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Tewari M, Pareek P, Kumar S. Correlating Amino Acid Interaction with Graphene-Based Materials Regulating Cell Function. J Indian Inst Sci 2022. [DOI: 10.1007/s41745-021-00272-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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2
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Ładniak A, Jurak M, Palusińska-Szysz M, Wiącek AE. The Influence of Polysaccharides/TiO 2 on the Model Membranes of Dipalmitoylphosphatidylglycerol and Bacterial Lipids. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27020343. [PMID: 35056656 PMCID: PMC8778854 DOI: 10.3390/molecules27020343] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/31/2021] [Accepted: 01/02/2022] [Indexed: 01/15/2023]
Abstract
The aim of the study was to determine the bactericidal properties of popular medical, pharmaceutical, and cosmetic ingredients, namely chitosan (Ch), hyaluronic acid (HA), and titanium dioxide (TiO2). The characteristics presented in this paper are based on the Langmuir monolayer studies of the model biological membranes formed on subphases with these compounds or their mixtures. To prepare the Langmuir film, 1,2-dipalmitoyl-sn-glycero-3-phospho-rac-(1-glycerol) (DPPG) phospholipid, which is the component of most bacterial membranes, as well as biological material-lipids isolated from bacteria Escherichia coli and Staphylococcus aureus were used. The analysis of the surface pressure-mean molecular area (π-A) isotherms, compression modulus as a function of surface pressure, CS-1 = f(π), relative surface pressure as a function of time, π/π0 = f(t), hysteresis loops, as well as structure visualized using a Brewster angle microscope (BAM) shows clearly that Ch, HA, and TiO2 have antibacterial properties. Ch and TiO2 mostly affect S. aureus monolayer structure during compression. They can enhance the permeability of biological membranes leading to the bacteria cell death. In turn, HA has a greater impact on the thickness of E. coli film.
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Affiliation(s)
- Agata Ładniak
- Department of Interfacial Phenomena, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Skłodowska University, M. Curie-Skłodowska Sq. 3, 20-031 Lublin, Poland; (M.J.); (A.E.W.)
- Laboratory of X-ray Optics, Centre for Interdisciplinary Research, Faculty of Science and Health, The John Paul II Catholic University of Lublin, Konstantynów 1J, 20-708 Lublin, Poland
- Correspondence:
| | - Małgorzata Jurak
- Department of Interfacial Phenomena, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Skłodowska University, M. Curie-Skłodowska Sq. 3, 20-031 Lublin, Poland; (M.J.); (A.E.W.)
| | - Marta Palusińska-Szysz
- Department of Genetics and Microbiology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland;
| | - Agnieszka Ewa Wiącek
- Department of Interfacial Phenomena, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Skłodowska University, M. Curie-Skłodowska Sq. 3, 20-031 Lublin, Poland; (M.J.); (A.E.W.)
