1,721,506 research outputs found
Extension of the AMBER force field to cyclic a,a dialkylated peptides
No full textThe popular biomolecular AMBER (ff99SB) force field (FF) has been extended with new
parameters for the simulations of peptides containing a,a dialkylated residues with cyclic side
chains. Together with the recent set of nitroxide parameters [E. Stendardo, A. Pedone, P. Cimino,
M. C. Menziani, O. Crescenzi and V. Barone, Phys. Chem. Chem. Phys., 2010, 12, 11697] this
extension allows treating the TOAC residue (TOAC, 2,2,6,6-tetramethylpiperidine-1-oxyl-4-
amino-4-carboxylic acid) widely used as a spin label in protein studies. All the conformational
minima of the Ac–Ac6C–NMe (Ac = acetyl, Ac6C = 1-aminocyclohexaneacetic acid, NMe =
methylamino) and Ac–TOAC–NMe dipeptides have been examined in terms of geometry and
relative energy stability by Quantum Mechanical (QM) computations employing an hybrid
density functional (PBE0) for an extended training set of conformers with various folds. A very
good agreement between QM and MM (molecular mechanics) data has been obtained in most of
the investigated properties, including solvent effects. Finally, the new set of parameters has been
validated by comparing the conformational and dynamical behavior of TOAC-labeled
polypeptides investigated by means of classical molecular dynamics (MD) simulations with QM
data and experimental evidence. The new FF accurately describes the tuning of conformational
and dynamical behavior of the Ac–TOAC–NMe dipeptide and double spin-labeled heptapeptide
Fmoc–(Aib–Aib–TOAC)2–Aib–OMe (Fmoc, fluorenyl-9-methoxycarbonyl; Aib,
a-aminoisobutyric acid; OMe, methoxy) by solvents with different polarity. In particular, we found
that the 310 helical structure of heptapeptide is the most stable one in vacuo, with a geometry very
similar to the X-ray crystallographic structure, whereas a conformational equilibrium between the
310- and a-helical structures is established in aqueous solution, in agreement with EPR data
Toward spectroscopic accuracy for open-shell systems: X2AB radicals as test cases
No full textThe structures, force fields and electro-magnetic properties of small molecules represent invaluable benchmarks for the most refined quantum mechanical (QM) approaches and an ideal playground where the accuracy of experimental and computational approaches rivals and synergically increases. At the same time, development and validation of the more approximate QM approaches, which are unavoidable for large systems, strongly benefit from the rich and variegate information issuing from sophisticate benchmark computations for the widest possible range of physico-chemical properties. On these grounds, very reliable extrapolation procedures have been developed and validated, which, however, mostly refer to closed-shell systems. The situation is more involved for open-shell systems due to both increased technical difficulties and to the paramount relevance of EPR spectroscopy, which requires, in turn, reliable computations of specific properties (especially isotropic hyperfine couplings) with peculiar method/basis set requirements [1]. At the same time, direct structural information are seldom available and assignments of vibrational frequencies are often not straightforward [2].
This prompted us to start a comprehensive research program on prototypical small organic X2AB radicals (with X=halogen atom, A=B,C,N and B=N,O) with the aim of extending the data base of highly accurate QM results to the structures, force fields and magnetic properties. All of these have been computed by the coupled cluster ansatz using a hierarchic series of basis sets and, in some cases, extrapolation procedures to reach the complete basis set limit. Methods rooted into the density functional theory have been used to estimate vibrational and environmental effects. The remarkable agreement with available experimental data confirms the reliability of the computational approach followed and suggests that our predictions for missing information should be highly reliable.
References
1. Improta R., Barone V., Chem. Rev. (Washington, D. C.) 2004, 104, 1231; Al Derzi A.R., Fau S., Bartlett R., J. Phys. Chem. A 2006, 110, 4473; Barone V., Cimino P., Stendardo E., J. Comp. Theor. Chem. 2008, 4, 751.
2. Sattelmeyer K.W., Schaefer III H.F., J. Chem. Phys. 2002, 117, 7914; Barone V., Carbonniere P., Pouchan C., J. Chem. Phys. 2005, 122, 224308
Antiproton-proton scattering experiments with polarization.
No full textPAX Collaboration Experimental Proposa
Quark matter in the colour-dielectric model with perturbative gluons
No full textThe possibility of describing simultaneously a single nucleon and quark matter in the framework of the colour-dielectric model (CDM) with perturbative gluons is investigated. It is pointed out that including the one-gluon exchange both in the hadronized and in the deconfined phase leads to a quark-hadron phase transition at anomalously small densities. This conclusion is independent of the choice of the model parameters, once these are constrained to yield the correct static properties of the nucleon. The unrealistic deconfinement densities that we find are determined by the large effective mass of quarks in the CDM
The Virtual Electron Paramagnetic Resonance Laboratory
No full textOur main objective in this Chapter has been to discuss the degree of advancement of the ICS to the interpretation of cw-EPR of organic radicals and biradicals in solvated environments, via combination of advanced quantum mechanical approaches and stochastic modelling of relaxation processes. The ICS ab initio prediction of cw-EPR spectra is able to assess molecular characteristics entirely from computational models and direct comparison with the experimental data. The sensitivity of the integrated methodology to the overall molecular geometry is proved, in all the cases discussed above, by the significant dependence of the calculated spectrum on arbitrary modifications of molecular geometry or dynamic properties. For instance, in the case of the heptapetide biradicals, the ICS is sensitive enough to distinguish between different helix conformations.
Some adjustment of computed magnetic tensors is probably unavoidable for a quantitative fitting of experimental spectra, particularly for large systems where only DFT approaches are feasible. However, the number of free parameters (if any) is limited enough that convergence to the true minimum can be granted. At the same time the allowed variation of parameters from their QM value is well within the difference between different structural models. Thus, pending further developments of DFT models, the ICS is already able to predict cw-EPR spectra of large molecular systems in solvents starting only from the chemical structure of the solute and some macroscopic solvent properties. Implementation in a user-friendly package finally could spread the systematic usage of the ICS in current real-life EPR laboratories, as much as standard QM packages for structural molecular properties are already diffuse in most modern chemistry research facilities
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