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The development of infrared difference spectroscopy provides unprecedented insights on structures of complex molecules like metalloproteins. However, the relevant information can be hard to find among the many bands of the vibrational spectra. The ab initio modeling is very helpful to assign the frequencies to vibrational modes but it is a challenge to process the huge quantity of data into descriptors useful for experimentalists. To this end, we developed a new tool called VIBMOL allowing to analyze vibrational modes of molecules from hessian matrices calculated with common quantum chemistry codes. VIBMOL program runs on Unix machines. Through a new graphical interface, the users can calculate the normal modes of molecules, visualize them, simulate infrared spectra, and explore the Potential Energy Distribution of normal modes among any set of vibration coordinates. It is combined with an interface program (gosdmu) formatting relevant data from the GAUSSIAN program. VIBMOL code is available upon request to the authors. A discussion is provided to help the readers to choose between a large choice of different software and it shows how VIBMOL can make the IR assignment easier in the context of collaborations with experimentalists. [ABSTRACT FROM AUTHOR]

We revise formal and numerical aspects of collinear and non-collinear density functional theories in the context of a two-component self-consistent treatment of spin–orbit coupling. Theoretical and numerical analyses of the non-collinear approaches confirm their ability to yield the proper collinear limit and provide rotational invariance of the total energy for functionals in the local-density or generalized-gradient approximations (GGAs). Calculations on simple molecules corroborate the formal considerations and highlight the importance of an effective screening algorithm to provide the sufficient level of numerical stability required for a rotationally invariant implementation of non-collinear GGA functionals. The illustrative calculations provide a first numerical comparison of both previously proposed non-collinear formulations for GGA functionals. The proposed screening procedure allows us to effectively deal with points of small magnetization, which would otherwise be problematic for the evaluation of the exchange–correlation energy and/or potential for non-collinear GGA functionals. Both previously suggested formulations for the non-collinear GGA are confirmed to be adequate for total energy calculations, provided that the screening is achieved on a sufficiently fine grid. All methods are implemented in the Crystal program. [ABSTRACT FROM AUTHOR]

Formal and computational aspects are discussed for a self-consistent treatment of spin-orbit coupling within the two-component generalization of the Hartree-Fock theory. A molecular implementation into the CRYSTAL program is illustrated, where the standard one-component code (typical of Hartree-Fock and Kohn-Sham spin-unrestricted methodologies) is extended to work in terms of two-component spinors. When passing from a one- to a two-component description, the Fock and density matrices become complex. Furthermore, apart from the αα and ββ diagonal spin blocks, one has also to deal with the αβ and βα off-diagonal spin blocks. These latter blocks require special care as, for open-shell electronic configurations, certain constraints of the one-component code have to be relaxed. This formalism intrinsically allows us to treat local magnetic torque as well as noncollinear magnetization and orbital current-density. An original scheme to impose a specified noncollinear magnetization on each atomic center as a starting guess to the self-consistent procedure is presented. This approach turns out to be essential to surpass local minima in the rugged energy landscape and allows possible convergence to the ground-state solution in all of the discussed test cases. [ABSTRACT FROM AUTHOR]

We revise formal and numerical aspects of collinear and noncollinear density functional theory (DFT) in the context of a two-component self-consistent treatment of spin-orbit coupling (SOC). While the extension of the standard one-component theory to a noncollinear magnetization is formally well-defined within the local density approximation, and therefore results in a numerically stable theory, this is not the case within the generalized gradient approximation (GGA). Previously reported formulations of noncollinear DFT based on GGA exchange-correlation potentials have several limitations: (i) they fail at reducing (either formally or numerically) to the proper collinear limit (i.e., when the magnetization is parallel or antiparallel to the z axis everywhere in space); (ii) they fail at ensuring a quantitative rotational invariance of the total energy and even a qualitative rotational invariance of the spatial distribution of the magnetization when a SOC operator is included in the Hamiltonian; (iii) they are numerically very unstable in regions of small magnetization. All of the above-mentioned problems are here shown (both formally and through test examples) to be solved by using instead a new formulation of noncollinear DFT for GGA functionals, which we call the "signed canonical" theory, as combined with an effective screening algorithm for unstable terms of the exchange-correlation potential in regions of small magnetization. All methods are implemented in the CRYSTAL program and tests are performed on simple molecules to compare the different formulations of noncollinear DFT. [ABSTRACT FROM AUTHOR]

New ab initio embedded-cluster calculations devoted to simulating the electronic spectroscopy of Bi3+ impurities in Y2O3 sesquioxide for substitutions in either S6 or C2 cationic sites have been carried out taking special care of the quality of the environment. A considerable quantitative improvement with respect to previous studies [F. Réal et al. J. Chem. Phys. 125, 174709 (2006); F. Réal et al. J. Chem. Phys. 127, 104705 (2007)] is brought by using environments of the impurities obtained via supercell techniques that allow the whole (pseudo) crystal to relax (WCR geometries) instead of environments obtained from local relaxation of the first coordination shell only (FSR geometries) within the embedded cluster approach, as was done previously. In particular the uniform 0.4 eV discrepancy of absorption energies found previously with FSR environments disappears completely when the new WCR environments of the impurities are employed. Moreover emission energies and hence Stokes shifts are in much better agreement with experiment. These decisive improvements are mainly due to a lowering of the local point-group symmetry (S6→C3 and C2→C1) when relaxing the geometry of the emitting (lowest) triplet state. This symmetry lowering was not observed in FSR embedded cluster relaxations because the crystal field of the embedding frozen at the genuine pure crystal positions seems to be a more important driving force than the interactions within the cluster, thus constraining the overall symmetry of the system. Variations of the doping rate are found to have negligible influence on the spectra. In conclusion, the use of WCR environments may be crucial to render the structural distortions occurring in a doped crystal and it may help to significantly improve the embedded-cluster methodology to reach the quantitative accuracy necessary to interpret and predict luminescence properties of doped materials of this type. [ABSTRACT FROM AUTHOR]