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3
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Pantaleone S, Rimola A, Ugliengo P, Sodupe M. First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO 2 (101) Anatase Surface Adopting a Full Periodic Approach. J Chem Inf Model 2021; 61:5484-5498. [PMID: 34752107 DOI: 10.1021/acs.jcim.1c00689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Computational modeling of protein/surface systems is challenging since the conformational variations of the protein and its interactions with the surface need to be considered at once. Adoption of first-principles methods to this purpose is overwhelming and computationally extremely expensive so that, in many cases, dramatically simplified systems (e.g., small peptides or amino acids) are used at the expenses of modeling nonrealistic systems. In this work, we propose a cost-effective strategy for the modeling of peptide/surface interactions at a full quantum mechanical level, taking the adsorption of polyglycine on the TiO2 (101) anatase surface as a test case. Our approach is based on applying the periodic boundary conditions for both the surface model and the polyglycine peptide, giving rise to full periodic polyglycine/TiO2 surface systems. By proceeding this way, the considered complexes are modeled with a drastically reduced number of atoms compared with the finite-analogous systems, modeling the polypeptide structures at the same time in a realistic way. Within our modeling approach, full periodic density functional theory calculations (including implicit solvation effects) and ab initio molecular dynamics (AIMD) simulations at the PBE-D2* theory level have been carried out to investigate the adsorption and relative stability of the different polyglycine structures (i.e., extended primary, β-sheet, and α-helix) on the TiO2 surface. It has been found that, upon adsorption, secondary structures become partially denatured because the peptide C═O groups form Ti-O═C dative bonds. AIMD simulations have been fundamental to identify these phenomena because thermal and entropic effects are of paramount importance. Irrespective of the simulated environments (gas phase and implicit solvent), adsorption of the α-helix is more favorable than that of the β-sheet because in the former, more Ti-O═C bonds are formed and the adsorbed secondary structure results less distorted with respect to the isolated state. Under the implicit water solvent, additionally, adsorbed β-sheet structures weaken with respect to their isolated states as the H-bonds between the strands are longer due to solvation effects. Accordingly, the results indicate that the preferred conformation upon adsorption is the α-helix over the β-sheet.
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Affiliation(s)
- Stefano Pantaleone
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia, Spain.,Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental Centre, Università degli Studi di Torino, Via P. Giuria 7, Torino 10125, Italy.,Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, Perugia I-06123, Italy
| | - Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia, Spain
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Inter-Departmental Centre, Università degli Studi di Torino, Via P. Giuria 7, Torino 10125, Italy
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia, Spain
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Kamel M, Raissi H, Hashemzadeh H, Mohammadifard K. Theoretical elucidation of the amino acid interaction with graphene and functionalized graphene nanosheets: insights from DFT calculation and MD simulation. Amino Acids 2020; 52:1465-1478. [PMID: 33098474 DOI: 10.1007/s00726-020-02905-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/18/2020] [Indexed: 11/26/2022]
Affiliation(s)
- Maedeh Kamel
- Department of Chemistry, Payame Noor University, 19395-4697, Tehran, Iran
| | - Heidar Raissi
- Department of Chemistry, University of Birjand, Birjand, Iran.
| | | | - Kamal Mohammadifard
- Department of Chemical Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
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5
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Sai Phani Kumar V, Verma M, Deshpande PA. On interaction of arginine, cysteine and guanine with a nano-TiO 2 cluster. Comput Biol Chem 2020; 86:107236. [PMID: 32220810 DOI: 10.1016/j.compbiolchem.2020.107236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/03/2020] [Accepted: 02/15/2020] [Indexed: 01/17/2023]
Abstract
Nanoscopic properties of TiO2 augmented with its physicochemical properties and biocompatibility make it a material interest in the biomedical field. Efficient methods to design of such materials require a thorough understanding of associated nano-bio interfaces. In the present study, density functional theory calculations were performed to study the interactions of arginine, cysteine and guanine with a nano-TiO2 cluster. Different configurations were sampled for the adsorption of arginine, cysteine and guanine to probe the nano-bio interface via the interaction of various functional groups present on biomolecules. Adsorption energies for arginine, cysteine and guanine were in a range of -25.0 to -57.6, -12.1 to -29.6 and -45.6 to -58.7 kcal/mol, respectively. From the change in adsorption energies and free energies, interaction of amino acids with carboxylic (COOH), thiol (SH) and amine (NH2) groups while the interaction of the nucleobase via O bonded to C and N of purine ring was found to be essential for thermodynamically stable and energetically favorable states. Density of states analysis also disclosed the prominent interactions of the biomolecules with the nano-TiO2 cluster. Decrease in band gaps on adsorption of the biomolecules was a pertinent phenomenon indicating the strong chemical interactions of the biomolecules with the nanoscopic TiO2 chosen for analysis in this study.
