Role of graphene in scavenging methyl cations: a DFT study.

DFT DNA methylation Graphene Methyl cation Radical scavenging

Journal

Journal of molecular modeling
ISSN: 0948-5023
Titre abrégé: J Mol Model
Pays: Germany
ID NLM: 9806569

Informations de publication

Date de publication:
30 Aug 2023
Historique:
received: 14 06 2023
accepted: 12 07 2023
medline: 30 8 2023
pubmed: 30 8 2023
entrez: 30 8 2023
Statut: epublish

Résumé

It is known that methylating agents methylate DNA by transferring a methyl cation (CH The spin polarised density functional theory (DFT) calculations employing PBE functional, ultrasoft pseudopotentials and plane wave basis set having kinetic energy cut-offs of 40 Ry and 400 Ry, respectively, for wave functions and charge densities were carried out to study the adsorption of CH

Identifiants

pubmed: 37646844
doi: 10.1007/s00894-023-05662-w
pii: 10.1007/s00894-023-05662-w
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

299

Informations de copyright

© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.

Références

Mattson MP (2003) Methylation and acetylation in nervous system development and neurodegenerative disorders. Ageing Res Rev 2:329–342
pubmed: 12726778
Clarke S (2003) Aging as war between chemical and biochemical processes: protein methylation and the recognition of age-damaged proteins for repair. Ageing Res Rev 2:263–285
pubmed: 12726775
Chen D, Meng L, Pei F, Zheng Y, Leng J (2017) A review of DNA methylation in depression. J Clin Neurosci 43:39–46
pubmed: 28645747
Drabløs F, Feyzi E, Aas PA, Vaagbø CB, Kavli B, Bratlie MS, Peña-Diaz J, Otterlei M, Slupphaug G, Krokan HE (2004) Alkylation damage in DNA and RNA—repair mechanisms and medical significance. DNA Repair 3:1389–1407
pubmed: 15380096
Robison SH, Munzer JS, Mrcp RT, Bradley WG (1987) Alzheimer’s disease cells exhibit defective repair of alkylating agent—induced DNA damage. Ann Neurol 21:250–258
pubmed: 3606032
Forde GK, Forde AE, Hill G, Ford A, Nazario A, Leszczynski J (2006) Comprehensive study of the effects of methylation on tautomeric equilibria of nucleic acid bases. J Phys Chem B 110:15564–15571
pubmed: 16884280
Shukla PK, Mishra PC, Suhai S (2007) Reactions of guanine with methyl chloride and methyl bromide: O6-methylation versus charge transfer complex formation. Int J Quantum Chem 107:1270–1283
Friedberg EC, Walker GC, Siede W (1995) DNA Repair and Mutagenesis. ASM Press, Washington, DC
Shooter KV, Howse R, Shah SA, Lawley PD (1974) The molecular basis for biological inactivation of nucleic acids. The action of methylating agents on the ribonucleic acid-containing bacteriophage R17. Biochemical Journal 137:303–312
pubmed: 4363111 pmcid: 1166118
Singer B, Gru¨nberger D, (1983) Molecular Biology of Mutagens and Carcinogens. Plenum Press, New York
Beranek DT (1990) Distribution of methyl and ethyl adducts following alkylation with monofunctional alkylating agents. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 231:11–30
pubmed: 2195323
Sedgwick B (2004) Repairing DNA-methylation damage. Nat Rev Mol Cell Biol 5:148–157
pubmed: 15040447
Lindahl T, Sedgwick B, Sekiguchi M, Nakabeppu Y (1988) Regulation and expression of the adaptive response to alkylating agents. Annu Rev Biochem 57:133–157
pubmed: 3052269
Bignami M, O’Driscoll M, Aquilina G, Karran P (2000) Unmasking a killer: DNA O6-methylguanine and the cytotoxicity of methylating agents. Mutat Res 462:71–82
pubmed: 10767619
Margison GP, Santibáñez Koref MF, Povey AC (2002) Mechanisms of carcinogenicity/chemotherapy by O6-methylguanine. Mutagenesis 17:483–487
