1
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Gowrisankar S, Bernhardt B, Becker J, Schreiner PR. Regioselective Synthesis of
meta
‐Tetraaryl‐Substituted Adamantane Derivatives and Evaluation of Their White Light Emission. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Saravanan Gowrisankar
- Institute of Organic Chemistry Justus Liebig University Heinrich-Buff-Ring 17 35392 Giessen Germany
- Center for Materials Research Heinrich-Buff-Ring 16 35392 Giessen Germany
| | - Bastian Bernhardt
- Institute of Organic Chemistry Justus Liebig University Heinrich-Buff-Ring 17 35392 Giessen Germany
- Center for Materials Research Heinrich-Buff-Ring 16 35392 Giessen Germany
| | - Jonathan Becker
- Institute of Inorganic and Analytical Chemistry Justus Liebig University 35392 Giessen Germany
| | - Peter R. Schreiner
- Institute of Organic Chemistry Justus Liebig University Heinrich-Buff-Ring 17 35392 Giessen Germany
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2
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Krongsuk S, Shinsuphan N, Amornkitbumrung V. Effect of the alkali metal (Li, Na, K) substitution on the geometric, electronic and optical properties of the smallest diamondoid: First principles calculations. Chin J Chem Eng 2019. [DOI: 10.1016/j.cjche.2018.05.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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3
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K K MJ, Padmanaban R. Effects of functionalization on the electronic and absorption properties of the smaller diamondoids: a computational study. J CHEM SCI 2018. [DOI: 10.1007/s12039-018-1505-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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4
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Sarap CS, Adhikari B, Meng S, Uhlig F, Fyta M. Optical Properties of Single- and Double-Functionalized Small Diamondoids. J Phys Chem A 2018; 122:3583-3593. [PMID: 29488764 DOI: 10.1021/acs.jpca.7b12519] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The rational control of the electronic and optical properties of small functionalized diamond-like molecules, the diamondoids, is the focus of this work. Specifically, we investigate the single- and double- functionalization of the lower diamondoids, adamantane, diamantane, and triamantane with -NH2 and -SH groups and extend the study to N-heterocyclic carbene (NHC) functionalization. On the basis of electronic structure calculations, we predict a significant change in the optical properties of these functionalized diamondoids. Our computations reveal that -NH2 functionalized diamondoids show UV photoluminescence similar to ideal diamondoids while -SH substituted diamondoids hinder the UV photoluminescence due to the labile nature of the S-H bond in the first excited state. This study also unveils that the UV photoluminescence nature of -NH2 diamondoids is quenched upon additional functionalization with the -SH group. The double-functionalized derivative can, thus, serve as a sensitive probe for biomolecule binding and sensing environmental changes. The preserved intrinsic properties of the NHC and the ideal diamondoid in NHC-functionalized-diamondoids suggests its utilization in diamondoid-based self-assembled monolayers (SAM), whose UV-photoluminescent signal would be determined entirely by the functionalized diamondoids. Our study aims to pave the path for tuning the properties of diamondoids through a selective choice of the type and number of functional groups. This will aid the realization of optoelectronic devices involving, for example, large-area SAM layers or diamondoid-functionalized electrodes.
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Affiliation(s)
- Chandra Shekar Sarap
- Institute for Computational Physics , Universität Stuttgart , Allmandring 3 , 70569 Stuttgart , Germany
| | - Bibek Adhikari
- Institute for Computational Physics , Universität Stuttgart , Allmandring 3 , 70569 Stuttgart , Germany
| | - Sheng Meng
- Institute of Physics , Chinese Academy of Sciences , Zhongguancun , Beijing 100190 , China
| | - Frank Uhlig
- Institute for Computational Physics , Universität Stuttgart , Allmandring 3 , 70569 Stuttgart , Germany
| | - Maria Fyta
- Institute for Computational Physics , Universität Stuttgart , Allmandring 3 , 70569 Stuttgart , Germany
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5
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Wang YT, Zhao YJ, Liao JH, Yang XB. Theoretical investigations on diamondoids (C nH m, n = 10-41): Nomenclature, structural stabilities, and gap distributions. J Chem Phys 2018; 148:014306. [PMID: 29306287 DOI: 10.1063/1.5004437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Combining the congruence check and the first-principles calculations, we have systematically investigated the structural stabilities and gap distributions of possible diamondoids (CnHm) with the carbon numbers (n) from 10 to 41. A simple method for the nomenclature is proposed, which can be used to distinguish and screen the candidates with high efficiency. Different from previous theoretical studies, the possible diamondoids can be enumerated according to our nomenclature, without any pre-determination from experiments. The structural stabilities and electronic properties have been studied by density functional based tight binding and first-principles methods, where a nearly linear correlation is found between the energy gaps obtained by these two methods. According to the formation energy of structures, we have determined the stable configurations as a function of chemical potential. The maximum and minimum energy gaps are found to be dominated by the shape of diamondoids for clusters with a given number of carbon atoms, while the gap decreases in general as the size increases due to the quantum confinement.