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Affiliation(s)
- V Sai Phani Kumar
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Manju Verma
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Parag A Deshpande
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
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6
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Rossi-Fernández AC, Villegas-Escobar N, Guzmán-Angel D, Gutiérrez-Oliva S, Ferullo RM, Castellani NJ, Toro-Labbé A. Theoretical study of glycine amino acid adsorption on graphene oxide. J Mol Model 2020; 26:33. [PMID: 31982975 DOI: 10.1007/s00894-020-4297-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 01/14/2020] [Indexed: 11/24/2022]
Abstract
The non-dissociative and dissociative adsorptions of zwitterionic Gly on graphene oxide (GO) was studied in the framework of DFT using a cluster model approach. In this work, the interaction with an epoxy group of GO basal plane was mainly considered. As a comparison, the non-dissociative and dissociative adsorptions of neutral Gly were also taken into account. The non-dissociative adsorption modes for zwitterionic and neutral Gly conformers show binding energies of 12.2 and 14.4 kcal mol-1, respectively. These molecules are thought to remain over the GO surface due to attractive noncovalent interactions. Two dissociative adsorption modes, for Z-Gly and N-Gly, show smaller binding energies of 7.2 and 8.4 kcal mol-1, where the deprotonated species links strongly through a C-O or C-N covalent bond to the GO surface. The results obtained in the present theoretical approach to the glycine/graphene oxide system support the fact that glycine can be attached to epoxy groups of graphene oxide basal planes in addition to the anchoring on edge oxidation groups. In summary, we conclude that glycine can be used as a reducing agent as well as a functionalizer of GO sheets.
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Affiliation(s)
- Ana C Rossi-Fernández
- Departamento de Química-Física, Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile. .,Instituto de Química del Sur (INQUISUR), CONICET-UNS, Universidad Nacional del Sur, Av. Alem 1253, 8000, Bahía Blanca, Argentina.
| | - Nery Villegas-Escobar
- Departamento de Química-Física, Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Daniela Guzmán-Angel
- Departamento de Química-Física, Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Soledad Gutiérrez-Oliva
- Departamento de Química-Física, Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Ricardo M Ferullo
- Instituto de Química del Sur (INQUISUR), CONICET-UNS, Universidad Nacional del Sur, Av. Alem 1253, 8000, Bahía Blanca, Argentina
| | - Norberto J Castellani
- Instituto de Física del Sur (IFISUR), CONICET-UNS, Universidad Nacional del Sur, Av. Alem 1253, 8000, Bahía Blanca, Argentina
| | - Alejandro Toro-Labbé
- Departamento de Química-Física, Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
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7
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Wang Q, She W, Lu X, Li P, Sun Y, Liu X, Pan W, Duan K. The interaction of hyaluronic acid and graphene tuned by functional groups: A density functional study. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.112559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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8
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Wang Q, Wang M, Lu X, Wang K, Fang L, Ren F, Lu G. Effects of atomic-level nano-structured hydroxyapatite on adsorption of bone morphogenetic protein-7 and its derived peptide by computer simulation. Sci Rep 2017; 7:15152. [PMID: 29123140 PMCID: PMC5680243 DOI: 10.1038/s41598-017-15219-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/23/2017] [Indexed: 11/17/2022] Open
Abstract
Hydroxyapatite (HA) is the principal inorganic component of bones and teeth and has been widely used as a bone repair material because of its good biocompatibility and bioactivity. Understanding the interactions between proteins and HA is crucial for designing biomaterials for bone regeneration. In this study, we evaluated the effects of atomic-level nano-structured HA (110) surfaces on the adsorption of bone morphogenetic protein-7 (BMP-7) and its derived peptide (KQLNALSVLYFDD) using molecular dynamics and density functional theory methods. The results indicated that the atomic-level morphology of HA significantly affected the interaction strength between proteins and HA substrates. The interactions of BMP-7 and its derived peptide with nano-concave and nano-pillar HA surfaces were stronger than those with flat or nano-groove HA surfaces. The results also revealed that if the groove size of nano-structured HA surfaces matched that of residues in the protein or peptide, these residues were likely to spread into the grooves of the nano-groove, nano-concave, and nano-pillar HA, further strengthening the interactions. These results are helpful in better understanding the adsorption behaviors of proteins onto nano-structured HA surfaces, and provide theoretical guidance for designing novel bioceramic materials for bone regeneration and tissue engineering.
