Conformational fluctuations and electronic properties in myoglobin

Abstract: In this article we use the recently developed perturbed matrix method (PMM) to investigate the effect of conformational fluctuations on the electronic properties of heme in Myoglobin. This widely studied biomolecule has been chosen as a benchmark for evaluating the accuracy of PMM in a large and complex system. Using a long, 80-ns, molecular dynamics simulation and unperturbed Configuration Interaction (CISD) calculations in PMM, we reproduced the main spectroscopic features of deoxy-Myoglobin. Moreover, in line with our previous results on a photosensitive protein, this study reveals a clear dynamical coupling between electronic properties and conformational fluctuations, suggesting that this correlation could be a general feature of proteins

Principal component analysis.

<p>Projection of the trajectories of Cα atoms from the larger artificial trajectory in the volume spanned by the first 3 eigenvectors obtained by the principal component analysis, from 2 different points of view. Frames have been represented as dots coloured in black (WT), blue (F429A), magenta (F429E), orange (F429H) and green (F429L).</p

A density functional theory study of hexafluoropropene: low-lying singlet excited states and primary photodissociation channel

Time-dependent density functional theory (TD-DFT) with different functional and related atomic basis sets, is applied to calculate the vertical transitions from the ground to the low-lying valence electronic excited states of hexafluoropropene in vacuum. The results are in satisfactory agreement with the recent high-resolution photoabsorption spectrum of hexafluoropropene in gas phase. The primary photodissociation channel was also studied and the binding energy of the weakest C-F bond of the molecule was determined. (C) 2004 Elsevier B.V. All rights reserved

RICERCA DI QUALITÀ E TECNOLOGIA D’AVANGUARDIA: UN BINOMIO VINCENTE PER LA CHIMICA COMPUTAZIONALE

L’analisi e il controllo dei meccanismi che governano i più interessanti processi biologici, tecnologici e ambientali richiedono una comprensione approfonditadelle caratteristiche strutturali e dinamiche di sistemi molecolari e supra-molecolari operanti in ambienti complessi. Anche se molte informazioni sperimentali indirette sono disponibili grazie a tecniche spettroscopiche sofisticate, l’organizzazione di tali informazioni e la loro interpretazione richiede strumenti computazionali accurati, efficienti e user friendly. Riveste, quindi, un ruolo determinante l’interazione costante tra innovazione scientifica e tecnologica

Nuove prospettive per i semiconduttori organici molecolari da studi in silico

Interaction of metal atoms with organic thin film is a fundamental issue to optimize performancesof novel devices. The computational investigations, based on density functionaltheory, reveal that a realistic description of the reactive processes is obtained whenthe organic thin film is modelled by its crystallographic structure.In this case, the metal atoms can react with multiple organic molecules present inthe solid forming complexes where they are bound both to O atoms and to aromatic Catoms of the molecules.Calculated band gap states, induced by chemical reaction upon deposition, reproducequite well the measured density of states as a function of the metal concentration inthe solid.Simulated core level shift spectra for N(1s), O(1s), Al (2p), in doped systems, are ingood agreement with experimental spectra and the electronic structure analysis providesa microscopic description of reaction processes.Interestingly, K atoms in PTCDA solid are ionically bound to anhydride O atoms andare able to form quasi mono-dimensional chain along the stack direction of the organicmaterial

Nuove prospettive per i semiconduttori organici molecolari da studi in silico

Interaction of metal atoms with organic thin film is a fundamental issue to optimize performancesof novel devices. The computational investigations, based on density functionaltheory, reveal that a realistic description of the reactive processes is obtained whenthe organic thin film is modelled by its crystallographic structure.In this case, the metal atoms can react with multiple organic molecules present inthe solid forming complexes where they are bound both to O atoms and to aromatic Catoms of the molecules.Calculated band gap states, induced by chemical reaction upon deposition, reproducequite well the measured density of states as a function of the metal concentration inthe solid.Simulated core level shift spectra for N(1s), O(1s), Al (2p), in doped systems, are ingood agreement with experimental spectra and the electronic structure analysis providesa microscopic description of reaction processes.Interestingly, K atoms in PTCDA solid are ionically bound to anhydride O atoms andare able to form quasi mono-dimensional chain along the stack direction of the organicmaterial

a,b) Cartoon representation of the CYP-2B4 crystal structure (PDB ID 1SUO) with specific domains coloured and labeled according to Scott et al.;[12] the heme group, the peroxide anion and Cys426 are shown as ball and stick. The enzyme is shown looking from the distal (a) or proximal (b) side of the heme group. To be coherent with the literature, the same color map reported in the original experimental work has been used. (c,d) Detail of the active site.

<p>The protein backbone is shown as a transparent cyan ribbon, while Cpd0 is shown in and stick style, together with the various rotamers of residue 429. Cys 436, residue 429 and the A and D propionate groups are labeled.</p