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Affiliation(s)
- Ya-Ting Wang
- Department of Physics, South China University of Technology, Guangzhou 510640, People's Republic of China
| | - Yu-Jun Zhao
- Department of Physics, South China University of Technology, Guangzhou 510640, People's Republic of China
| | - Ji-Hai Liao
- Department of Physics, South China University of Technology, Guangzhou 510640, People's Republic of China
| | - Xiao-Bao Yang
- Department of Physics, South China University of Technology, Guangzhou 510640, People's Republic of China
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6
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Adhikari B, Sivaraman G, Fyta M. Diamondoid-based molecular junctions: a computational study. NANOTECHNOLOGY 2016; 27:485207. [PMID: 27819796 DOI: 10.1088/0957-4484/27/48/485207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this work, we deal with the computational investigation of diamondoid-based molecular conductance junctions and their electronic transport properties. A small diamondoid is placed between the two gold electrodes of the nanogap and is covalently bonded to the gold electrodes through two different molecules, a thiol group and a N-heterocyclic carbene molecule. We have shown that the thiol linker is more efficient as it introduces additional electron paths for transport at lower energies. The influence of doping the diamondoid on the properties of the molecular junctions has been investigated. We find that using a nitrogen atom to dope the diamondoids leads to a considerable increase of the zero bias conductance. For the N-doped system we show an asymmetric feature of the I-V curve of the junctions resulting in rectification within a very small range of bias voltages. The rectifying nature is the result of the characteristic shift in the bias-dependent highest occupied molecular orbital state. In all cases, the efficiency of the device is manifested and is discussed in view of novel nanotechnological applications.
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Affiliation(s)
- Bibek Adhikari
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
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7
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Sivaraman G, Amorim RG, Scheicher RH, Fyta M. Benchmark investigation of diamondoid-functionalized electrodes for nanopore DNA sequencing. NANOTECHNOLOGY 2016; 27:414002. [PMID: 27607107 DOI: 10.1088/0957-4484/27/41/414002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Small diamond-like particles, diamondoids, have been shown to effectively functionalize gold electrodes in order to sense DNA units passing between the nanopore-embedded electrodes. In this work, we present a comparative study of Au(111) electrodes functionalized with different derivatives of lower diamondoids. Focus is put on the electronic and transport properties of such electrodes for different DNA nucleotides placed within the electrode gap. The functionalization promotes a specific binding to DNA leading to different properties for the system, which provides a tool set to systematically improve the signal-to-noise ratio of the electronic measurements across the electrodes. Using quantum transport calculations, we compare the effectiveness of the different functionalized electrodes in distinguishing the four DNA nucleotides. Our results point to the most effective diamondoid functionalization of gold electrodes in view of biosensing applications.
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Affiliation(s)
- Ganesh Sivaraman
- Institute for Computational Physics, Universität Stuttgart, Stuttgart, Germany
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8
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Adhikari B, Meng S, Fyta M. Carbene-mediated self-assembly of diamondoids on metal surfaces. NANOSCALE 2016; 8:8966-8975. [PMID: 27074198 DOI: 10.1039/c5nr08709k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
N-heterocyclic carbenes (NHC)s are emerging as an alternative class of molecules to thiol-based self-assembled monolayers (SAMs), making carbene-based SAMs much more stable under harsh environmental conditions. In this work, we have functionalized tiny diamondoids using NHCs in order to prepare highly stable carbene-mediated diamondoid SAMs on metal substrates. Using quantum-mechanical simulations and two different configurations for the carbene-functionalized diamondoids attached on gold, silver, and platinum surfaces we were able to study in detail these materials. Specifically, we focus on the binding characteristics, stability, and adsorption of the NHC-mediated diamondoid SAMs on the metal surfaces. A preferential binding to platinum surfaces was found, while a modulation of the work function in all cases was clear. The surface morphology of all NHC-based diamondoid SAMs was revealed through simulated STM images, which show characteristic features for each surface.
