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Demir Gİ, Tekin A. NICE-FF: A non-empirical, intermolecular, consistent, and extensible force field for nucleic acids and beyond. J Chem Phys 2023; 159:244117. [PMID: 38153156 DOI: 10.1063/5.0176641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
A new non-empirical ab initio intermolecular force field (NICE-FF in buffered 14-7 potential form) has been developed for nucleic acids and beyond based on the dimer interaction energies (IEs) calculated at the spin component scaled-MI-second order Møller-Plesset perturbation theory. A fully automatic framework has been implemented for this purpose, capable of generating well-polished computational grids, performing the necessary ab initio calculations, conducting machine learning (ML) assisted force field (FF) parametrization, and extending existing FF parameters by incorporating new atom types. For the ML-assisted parametrization of NICE-FF, interaction energies of ∼18 000 dimer geometries (with IE < 0) were used, and the best fit gave a mean square deviation of about 0.46 kcal/mol. During this parametrization, atom types apparent in four deoxyribonucleic acid (DNA) bases have been first trained using the generated DNA base datasets. Both uracil and hypoxanthine, which contain the same atom types found in DNA bases, have been considered as test molecules. Three new atom types have been added to the DNA atom types by using IE datasets of both pyrazinamide and 9-methylhypoxanthine. Finally, the last test molecule, theophylline, has been selected, which contains already-fitted atom-type parameters. The performance of NICE-FF has been investigated on the S22 dataset, and it has been found that NICE-FF outperforms the well-known FFs by generating the most consistent IEs with the high-level ab initio ones. Moreover, NICE-FF has been integrated into our in-house developed crystal structure prediction (CSP) tool [called FFCASP (Fast and Flexible CrystAl Structure Predictor)], aiming to find the experimental crystal structures of all considered molecules. CSPs, which were performed up to 4 formula units (Z), resulted in NICE-FF being able to locate almost all the known experimental crystal structures with sufficiently low RMSD20 values to provide good starting points for density functional theory optimizations.
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Affiliation(s)
- Gözde İniş Demir
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Türkiye
| | - Adem Tekin
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Türkiye
- Research Institute for Fundamental Sciences (TÜBİTAK-TBAE), Kocaeli, Türkiye
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Demir Gİ, Demir S, Tekin A. 2D‐FFCASP—A New Approach for 2D Structure Prediction Applied to Self‐Assemblies of DNA Bases. ADVANCED THEORY AND SIMULATIONS 2022. [DOI: 10.1002/adts.202200308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Gözde İniş Demir
- Informatics Institute Istanbul Technical University Maslak Istanbul 34469 Turkey
| | - Samet Demir
- Informatics Institute Istanbul Technical University Maslak Istanbul 34469 Turkey
- TÜBİTAK Research Institute for Fundamental Sciences Gebze Kocaeli 41470 Turkey
| | - Adem Tekin
- Informatics Institute Istanbul Technical University Maslak Istanbul 34469 Turkey
- TÜBİTAK Research Institute for Fundamental Sciences Gebze Kocaeli 41470 Turkey
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3
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Milovanović B, Etinski M, Popov I. Self-assembly of rylene-decorated guanine ribbons on graphene surface for optoelectronic applications: a theoretical study. NANOTECHNOLOGY 2021; 32:435405. [PMID: 34284367 DOI: 10.1088/1361-6528/ac162c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
We are witnessing a change of paradigm from the conventional top-down to the bottom-up fabrication of nanodevices and particularly optoelectronic devices. A promising example of the bottom-up approach is self-assembling of molecules into layers with predictable and reproducible structural, electronic and optical properties. Nucleobases possess extraordinary ability to self-assembly into one-, two-, and three-dimensional structures. Optical properties of nucleotides are not suitable for wider application to optoelectronics and photovoltaics due to their large optical band gap, which is in contrast to rylene-based dyes that have been intensively investigated in organic optoelectronics. However, these lack the self-assembly capability of nucleobases. Combinations of covalently decorated guanine molecules with rylene type chromophores present 'the best of the both worlds'. Due to the large size of such compounds and its flexible nature their self-assemblies have not been fully understood yet. Here, we use a theoretical approach to study the structural, energetic and optical properties of rylene-based dye decorated guanine (GPDI), as self-assembled on a graphene sheet. Particularly we utilize the density-functional based tight-binding method to study atomic structure of these systems including the potential energy surface of GPDI and stability and organization of single- and multilayered GPDIs on graphene sheet. Using density-functional theory (DFT) we employ the energy decomposition analysis to gain a deeper insight into the contributions of different moieties to stability of GPDI films. Using time dependent DFT we analyze optical properties of these systems. We find that atomically thin films consisting of only a few molecular layers with large surface areas are more favorable than isolated thick islands. Our study of excited states indicates existence of charge separated states similar to ones found in the well-studied hydrogen bonded organic frameworks. The self-assembly characterized with a large homogeneous coverage and long-living charge-separated states provide the great potential for optoelectronic applications.
