Search results for "Density Functional Theory"

Theoretical Study on the Photo-Oxidation and Photoreduction of an Azetidine Derivative as a Model of DNA Repair

2021

Photocycloreversion plays a central role in the study of the repair of DNA lesions, reverting them into the original pyrimidine nucleobases. Particularly, among the proposed mechanisms for the repair of DNA (6-4) photoproducts by photolyases, it has been suggested that it takes place through an intermediate characterized by a four-membered heterocyclic oxetane or azetidine ring, whose opening requires the reduction of the fused nucleobases. The specific role of this electron transfer step and its impact on the ring opening energetics remain to be understood. These processes are studied herein by means of quantum-chemical calculations on the two azetidine stereoisomers obtained from photocyc…

Density functional theory studies of OH-modified open-ended single-wall zigzag carbon nanotubes (SWCNTs)

2010

Abstract Functionalized carbon nanotubes (CNTs) are often formed as result of oxidation and cleaning of raw product grown on metal catalyst. Structure and energy of ideal and OH-modified single-wall nanotubes (SWCNTs) of different length (2.8, 7.0 and 13.5 A) were obtained at the DFT-B3LYP level. From one to nine OH groups were added at the end of the nanotube and a nonadditive dependence of attachment energy on the number of substituents was observed. The energetics of SWCNT end substitution with OH groups was supported by high level MP2 and CCSD(T) determination of reaction energy: R – H + 1 / 2 O 2 → R – OH + Δ E for methane, benzene and anthracene. In addition, a vibrational analysis of…

Insight into the Mechanism of Action of Marine Cytotoxic Thiazinoquinones

2017

The electrochemical response of four natural cytotoxic thiazinoquinones isolated from the Aplidium species was studied using conventional solution-phase and solid-state techniques, based on the voltammetry of immobilized particles methodology. The interaction with O-2 and electrochemically generated reactive oxygen species (ROS) was electrochemically monitored. At the same time, a molecular modeling study including density functional theory (DFT) calculations was performed in order to analyze the conformational and electronic properties of the natural thiazinoquinones, as well as those of their reduced intermediates. The obtained electrochemical and computational results were analyzed and c…

A quantum mechanics-molecular mechanics study of dissociative electron transfer : The methylchloride radical anion in aqueous solution

2002

The dissociative electron transfer reaction CH3Cl+e−→CH3•+Cl− in aqueous solution is studied by using a QM/MM method. In this work the quantum subsystem (a methylchloride molecule plus an electron) is described using density functional theory while the solvent (300 water molecules) is described using the TIP3P classical potential. By means of molecular dynamics simulations and the thermodynamic integration technique we obtained the potential of mean force (PMF) for the carbon–chlorine bond dissociation of the neutral and radical anion species. Combining these two free energy curves we found a quadratic dependence of the activation free energy on the reaction free energy in agreement with Ma…

Hole Localization and Thermochemistry of Oxidative Dehydrogenation of Aqueous Rutile TiO2(110)

2012

The Silica-Water Interface: How the Silanols Determine the Surface Acidity and Modulate the Water Properties.

2015

Silica is the most abundant metal oxide and the main component of the Earth's crust. Its behavior in contact with water plays a critical role in a variety of geochemical and environmental processes. Despite its key role, the details of the aqueous silica interface at the microscopic molecular level are still elusive. Here we provide such a detailed understanding of the molecular behavior of the silica-water interface, using density functional theory based molecular dynamics (DFTMD) simulations, where a consistent treatment of the electronic structure of solvent and surface is provided. We have calculated the acidity of the silanol groups at the interface directly from the DFTMD simulations,…

Thermodynamics of titanium and vanadium reduction in non-aqueous environment calculated at various levels of theory.

2012

Reduction of titanium and vanadium compounds is a process accompanying the activation of coordinative olefin polymerization catalysts. Four density functional theory (DFT) functionals, coupled cluster with single, double, and perturbative triple excitations method CCSD(T) as well as complete active-space second-order perturbation theory method CASPT2 with a complete active-space self-consistent field CASSCF reference wave function were applied to investigate the thermodynamics of titanium and vanadium reduction. The performance of these theoretical methods was assessed and compared with experimental values. The calculations indicate that vanadium(IV) chloride is more easily reduced by trime…

Sensitivity of noble gas NMR parameters to the heterocyclic ring proximity. Density functional theory studies of Ne–furan and Ar–furan complexes

2014

Theoretical modeling of noble gas interaction with furan as a simple heterocyclic ring was performed. The structures of neon–furan and argon–furan complexes were calculated at the MP2, M06-2X, CAM-B3LYP, APFD, and VSXC levels of theory using 6-311++G** basis set. The predicted 21Ne and 39Ar NMR chemical shifts for the Ne–furan and Ar–furan complexes calculated with pcS-3 and aug-pcS-3 basis sets were sensitive to the presence of the aromatic furan ring. Our results indicate a higher sensitivity of the neon and argon NMR probes than the previously reported 3He NMR spectroscopic parameters in studies of small heterocyclic rings containing the oxygen atom.

Ab initio angle- and energy-resolved photoelectron spectroscopy with time-dependent density-functional theory

2012

We present a time-dependent density-functional method able to describe the photoelectron spectrum of atoms and molecules when excited by laser pulses. This computationally feasible scheme is based on a geometrical partitioning that efficiently gives access to photoelectron spectroscopy in time-dependent density-functional calculations. By using a geometrical approach, we provide a simple description of momentum-resolved photoemission including multiphoton effects. The approach is validated by comparison with results in the literature and exact calculations. Furthermore, we present numerical photoelectron angular distributions for randomly oriented nitrogen molecules in a short near-infrared…

A theoretical investigation on the Cd doping of Cu-depleted CuInSe<inf>2</inf> materials

2011

Because of their outstanding characteristics and affordable price, polycrystalline thin film solar cells based on CuIn 1−x Ga x Se 2 (CIGS) absorber layer have emerged to be one of the most promising materials for photovoltaic applications [1–2]. To further enhance the efficiency of these solar cells much effort is spent on the in-depth investigation of the production methods. However, the effect of structural defects and dopants upon the macroscopic properties and morphology of epitaxially grown CIGS films is not yet fully understood [3]. More importantly, it is well established that the best cells can be prepared by growing the CIGS absorber layer under Cu-poor conditions [4]. Thus, it is…