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Affiliation(s)
- Bibek Adhikari
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
| | - Sheng Meng
- Institute of Physics, Chinese Academy of Sciences, Zhongguancun, Beijing, 100190, China
| | - Maria Fyta
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
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9
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Electron-vibration coupling induced renormalization in the photoemission spectrum of diamondoids. Nat Commun 2016; 7:11327. [PMID: 27103340 PMCID: PMC4844694 DOI: 10.1038/ncomms11327] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 03/16/2016] [Indexed: 01/03/2023] Open
Abstract
The development of theories and methods devoted to the accurate calculation of the electronic quasi-particle states and levels of molecules, clusters and solids is of prime importance to interpret the experimental data. These quantum systems are often modelled by using the Born–Oppenheimer approximation where the coupling between the electrons and vibrational modes is not fully taken into account, and the electrons are treated as pure quasi-particles. Here, we show that in small diamond cages, called diamondoids, the electron–vibration coupling leads to the breakdown of the electron quasi-particle picture. More importantly, we demonstrate that the strong electron–vibration coupling is essential to properly describe the overall lineshape of the experimental photoemission spectrum. This cannot be obtained by methods within Born–Oppenheimer approximation. Moreover, we deduce a link between the vibronic states found by our many-body perturbation theory approach and the well-known Jahn–Teller effect. The electron–vibration coupling is essential to describe the photoelectron properties of molecules. Here, the authors show theoretically and experimentally that the electron–vibration coupling is very large in diamonoids, and link the deduced vibronic states to the well-known Jahn–Teller effect.
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10
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Banerjee S, Baiardi A, Bloino J, Barone V. Temperature Dependence of Radiative and Nonradiative Rates from Time-Dependent Correlation Function Methods. J Chem Theory Comput 2016; 12:774-86. [DOI: 10.1021/acs.jctc.5b01017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shiladitya Banerjee
- Scuola Normale Superiore, piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Consiglio Nazionale
delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Alberto Baiardi
- Scuola Normale Superiore, piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Julien Bloino
- Scuola Normale Superiore, piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Consiglio Nazionale
delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, piazza
dei Cavalieri 7, I-56126 Pisa, Italy
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11
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Banerjee S, Stüker T, Saalfrank P. Vibrationally resolved optical spectra of modified diamondoids obtained from time-dependent correlation function methods. Phys Chem Chem Phys 2015; 17:19656-69. [PMID: 26151912 DOI: 10.1039/c5cp02615f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Optical properties of modified diamondoids have been studied theoretically using vibrationally resolved electronic absorption, emission and resonance Raman spectra. A time-dependent correlation function approach has been used for electronic two-state models, comprising a ground state (g) and a bright, excited state (e), the latter determined from linear-response, time-dependent density functional theory (TD-DFT). The harmonic and Condon approximations were adopted. In most cases origin shifts, frequency alteration and Duschinsky rotation in excited states were considered. For other cases where no excited state geometry optimization and normal mode analysis were possible or desired, a short-time approximation was used. The optical properties and spectra have been computed for (i) a set of recently synthesized sp(2)/sp(3) hybrid species with C[double bond, length as m-dash]C double-bond connected saturated diamondoid subunits, (ii) functionalized (mostly by thiol or thione groups) diamondoids and (iii) urotropine and other C-substituted diamondoids. The ultimate goal is to tailor optical and electronic features of diamondoids by electronic blending, functionalization and substitution, based on a molecular-level understanding of the ongoing photophysics.
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Affiliation(s)
- Shiladitya Banerjee
- Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Straße 24-25, D-14476 Potsdam-Golm, Germany.