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Affiliation(s)
- Branislav Milovanović
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, Belgrade, Serbia
| | - Mihajlo Etinski
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, Belgrade, Serbia
| | - Igor Popov
- Institute for Multidisciplinary Research, University of Belgrade, Kneza Višeslava 1, Belgrade, Serbia
- Institut of Physics, University of Belgrade, Pregrevica 118, Belgrade, Serbia
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4
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Li X, Huang Z, Li S, Song A, Hao J, Liu HG. A new approach to construct and modulate G-quadruplex by cationic surfactant. J Colloid Interface Sci 2020; 578:338-345. [PMID: 32535416 DOI: 10.1016/j.jcis.2020.06.012] [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: 04/26/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 10/24/2022]
Abstract
HYPOTHESIS G-quadruplex structure has raised increasing attention in supramolecular chemistry as an effective template for ordered functional materials. Thus, it is of practical significance to advance our understanding regarding G-quadruplex structures. Typically, G-quadruplex structures are formed in the presence of suitable metal ions. New methods to construct such structures need to be explored. EXPERIMENTS The supramolecular assembly between CTAB and a guanosine derivative at different molar ratios was systematically studied, including assembly mechanisms, morphology, and macroscopic properties. Cationic surfactants with different alkyl chains were studied as control experiments. FINDINGS A novel strategy to construct G-quadruplex with the promotion of the cationic surfactant CTAB is presented in this work. The structure-property relationships of G-quadruplex gels are characterized by rheology and shrinkage ratio experiments. MacKintosh's theory was used to rationalize the relationship between gel elasticity and water content. The transition of G-quadruplex structures could be easily enabled by modulating CTAB concentration, which promotes the phase transition from gel/sol biphase to homogeneous sol phase. This work will provide a new viewpoint for the construction and modulation of G-quadruplex structures.
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Affiliation(s)
- Xiaoyang Li
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, Shandong University, PR China
| | - Zhaohui Huang
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, Shandong University, PR China
| | - Shuman Li
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, Shandong University, PR China
| | - Aixin Song
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, Shandong University, PR China
| | - Jingcheng Hao
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, Shandong University, PR China
| | - Hong-Guo Liu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, Shandong University, PR China.
