Thymine Molecules Research Articles

{5′-O-[Bis(4-methoxyphenyl)(phenyl)methyl]-2′-deoxy-β-D-threopentofuranosyl}thymine ethyl acetate 0.25-solvate

The title compound, C(31)H(32)N(2)O(7)·0.25C(4)H(8)O(2), is a key intermediate in the synthesis of [(18)F]fluorine-labelled thymidine ((18)F-FLT), which is the most widely used molecular imaging probe for positron emission tomography (PET). The crystallographic asymmetric unit contains two independent thymine molecules plus one partially occupied site for an ethyl acetate molecule. The two independent thymine molecules show similar geometrical features, except that the dimethoxytrityl groups adopt different orientations with respect to the remainder of the molecule. Each thymine base adopts an anti conformation with respect to the attached deoxyribose ring, and the deoxyribose rings show C3-endo puckering. The conformation of the side chain at the C1 position of the deoxyribose ring is gauche+. Intermolecular N-H···O and O-H···O hydrogen bonds link the molecules into one-dimensional chains.

Comment on “Experimental and theoretical study of the triple-differential cross section for electron-impact ionization of thymine molecules”

In their recent paper, Bellm et al. [Phys. Rev. A 85, 022710 (2012)] performed ($e$,2$e$) experiments on thymine at an incident energy of 250 eV. They wrote in the conclusion that a model based on the first Born approximation using the completely neglected differential overlap description is in very good agreement with the experimental data. On the contrary, we argue that this model fails to describe experiments on water performed at the same incident energy and is unable to explain any shift of the binary or recoil peaks.

Triple-differential cross sections for the ionization of thymine by electrons and positrons

We apply the second Born approximation and the BBK methods to study triple-differential cross sections for the ionization of valence orbitals of a thymine molecule by electrons and positrons. Calculations have been performed for a coplanar geometry at an incident energy of 250 eV and an ejected-electron energy of 20 eV, while the angle of scattering is fixed at 10°. We use an accurate single-centre wavefunction for the initial state of the target and the well-known CNDO model. The present second Born approximation (with the single-centre wavefunction for the initial state) and the BBK model (with the CNDO model) yield cross sections in good agreement with the recent experimental data for electron impact. In the case of positron impact, we find that the contribution of the second term of the Born series is not insignificant for the present kinematics.

Bonded exciplex formation from stacked thymine and adenine: semiclassical simulations

The nonradiative decay of a π-stacked adenine and thymine, following excitation of thymine by an ultrafast laser pulse, was studied by semiclassical dynamics simulations. The simulation found that a bonded exciplex is formed after excitation due to strong interaction between the stacked bases. The strong interaction significantly lowers the energy gap between the LUMO and HOMO and consequently facilitates the deactivation of the electronically excited molecule. It also restricts the deformation vibration of the excited thymine molecule, which slows down the coupling between the HOMO and LUMO energy levels and delays the deactivation of the excited adenine molecule to the electronic ground state.

Systematic studies of the methylation of DNA base molecules from first-principles

We have studied selected DNA base molecules, such as guanine, cytosine, adenine, and thymine, and methylated DNA base molecules from first-principles. The impact of methylation and the rearrangement of the hydrogen atoms of the DNA base molecules on the geometries and the electronic properties are explained with the bond orders, the steric effects, and the molecular topologies. A DNA base molecule without methylation and a corresponding methylated DNA base molecule with the same bond order are expected to have similar HOMO-LUMO energy gaps.

Erratum: Experimental and theoretical study of the triple-differential cross section for electron-impact ionization of thymine molecules [Phys. Rev. A85, 022710 (2012)

Erratum: Experimental and theoretical study of the triple-differential cross section for electron-impact ionization of thymine molecules [Phys. Rev. A<b>85</b>, 022710 (2012)

The self assembly of thymine at Au(110)/liquid interfaces

AbstractWe show that thymine self‐assembles into an ordered structure when adsorbed at a Au(110)/liquid interface. Reflection anisotropy spectroscopy (RAS) shows that as found for cytosine and adenine the adsorbed thymine molecules are oriented essentially vertically on the Au(110) surface with the molecule aligned along one of the principal axes of the Au(110) surface. Simulations of the RA spectra to an empirical model indicates that as found for adsorbed cytosine and adenine, thymine is aligned along the [$1{\bar {1}}0$] direction on the Au(110) surface.