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12
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Adhikari B, Fyta M. Towards double-functionalized small diamondoids: selective electronic band-gap tuning. NANOTECHNOLOGY 2015; 26:035701. [PMID: 25549002 DOI: 10.1088/0957-4484/26/3/035701] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Diamondoids are nanoscale diamond-like cage structures with hydrogen terminations, which can occur in various sizes and with a diverse type of modifications. In this work, we focus on the structural alterations and the effect of doping and functionalization on the electronic properties of diamondoids, from the smallest adamantane to heptamantane. The results are based on quantum mechanical calculations. We perform a self-consistent study, starting with doping the smallest diamondoid, adamantane. Boron, nitrogen, silicon, oxygen, and phosphorus are chosen as dopants at sites which have been previously optimized and are also consistent with the literature. At a next step, an amine- and a thiol- group are separately used to functionalize the adamantane molecule. We mainly focus on a double functionalization of diamondoids up to heptamantane using both these atomic groups. The effect of isomeration in the case of tetramantane is also studied. We discuss the higher efficiency of a double-functionalization compared to doping or a single-functionalization of diamondoids in tuning the electronic properties, such as the electronic band-gap, of modified small diamondoids in view of their novel nanotechnological applications.
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Affiliation(s)
- Bibek Adhikari
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
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13
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Clay WA, Dahl JEP, Carlson RMK, Melosh NA, Shen ZX. Physical properties of materials derived from diamondoid molecules. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:016501. [PMID: 25551840 DOI: 10.1088/0034-4885/78/1/016501] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Diamondoids are small hydrocarbon molecules which have the same rigid cage structure as bulk diamond. They can be considered the smallest nanoparticles of diamond. They exhibit a mixture of properties inherited from bulk cubic diamond as well as a number of unique properties related to their size and structure. Diamondoids with different sizes and shapes can be separated and purified, enabling detailed studies of the effects of size and structure on the diamondoids' properties and also allowing the creation of chemically functionalized diamondoids which can be used to create new materials. Most notable among these new materials are self-assembled monolayers of diamondoid-thiols, which exhibit a number of unique electron emission properties.
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Affiliation(s)
- W A Clay
- Stanford Institute for Materials and Energy Science, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA. Geballe Laboratory for Advanced Materials, Department of Physics and Applied Physics, Stanford University, CA 94305
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14
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Maier FC, Sivaraman G, Fyta M. The role of a diamondoid as a hydrogen donor or acceptor in probing DNA nucleobases. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2014; 37:95. [PMID: 25339284 DOI: 10.1140/epje/i2014-14095-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/01/2014] [Indexed: 06/04/2023]
Abstract
It has been shown that diamondoids can interact with DNA by forming relatively strong hydrogen bonds to DNA units, such as nucleobases. For this interaction to occur the diamondoids must be chemically modified in order to provide donor/acceptor groups for the hydrogen bond. We show here that the exact arrangement of an amine-modified adamantane with respect to a neighboring nucleobase has a significant influence on the strength of the hydrogen bond. Whether the diamondoid acts as a hydrogen donor or acceptor in the hydrogen binding to the nucleobase affects the electronic structure and thereby the electronic band-gaps of the diamondoid-nucleobase complex. In a donor arrangement of the diamondoid close to a nucleobase, the interaction energies are weak, but the electronic band-gaps differ significantly. Exactly the opposite trend is observed in an acceptor arrangement of the diamondoid. In each of these cases the frontier orbitals of the diamondoid and the nucleobase play a different role in the binding. The results are discussed in view of a diamondoid-based biosensing device.
