Electronic structures of 3d-metal mononitrides

Bond distances, vibrational frequencies, electron affinities, ionization potentials, and dissociation energies of the title molecules in neutral, positively, and negatively charged ions were studied by use of density functional methods B3LYP, BLYP, BHLYP, BPW91, and B3PW91. The calculated results are compared with experiments and previous theoretical studies. It was found that the calculated properties are highly dependent on the functionals employed, in particular for the dissociation energy and vibrational frequency. For neutral species, pure density functional methods BLYP and BPW91 have relatively good performance in reproducing the experimental bond distance and vibrational frequency. For cations, hybrid exchange functional methods B3LYP and B3PW91 are good in predicting the dissociation energy. For both neutral and charged species, BHLYP tends to give smaller dissociation energy.

Electron shell contributions to gamma-ray spectra of positron annihilation in noble gases

Gamma-ray positron annihilation spectra of the noble gases are simulated using computational chemistry tools for the bound electron wavefunctions and plane-wave approximation for the low-energy positron. The present annihilation line shapes, i.e. the full width at half maximum, Delta epsilon, of the gamma-ray annihilation spectra for He and Ar (valence) agree well with available independent atomic calculations using a different algorithm. For other noble gases they achieve moderate agreement with the experimental measurements. It is found that the contributions of various atomic electron shells to the spectra depend significantly on their principal quantum number n and orbital angular momentum quantum number l. The present study further reveals that the outermost ns electrons of the noble gases exhibit spectral line shapes in close agreement with those measured, indicating (as expected) that the measurements are not due to a simple sum over the momentum densities for all atomic electrons. The robust nature of the present approach makes it possible for us to proceed to more complex molecular systems using the tools of modern computational chemistry.

The structural information content of chemical networks

We present an information-theoretic method to measure the structural information content of networks and apply it to chemical graphs. As a result, we find that our entropy measure is more general than classical information indices known in mathematical and computational chemistry. Further, we demonstrate that our measure reflects the essence of molecular branching meaningfully by determining the structural information content of some chemical graphs numerically.

Electronic states and spin-forbidden cooling transitions of AlH and AlF

The feasibility of laser cooling AlH and AlF is investigated using ab initio quantum chemistry. All the electronic states corresponding to the ground and lowest two excited states of the Al atom are calculated using multi-reference configuration interaction (MRCI) and the large AV6Z basis set for AlH. The smaller AVQZ basis set is used to calculate the valence electronic states of AlF. Theoretical Franck-Condon factors are determined for the A(1)Pi -> X(1)Sigma(+) transitions in both radicals and found to agree with the highly diagonal factors found experimentally, suggesting computational chemistry is an effective method for screening suitable laser cooling candidates. AlH does not appear to have a transition quite as diagonal as that in SrF (which has been laser cooled) but the A(1)Pi -> X(1)Sigma(+) transition transition of AlF is a strong candidate for cooling with just a single laser, though the cooling frequency is deep in the UV. Furthermore, the a (3)Pi -> X(1)Sigma(+) transitions are also strongly diagonal and in AlF is a practical method for obtaining very low final temperatures around 3 mu K.

STO and GTO field-induced polarization functions for H to Kr

Field-induced polarization (FIP) functions were proposed over two decades ago to improve the accuracy of calculated response properties, and the FIP functions in GTO form for H and C to F were tested on small molecules, with encouraging results. The concept of FIP,is now extended to all atoms up to Kr. New simplifying approximations for the description of asymptotic highest occupied atomic orbitals. (HOAOs) are introduced in this study. They provide the basis for STO and GTO exponents of a complete set of FIP functions from H to Kr, which are both listed for the convenience of the users. Tests on the polarizabilities of a series of atoms and molecules demonstrate that addition of the FIP basis functions to a series' of standard basis sets drastically improves the performance of all these basis sets compared to converged results. Moreover, the byproduct of this study (approximate asymptotic HOAOs) provides information for the construction of accurate basis sets for long-range ground state properties. (C) 2003 Wiley Periodicals, Inc.