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5
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Li X, Sánchez-Ferrer A, Bagnani M, Adamcik J, Azzari P, Hao J, Song A, Liu H, Mezzenga R. Metal ions confinement defines the architecture of G-quartet, G-quadruplex fibrils and their assembly into nematic tactoids. Proc Natl Acad Sci U S A 2020; 117:9832-9839. [PMID: 32317383 PMCID: PMC7211958 DOI: 10.1073/pnas.1919777117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
G-quadruplex, assembled from a square array of guanine (G) molecules, is an important structure with crucial biological roles in vivo but also a versatile template for ordered functional materials. Although the understanding of G-quadruplex structures is the focus of numerous studies, little is known regarding the control of G-quartet stacking modes and the spontaneous orientation of G-quadruplex fibrils. Here, the effects of different metal ions and their concentrations on stacking modes of G-quartets are elucidated. Monovalent cations (typically K+) facilitate the formation of G-quadruplex hydrogels with both heteropolar and homopolar stacking modes, showing weak mechanical strength. In contrast, divalent metal ions (Ca2+, Sr2+, and Ba2+) at given concentrations can control G-quartet stacking modes and increase the mechanical rigidity of the resulting hydrogels through ionic bridge effects between divalent ions and borate. We show that for Ca2+ and Ba2+ at suitable concentrations, the assembly of G-quadruplexes results in the establishment of a mesoscopic chirality of the fibrils with a regular left-handed twist. Finally, we report the discovery of nematic tactoids self-assembled from G-quadruplex fibrils characterized by homeotropic fibril alignment with respect to the interface. We use the Frank-Oseen elastic energy and the Rapini-Papoular anisotropic surface energy to rationalize two different configurations of the tactoids. These results deepen our understanding of G-quadruplex structures and G-quadruplex fibrils, paving the way for their use in self-assembly and biomaterials.
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Affiliation(s)
- Xiaoyang Li
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Jinan, Shandong 250100, China
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China
- Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | | | - Massimo Bagnani
- Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Jozef Adamcik
- Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Paride Azzari
- Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Jingcheng Hao
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Jinan, Shandong 250100, China;
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China
| | - Aixin Song
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Jinan, Shandong 250100, China
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China
| | - Hongguo Liu
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Jinan, Shandong 250100, China
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland;
- Department of Materials, ETH Zürich, 8093 Zürich, Switzerland
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6
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Farkhondeh H, Rahsepar FR, Zhang L, Leung KT. Structural and Chemical Evolution of l-Cysteine Nanofilm on Si(111)-√3×√3-Ag: From Preferential Growth at Step Edges and Antiphase Boundaries at Room Temperature to Adsorbate-Mediated Metal Cluster Formation at Elevated Temperature. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:16185-16200. [PMID: 31661626 DOI: 10.1021/acs.langmuir.9b02852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The interaction of cysteine molecules with the Si(111)-√3×√3-Ag surface has been investigated over the submonolayer to multilayer regime using X-ray photoelectron spectroscopy, scanning tunneling microscopy, and density functional theory calculations. With both upper step and lower step terraces, step edges, and antiphase boundaries, the √3×√3-Ag overlayer supported on Si(111) provides a rich two-dimensional template for studying site-specific biomolecular interactions. As an amino acid with three functional groups, cysteine is found to chemisorb through S-H bond cleavage and S-Ag bond linkage first at step edges and antiphase boundaries followed by island formation and expanded growth onto terraces. Intermolecular interactions are dominated by zwitterionic hydrogen bonding at higher coverages, producing a porous unordered interfacial layer composed of cysteine agglomerates at room temperature. Upon annealing, cysteine adsorbates induce structural transformation of the uniform √3×√3-Ag reconstructed surface lattice into metallic Ag clusters with a narrow size distribution and short-range ordering. Preferential nanoaggregate formation of cysteine at defect sites and cysteine-induced metal cluster formation promise a new approach to fabricating nanoclusters for potential applications in chemical sensing and catalysis.