Experimental and theoretical study of the triple-differential cross section for electron-impact ionization of thymine molecules

Triply differential cross sections for the electron-impact ionization of inner valence orbitals of thymine have been measured using the ($e$,2$e$) technique at an incident electron energy of 250 eV. The measurements have been performed with coplanar asymmetric kinematics for scattered electron angles of --10\ifmmode^\circ\else\textdegree\fi{} and --15\ifmmode^\circ\else\textdegree\fi{} and with an ejected-electron energy of 20 eV. Theoretical calculations have been performed within the first-order Born approximation and are in very good agreement with the experimental data.

Quantum Simulation Study of DNA nucleotide Thymine for use in Molecular Devices

The soft-computing techniques provide us with tools that can be used to calculate the various parameters that cannot be measured easily. In this paper computational study of DNA base Thymine has been carried out using two probe set up. The metal-molecule-metal assembly was realized by inserting Thymine molecule between two gold terminals and analyzed for current-voltage characteristics. The current- voltage characteristics are obtained using Density Functional theory within Non-equilibrium Green's function formalism (NEGF-DFT). Negative differential resistance is exhibited in the characteristics of Thymine. In two probe set-up without using gate, oscillating behavior of current through thymine is observed rendering its use to drive electronic circuits. It is also observed that the current-voltage characteristics of Thymine can be modulated by gating the two probe setup. The analysis shows that Thymine is suitable for use in two and three terminal Nanoelectronic devices. The development of electronic industry in terms of size and speed is pushing electronic devices into the realm of molecular electronics. Molecular electronics attempts to find the use of single molecule or group of molecules to function as basic element of electronic devices. Molecular electronic uses material having dimensions below 100 nm, such as organic molecules, carbon nanotubes, and nanowire as substitute for the solid-state layers of traditional semiconductor devices. To accumulate knowledge of molecules and to investigate the electronic properties of molecules interdisciplinary approach is used. Chemistry tools synthesize various molecular architectures. Electrochemical and spectroscopic tools are used to characterize the molecules. Nanofabrication tools are used to fabricate functional single molecule devices for measurement at cryogenic temperature , which help to understand precisely the quantum mechanical nature of current flowing through individual molecules. Similarly computational design tools are contributing for understanding the theoretical model for such devices. Simulation techniques provide us with an excellent solution to probe the various parameters of a system. Simulation helps in predicting the behavior of a system before realizing the actual system. So, to analyze the electronic properties of molecules also we take aid of simulation and computational methods. In this paper we are analyzing the current-voltage characteristics of thymine for use in electronic circuits. DNA a natural nanowire is proving itself the leading candidate for molecular electronics. Due to its two important features self assembly and self replication it could produce structures in the nano range that does not seem possible with classical technologies. For DNA molecule to work as single electronic devices, it is necessary for it to be workable at room temperature. For operations like quantum tunneling and coulomb blockade (CB) the HOMO-LUMO gaps should be larger than thermal energy at room temperature (300K) which is equivalent to 0.026eV. Researchers have observed that HOMO-LUMO gap for all DNA Bases is larger than the thermal energy at room temperature (1).

A Semiclassical Dynamics Simulation on Charge Transfer and Radiationless Deactivation Excited State of &lt;em&gt;&amp;pi;&lt;/em&gt;-Stacked Adenine-Thymine System

A semiclassical electronic radiation ion dynamics (SERID) simulation was used to study the photophysical deactivation of π-stacked adenine and thymine. A laser was only applied to the thymine molecule during the simulations. The results showed that an (A + T - ) * type exciplex was formed between excited thymine and unexcited adenine as a consequence of charge transfer. When the intermolecular distance was less than 0.300 nm, the stacked system was recovered to electronic neutrality by charge recombination because of the orbital delocalization effect. When the torsion angle of the C4ʹ-C5ʹ bond of the adenine molecule reached its maximum, the exciplex decayed to its ground state via an avoided crossing. The deactivation channel of the exciplex was found to be dependent on the intermolecular distance and deformation of the adenine molecule. It was difficult for the adenine molecule to undergo strong twist required for deactivation because of the steric hindrance encountered by the C4ʹ and C5ʹ atoms. Consequently, the lifetime of the A-T exciplex was clearly longer than that of the T-T exciplex. (Article)

Molecular Dynamics Simulation Study of Adsorption and Patterning of DNA Bases on the Au(111) Surface

