Biomedical subjects

R Dovesi

Publications and source records attributed to R Dovesi.

At least 19 recordsLinked to original sources

PubMed2006

Vibrational spectrum of katoite Ca3Al2[(OH)4]3: a periodic ab initio study.

The vibrational spectrum of the Si-free katoite hydrogarnet (116 atoms in the unit cell) has been calculated at the periodic ab initio quantum mechanical level with the CRYSTAL program, by using a Gaussian type basis set and the hybrid B3LYP Hamiltonian. The harmonic frequencies at the Gamma point have been obtained by diagonalizing the mass-weighted Hessian matrix, that is evaluated by numerical differentiation of the analytical first derivatives of the energy with respect to the atomic Cartesian coordinates. The parameters controlling the numerical differentiation, as well as the numerical integration of the exchange-correlation functional for the self-consistent field (SCF) calculation, are shown to affect the obtained frequencies by less than 3 cm-1. Before diagonalization, the dynamical matrix is transformed to a block diagonal form according to the irreducible representations of the point group, so that the 345 vibrational modes are automatically classified by symmetry. Various tools are adopted (graphical representation, isotopic substitution, "freezing" part of the unit cell) that permit a complete classification of normal modes and, in particular, an analysis of the modes in terms of simple models (octahedra modes, Ca modes, H stretching, bending, rotations). The harmonic OH stretching band (48 modes) is quite narrow (20 cm-1), indicating that the interaction among OH groups is very weak. As the OH stretching modes are known to be totally separable from the other modes and strongly anharmonic, the one-dimensional Schroedinger equation for the anharmonic oscillator is solved numerically for the two extreme situations, corresponding to the vibration of one decoupled OH and of all 48 OH groups moving in phase. The anharmonic frequencies are 3682 and 3673 cm-1, respectively, in good agreement with IR experiments (a single band at 3661 cm-1 with a width at half band height of 33 cm-1) and confirming that the interaction between OH groups is extremely weak.

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PubMed2005

Vibration frequencies of Ca3Fe2Si3O12 andradite: an ab initio study with the CRYSTAL code.

The vibrational spectrum of Ca3Fe2Si3O12 andradite is calculated at the Gamma point by using the periodic ab initio CRYSTAL program that adopts an all-electron Gaussian-type basis set and the B3LYP Hamiltonian. The full set of frequencies (17 IR active, 25 Raman active, and 55 inactive modes) is calculated. The effect of the basis set on the calculated frequencies is discussed. The modes are characterized by direct inspection of the eigenvectors and isotopic substitution. The present calculations permit us to clarify some of the assignment problems raised by experiments. The mean absolute differences of the various modes with respect to the available experimental IR and Raman data are as small as 9 and 5 cm(-1), respectively.

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PubMed2005

Local-MP2 electron correlation method for nonconducting crystals.

Rigorous methods for the post-HF (HF-Hartree-Fock) determination of correlation corrections for crystalline solids are currently being developed following different strategies. The CRYSTAL program developed in Torino and Daresbury provides accurate HF solutions for periodic systems in a basis set of Gaussian type functions; for insulators, the occupied HF manifold can be represented as an antisymmetrized product of well localized Wannier functions. This makes possible the extension to nonconducting crystals of local correlation linear scaling On techniques as successfully and efficiently implemented in Stuttgart's MOLPRO program. These methods exploit the fact that dynamic electron correlation effects between remote parts of a molecule (manifesting as dispersive interactions in intermolecular perturbation theory) decay as an inverse sixth power of the distance R between these fragments, that is, much more quickly than the Coulomb interactions that are treated already at the HF level. Translational symmetry then permits the crystalline problem to be reduced to one concerning a cluster around the reference zero cell. A periodic local correlation program (CRYSCOR) has been prepared along these lines, limited for the moment to the solution of second-order Moller-Plesset equations. Exploitation of point group symmetry is shown to be more important and useful than in the molecular case. The computational strategy adopted and preliminary results concerning five semiconductors with tetrahedral structure (C, Si, SiC, BN, and BeS) are presented and discussed.

