Adsorption Of Cytosine Research Articles

Adsorption of cytosine on Si and Ge doped graphene: A DFT study

This study describes how the cytosine adsorption on Si and Ge-doped Graphene uses density functional theory (DFT) calculations. The adsorption energies of cytosine on Si and Ge-doped Graphene are computed. The method used a hybrid B3LYP approach with 6-31G (d,p) and LANL2DZ basis sets to determine the Highest Occupied Molecular Orbital -Lowest Unoccupied Molecular Orbital HOMO and LUMO states and descriptors; and charge distribution potential. According to charge distributions, both Ge-doped and Si-doped graphene structures are sensitive to the cytosine base. The DNA base cytosine plays a crucial role as an adsorbent. When cytosine was adsorbed on Ge- and Si-doped graphene structures, the Highest Occupied Molecular Orbital -Lowest Unoccupied Molecular Orbital (HOMO-LUMO) gap decreased. This finding implies that the electrical conductivity of both systems has increased. The result shows that the Ge- and Si-doped graphene structures might be introduced as strong adsorbents for biosensor applications in various fields.

Adsorption of cytosine on prebiotic siliceous clay surface induced with metal dications: Relevance to origin of life

Adsorption of protobiomolecules on primigenial mineral surfaces transacts a very specific and selective role in prebiotic chemical evolution. Cytosine (CYN) is a core constituent of genetic macromolecules i.e., DNA and RNA. A prebiotic simulation experiment following adsorption behaviour of a nucleic acid base CYN, as a function of pH, concentration, time and temperature on the surface of Montmorillonite (MMT), a prominent siliceous clay of smectite group having specific surface area, was studied systematically and methodically using UV, FTIR, SEM and XRD. Biologically significant metal dication [M2+ = Mg2+, Ca2+, Fe2+ and Cu2+] embeded surfaces of MMT (MMT-M2+) were prepared separately by cation-exchange approach. Results observed through UV spectral data reveal a very significant role of metal ions on the quantity of CYN adsorbed on different solid surfaces. The adsorption behaviour fitted well with Langmuir isotherm model and the adsorption isotherm shows monolayer formation of CYN (as adsorbate) on the surface of MMT and MMT-M2+(as adsorbent) showing Langmuir type adsorption. The calculated Langmuir adsorption parameters (KL& Xm) delineate appreciable interaction of CYN on MMT-Fe2+ surface following MMT-Cu2+ as compared to MMT alone and to other metal induced MMTs.In terms of % binding and Xm data, the effectiveness of various adsorbents in adsorption of CYN on MMT/MMT-M2+ at pH 6.6 and temperature 298K was found in the order; MMT-Fe2+> MMT-Cu2+> MMT > MMT-Ca2+> MMT-Mg2+. The results were further confirmed by SEM, XRD and FTIR which also support the outcomes. The present work throws light on the affinity of MMT clay (having multifarious applications in biological systems) with and without biogenic metal diions towards the surface interaction of nucleic acid base mimicking primeval sea shore/sea bed or hydrothermal vent conditions deciphering the phenomena that how biomonomers could have been protected from extreme hazardous conditions of primitive Earth and stabilized during chemical evolution and availed them for consecutive molecular evolution. Results further embark better adsorption capability of transition metal ion incorporated MMTs than the clay without metal ion and exchanged with alkaline Earth dications.

Effects of Potential and Anions on the Adsorption of Cytosine on the Au(111) Electrode in Neutral Media

Effects of Potential and Anions on the Adsorption of Cytosine on the Au(111) Electrode in Neutral Media

A STM view of the reorientation of cytosine adsorbed on the Au(111) – (1 × 1) electrode in sulfuric and perchloric acids

The adsorption of cytosine (C) on gold electrode has been studied to gain a fundamental understanding of the interaction between biomolecule and metal entity, which has important ramifications in the modern research on biological surface science. The characteristics of tautomerization and acid-base equilibrium of C at Au(111) electrode are intriguing and challenging to the modern study of electrified interface. Although this system has been studied by using in situ scanning tunneling microscopy (STM) and vibrational spectroscopy, many critical issues such as intermolecular interaction, substrate structure, and concentration of C are yet to be explored. High-resolution STM was used in the current study to probe the structure of C adsorbed on an Au(111) electrode in sulfuric and perchloric acids as a function of potential and [C]. C molecules arranged differently on the Au(111) – (1 × 1) substrate in 0.1 M H2SO4 and HClO4 containing 1 mM C, indicating that anion was coadsorbed with C admolecule. Adsorbed C was protonated at the negative potential, but deprotonated at the positive potential. Meanwhile, C admolecule reoriented from horizontal to upright configuration, as inferred from the ordered structures observed at different potentials. The surface coverage of C on Au(111), evaluated from the ordered structures, increased with more positive potential and grew into a multilayer film in 1 mM C in these acids.