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Affiliation(s)
- Qun Wang
- Key Lab of Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, Sichuan, China
- College of Life Science and Biotechnology, MianYang Teachers' College, Mianyang, 621006, Sichuan, China
| | - Menghao Wang
- Key Lab of Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, Sichuan, China
| | - Xiong Lu
- Key Lab of Advanced Technologies of Materials, Ministry of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, Sichuan, China
| | - Kefeng Wang
- National Engineering Research Center for Biomaterials, Genome Research Center for Biomaterials, Sichuan University, Chengdu, 610065, Sichuan, China.
| | - Liming Fang
- Department of Polymer Science and Engineering, School of Materials Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Fuzeng Ren
- Department of Materials Science and Engineering, South University of Science and Technology of China, Shenzhen, Guangdong, 518055, China
| | - Guoming Lu
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
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9
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Wang Q, Wang MH, Lu X, Wang KF, Fang LM. Combined effects of dopants and electric field on interactions of dopamine with graphene. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Wang MH, Wang Q, Lu X, Wang KF, Fang L, Ren F, Lu G, Zhang H. Interaction Behaviors of Fibrinopeptide-A and Graphene with Different Functional Groups: A Molecular Dynamics Simulation Approach. J Phys Chem B 2017; 121:7907-7915. [DOI: 10.1021/acs.jpcb.7b07170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Meng-hao Wang
- Key
Lab of Advanced Technologies of Materials, Ministry of Education,
School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, Sichuan China
| | - Qun Wang
- Key
Lab of Advanced Technologies of Materials, Ministry of Education,
School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, Sichuan China
- College
of Life Science and Biotechnology, Mianyang Teachers’ College, Mianyang 621006, Sichuan, China
| | - Xiong Lu
- Key
Lab of Advanced Technologies of Materials, Ministry of Education,
School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, Sichuan China
- Genome
Research Center for Biomaterials, Sichuan University, Chengdu 610065, Sichuan China
| | - Ke-feng Wang
- National
Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610065, Sichuan China
- Genome
Research Center for Biomaterials, Sichuan University, Chengdu 610065, Sichuan China
| | - Liming Fang
- Department
of Polymer Science and Engineering, School of Materials Science and
Engineering, South China University of Technology, Guangzhou 510641, China
| | - Fuzeng Ren
- Department
of Materials Science and Engineering, South University of Science and Technology of China, Shenzhen, Guangdong 518055, China
| | - Guoming Lu
- School of
Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, Sichuan China
| | - Hongping Zhang
- Engineering
Research Center of Biomass Materials, Ministry of Education, School
of Materials Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
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11
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Dias Ledo RM, Leal LA, de Brito Silva PP, da Cunha WF, de Souza LE, Almeida Fonseca AL, Ceschin AM, da Silva Filho DA, Ribeiro Junior LA. Modeling optical properties of polymer–solvent complexes: the chloroform influence on the P3HT and N2200 absorption spectra. J Mol Model 2017; 23:37. [DOI: 10.1007/s00894-016-3196-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 12/16/2016] [Indexed: 10/20/2022]
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Abstract
Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.
