Search results for "density functional"
showing 10 items of 1070 documents
Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome
2019
The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that …
Ag11(SG)7 : A New Cluster Identified by Mass Spectrometry and Optical Spectroscopy
2014
We report a one-step and high yield synthesis of a red-luminescent silver cluster with the molecular formula, Ag11(SG)7 (SG: glutathionate) via reduction of silver ions by sodium borohydride in the presence of the tripeptide, glutathione (GSH). The as-prepared cluster shows prominent absorption features at 485 and 625 nm in its UV-vis absorption spectrum. Aging of the as-prepared cluster solution led to the disappearance of the 625 nm peak, followed by broadening of the 485 nm peak to give three maxima at ?487, 437, and 393 nm in its absorption spectrum. These peaks remain unchanged even after polyacrylamide gel electrophoresis (PAGE), where a single band was observed confirming high purity…
Cladosins L-O, new hybrid polyketides from the endophytic fungus Cladosporium sphaerospermum WBS017
2019
Abstract The endophytic fungus Cladosporium sphaerospermum WBS017 was obtained from healthy bulbs of Fritillaria unibracteata var. wabuensis. Fermentation of C. sphaerospermum on solid rice medium yielded three new hybrid polyketides, cladosins L−N (1–3), and a known derivative cladodionen (4). Further cultivation of this fungus on white bean medium afforded an additional new hybrid polyketide, cladosin O (5) along with three known analogues (6–8). The structures of the new compounds were elucidated using a combination of NMR and HRESIMS data. The absolute configurations of compounds 2 and 3 were determined by Mosher’s method and TDDFT-ECD calculations. All isolated compounds were evaluated…
Microscopic Insights into the Fluorite/Water Interfaces from Vibrational Sum Frequency Generation Spectroscopy
2016
Water/mineral interfaces are central to a wide range of environmental and technological processes. In this report we provide a quantitative, molecular-level understanding of the CaF2/water interface using Density Functional Theory-based molecular dynamics simulations. In particular through the comparison of calculated Vibrational Sum Frequency Generation spectra to the experimental ones, we give a structural characterisation of the interface at different pH. At low pH, the surface is positively charged, causing a substantial degree of water ordering. Our results suggest that the surface charge originates from the dissolution of fluoride ions of the topmost layer, rather than from proton ads…
Aminoacid zwitterions in solution : Geometric, energetic, and vibrational analysis using density functional theory-continuum model calculations
1998
Glycine and alanine aminoacids chemistry in solution is explored using a hybrid three parameters density functional (B3PW91) together with a continuum model. Geometries, energies, and vibrational spectra of glycine and alanine zwitterions are studied at the B3PW91/6-31+G∗∗ level and the results compared with those obtained at the HF and MP2/6-31+G∗∗ levels. Solvents effects are incorporated by means of an ellipsoidal cavity model with a multipolar expansion (up to sixth order) of the solute’s electrostatic potential. Our results confirm the validity of the B3PW91 functional for studying aminoacid chemistry in solution. Taking into account the more favorable scaling behavior of density funct…
DFT study of N–H···O hydrogen bond between model dehydropeptides and water molecule
2013
The strength of the hydrogen bond formed between a water molecule and two α,β-dehydroalanine derivatives including Ac-ΔAla-NMe2 (1) and Ac-ΔAla-NHMe (2) in comparison with standard amino acid Ac-Ala-NMe2 (3) is studied by density functional theory (with M06-2X and B3LYP functionals). Calculations were conducted for two different conformations of the peptides: extended (C5) and bent (β) with polyproline II backbone dihedral angles. The obtained results show that both dehydro and standard peptides in bent conformation form stronger hydrogen bonds with water than in the extended ones. Moreover, due to higher polarity of the N–H group of α,β-dehydroalanine residues, the H-bond in their complexe…
First signals of electrochemically oxidized species of TTF and TMT-TTF : a study by in situ spectroelectrochemical FTIR and DFT calculations
2003
A first study by in situ FTIR spectroelectrochemistry of TTF and TTM-TTF has been undertaken. The oxidation, in this case, is caused only by electrochemistry, which constitutes a clear advantage over chemical oxidation since no side products are present in the solution. In this context, we obtained the signals of neutral, radical cation, and dication species of TTF and TTM-TTF. The experimental conditions were chosen in order to avoid the possible formation of π-dimer species and to obtain a satisfactory signal-to-noise ratio. A weak signal was detected for TTF and a stronger one for TTM-TTF. The changes induced by the oxidation process in the IR spectra of TTF and TTM-TTF have been analyze…
Theoretical study on the influence of electric field direction on the photovoltaic performance of aryl amine organic dyes for dye-sensitized solar ce…
2019
It is very important to reveal the influence of different electric field directions on dye sensitizers. Thus, in this study, we investigated the electronic structures and optical properties of six designed aryl amine organic dye models under different electric fields using density functional theory (DFT) and time-dependent density functional theory (TD-DFT). Moreover, the electronic structures and optical properties of these studied dyes with different electric field in tetrahydrofuran (THF) were also calculated. The key parameters of the short-circuit current density (Jsc), including light harvesting efficiency (LHE) and intra-molecular charge transfer (ICT), are discussed in detail. With …
Solution of the Skyrme-Hartree–Fock–Bogolyubovequations in the Cartesian deformed harmonic-oscillator basis. (VIII) hfodd (v2.73y): A new version of …
2017
We describe the new version (v2.73y) of the code HFODD which solves the nuclear Skyrme Hartree-Fock or Skyrme Hartree-Fock-Bogolyubov problem by using the Cartesian deformed harmonic-oscillator basis. In the new version, we have implemented the following new features: (i) full proton-neutron mixing in the particle-hole channel for Skyrme functionals, (ii) the Gogny force in both particle-hole and particle-particle channels, (iii) linear multi-constraint method at finite temperature, (iv) fission toolkit including the constraint on the number of particles in the neck between two fragments, calculation of the interaction energy between fragments, and calculation of the nuclear and Coulomb ene…
Thouless-Valatin Rotational Moment of Inertia from the Linear Response Theory
2017
Spontaneous breaking of continuous symmetries of a nuclear many-body system results in appearance of zero-energy restoration modes. Such modes introduce a non-physical contributions to the physical excitations called spurious Nambu-Goldstone modes. Since they represent a special case of collective motion, they are sources of important information about the Thouless-Valatin inertia. The main purpose of this work is to study the Thouless-Valatin rotational moment of inertia as extracted from the Nambu-Goldstone restoration mode that results from the zero-frequency response to the total angular momentum operator. We examine the role and effects of the pairing correlations on the rotational cha…