Computational Insights into Molecular Adsorption Characteristics of Methylated DNA on Graphene Oxide for Multicancer Early Detection.

DNA methylation is an epigenetic modification involving the transfer of a methyl group to cytosine residues of a DNA molecule. Altered DNA methylation of certain genes is associated with several diseases including cancer. Nanomaterials, such as graphene oxide (GO), offer great potential as sensing elements for methylated DNA (mDNA) detection due to their distinct properties. Understanding molecular interactions between mDNA and GO can make provision for developing a universal cancer screening test. Molecular dynamics (MD) simulation and density functional theory (DFT) calculation have been employed for investigating their detailed macro- and microscale interactions. Based upon the MD simulation, different adsorption levels of methylated and unmethylated DNAs on GO were represented by a contacting surface area (CSA), which depends on surrounding conditions (in water or a MgCl2 solution). In water, the CSAs of the methylated and unmethylated single-stranded DNA (ssDNA) were ≈13 and ≈5 nm2, respectively, representing more preferable adsorption on GO for the methylated ssDNA. In the presence of divalent ions (Mg2+), the CSAs of both methylated and unmethylated DNA molecules were ≈8 nm2, suggesting that there was no significant difference in adsorption in a saline solution. To reveal the electrical property of GO covered by either methylated or unmethylated DNA, its electronic structure was investigated by the DFT calculation. The energy gaps of pristine graphene (pG) and GO adsorbed by 5-methylcytosine (5mC) were 1.6 and 12.9 meV, respectively, while cytosine adsorption resulted in lower energy gaps (1.2 meV for pG and 9.5 meV for GO). When comparing methylated DNA-covered GO with that covered with unmethylated DNA, remarkable differences in electrical conductivity, which were caused by the electronic structure of GO, were observed. These findings will provide a new route for an efficient detection method of DNA methylation, which can further be used to develop a universal cancer test.

A DFT study on the adsorption of nucleobases with Au20.

The interactions of nucleobase with Au20 cluster were studied utilizing density functional theory (DFT). We find that the nucleobases were attached with Au20 through Au-N or Au-O bonds. The orders of calculated adsorption energy are cytosine > adenine > guanine > thymine. The maximum adsorption energy is - 0.787eV which belongs to the adsorption of cytosine on Au20 cluster. Our calculations show that the HOMO-LUMO gaps of Au20 are significantly decreased by the nucleobase adsorption, suggesting the potential detection for nucleobases. The interactions between Au20 and nucleobases are revealed through the QTAIM analysis. The NBO analysis was investigated for the electron transfer of donor-acceptor of all types of complexes. The IR and UV-vis spectra were simulated for the further identification in the experiment.

Density Functional Theory Calculations of the Adsorption of Cytosine on Si(100)

We have performed density functional theory (DFT) calculations to investigate the adsorption structures of cytosine on Si(100). Multiple adsorption configurations that could result from Lewis acid–base reactions or cycloadditions were optimized, and the structural and energetic parameters of the obtained adsorption structures were compared. Row‐bridged bidentate configurations with SiOCNCNSi linkages to two silicon atoms in adjacent dimer rows were found to be more stable than other configurations. The SiN bond was formed by NH dissociative adsorption, while the SiO bond was dative. In the monodentate structures, the CH or NH dissociative adsorption structures were more energetically favorable than the datively bonded ones. Cycloaddition through the π‐electrons of the CN or CC bonds of the cytosine ring resulted in relatively unstable adsorption products.

Theoretical Model for Surface Forces between Cytosine and CNT(6,6-6) Nanotube: Geometry Optimization, Molecular Structure, Intermolecular Hydrogen Bond, Spectroscopic (NMR, UV/Vis, Excited State), FMO, MEP, and HOMO–LUMO Investigations

In the present work, the adsorption of the molecule cytosine on carbon nanotube [CNT] (6,6-6) was investigated for the first time using density functional theory (DFT) calculations in the gas phase. The non-bonded interaction effect of compounds cytosine and CNT(6,6-6) nanotube on the electronic properties, chemical shift tensors and natural charge was investigated. The electronic properties of the obtained complex change after cytosine adsorption. The natural charge analysis showed that the charge transfer occurs between cytosine and CNT(6,6-6) nanotube and it was induced the dipole moment to the CNT(6,6-6) nanotube. Moreover, the formation of an intermolecular hydrogen bond between cytosine and CNT(6,6-6) nanotube has been investigated. The electronic spectra of the isolated molecule cytosine and the complex CNT(6,6-6)/cytosine in the gas phase were calculated by time dependent density functional theory (TD-DFT). The various parameters such as equilibrium geometry, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO) of the cytosine and CNT(6,6-6) nanotube were calculated and discussed consequently.

