, the electronic structure, and the specific role of the molecular properties of the nucleobase-Au13 system. The primary outcomes of this comprehensive research illuminated that nucleic bases have potent affinity for binding to the Au cluster being chemisorption type and following the trend: Adenine > Cytosine > Guanine > Thymine. The AIM analysis indicated that the binding nature of the interacting species was predominantly partial covalent and high polar. We discuss the bearing of our findings in view of gene-nanocarrier, biosensing applications as well as nanodevices for sequencing of DNA.
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Muñoz ADO, Escobedo-Morales A, Skakerzadeh E, Anota EC. Effect of homonuclear boron bonds in the adsorption of DNA nucleobases on boron nitride nanosheets. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114951] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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15
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Rahman H, Hossain MR, Ferdous T. The recent advancement of low-dimensional nanostructured materials for drug delivery and drug sensing application: A brief review. J Mol Liq 2020; 320:114427. [PMID: 33012931 PMCID: PMC7525470 DOI: 10.1016/j.molliq.2020.114427] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 01/07/2023]
Abstract
In this review article, we have presented a detailed analysis of the recent advancement of quantum mechanical calculations in the applications of the low-dimensional nanomaterials (LDNs) into biomedical fields like biosensors and drug delivery systems development. Biosensors play an essential role for many communities, e.g. law enforcing agencies to sense illicit drugs, medical communities to remove overdosed medications from the human and animal body etc. Besides, drug delivery systems are theoretically being proposed for many years and experimentally found to deliver the drug to the targeted sites by reducing the harmful side effects significantly. In current COVID-19 pandemic, biosensors can play significant roles, e.g. to remove experimental drugs during the human trials if they show any unwanted adverse effect etc. where the drug delivery systems can be potentially applied to reduce the side effects. But before proceeding to these noble and expensive translational research works, advanced theoretical calculations can provide the possible outcomes with considerable accuracy. Hence in this review article, we have analyzed how theoretical calculations can be used to investigate LDNs as potential biosensor devices or drug delivery systems. We have also made a very brief discussion on the properties of biosensors or drug delivery systems which should be investigated for the biomedical applications and how to calculate them theoretically. Finally, we have made a detailed analysis of a large number of recently published research works where theoretical calculations were used to propose different LDNs for bio-sensing and drug delivery applications.
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Affiliation(s)
- Hamidur Rahman
- Department of Physics, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md Rakib Hossain
- Department of Physics, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Tahmina Ferdous
- Department of Physics, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
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Vaidyanathan A, Mathew M, Radhakrishnan S, Rout CS, Chakraborty B. Theoretical Insight on the Biosensing Applications of 2D Materials. J Phys Chem B 2020; 124:11098-11122. [PMID: 33232607 DOI: 10.1021/acs.jpcb.0c08539] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The research on the design of efficient, reliable, and cost-effective biosensors is expanding given its high demand in various fields such as health care, environmental surveillance, agriculture, diagnostics, industries, and so forth. In the last decade, various fascinating and interesting 2D materials with extraordinary properties have been experimentally synthesized and theoretically predicted. 2D materials have been explored for the sensing of different biomolecules because of their large surface area and strong interaction with different biomolecules. Theoretical simulations can bring important insight on the interaction of biomolecules on 2D materials, charge transfer, orbital interactions, and so forth and may play an important role in the development of efficient biosensors. Quantum simulation techniques, such as density functional theory (DFT), are very powerful and are gaining popularity especially with the advent of high-speed computing facilities. This review article provides theoretical insight regarding the interaction of various biomolecules on different 2D materials and the charge transfer between the biomolecules and 2D materials leading to electrochemical signals, which can then provide experimentalists the useful design parameters for fabrication of biosensors. It also includes an overview of quantum simulations, use of the DFT method for simulating biomolecules on 2D materials, parameters obtained from theoretical simulations and sensitivity, and limitations of computational techniques for sensing biomolecules on 2D materials. Furthermore, this review summarizes the recent work in first-principles investigation of 2D materials for the purpose of biomolecule sensing. Beyond the traditional graphene or 2D transition-metal dichalcogenides, some novel and recently proposed 2D materials such as pentagraphene, haeckelite, MXenes, and so forth which have exhibited good sensing applications have also been highlighted.
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Affiliation(s)
- Antara Vaidyanathan
- Department of Chemistry, Ramnarain Ruia Autonomous College, Matunga, Mumbai 400019, India
| | - Minu Mathew
- Centre for Nano and Material Science, Jain University, Jain Global Campus, Jakkasandra, Ramanagara, Bangalore 562112, India
| | - Sithara Radhakrishnan
- Centre for Nano and Material Science, Jain University, Jain Global Campus, Jakkasandra, Ramanagara, Bangalore 562112, India
| | - Chandra Sekhar Rout
- Centre for Nano and Material Science, Jain University, Jain Global Campus, Jakkasandra, Ramanagara, Bangalore 562112, India
| | - Brahmananda Chakraborty
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India.,Homi Bhabha National Institute, Mumbai 400094, India
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Mir SH, Yadav VK, Singh JK. Boron-Carbon-Nitride Sheet as a Novel Surface for Biological Applications: Insights from Density Functional Theory. ACS OMEGA 2019; 4:3732-3738. [PMID: 31459586 PMCID: PMC6648852 DOI: 10.1021/acsomega.8b03454] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/12/2019] [Indexed: 06/10/2023]
Abstract
Understanding the interaction between nanoscale materials and nucleobases is essential for their use in nanobiotechnology and nanomedicine. Our ab initio calculations indicate that the interaction of nucleobases [adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U)] with boron-carbon-nitride (BCN) is mainly governed by van der Waals interactions. The adsorption energies, ranging from -0.560 to -0.879 eV, decrease in the order of G > A > T > C > U, which can be attributed to π-π interactions and different side groups of the nucleobases. We found that anions (N and O atoms) of nucleobases prefer to stay on top of cation (B) of the substrate. The results also showed that BCN exhibits superior binding strength than graphene and boron-nitride-based materials. We also found that upon adsorption, the fundamental properties of BCN and nucleobases remains unaltered, which suggests that BCN is a promising template for self-assembly of nucleobases.
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Roondhe B, Jha PK. "Haeckelite", a new low dimensional cousin of boron nitride for biosensing with ultra-fast recovery time: a first principles investigation. J Mater Chem B 2018; 6:6796-6807. [PMID: 32254696 DOI: 10.1039/c8tb01649f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We performed state-of-the-art first principles calculations under the framework of dispersion corrected density functional theory to investigate the electronic and vibrational properties of a recently found allotrope of BN, with octagonal and square ring forming planar haeckelite structures (haeck-BN). We further investigated the adsorption mechanism of five nucleobases adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U) over haeck-BN to explore its applicability in biosensing. The dispersion correction (DFT-D2) is included to appropriately consider van der Waals interactions. The order of adsorption energy of nucleobases over haeck-BN has the following order: G > T > A ≈ C > U. Significant variation in electronic properties, density of states and work function confirm the adsorption of nucleobases. To check the reusability of haeck-BN as a biosensor toward nucleobases, we calculated the recovery time. Ultrafast recovery times (in millisecond) of 292 ms, 130 ms, 120 ms, 160 ms and 0.6 ms were predicted for G, A, C, T and U, respectively. Our finding suggests that haeck-BN can be utilized as a biosensor for the detection of nucleobases due to its superiority to graphene, h-BN and boron nitride nanotubes, and can be further explored for photocatalysis.
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Affiliation(s)
- Basant Roondhe
- Department of Physics, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara-390002, India.
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