pubmed: 12435845
Wyatt MD, Pittman DL (2006) Methylating agents and DNA repair responses: methylated bases and sources of strand breaks. Chem Res Toxicol 19:1580–1594
pubmed: 17173371 pmcid: 2542901
Christmann M, Roos WP, Kaina B (2007) DNA Methylation Damage: Formation, Repair and Biological Consequences. In: Obe G, Vijayalaxmi (eds) Chromosomal Alterations. Springer, Berlin, Heidelberg
Mishina Y, Duguid EM, He C (2006) Direct reversal of DNA alkylation damage. Chem Rev 106:215–232
pubmed: 16464003 pmcid: 2432087
Meikrantz W, Bergom MA, Memisoglu A, Samson L (1998) O6-alkylguanine DNA lesions trigger apoptosis. Carcinogenesis 19:369–372
pubmed: 9498291
Boysen G, Pachkowski BF, Nakamura J, Swenberg JA (2009) The formation and biological significance of N7-guanine adducts. Mutat Res Genet Toxicol Environ Mutagen 678:76–94
Ekanayake KS, LeBreton PR (2006) Activation barriers for DNA alkylation by carcinogenic methane diazonium ions. J Comput Chem 27:277–286
pubmed: 16342081
Bhattacharjee K, Shukla PK (2014) A DFT study of reactions of methyldiazonium ion with DNA/RNA nucleosides: investigating effect of sugar moiety on methylation pattern of bases. Int J Quantum Chem 114:1637–1644
Olah GA (1970) Stable Carbonium Ions in Solution: New superacid solvents and nuclear magnetic resonance spectroscopy permit direct study. Science 168:1298–1311
pubmed: 17731033
Olah GA (1973) Carbocations and electrophilic reactions. Angew Chem, Int Ed Engl 12:173–212
Dahlquist FW, Rand-Meir T, Raftery MA (1968) Demonstration of Carbonium ion intermediate during lysozyme catalysis. Chemistry 61:1194–1198
Murata M, Takahashi A, Saito I, Kawanishi S (1999) Site-specific DNA methylation and apoptosis: induction by diabetogenic streptozotocin. Biochem Pharmacol 57:881–887
pubmed: 10086321
Shukla PK, Ganapathy V, Mishra PC (2011) A quantum theoretical study of reactions of methyldiazonium ion with DNA base pairs. Chem Phys 388:31–37
Wurdeman RL, Church KM, Gold B (1989) DNA methylation by N-methyl-N-nitrosourea, N-methyl-N′-nitro-N-nitrosoguanidine, N-nitroso (1-acetoxyethyl) methylamine, and diazomethane. The mechanism for the formation of N7-methylguanine in sequence-characterized 5′-[32P]-end-labeled DNA. J Am Chem Soc 111:6408–6412
Gold B, Marky LM, Stone MP, Williams LD (2006) A review of the role of the sequence-dependent electrostatic landscape in DNA alkylation patterns. Chem Res Toxicol 19:1402–1414
pubmed: 17112226 pmcid: 2532758
Spratt TE, Zydowsky TM, Floss HG (1997) Stereochemistry of the in vitro and in vivo Methylation of DNA by (R)-and (S)-N-[2H1, 3H] Methyl-N-nitrosourea and (R)-and (S)-N-Nitroso-N-[2H1, 3H] methyl-Nmethylamine. Chem Res Toxicol 10:1412–1419
pubmed: 9437533
Ekanayake KS, Lebreton PR (2007) Model transition states for methane diazonium ion methylation of guanine runs in oligomeric DNA. J Comput Chem 28:2352–2365
pubmed: 17476668
Fowler JD, Allen MJ, Tung VC, Yang Y, Kaner RB, Weiller BH (2009) Practical chemical sensors from chemically derived graphene. ACS Nano 3:301–306
pubmed: 19236064
Gilje S, Han S, Wang M, Wang KL, Kaner RB (2007) A chemical route to graphene for device applications. Nano Lett 7:3394–3398
pubmed: 17944523
Yoo E, Okata T, Kohyama M, Nakamura J, Honma I (2009) Enhanced electrocatalytic activity of Pt subnanoclusters on graphene nanosheet surface. Nano Lett 9:2255–2259
pubmed: 19405511
Schedin F, Geim AK, Morozov SV, Hill EW, Blake P, Katsnelson MI, Novoselov KS (2007) Detection of individual gas molecules adsorbed on graphene. Nature mater 6:652–655