In situ surface enhanced infrared absorption spectroscopy study of the adsorption of cytosine on gold electrodes

The structural facilities provided by the ‘in situ’ Surface-Enhanced Infrared Absorption Spectroscopy in the Attenuated Total Reflection mode (ATR-SEIRAS) are exploited for the characterization of cytosine adsorption on gold thin-film electrodes from acid, neutral and basic solutions, using H2O and D2O as solvents. The experimental conditions are selected in order to consider the two forms involved in the first acid-base equilibrium and in the tautomeric keto-enol and amino-imino equilibria of the molecule. The results are compared with the corresponding absorption FT-IR spectra of cytosine in solution. DFT calculations are used to optimize the molecular geometries and to estimate the vibrational properties of the different acid-base and tautomeric forms, either in solution or in the adsorbed state on gold surfaces.The comparison between the spectra in solution and in the adsorbed state indicates the adsorption of the deprotonated form even at pH bellow the first pKa of cytosine. Therefore, only the tautomeric forms of the deprotonated cytosine are considered: the keto-amino (C1 and C4), the enol-amino (C2) and the keto-imino (C3) tautomers of cytosine and of deuterated cytosine molecules.Interpretations of the absorption FT-IR spectra of the molecules in solution based on DFT calculations suggest the preponderance of the C1 tautomer in solution but with contributions of the C3 tautomer, in neutral and basic media. However, the interpretations of the ATR-SEIRAS experiments show the preponderance of tautomer C3 in the adsorbed state with contributions of tautomer C1 depending not only on the pH of the solution, but also on the potential applied to the electrode.

Adsorption behavior of cytosine and guanine nucleobases on graphyne nanosheets: A DFT study

We explored the cytosine and guanine nitrogenous bases adsorption over pure and boron substituted graphyne (Gpn) nanosheet. Initially, the stability of Gpn nanosheet is ascertained by formation energy and found to be stable. Also, the energy gap and density of states (DOS) spectrum are investigated for isolated condition and cytosine, and guanine adsorbed Gpn nanosheet. The adsorption energy shows physisorption type of adsorption for cytosine and guanine bases on Gpn nanosheet. Further, the charge transfer and energy gap deviation are also observed upon cytosine and guanine adsorption. The results reveal that pure and boron substituted Gpn nanosheet are promising nanostructures for adsorption of cytosine and guanine nucleobases.

ONIOM DFT study of the adsorption of cytosine on the Au/Ag and Ag/Au bimetallic nanosurfaces: The effect of sublayer

In this work, the adsorption of cytosine (CYT) on the Au/Ag and Ag/Au bimetallic nanosurfaces has been studied using density functional theory (DFT) in the scheme of the “our own n-layered integrated molecular orbital and molecular mechanics” (ONIOM) and compared with its adsorption on pure Au and Ag nanosurfaces, respectively. It was found the arrangement of Au and Ag layers on each other in the nanosurface has considerable effect on the adsorption energy (Ead), adsorption mode and the charge transfer between the CYT and nanosurface. The presence of Ag as sublayer in the Au/Ag nanosurface decreases the Ead of the CYT, increases the vertical distance of the CYT from the surface and changes its tilting direction from its oxygen atom to nitrogen atom of ring CN compared to the adsorption of the CYT on pure Au nanosurface. The opposite trend has been seen for the adsorption of the CYT on the Ag/Au nanosurface which Au is as sublayer compared to the adsorption of the CYT on pure Ag surface. The tilting of the CYT from its oxygen atom on the Ag/Au nanosurface increases compared to that on pure Ag surface. Also, it has been shown that the Ag sublayers increase the charge transfer from the CYT to the Au/Ag nanosurface while the Au sublayers decrease the charge transfer from the CYT to the Ag/Au nanosurface, significantly. The quantum theory of atoms in molecules (QTAIM) has been also used to determine the interatomic interaction lines between the CYT and nanosurfaces to determine which atoms of the CYT and first layer of nanosurfaces are in local interactions with each other. The interaction energies of the CYT with the selected nanosurfaces have also been calculated at the Hartree-Fock (HF) level of theory and compared with those obtained using the DFT method to understand the reason of the change of Eint due to the sublayers.