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Affiliation(s)
- Frank C Maier
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, 70596, Stuttgart, Germany
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15
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Savoca M, Langer J, Harding DJ, Palagin D, Reuter K, Dopfer O, Fielicke A. Vibrational spectra and structures of bare and Xe-tagged cationic SinOm+ clusters. J Chem Phys 2014; 141:104313. [DOI: 10.1063/1.4894406] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Marco Savoca
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
| | - Judith Langer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
| | - Dan J. Harding
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
| | - Dennis Palagin
- Lehrstuhl für Theoretische Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Karsten Reuter
- Lehrstuhl für Theoretische Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
| | - André Fielicke
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
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16
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Maier FC, Fyta M. Type-dependent identification of DNA nucleobases by using diamondoids. Chemphyschem 2014; 15:3466-75. [PMID: 25145625 DOI: 10.1002/cphc.201402335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Indexed: 01/16/2023]
Abstract
The possibility of distinguishing between DNA nucleobases of different sizes is manifested here through quantum-mechanical simulations. By using derivatives of small, modified diamond clusters, known as diamondoids, it is possible to separate the pyrimidines (cytosine and thymine) from the larger purines (adenine and guanine), according to the collective electronic and binding properties of these DNA nucleobases and the diamondoid. The latter acts as a probe with which these properties can be examined in detail. Short single-stranded DNA is built up from single nucleobases to reveal the effect of each DNA unit on the sensing abilities of the diamondoid probe. Several ways of orienting the nucleobases, nucleosides, nucleotides, and short single-stranded DNA are investigated; these lead to quite different electronic properties and may or may not enhance the possibility of separating the DNA nucleobases. For the optimum orientation, that is, one that promotes stronger hydrogen bonding of the diamondoid to the short DNA strand, it is found that the electronic band gaps of a purine strand lie in a completely different range to the band gaps of a pyrimidine strand. This difference can be over 1 eV, which is measurable and shows the potential of using diamondoids and their derivatives in biosensing devices.
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Affiliation(s)
- Frank C Maier
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, 70569 Stuttgart (Germany)
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17
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Demján T, Vörös M, Palummo M, Gali A. Electronic and optical properties of pure and modified diamondoids studied by many-body perturbation theory and time-dependent density functional theory. J Chem Phys 2014; 141:064308. [DOI: 10.1063/1.4891930] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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18
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Sivaraman G, Fyta M. Chemically modified diamondoids as biosensors for DNA. NANOSCALE 2014; 6:4225-4232. [PMID: 24608602 DOI: 10.1039/c3nr06417d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Understanding the interaction of biological molecules with materials is essential in view of the novel potential applications arising when these two are combined. To this end, we investigate the interaction of DNA with diamondoids, a broad family of tiny hydrogen-terminated diamond clusters with high technological potential. We model this interaction through quantum-mechanical computer simulations and focus on the hydrogen bonding possibilities of the different DNA nucleobases to the lower amine-modified diamondoids with respect to their relative distance and orientation. Our aim is to promote the binding between these two units, and probe this through the association energy, the electronic structure of the nucleobase-diamondoid system, and the specific role of their frontier orbitals. We discuss the relevance of our results in view of biosensing applications and specifically nanopore sequencing of DNA.
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Affiliation(s)
- Ganesh Sivaraman
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
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19
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Banerjee S, Saalfrank P. Vibrationally resolved absorption, emission and resonance Raman spectra of diamondoids: a study based on time-dependent correlation functions. Phys Chem Chem Phys 2014; 16:144-58. [DOI: 10.1039/c3cp53535e] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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20
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Rander T, Staiger M, Richter R, Zimmermann T, Landt L, Wolter D, Dahl JE, Carlson RMK, Tkachenko BA, Fokina NA, Schreiner PR, Möller T, Bostedt C. Electronic structure tuning of diamondoids through functionalization. J Chem Phys 2013; 138:024310. [DOI: 10.1063/1.4774268] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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21
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Vörös M, Demjén T, Szilvási T, Gali A. Tuning the optical gap of nanometer-size diamond cages by sulfurization: a time-dependent density functional study. PHYSICAL REVIEW LETTERS 2012; 108:267401. [PMID: 23005011 DOI: 10.1103/physrevlett.108.267401] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Indexed: 06/01/2023]
Abstract
The optical gap of nanometer sized diamond cages, i.e., diamondoids, lies in the ultraviolet spectral region. Here we show by hybrid functional based time-dependent density-functional calculations that, by varying the number of C=S double bonds at the surface of diamondoids, the absorption onset can be tuned toward the infrared spectral region. Our finding has an important implication for in vivo biological applications where toxic and unstable dye molecules may be substituted by the luminescent sulfurized diamondoids.
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Affiliation(s)
- Márton Vörös
- Department of Atomic Physics, Budapest University of Technology and Economics, Budafoki út 8., H-1111, Budapest, Hungary
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