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Affiliation(s)
- Hanieh Farkhondeh
- WATLab and Department of Chemistry , University of Waterloo , Waterloo , Ontario N2L3G1 , Canada
| | - Fatemeh R Rahsepar
- WATLab and Department of Chemistry , University of Waterloo , Waterloo , Ontario N2L3G1 , Canada
| | - Lei Zhang
- WATLab and Department of Chemistry , University of Waterloo , Waterloo , Ontario N2L3G1 , Canada
| | - Kam Tong Leung
- WATLab and Department of Chemistry , University of Waterloo , Waterloo , Ontario N2L3G1 , Canada
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7
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Abdelaziz A, Zaitsau DH, Kuratieva NV, Verevkin SP, Schick C. Melting of nucleobases. Getting the cutting edge of "Walden's Rule". Phys Chem Chem Phys 2019; 21:12787-12797. [PMID: 30888011 DOI: 10.1039/c9cp00716d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Walden's Rule is an empirical observation of an invariant fusion entropy during fusion of non-associated organic compounds. For the five nucleobases, adenine, thymine, cytosine, guanine, and uracil, surprisingly high fusion temperatures and enthalpies have been measured using a specially developed fast scanning calorimetry method that prevents decomposition. Even when nucleobases admittedly possess very high fusion temperatures, e.g. the value of 862 K measured for guanine really exceeds all expectations of the feasible dimension of the fusion temperature for such a relatively small and simple organic molecule. Hirshfeld surface analysis has been applied in order to find out an explanation for such extremely unusual thermal behavior of nucleobases. We rationalized the observed trends in terms of fusion entropy (Walden's constant = 56.5 J K-1 mol-1) as the entropic penalty of fusion not only for "non-associated", as proposed by Walden in 1908, but also for "ideal associated" systems like nucleobases.
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Affiliation(s)
- A Abdelaziz
- University of Rostock, Institute of Physics, Albert-Einstein-Str. 23-24, 18051 Rostock, Germany. and University of Rostock, Faculty of Interdisciplinary Research, Competence Centre CALOR, Albert-Einstein-Str. 25, 18051 Rostock, Germany.
| | - D H Zaitsau
- University of Rostock, Institute of Chemistry, Dr-Lorenz-Weg 2, 18059 Rostock, Germany
| | - N V Kuratieva
- Nikolaev Institute of Inorganic Chemistry of Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - S P Verevkin
- University of Rostock, Faculty of Interdisciplinary Research, Competence Centre CALOR, Albert-Einstein-Str. 25, 18051 Rostock, Germany. and University of Rostock, Institute of Chemistry, Dr-Lorenz-Weg 2, 18059 Rostock, Germany and Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russian Federation
| | - C Schick
- University of Rostock, Institute of Physics, Albert-Einstein-Str. 23-24, 18051 Rostock, Germany. and University of Rostock, Faculty of Interdisciplinary Research, Competence Centre CALOR, Albert-Einstein-Str. 25, 18051 Rostock, Germany. and Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russian Federation
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8
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Zhang J, Li X, Sun X, Liu Y, Hao J, Tan Y, Song A. G-Quadruplex based hydrogels stabilized by a cationic polymer as an efficient adsorbent of picric acid. NEW J CHEM 2019. [DOI: 10.1039/c9nj03143j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hydrogels based on G-quadruplexes (G-hydrogels) were prepared using guanosine 5′-monophosphate disodium salt, GMP, with a hyperbranched poly(ethylenimine), PEI, containing abundant –NH2 groups.
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Affiliation(s)
- Jin Zhang
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Xiaoyang Li
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Xiuping Sun
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Yihan Liu
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Jingcheng Hao
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Yebang Tan
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Aixin Song
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
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9
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Grüber R, Aranda J, Bellili A, Tuñón I, Dumont E. Free energy profiles for two ubiquitous damaging agents: methylation and hydroxylation of guanine in B-DNA. Phys Chem Chem Phys 2017; 19:14695-14701. [PMID: 28537602 DOI: 10.1039/c6cp07966k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA methylation and hydroxylation are two ubiquitous reactions in DNA damage induction, yet insights are scarce concerning the free energy of activation within B-DNA. We resort to multiscale simulations to investigate the attack of a hydroxyl radical and of the primary diazonium onto a guanine embedded in a solvated dodecamer. Reaction free energy profiles characterize two strongly exergonic processes, yet allow unprecedented quantification of the barrier towards this damage reaction, not higher than 6 kcal mol-1 and sometimes inexistent, and of the exergonicities. In the case of the [G(C8)-OH]˙ intermediate, we challenge the functional dependence of such simulations: recently-proposed functionals, such as M06-2X and LC-BLYP, agree on a ∼4 kcal mol-1 barrier, whereas the hybrid GGA B3LYP functional predicts a barrier-less pathway. In the long term, multiscale approaches can help build up a unified panorama of DNA lesion induction. These results stress the importance of DFT/MM-MD simulations involving new functionals towards the sound modelling of biomolecule damage even in the ground state.