Stankovich S, Dikin DA, Dommett GH, Kohlhaas KM, Zimney EJ, Stach EA, Piner RD, Nguyen ST, Ruoff RS (2006) Graphene-based composite materials. Nature 442:282–286
pubmed: 16855586
Eda G, Chhowalla M (2009) Graphene-based composite thin films for electronics. Nano Lett 9:814–818
pubmed: 19173637
Ramanathan T, Abdala AA, Stankovich S, Dikin DA, Herrera-Alonso M, Piner RD, Adamson DH, Schniepp HC, Chen X, Ruoff RS, Nguyen ST, Aksay IA, Prud’Homme RK, Brinson LC (2008) Functionalized graphene sheets for polymer nanocomposites. Nat Nanotechnol 3:327–331
pubmed: 18654541
Barbolina II, Novoselov KS, Morozov SV, Dubonos SV, Missous M, Volkov AO, Christian DA, Grigorieva IV, Geim AK (2006) Submicron sensors of local electric field with single-electron resolution at room temperature. Appl Phys Lett 88:013901
Di C-a, Wei D, Yu G, Liu Y, Guo Y, Zhu D (2008) Patterned graphene as source/drain electrodes for bottom-contact organic field-effect transistors. Adv Mater 20:3289–3293
Wang X, Zhi L, Müllen K (2008) Transparent, conductive graphene electrodes for dye-sensitized solar cells. Nano Lett 8:323–327
pubmed: 18069877
Chung C, Kim Y-K, Shin D, Ryoo S-R, Hong BH, Min D-H (2013) Biomedical applications of graphene and graphene oxide. Acc Chem Res 46:2211–2224
pubmed: 23480658
McCallion C, Burthem J, Rees-Unwin K, Golovanov A, Pluen A (2016) Graphene in therapeutics delivery: problems, solutions and future opportunities. Eur J Pharm Biopharm 104:235–250
pubmed: 27113141
Reina G, González-Domínguez JM, Criado A, Vázquez E, Bianco A, Prato M (2017) Promises, facts and challenges for graphene in biomedical applications. Chem Soc Rev 46:4400–4416
pubmed: 28722038
Wang Z, Colombi Ciacchi L, Wei G (2017) Recent advances in the synthesis of graphene-based nanomaterials for controlled drug delivery. Appl Sci 7:1175
Ghosal K, Sarkar K (2018) Biomedical applications of graphene nanomaterials and beyond. ACS Biomater Sci Eng 4:2653–2703
pubmed: 33434995
Arvidsson R, Boholm M, Johansson M, de Montoya ML (2018) “Just carbon”: ideas about graphene risks by graphene researchers and innovation advisors. Nanoethics 12:199–210
pubmed: 30546498 pmcid: 6267168
Malhotra R, Halbig CE, Sim YF, Lim CT, Leong DT, Neto AC, Garaj S, Rosa V (2022) Cytotoxicity survey of commercial graphene materials from worldwide. npj 2D Materials and Applications 6:65
Mohanty N, Berry V (2008) Graphene-based single-bacterium resolution biodevice and DNA transistor: interfacing graphene derivatives with nanoscale and microscale biocomponents. Nano Lett 8:4469–4476
pubmed: 19367973
Lu CH, Yang HH, Zhu CL, Chen X, Chen GN (2009) A graphene platform for sensing biomolecules. Angew Chem Int Ed Engl 121:4879–4881
Tang Z, Wu H, Cort JR, Buchko GW, Zhang Y, Shao Y, Aksay IA, Liu J, Lin Y (2010) Constraint of DNA on functionalized graphene improves its biostability and specificity. Small 6:1205–1209
pubmed: 20461727
Tang LAL, Wang J, Loh KP (2010) Graphene-based SELDI probe with ultrahigh extraction and sensitivity for DNA oligomer. J Am Chem Soc 132:10976–10977
pubmed: 20698647
Chen RJ, Choi HC, Bangsaruntip S, Yenilmez E, Tang X, Wang Q, Chang YL, Dai H (2004) An investigation of the mechanisms of electronic sensing of protein adsorption on carbon nanotube devices. J Am Chem Soc 126:1563–1568
pubmed: 14759216
Ghaderi N, Peressi M (2010) First-principle study of hydroxyl functional groups on pristine, defected graphene, and graphene epoxide. J Phys Chem C 114:21625–21630
Fan X, Zheng W, Kuo J-L (2013) Oxygen reduction reaction on active sites of heteroatom-doped graphene. RSC Adv 3:5498–5505
