Search results for "Density Functional Theory"
showing 10 items of 981 documents
Capping Parallel β-Sheets of Acetyl(Ala)6NH2 with an Acetyl(Ala)5ProNH2 Can Arrest the Growth of the Sheet, Suggesting a Potential for Curtailing Amy…
2014
We present ONIOM calculations using B3LYP/d95(d,p) as the high level and AM1 as the medium level on parallel β-sheets containing four strands of Ac-AAAAAA-NH2 capped with either Ac-AAPAAA-NH2 or Ac-AAAPAA-NH2. Because Pro can form H-bonds from only one side of the peptide linkage (that containing the C═O H-bond acceptor), only one of the two Pro-containing strands can favorably add to the sheet on each side. Surprisingly, when the sheet is capped with AAPAAA-NH2 at one edge, the interaction between the cap and sheet is slightly more stabilizing than that of another all Ala strand. Breaking down the interaction enthalpies into H-bonding and distortion energies shows the favorable interaction…
The Right Answer for the Right Electrostatics: Force Field Methods Are Able to Describe Relative Energies of DNA Guanine Quadruplexes
2014
Different force fields and approximate density functional theory were applied in order to study the rotamer space of the telomeric G-quadruplex DNA. While some force fields show an erratic behavior when it comes to the reproduction of the higher-order DNA conformer space, OPLS and MMFF implementations are able to reproduce the experimentally known energy order. The stabilizing effect of the AA (anti−anti) versus SA (syn−anti) conformer is analyzed applying mechanical bond strength descriptors (compliance constants). The fact that we observe the correct energy order using appropriate force fields is in contrast with results previously reported, which suggested the general inappropriateness o…
Influence of F centres on structural and electronic properties of AlN single-walled nanotubes
2007
We analyse the influence of uncharged N vacancies (neutral F centres), created either under conditions of AlN nanotube growth or by its soft irradiation, on the atomic and electronic structure. Periodic one-dimensional (1D) density functional theory (DFT) calculations on models of defective single-walled nanotubes (SW NTs) allow us to analyse how NT chirality and concentration of F centres change their properties compared to the corresponding defect-free nanotubes. We have simulated reconstruction around periodically repeated F centres on 1 nm AlN SW NTs with armchair- and zigzag-type chiralities. To achieve the limit of an isolated vacancy for both chiralities, we have considered different…
SrTiO3 Nanotubes with Negative Strain Energy Predicted from First Principles
2011
On the basis of hybrid density functional theory calculations, we predict that the most energetically favorable single-walled SrTiO3 nanotubes with negative strain energy can be folded from SrTiO3 (110) nanosheets of rectangular morphology. Further formation of multiwalled tubular nanostructure with interwall distance of ∼0.46 nm yields an additional gain in energy of 0.013 eV per formula unit. (The formation energy of the most stable nanotube is 1.36 eV/SrTiO3.) Because of increase in the Ti–O bond covalency in the outer shells, SrTiO3 nanotubes can demonstrate an enhancement of their adsorption properties. Quantum confinement leads to a widening of the energy band gap of single-walled SrT…
[pi]-strain-induced electrophilicity in small cycloalkynes: a dft analysis of the polar cycloaddition of cyclopentyne towards enol ethers
2006
Small cycloalkynes possess a π-strain-induced electrophilicity related to the bending of the C–Csp–Csp bond angle. For cyclopentyne and benzyne, the electrophilicity index defined in the context of density functional theory gives a coherent rationale for the reactivity of these cycloalkynes, which may act as electrophiles in polar cycloaddition reactions toward enol ethers. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
The transfer of tin and germanium atoms from N-heterocyclic stannylenes and germylenes to diazadienes.
2005
New N-heterocyclic stannylenes and germylenes were synthesized by transamination of E[N(SiMe3)2] (E = Ge, Sn) with alpha-amino-aldimines or ethylidene-1,2-diamines and were characterized by spectroscopic methods and in the case of the germylene 10 g by X-ray diffraction. The reactions of several germylenes and stannylenes with diazadienes were studied by using dynamic NMR and computational methods. Experimental and theoretical studies confirmed that metathesis with exchange of the Group 14 atom is feasible for both stannylenes and germylenes, with exchange rates being generally higher for stannylenes. The metathesis of the diazadiene 3 b and the stannylene 1 b follows second-order kinetics …
UV–Vis, IR, Raman and theoretical characterization of a novel quinoid oligothiophene molecular material
2003
A quinoid-type oligothiophene, 3 0 ,4 0 -dibutyl-5,5 00 -bis(dicyanomethylene)-5,5 00 -dihidro-2,2 0 :5 0 ,2 00 -terthiophene, which can be viewed as an analog of TCNQ, has been investigated by spectroelectrochemistry and density functional theory calculations, in its neutral and dianionic states. Electrochemical data show that the molecule can be both reduced and oxidized at relatively low potentials. Upon reduction, both experiments and theory agree well with the generation of a dianionic charged species. The model shows that the electronic structure of the dianion is consistent with two anionic dicyanomethylene groups attached to a central terthienyl spine having an aromatic structure. T…
Low-pressure pyrolysis of tBu2SO: synthesis and IR spectroscopic detection of HSOH.
2005
Sulfenic acid (HSOH, 1) has been synthesized in the gas-phase by low-pressure high-temperature (1150 degrees C) pyrolysis of di-tert-butyl sulfoxide (tBu(2)SO, 2) and characterized by means of matrix isolation and gas-phase IR spectroscopy. High-level coupled-cluster (CC) calculations (CCSD(T)/cc-pVTZ and CCSD(T)/cc-pVQZ) support the first identification of the gas-phase IR spectrum of 1 and enable its spectral characterization. Five of the six vibrational fundamentals of matrix-isolated 1 have been assigned, and its rotational-resolved gas-phase IR spectrum provides additional information on the O-H and S-H stretching fundamentals. Investigations of the pyrolysis reaction by mass spectrome…
Theoretical description of the Raman spectrum of a vinylene-bridged quaterthiophene oligomer
2003
The Raman spectrum of a quaterthiophene oligomer incorporating a central vinylene spacer has been investigated using density functional theory B3LYP/6-31G** calculations. The spectrum has been fully assigned with the aid of the calculations and in comparison with unsubstituted quaterthiophene. The spectrum preserves most of the vibrational features of linear oligothiophenes. The vibrations of the vinylene spacer are clearly differentiated from those of the rest of the chain. The vinylene spacer increases the conjugation length of the molecule and induces a frequency downshift of < 20 cm 21 for the normal modes associated with the nas(CyC) and ns(CyC) vibrations of the thiophene rings. The m…
1,3-Dipolar cycloaddition of 1H-pyrazinium-3-olate and N1- and C-methyl substituted pyrazinium-3-olates with methyl acrylate: a density functional th…
2011
Abstract A DFT study of the 1,3-dipolar cycloaddition of methyl acrylate to 1H-pyrazinium-3-olate and N1- and C-methyl substituted pyrazinium-3-olates, in the gas phase and in THF, has been carried out at the B3LYP/6-31G(d) level. Two stereoisomeric pathways, endo and exo, and two regioisomeric channels, 2-oxo-3,8-diazabicyclo[3.2.1]octane-6-ester and 7-ester products, have been considered. Thermodynamic and kinetic parameters calculated at room temperature have been analyzed. The regioselectivity has been interpreted using reactivity indices. It is generally found that the exo pathway is preferred and the formation of the 6-esters is dominant. The theoretical data obtained for the cycloadd…