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13
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Wang Q, Wang MH, Wang KF, Zhao YC, Wang WL, Zhang LP. Interactions of Anionic and Neutral Serine with Pure and Metal-doped Graphene Studied by Density Functional Theory. CHINESE J CHEM PHYS 2016. [DOI: 10.1063/1674-0068/29/cjcp1512250] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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14
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Carballeira DL, Ramos-Berdullas N, Pérez-Juste I, Fajín JLC, Cordeiro MNDS, Mandado M. A computational study of the interaction of graphene structures with biomolecular units. Phys Chem Chem Phys 2016; 18:15312-21. [DOI: 10.1039/c6cp00545d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemical sensors constructed from graphene nanostructures have raised recently a great interest. In this work we analyse using DFT the electronic factors responsible for the large affinity of biomolecular units for graphene surface.
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Affiliation(s)
| | | | | | - José Luis Cagide Fajín
- LAQV-REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
- 4169-007 Porto
| | - M. Natália D. S. Cordeiro
- LAQV-REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
- 4169-007 Porto
| | - Marcos Mandado
- Department of Physical Chemistry
- University of Vigo
- 36310 Vigo
- Spain
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15
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Graphdiyne as a promising material for detecting amino acids. Sci Rep 2015; 5:16720. [PMID: 26568200 PMCID: PMC4644954 DOI: 10.1038/srep16720] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/19/2015] [Indexed: 01/15/2023] Open
Abstract
The adsorption of glycine, glutamic acid, histidine and phenylalanine on single-layer graphdiyne/ graphene is investigated by ab initio calculations. The results show that for each amino acid molecule, the adsorption energy on graphdiyne is larger than the adsorption energy on graphene and dispersion interactions predominate in the adsorption. Molecular dynamics simulations reveal that at room temperature the amino acid molecules keep migrating and rotating on graphdiyne surface and induce fluctuation in graphdiyne bandgap. Additionally, the photon absorption spectra of graphdiyne-amino-acid systems are investigated. We uncover that the presence of amino acid molecules makes the photon absorption peaks of graphdiyne significantly depressed and shifted. Finally, quantum electronic transport properties of graphdiyne-amino-acid systems are compared with the transport properties of pure graphdiyne. We reveal that the amino acid molecules induce distinct changes in the electronic conductivity of graphdiyne. The results in this paper reveal that graphdiyne is a promising two-dimensional material for sensitively detecting amino acids and may potentially be used in biosensors.
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16
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Bukowski B, Deskins NA. The interactions between TiO2 and graphene with surface inhomogeneity determined using density functional theory. Phys Chem Chem Phys 2015; 17:29734-46. [PMID: 26477857 DOI: 10.1039/c5cp04073f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
TiO2/graphene composites have shown promise as photocatalysts, leading to improved electronic properties. We have modeled using density functional theory TiO2/graphene interfaces formed between graphene with various defects/functional groups (C vacancy, epoxide, and hydroxyl) and TiO2 clusters of various sizes. We considered clusters from 3 to 45 atoms, the latter a nanoparticle of ∼1 nm in size. Our results show that binding to pristine graphene is dominated by van der Waals forces, and that C vacancies or epoxide groups lead to much stronger binding between the graphene and TiO2. Such sites may serve to anchor TiO2 to graphene. Graphene surfaces with hydroxyls however lead to OH transfer to TiO2 and weak interactions between the graphene and the hydroxylated TiO2 cluster. Charge transfer may occur between TiO2 and graphene in various directions (graphene to TiO2 or TiO2 to graphene), depending on the state of the graphene surface, based on overlap of the density of states. Our work indicates that graphene surface defects or functional groups may have a significant effect on the stability, structure, and photoactivity of these materials.
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Affiliation(s)
- Brandon Bukowski
- Worcester Polytechnic Institute, Department of Chemical Engineering, Worcester, MA 01609, USA.
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17
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Encapsulated β-carotene in ZnO nanotubes: Theoretical insight into the stabilization dynamics. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.07.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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Wang Q, Wang MH, Wang KF, Liu Y, Zhang HP, Lu X, Zhang XD. Computer simulation of biomolecule–biomaterial interactions at surfaces and interfaces. Biomed Mater 2015; 10:032001. [DOI: 10.1088/1748-6041/10/3/032001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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