Potential of metal–fullerene hybrids as strong nanocarriers for cytosine and guanine nucleobases: A detailed DFT study

In this article, the adsorption of cytosine and guanine molecules on the surface of Cr-doped C20 fullerene (C19Cr) and Ni-doped C20 fullerene (C19Ni) are studied using first-principles density functional theory (DFT) calculations. In order to thoroughly comprehend the influences of the molecules on the metal-fullerene complexes, the geometric parameters, the binding energies, transferred charges, the magnitude of dipole moments, thermochemical parameters, frontier molecular orbitals, and the global indices of activities are calculated. The results highlighted that the interactions of both cytosine and guanine molecules with metal-fullerene complexes are highly exothermic, suggesting that these molecules might be chemisorbed on their adsorbents. The C19Cr exhibits a better adsorption behavior toward the molecules compared to C19Ni, and cytosine has the higher binding energies with metal-fullerene complexes in comparison with guanine. Further analyses showed that the C19Cr experiences significant changes in its electronic properties upon adsorption of the cytosine molecule. However, the small variations in the electronic properties of C19Ni after complexation with guanine indicate that this complex is not sensitive to the guanine. Furthermore, the results of frontier molecular orbital reveal the strong (moderate) interactions between the C19Cr with the cytosine (guanine) molecule and moderate (weak) interactions between the C19Ni with the cytosine (guanine) molecule. Therefore, the C19Cr and C19Ni have moderate sensitivities to cytosine and guanine molecules. More excitingly, our findings divulge promising potential of the Cr-fullerene complex as a biochemical adsorbent for cytosine.

Surface study of gallium- and aluminum- doped graphenes upon adsorption of cytosine: DFT calculations

The adsorption of cytosine molecule on Al- and Ga- doped graphenes is studied using first-principles density functional theory (DFT) calculations. The energetically most stable geometries of cytosine on both Al- and Ga- doped graphenes are determined and the adsorption energies are calculated. The net charge of transfer as well as local charge of doped atoms upon adsorption of cytosine are studied by natural bond orbitals (NBO) analysis. Orbital hybridizing of complexes was searched by frontier molecular orbital theory (FMO), and density of states (DOS). Depending on the side of cytosine, there are four possible sites for its adsorption on doped graphene; denoted as P1, P2, P3, and P4, respectively. The order of binding energy in the case of Al-doped graphene is found as P1˃P4˃P3˃P2. Interestingly, the order in the case of Ga-doped graphene changes to: P4∼P1˃P3˃P2. Both surfaces show superior adsorbent property, resulting chemisorption of cytosine, especially at P1 and P4 position configurations. The NBO charge analysis reveals that the charge transfers from Al- and Ga- doped graphene sheets to cytosine. The electronic properties of both surfaces undertake important changes after cytosine adsorption, which indicates notable change in its electrical conductivity.

Adsorption of Cytosineon Single-walled Carbon Nanotubes

The adsorption of cytosine on metallic pristine single walled carbon nanotubes (SWNT) surface is investigated using density functional theory with local density approximation. On the SWNT, cytosine is physis orbed by taking the π-π interaction. Binding energy reported in this case is around -0.38 eV. By introducing metal atoms to the cytosine- SWNT, interaction can be strongly enhanced. The enhanced binding energies increases to -0.56 and -2.20 eV in presence of Li and Co atoms. Using pristine SWNT, electric sensor based on Co- doped SWNT depicts more sensitivity. Reported work gives insight into SWNT-based bio- sensors enhanced by doping appropriate metal atoms.

A computational study of adenine, uracil, and cytosine adsorption upon AlN and BN nano-cages

Density-functional theory calculations are used to investigate the interaction of Al12N12 and B12N12 clusters with the adenine (A), uracil (U), and cytosine (C) molecules. The current calculations demonstrate that these hybrid adsorbent materials are able to adsorb the adenine, uracil, and cytosine molecules through exothermic processes. Our theoretical results reveal improvement in the adsorption of adenine, uracil, and cytosine on Al12N12 and B12N12. It is observed that B12N12 is highly sensitive to adenine, uracil, and cytosine compared with Al12N12 to serve as a biochemical sensor.