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PubMed2004

Calculation of the vibration frequencies of alpha-quartz: the effect of Hamiltonian and basis set.

The central-zone vibrational spectrum of alpha-quartz (SiO2) is calculated by building the Hessian matrix numerically from the analytical gradients of the energy with respect to the atomic coordinates. The nonanalytical part is obtained with a finite field supercell approach for the high-frequency dielectric constant and a Wannier function scheme for the evaluation of Born charges. The results obtained with four different Hamiltonians, namely Hartree-Fock, DFT in its local (LDA) and nonlocal gradient corrected (PBE) approximation, and hybrid B3LYP, are discussed, showing that B3LYP performs far better than LDA and PBE, which in turn provide better results than HF, as the mean absolute difference from experimental frequencies is 6, 18, 21, and 44 cm(-1), respectively, when a split valence basis set containing two sets of polarization functions is used. For the LDA results, comparison is possible with previous calculations based on the Density Functional Perturbation Theory and usage of a plane-wave basis set. The effects associated with the use of basis sets of increasing size are also investigated. It turns out that a split valence plus a single set of d polarization functions provides frequencies that differ from the ones obtained with a double set of d functions and a set of f functions on all atoms by on average less than 5 cm(-1).

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PubMed2004

The katoite hydrogarnet Si-free Ca3Al2([OH]4)3: a periodic Hartree-Fock and B3-LYP study.

The structure of the Si-free katoite hydrogarnet (116 atoms in the unit cell) has been investigated at the periodic ab initio quantum mechanical level with the CRYSTAL program, by using a Gaussian type basis set and both the HF and the hybrid B3-LYP Hamiltonians. The structure has been fully optimized at various pressures in the 0-46 GPa range; the modifications of the structure, and in particular of the (OH)4 group, as a function of pressure are analyzed. At the B3-LYP level and P greater than 15 GPa, a O-H...O interaction of increasing strength appears, with important modifications in the local geometry of the tetrahedral site. The calculated omega01(O-H) fundamental vibrational frequency at zero pressure is in excellent agreement with experiment (3674 and 3663 cm(-1), respectively); the omega01(O-H) stretching frequency remains essentially constant in the 0-15 GPa interval, whereas it dramatically decreases at higher pressures with a corresponding anharmonicity increase, as a consequence of the formation of a strong hydrogen bond. The hydration energy of grossular and the formation energy of Si-free katoite have also been computed, and the B3-LYP results are in quite good agreement with experiment.

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PubMed2004

The calculation of the vibrational frequencies of crystalline compounds and its implementation in the CRYSTAL code.

The problem of numerical accuracy in the calculation of vibrational frequencies of crystalline compounds from the hessian matrix is discussed with reference to alpha-quartz (SiO(2)) as a case study and to the specific implementation in the CRYSTAL code. The Hessian matrix is obtained by numerical differentiation of the analytical gradient of the energy with respect to the atomic positions. The process of calculating vibrational frequencies involves two steps: the determination of the equilibrium geometry, and the calculation of the frequencies themselves. The parameters controlling the truncation of the Coulomb and exchange series in Hartree-Fock, the quality of the grid used for the numerical integration of the Exchange-correlation potential in Density Functional Theory, the SCF convergence criteria, the parameters controlling the convergence of the optimization process as well as those controlling the accuracy of the numerical calculation of the Hessian matrix can influence the obtained vibrational frequencies to some extent. The effect of all these parameters is discussed and documented. It is concluded that with relatively economical computational conditions the uncertainty related to these parameters is smaller than 2-4 cm(-1). In the case of the Local Density Approximation scheme, comparison is possible with recent calculations performed with a Density Functional Perturbation Theory method and a plane-wave basis set.

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PubMed1995