Laskar BI, Shukla PK (2021) Adsorption of HOOO
Wang FT, Chen L, Tian CJ, Meng Y, Wang ZG, Zhang RQ, Jin MX, Zhang P, Ding DJ (2011) Interactions between free radicals and a graphene fragment: Physical versus chemical bonding, charge transfer, and deformation. J Comput Chem 32:3264–3268
pubmed: 21953559
Tachikawa H (2019) Methyl radical addition to the surface of graphene nanoflakes: A density functional theory study. Surf Sci 679:196–201
Mandeltort L, Choudhury P, Johnson JK, Yates JT Jr (2012) Reaction of the Basal Plane of Graphite with the Methyl Radical. J Phys Chem Lett 3:1680–1683
pubmed: 26285728
Mandeltort L, Choudhury P, Johnson JK, Yates JT Jr (2012) Methyl Radical Reactivity on the Basal Plane of Graphite. J Phys Chem C 116:18347–18357
Kim H, Mattevi C, Calvo MR, Oberg JC, Artiglia L, Agnoli S, Hirjibehedin CF, Chhowalla M, Saiz E (2012) Activation Energy Paths for Graphene Nucleation and Growth on Cu. ACS Nano 6:3614–3623
pubmed: 22443380
Perdew JP, Burke K, Ernzerhof M (1996) Generalized gradient approximation made simple. Phys Rev Lett 77:3865
pubmed: 10062328
Vanderbilt D (1990) Soft self-consistent pseudopotentials in a generalized eigenvalue formalism. Phys Rev B 41:7892
Grimme S (2006) Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J Comput Chem 27:1787–1799
pubmed: 16955487
Bengtsson L (1999) Dipole correction for surface supercell calculations. Phys Rev B 59:12301
Marzari N, Vanderbilt D, De Vita A, Payne MC (1999) Thermal contraction and disordering of the Al (110) surface. Phys Rev Lett 82:3296
Monkhorst HJ, Pack JD (1976) Special points for Brillouin-zone integrations. Phys Rev B 13:5188
Broyden CG (1970) The convergence of a class of double-rank minimization algorithms 1. general considerations. IMA J Appl Math 6:76–90
Fletcher R (1970) A new approach to variable metric algorithms. Comput J 13:317–322
Goldfarb D (1970) A family of variable-metric methods derived by variational means. Math Comput 24:23–26
Shanno DF (1970) Conditioning of quasi-Newton methods for function minimization. Math Comput 24:647–656
Tang W, Sanville E, Henkelman G (2009) A grid-based Bader analysis algorithm without lattice bias. J Phys: Condens Matter 21:084204
pubmed: 21817356
Sanville E, Kenny SD, Smith R, Henkelman G (2007) Improved grid-based algorithm for Bader charge allocation. J Comput Chem 28:899–908
pubmed: 17238168
Henkelman G, Arnaldsson A, Jónsson H (2006) A fast and robust algorithm for Bader decomposition of charge density. Comput Mater Sci 36:354–360
Andreussi O, Dabo I, Marzari N (2012) Revised self-consistent continuum solvation in electronic-structure calculations. J Chem Phys 136:064102–064120
pubmed: 22360164
Giannozzi P, Andreussi O, Brumme T, Bunau O, Nardelli MB, Calandra M, Car R, Cavazzoni C, Ceresoli D, Cococcioni M, Colonna N (2017) Advanced capabilities for materials modelling with Quantum ESPRESSO. J Phys: Condens Matter 29:465901
pubmed: 29064822
Giannozzi P, Baroni S, Bonini N, Calandra M, Car R, Cavazzoni C, Ceresoli D, Chiarotti GL, Cococcioni M, Dabo I (2009) QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials. J Phys: Condens Matter 21:395502
pubmed: 21832390

Auteurs

Baharul Islam Laskar (BI)

Department of Physics, Assam University, Silchar - 788 011, Assam, India.

Abhishek Kumar Mishra (AK)

Department of Physics, Applied Science Cluster, University of Petroleum and Energy Studies, Dehradun, 248007, India.

Pradeep Kumar Shukla (PK)

Department of Physics, Assam University, Silchar - 788 011, Assam, India. pkshukla@ymail.com.

Classifications MeSH