To understand of the mechanism of self-assembly of DNA base molecules on the Au(111) surface, molecular dynamics simulations of different surface coverage of guanine, adenine, cytosine, and thymine molecules at 300 and 400 K are performed. At low coverage, guanine, adenine, and thymine form hydrogen bonded chains on the surface, while cytosine molecules cluster into islands. At larger coverage, simulations indicate that adenine molecules form ordered two-dimensional hexagonal structures, while guanine, cytosine, and thymine molecules aggregate into small random clusters. These observations agree with scanning tunneling microscopy (STM) experiments of the DNA bases on gold surfaces. The simulations show that arrangement of the molecules on the gold surface is controlled by base–base interactions. The hydrogen bond interactions and stability of base–base homopairs, which are the smallest components of the self-assembled structures on the Au(111) surface, are calculated and compared with calculations of the homopairs in the gas phase and with values available in the literature. The binding energies per base on the surface initially decrease in magnitude with increasing surface coverage and then reach a constant plateau at large coverages. The mechanisms of molecular mobility for the bases with one and two molecule coverage on the surface are analyzed at two temperatures.

Surface‐enhanced Raman scattering‐based approach for DNA detection at low concentrations via polyvinyl alcohol‐protected silver grasslike patterns

A simple method is demonstrated to detect DNA at low concentrations on the basis of surface‐enhanced Raman scattering (SERS) via polyvinyl alcohol‐protected silver grasslike patterns (PVA‐Ag GPs) grown on the surface of the common Al substrate. By the SERS measurements of sodium citrate and thymine, the PVA‐Ag GPs are shown to be an excellent SERS substrate with good activity, stability and reproducibility. With the use of the tested molecule of thymine, the enhancement factor of the PVA‐Ag GPs is up to ~1.4 × 108. The PVA‐Ag GPs are also shown to be an excellent SERS substrate with good biocompatibility for DNA detection, and the detection limit is down to ~10−5 mg/g. Meanwhile, the assignations of the Raman bands and the adsorption behaviors of the DNA molecules are also analyzed. In this work, the geometry optimization and the wavenumber analysis of adenine–Ag and guanine–Ag complexes for the ground states are performed using density functional theory, B3LYP functional and the LanL2DZ basis set. The transition energies and the oscillator strengths of adenine–Ag and guanine–Ag for the lowest six singlet excited states were calculated by using the time‐dependent density functional theory method with the same functional and basis set. The results show that the charge transfer in the adenine–Ag and guanine–Ag complexes should be the chemical factor for the SERS of the DNA molecules. Lastly, this method may be employed in large‐scale preparation of substrates that have been widely applied in the Raman analysis of DNA because the fabrication process is simple and inexpensive. Copyright © 2011 John Wiley &amp; Sons, Ltd.

Second-order Born approximation for the ionization of molecules by electron and positron impact

Second-order Born approximation is applied to study the ionization of molecules. The initial and final states are described by single-center wave functions. For the initial state a Gaussian wave function is used while for the ejected electron it is a distorted wave. Results of the present model are compared with recent ($e,2e$) experiments on the water molecule. Preliminary results are also presented for the ionization of the thymine molecule by electrons and positrons.

Low-energy Electron Collisions with Gas-phase Thymine Molecule

The paper presents an investigation of the negative ion formation of the thymine (T) molecule. The formation of negative ions by electron impact of this molecule is measured. The quantum mechanical investigations are performed to calculate the electron attachment cross section, the force constants, the resulting vibrational frequencies and intensities. The absorption spectrum and their nature are investigated too. The obtained results allows us to foresee the mechanism of production of the [T-H]- ion and explain the origin of some features in the experimental negative ion formation of the thymine molecule.http://dx.doi.org/10.5755/j01.ms.17.3.601

Specific Photodynamics in Thymine Clusters: The Role of Hydrogen Bonding

A photoionization detected IR study of thymine and 1-methylthymine monohydrates and of their homodimers was carried out to shed some light on the structure of the thymine clusters whose complex photodynamics has recently been the subject of great interest. Under supersonic jet conditions, thymine forms doubly H-bonded cyclic clusters with water or another base preferentially via its N1-H group and the adjacent carbonyl group. This hydrate is of no biological relevance since the N1-H group is the sugar binding site in thymidine. On the other hand, 1-methylthymine forms the donor H-bonds only via the N3-H group. Hence, properties of the N1-H and the N3-H bound clusters of thymine can be studied using thymine and 1-methylthymine molecules, respectively. No biologically relevant conformations of the dimers and hydrates of thymine, contrary to those of 1-methylthymine, are observed under supersonic jet conditions. Thymine homodimer, which extensively fragments upon UV ionization by formation of a protonated monomer, exhibits two N1-H···O═C2 hydrogen bonds. The photodynamics of hydrated thymines is found to be extremely sensitive to the hydration site: ranging from an ultrafast relaxation in less than 100 fs up to formation of a dark state with the lifetime on the microsecond time scale.