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Affiliation(s)
- R Grüber
- Univ. Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France.
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10
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Paragi G, Fonseca Guerra C. Cooperativity in the Self-Assembly of the Guanine Nucleobase into Quartet and Ribbon Structures on Surfaces. Chemistry 2017; 23:3042-3050. [DOI: 10.1002/chem.201604830] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Indexed: 01/12/2023]
Affiliation(s)
- Gábor Paragi
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- MTA-SZTE; Supramolecular and Nanostructured Materials Research Group; Dóm tér 8 Szeged Hungary
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
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11
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Ciesielski A, El Garah M, Masiero S, Samorì P. Self-assembly of Natural and Unnatural Nucleobases at Surfaces and Interfaces. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:83-95. [PMID: 26488679 DOI: 10.1002/smll.201501017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/19/2015] [Indexed: 06/05/2023]
Abstract
The self-assembly of small organic molecules interacting via non-covalent forces is a viable approach towards the construction of highly ordered nanostructured materials. Among various molecular components, natural and unnatural nucleobases can undergo non-covalent self-association to form supramolecular architectures with ad hoc structural motifs. Such structures, when decorated with appropriate electrically/optically active units, can be used as scaffolds to locate such units in pre-determined positions in 2D on a surface, thereby paving the way towards a wide range of applications, e.g., in optoelectronics. This review discusses some of the basic concepts of the supramolecular engineering of natural and unnatural nucleobases and derivatives thereof as well as self-assembly processes on conductive solid substrates, as investigated by scanning tunnelling microscopy in ultra-high vacuum and at the solid/liquid interface. By unravelling the structure and dynamics of these self-assembled architectures with a sub-nanometer resolution, a greater control over the formation of increasingly sophisticated functional systems is achieved. The ability to understand and predict how nucleobases interact, both among themselves as well as with other molecules, is extremely important, since it provides access to ever more complex DNA- and RNA-based nanostructures and nanomaterials as key components in nanomechanical devices.
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Affiliation(s)
- Artur Ciesielski
- ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Mohamed El Garah
- ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Stefano Masiero
- Dipartimento di Chimica "G. Caimician", Alma Mater Studiorum - Università di Bologna, v. San Giacomo, 11 - 40126, Bologna, Italy
| | - Paolo Samorì
- ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000, Strasbourg, France
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12
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Conti S, del Rosso MG, Ciesielski A, Weippert J, Böttcher A, Shin Y, Melinte G, Ersen O, Casiraghi C, Feng X, Müllen K, Kappes MM, Samorì P, Cecchini M. Perchlorination of Coronene Enhances its Propensity for Self-Assembly on Graphene. Chemphyschem 2015; 17:352-7. [PMID: 26663716 DOI: 10.1002/cphc.201501113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Indexed: 11/11/2022]
Abstract
Providing a quantitative understanding of the thermodynamics involved in molecular adsorption and self-assembly at a nanostructured carbon material is of fundamental importance and finds outstanding applications in the graphene era. Here, we study the effect of edge perchlorination of coronene, which is a prototypical polyaromatic hydrocarbon, on the binding affinity for the basal planes of graphite. First, by comparing the desorption barrier of hydrogenated versus perchlorinated coronene measured by temperature-programmed desorption, we quantify the enhancement of the strength of physisorption at the single-molecule level though chlorine substitution. Then, by a thermodynamic analysis of the corresponding monolayers based on force-field calculations and statistical mechanics, we show that perchlorination decreases the free energy of self-assembly, not only enthalpically (by enhancing the strength of surface binding), but also entropically (by decreasing the surface concentration). The functional advantage of a chemically modulated 2D self-assembly is demonstrated in the context of the molecule-assisted liquid-phase exfoliation of graphite into graphene.