Adsorption of Cytosine and AZA Derivatives of Cytidine on Au Single Crystal Surfaces

The adsorption of cytosine on the Au(111) and Au(110) surfaces has been studied using both aqueous deposition and evaporation in vacuum to prepare the samples. Soft X-ray photoelectron spectroscopy (XPS) and near edge X-ray absorption fine structure spectroscopy (NEXAFS) were used to determine the electronic structure and orientation of the adsorbates. In addition, three derivatives of cytosine, 6-azacytosine, 6-azacytidine and 5- azacytidine, were studied. Monolayer films of the latter three samples were adsorbed on Au(111) from aqueous solution, and the nature of bonding was determined. Spectra have been interpreted in the light of published calculations of free cytosine molecules and new ab initio calculations of the other compounds. Surface core level shifts of Au 4f imply that all of these compounds are chemisorbed. Cytosine adsorbs as a single tautomer, but in two chemical states with different surface-molecule bonding. For deposition in vacuum, a flat-lying molecular state bonded through the N(3) atom of the pyrimidine ring dominates, but a second state is also present. For deposition from solution, the second state dominates, with the molecular plane no longer parallel to the surface. This state also bonds through the N(3) atom, but in addition interacts with the surface via the amino group. Two tautomers of 6-azacytosine were observed, and they and 6-azacytidine adsorb with similar geometries, chemically bonding via the azacytosine ring. The ribose ring does not appear to perturb the adsorption of azacytidine compared with azacytosine. The azacytosine ring is nearly but not perfectly parallel to the surface, like 5-azacytidine, which adsorbs as an imino tautomer. ...

Interaction of DNA Bases with Gold Substrates

The interaction of molecules with inorganic substrates is a crucial issue forapplications in molecular electronics. It influences important factors suchas the immobilization efficiency and the charge injection through the inter-face. Moreover, mechanical aspects connected to the unfolding of biologicalmolecules are important.We hereby present recent efforts in our group to tackle these problems,based on density functional theory calculations. In particular, we discussour results on the adsorption of cytosine on Au(111) and on the interactionof guanine, in its natural and size-expanded forms, with small Au clusters.We find that cytosine binds to the Au(111) surface with a mechanism thatinvolves charge sharing, intermediate between chemisorption and physisorp-tion. The investigation of small complexes between guanine and gold clustersreveals the formation of hydrogen bonds: these configurations with unusualbonds are relevant at the corners of nanoparticles, while they can probably beneglected when DNA binds on flat extended metal surfaces.

A Density Functional Theory Study of Cytosine on Au(111)

The adsorption of cytosine on Au(111) is investigated using density functional theory with the nonlocal van der Waals density functional. Test calculations performed on the benzene stacked dimer and on a benzene molecule adsorbed on Au(111) allow us to assess the methodology and reveal the accuracy and predictivity of the van der Waals density funcional relative to experimental outcome. Our results for cytosine on Au(111) indicate that the inclusion of dispersion interactions is crucial for the treatment of this system. In fact, such terms enhance the value of the adsorption energy and also affect the cytosine bonding geometry: in particular, we find that a tilted geometry is always favorable relative to a parallel geometry, which was not found in standard density functional theory investigations. The combined new data for energetics and geometry lead to conclusions that contrast the common opinion that the surface–molecule interaction is negligible in the process of monolayer formation.

Prevention of surface reconstruction at the Au(110)/electrolyte interface by the adsorption of cytosine

It is shown that the adsorption of cytosine at the Au(110)/liquid interface at a potential of 0.0 V "freezes" the Au(110) surface in the (1x1) structure and that the molecule does not change its orientation on the surface as the potential is varied. In contrast the adsorption of adenine does not freeze the Au(110) surface even though both molecules adopt a base stacking structure with individual molecules oriented in a plane vertical to the Au(110) surface with their long axes along [110] rows. It is suggested that cytosine bonds to three Au atoms through the NH(2) group, the N(3) and O(8) sites, and that this arrangement stabilizes the Au(110) surface and prevents its reconstruction to the more open (1x2) and (1x3) structures as the applied voltage is varied. The weaker bonding of the adenine molecule with the gold surface is unable to prevent the voltage induced reconstruction of the Au(110) surface.

FIRST PRINCIPLES STUDY OF CYTOSINE ADSORPTION ON GRAPHENE

The adsorption of cytosine on graphene surface is studied using density functional theory with local density approximation. The cytosine is physisorbed onto graphene through π–π interaction, with a binding energy around -0.39 eV. Due to the weak interaction, the electronic properties of graphene show little change upon adsorption. The cytosine/graphene interaction can be strongly enhanced by introducing metal atoms. The binding energies increase to -0.60 and -2.31 eV in the presence of Li and Co atoms, respectively. The transport behavior of an electric sensor based on Co -doped graphene shows a sensitivity one order of magnitude higher than that of a similar device using pristine graphene. This work reveals that the sensitivity of graphene-based bio-sensors could be drastically improved by introducing appropriate metal atoms.