Thymine quintets and their higher order assemblies studied by electrospray ionization mass spectrometry and theoretical calculation

We previously reported that thymine molecules can specifically form a pentameric magic number cluster named as thymine quintet in the presence of K(+) , Rb(+) and Cs(+) . Actually, thymine decamer and doubly charged thymine 15-mer metaclusters can be observed along with thymine quintet in the ESI mass spectra of thymine with the addition of K(+) , Rb(+) and Cs(+) . The product ion spectra of these metaclusters, especially the 15-mer with hetero central ions, indicate that they are higher order assemblies of thymine quintets. The collision-induced dissociation experiments show that the gas-phase stabilities of these metaclusters depend on the size of the central ions, following the order Cs(+) > Rb(+) > K(+) , while K(+) leads to the highest dissociation energy of a thymine quintet. The optimized structures of thymine quintet and decamer were provided by density functional theory calculations, which showed that thymine quintet is bowl-shaped and its tilting angle increases with the size of the central ion. Furthermore, the chirality of thymine quintet was defined for the first time and the resulting different diastereoisomers of thymine decamers were also revealed by the calculation study. Copyright © 2011 John Wiley & Sons, Ltd.

Observation and Analysis of Small Inclination of Thymine Molecules on Graphite

The orientation of vacuum-sublimated thymine molecules on graphite was studied by ultraviolet photoelectron spectroscopy (UPS) and metastable atom electron spectroscopy (MAES). MAES gave pronounced band intensity enhancement for π molecular orbitals, which confirms the nearly lying-down orientation of the molecules proposed by Uchihashi et al. (Appl. Surf. Sci. 2000, 157, 244). In UPS, a lowering of the vacuum level was observed upon monolayer formation and attributed to inclination of the molecular dipoles from the surface. The tilt angle of the molecular plane was estimated to be 2.1−4.4° by applying the Helmholtz equation to the vacuum level shift.

Label free sub-picomole level DNA detection with Ag nanoparticle decorated Au nanotip arrays as surface enhanced Raman spectroscopy platform

Label free optical sensing of adenine and thymine oligonucleotides has been achieved at the sub-picomole level using self assembled silver nanoparticles (AgNPs) decorated gold nanotip (AuNT) arrays. The platform consisting of the AuNTs not only aids in efficient bio-immobilization, but also packs AgNPs in a three dimensional high surface area workspace, assisting in surface enhanced Raman scattering (SERS). The use of sub-10 nm AgNPs with optimum inter-particle distance ensures amplification of the chemically specific Raman signals of the adsorbed adenine, thymine, cytosine and guanine molecules in SERS experiments. High temporal stability of the Raman signals ensured reliable and repeatable DNA detection even after three weeks of ambient desk-top conservation. This facile architecture, being three dimensional and non-lithographic, differs from conventional SERS platforms.

Effect of hydrogen bonding on the structure and vibrational spectra of the complementary pairs of nucleic acid bases. II. adenine-thymine

The vibrational spectra of an isolated complementary adenine-thymine pair are calculated in the B3LYP/6-311++G(d,p) approximation and analyzed. The effect of hydrogen bonds on the structure is shown along with the position of frequencies and intensities of normal vibrations of the pair in comparison with the spectra of isolated thymine and adenine molecules. A comparative analysis of the hydrogen bonding effect on the IR and Raman spectra of thymine and adenine is performed

Internal Energies of Ion-Sputtered Neutral Tryptophan and Thymine Molecules Determined by Vacuum Ultraviolet Photoionization

Vacuum ultraviolet photoionization coupled to secondary neutral mass spectrometry (VUV-SNMS) of deposited tryptophan and thymine films are performed at the Chemical Dynamics Beamline. The resulting mass spectra show that while the intensity of the VUV-SNMS signal is lower than the corresponding secondary ion mass spectroscopy (SIMS) signal, the mass spectra are significantly simplified in VUV-SNMS. A detailed examination of tryptophan and thymine neutral molecules sputtered by 25 keV Bi(3)(+) indicates that the ion-sputtered parent molecules have approximately 2.5 eV of internal energy. While this internal energy shifts the appearance energy of the photofragment ions for both tryptophan and thymine, it does not change the characteristic photoionizaton efficiency (PIE) curves of thymine versus photon energy. Further analysis of the mass spectral signals indicate that approximately 80 neutral thymine molecules and 400 tryptophan molecules are sputtered per incident Bi(3)(+) ion. The simplified mass spectra and significant characteristic ion contributions to the VUV-SNMS spectra indicate the potential power of the technique for organic molecule surface analysis.