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Affiliation(s)
- Simone Conti
- Laboratoire d'Ingénierie des Fonctions Moléculaires, ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000, Strasbourg (France
| | - Maria G del Rosso
- Nanochemistry Laboratory, ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000, Strasbourg (France
| | - Artur Ciesielski
- Nanochemistry Laboratory, ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000, Strasbourg (France
| | - Jürgen Weippert
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131, Karlsruhe (Germany
| | - Artur Böttcher
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131, Karlsruhe (Germany
| | - Yuyoung Shin
- School of Chemistry, University of Manchester, Oxford road, Manchester, M13 9PL (UK
| | - Georgian Melinte
- Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS), UMR 7504, 23, rue du Loess, 67037 Cedex 08, Strasbourg (France
| | - Ovidiu Ersen
- Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS), UMR 7504, 23, rue du Loess, 67037 Cedex 08, Strasbourg (France
| | - Cinzia Casiraghi
- School of Chemistry, University of Manchester, Oxford road, Manchester, M13 9PL (UK
| | - Xinliang Feng
- Max Plank Institute for Polymer Research, Ackermannweg 10, 55128, Mainz (Germany.,Center for Advancing Electronics Dresden (CFAED) & Department of Chemistry and Food Chemistry, Technische Universitaet Dresden, 01062, Dresden (Germany
| | - Klaus Müllen
- Max Plank Institute for Polymer Research, Ackermannweg 10, 55128, Mainz (Germany
| | - Manfred M Kappes
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131, Karlsruhe (Germany.
| | - Paolo Samorì
- Nanochemistry Laboratory, ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000, Strasbourg (France.
| | - Marco Cecchini
- Laboratoire d'Ingénierie des Fonctions Moléculaires, ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000, Strasbourg (France.
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13
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Zhong D, Blömker T, Mück-Lichtenfeld C, Zhang H, Kehr G, Erker G, Fuchs H, Chi L. Thymine and adenine tetrads formed on anisotropic metal surfaces. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:265-270. [PMID: 24605377 DOI: 10.1002/smll.201301595] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The interplay of the Au(110) surface and alkyl-substituted DNA bases induces reorganization of the surface with parallel atomic grooves, while the enhanced surface anisotropy constrains the substituent alkyl chains along the grooves. Every four molecules are bound together through H-bonds while further possible H-bonds are prohibited by either the alkyl chains or the groove borders, resulting in separated tetrad structures located in the grooves.
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Liu L, Xia D, Klausen LH, Dong M. The self-assembled behavior of DNA bases on the interface. Int J Mol Sci 2014; 15:1901-14. [PMID: 24473140 PMCID: PMC3958828 DOI: 10.3390/ijms15021901] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 12/31/2013] [Accepted: 01/07/2014] [Indexed: 11/16/2022] Open
Abstract
A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures. In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. From the ideal condition to a more realistic environment, the self-assembled behaviors of DNA bases are introduced. In a vacuum system, the energetic advantages will dominate the assembly formation of DNA bases, while at ambient condition, more factors such as conformational freedom and the biochemical environment will be considered. Therefore, the assemblies of DNA bases at ambient condition are different from the ones obtained under vacuum. We present the ordered nanostructures formed by DNA bases at both vacuum and ambient condition. To construct and tailor the nanostructure through the interaction between DNA bases, it is important to understand the assembly behavior and features of DNA bases and their derivatives at ambient condition. The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface.