The energy levels of the 5f configuration of U5+ and 5f2 configuration of U4+ have been calculated in a dressed effective Hamiltonian relativistic spin-orbit configuration interaction framework. Electron correlation is treated in the scalar relativistic scheme with either the multistate multireference second-order multiconfigurational perturbation theory (MS-CASPT2) or with the multireference single and double configuration interaction (MRCI) and its size-extensive Davidson corrected variant. The CASPT2 method yields relative energies which are lower than those obtained with the MRCI method, the differences being the largest for the highest state 1S0 of the 5f2 manifold. Both valence correlation effects and spin-orbit polarization of the outer-core orbitals are shown to be important. The satisfactory agreement of the results with experiments and four-component correlated calculations illustrates the relevance of dressed spin-orbit configuration interaction methods for spectroscopy studies of heavy elements. [ABSTRACT FROM AUTHOR]

The ab initio embedded cluster method coupled with correlated spin-orbit calculations has been used to interpret the excitation spectrum of a Bi3+-doped yttria crystal. Our results indicate that the Bi3+ impurity can absorb light over a wider energy range in the C2 site than in the S6 site. Even if the computed absorption energies seem to be about 0.4 eV too high with respect to the experimental peaks for both sites, it is noteworthy that the embedded cluster model renders 93% of the large crystal redshift, about 6 eV. The determination of the geometry relaxation of the first shell of oxygen neighbors upon electronic excitation shows that the Stokes shift is smaller in the S6 site than in the C2 site. Combining all these results confirms the assignment of the violet emission to the S6 site and that of the green emission to the C2 site, as proposed by Boulon [J. Phys. (Paris) 32, 333 (1971)]. In addition, the nature of the metastable states which lie below the emitting ones and are responsible for the temperature dependence of the fluorescence lifetimes is discussed. [ABSTRACT FROM AUTHOR]

Ab initio study of excitation energies and oscillator strengths for absorption towards the 3P1 and 1P1 states of the Bi3+ ion has been performed for the Bi3+ ion in gas phase and as a dopant of the cubic elpasolite Cs2NaYCl6 and the yttria Y2O3 crystal using the ab initio embedded-cluster method. The ground and excited states were computed with a relativistic spin-orbit configuration interaction approach suited for heavy elements. Electron correlation was treated in the scalar relativistic scheme with perturbative, variational, and coupled-cluster methods. Intermediate coupling is included via an effective-Hamiltonian based spin-orbit configuration interaction approach. Small-core (60 electrons) and large-core (78 electrons) relativistic effective core potentials (ECPs) have been used to describe the bismuth ion. The best match with experiment was obtained with the small-core ECP. The accuracy of excitation energies strongly depends on the electron correlation method used. The agreement between experimental data and the results obtained using second-order multiconfigurational perturbation theory is greatly improved with the shifted zeroth-order Hamiltonian proposed by Ghido et al. [Chem. Phys. Lett. 396, 142 (2004)]. Although quite time consuming, coupled-cluster and variational methods yield good agreement with experimental data. The first absorption band recorded for the doped elpasolite crystal is positioned with an excellent accuracy while the computed energy of the second absorbing manifold is in poorer agreement with experimental data. This suggests that interactions with neglected close-lying excited states with a ligand-to-metal charge transfer character may be significant. Calculations of the spectrum of Bi3+ doping yttria in both the S6 and C2 site symmetries indicate that the absorbing manifold arises from electronic excitations localized on the Bi3+ doping ion with main triplet 6s6p character. Our results predict the first absorbing peak to lie about 0.5 eV lower for the S6 sites than for the C2 site, thus attributing the violet and the green emission wavelengths to the S6 and C2 sites, respectively. A subsequent study of Stokes shift and emission wavelength should hopefully lead to a final assignment of the measured excitation spectra. [ABSTRACT FROM AUTHOR]

Reports on molecular dynamic studies of three water clusters. Analysis of trajectories using structural local index. Existence of a dynamical equilibrium among molecules in states involving protons in hydrogen bonds; Range of enthalpy and entropy changes for the three clusters; Characterization of the dynamical properties of water systems.

Describes a theoretical study of several water/ammonia/formaldehyde cyclic trimers. Water/ammonia WN and NW heterodimers; Ammonia dimer; Water/formaldehyde and ammonia/formaldehyde dimers; Energy results for trimers; Water/ammonia heterotrimers W[sub 2]N and WN[sub 2]; Ammonia homotrimer N[sub 3]; Trends of cooperative effects in cyclic trimers.

Investigates hydrogen bond (HB) properties and cooperative effect relationships in methanol/water, ethanol/water and dimethylether/water corrections. Ab initio methods used; Analysis of ab initio results for dimers and cyclic trimers; Comparison of cooperative effects in trimers and heterodimers.

Analyzes flexible models, classical many-body polarization, pairwise and topological and classical many-body polarization effects, used to study interactions in water clusters. Decomposition of interaction energies; Topological origin of hydrogen bonding; Parameters of the models derived from calculations on water dimer structures and the cyclic water trimer.

The majority of the discussion in the article surrounded the rotational invariance and reduction to the collinear limit of different non-collinear formulations of the GGA. It has, however, unfortunately come to the attention of all three authors of the article that a programming mistake was present in the relevant implementation of the non-collinear GGA formulations. [1] The article discussed an implementation of collinear and non-collinear formulations of the local-density approximation and generalized-gradient approximation (GGA) of the density-functional theory (DFT). [Extracted from the article]