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Affiliation(s)
- Lei Liu
- Institute for Advanced Materials, Jiangsu University, 301 Xuefu Road, Jiangsu 212013, China.
| | - Dan Xia
- Interdisciplinary nanoscience Center (iNANO), Gustav Wieds vej 14, DK-8000 Aarhus C, Denmark.
| | - Lasse H Klausen
- Interdisciplinary nanoscience Center (iNANO), Gustav Wieds vej 14, DK-8000 Aarhus C, Denmark.
| | - Mingdong Dong
- Interdisciplinary nanoscience Center (iNANO), Gustav Wieds vej 14, DK-8000 Aarhus C, Denmark.
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15
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Liang LJ, Wang Q, Wu T, Sun TY, Kang Y. Contribution of Water Molecules in the Spontaneous Release of Protein by Graphene Sheets. Chemphyschem 2013; 14:2902-9. [DOI: 10.1002/cphc.201300414] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/24/2013] [Indexed: 11/07/2022]
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16
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Howorka S. DNA nanoarchitectonics: assembled DNA at interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:7344-7353. [PMID: 23373872 DOI: 10.1021/la3045785] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
DNA is a powerful biomaterial for creating rationally designed and functionally enhanced nanostructures. DNA nanoarchitectures positioned at substrate interfaces can offer unique advantages leading to improved surface properties relevant to biosensing, nanotechnology, materials science, and cell biology. This Perspective highlights the benefits and challenges of using assembled DNA as a nanoscale building block for interfacial layers and surveys their applications in three areas: homogeneous dense surface coatings, bottom-up nanopatterning, and 3D nanoparticle lattices. Possible future research developments are discussed at the end of the Perspective.
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Affiliation(s)
- Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, England, United Kingdom.
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17
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Chen JJ, Li WW, Yu HQ, Li XL. Capture of H2S from binary gas mixture by imidazolium-based ionic liquids with nonfluorous anions: A theoretical study. AIChE J 2013. [DOI: 10.1002/aic.14111] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jie-Jie Chen
- Dept. of Chemistry; University of Science & Technology of China; Hefei 230026 China
| | - Wen-Wei Li
- Dept. of Chemistry; University of Science & Technology of China; Hefei 230026 China
| | - Han-Qing Yu
- Dept. of Chemistry; University of Science & Technology of China; Hefei 230026 China
| | - Xue-Liang Li
- Anhui Key Laboratory of Controllable Chemistry Reaction & Material Chemical Engineering, School of Chemical Engineering; Hefei University of Technology; Hefei 230009 China
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18
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Paragi G, Kupihár Z, Guerra CF, Bickelhaupt FM, Kovács L. Supramolecular ring structures of 7-methylguanine: a computational study of its self-assembly and anion binding. Molecules 2012; 18:225-35. [PMID: 23271462 PMCID: PMC6269867 DOI: 10.3390/molecules18010225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/14/2012] [Accepted: 12/21/2012] [Indexed: 11/29/2022] Open
Abstract
The density functional theory calculations of 7-methylguanine clusters revealed that stable ring assemblies can be formed with or without anions in the center position and hexameric clusters are the most stable and most planar ones. The coordination of anions (Cl−, Br−, NO3−) stabilizes and thus favors the formation of planar aggregates. We believe that the predicted planar structures stabilized by anions are good models for self-assembly structures formed at solid-liquid or solid-gas interfaces. Comparing the bonding and average H-bond energy to reference ribbon calculations we pointed out the presence of the previously introduced cooperativity effect in circular supramolecular structures of 7-methylguanine.
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Affiliation(s)
- Gábor Paragi
- Supramolecular and Nanostructured Materials Research Group of the Hungarian Academy of Sciences, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +36-62-544-593; Fax: +36-62-545-971
| | - Zoltán Kupihár
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary; E-Mails: (Z.K.); (L.K.)
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands; E-Mails: (C.F.G.); (F.M.B.)
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands; E-Mails: (C.F.G.); (F.M.B.)
| | - Lajos Kovács
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary; E-Mails: (Z.K.); (L.K.)
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