Assessing the Reproducibility of Clustering of Molecular Dynamics Conformations on Self-Organizing Maps

The goal of most clustering algorithms is to find the optimal number of clusters (i.e. fewest number of clusters). However, analysis of molecular conformations of biological macromolecules obtained from computer simulations may benefit from a larger array of clusters. The Self-Organizing Map (SOM) clustering method has the advantage of generating large numbers of clusters, but often gives ambiguous results. In this work, SOMs have been shown to be reproducible when the same conformational dataset is independently clustered multiple times (~100), with the help of the Cramérs V-index (C_v). The ability of C_v to determine which SOMs are reproduced is generalizable across different SOM source codes. The conformational ensembles produced from MD (molecular dynamics) and REMD (replica exchange molecular dynamics) simulations of the penta peptide Met-enkephalin (MET) and the 34 amino acid protein human Parathyroid Hormone (hPTH) were used to evaluate SOM reproducibility. The training length for the SOM has a huge impact on the reproducibility. Analysis of MET conformational data definitively determined that toroidal SOMs cluster data better than bordered maps due to the fact that toroidal maps do not have an edge effect. For the source code from MATLAB, it was determined that the learning rate function should be LINEAR with an initial learning rate factor of 0.05 and the SOM should be trained by a sequential algorithm. The trained SOMs can be used as a supervised classification for another dataset. The toroidal 10×10 hexagonal SOMs produced from the MATLAB program for hPTH conformational data produced three sets of reproducible clusters (27%, 15%, and 13% of 100 independent runs) which find similar partitionings to those of smaller 6×6 SOMs. The χ^2 values produced as part of the C_v calculation were used to locate clusters with identical conformational memberships on independently trained SOMs, even those with different dimensions. The χ^2 values could relate the different SOM partitionings to each other.

Neutral atoms in ionic lattices: Excited states of KCl:Ag(0)

The optical-absorption spectrum of a cationic Ag0 atom in a KCl crystal has been studied theoretically by means of a series of cluster models of increasing size. Excitation energies have been determined by means of a multiconfigurational self-consistent field procedure followed by a second-order perturbation correlation treatment. Moreover results obtained within the density-functional framework are also reported. The calculations confirm the assignment of bands I and IV to transitions of the Ag-5s electron into delocalized states with mainly K-4s,4p character. Bands II and III have been assigned to internal transitions on the Ag atom, which correspond to the atomic Ag-4d to Ag-5s transition. We also determine the lowest charge transfer (CT) excitation energy and confirm the assignment of band VI to such a transition. The study of the variation of the CT excitation energy with the Ag-Cl distance R gives additional support to a large displacement of the Cl ions due to the presence of the Ag0 impurity. Moreover, from the present results, it is predicted that on passing to NaCl:Ag0 the CT onset would be out of the optical range while the 5s-5p transition would undergo a redshift of 0.3 eV. These conclusions, which underline the different character of involved orbitals, are consistent with experimental findings. The existence of a CT transition in the optical range for an atom inside an ionic host is explained by a simple model, which also accounts for the differences with the more common 3d systems. The present study sheds also some light on the R dependence of the s2-sp transitions due to s2 ions like Tl+.

Ground- and excited-state properties of M-center oxygen vacancy aggregates in the bulk and the surface of MgO

Aggregates of oxygen vacancies (F centers) represent a particular form of point defects in ionic crystals. In this study we have considered the combination of two oxygen vacancies, the M center, in the bulk and on the surface of MgO by means of cluster model calculations. Both neutral and charged forms of the defect M and M+ have been taken into account. The ground state of the M center is characterized by the presence of two doubly occupied impurity levels in the gap of the material; in M+ centers the highest level is singly occupied. For the ground-state properties we used a gradient corrected density functional theory approach. The dipole-allowed singlet-to-singlet and doublet-to-doublet electronic transitions have been determined by means of explicitly correlated multireference second-order perturbation theory calculations. These have been compared with optical transitions determined with the time-dependent density functional theory formalism. The results show that bulk M and M+ centers give rise to intense absorptions at about 4.4 and 4.0 eV, respectively. Another less intense transition at 1.3 eV has also been found for the M+ center. On the surface the transitions occur at 1.6 eV (M+) and 2 eV (M). The results are compared with recently reported electron energy loss spectroscopy spectra on MgO thin films.

Theoretical modeling of photon and electron-stimulated Na and K desorption from SiO2

The mechanism of generation of atomic Na and K from SiO2 samples has been studied using explicitly correlated wave function and density functional theory cluster calculations. Possible pathways for the photon and electron stimulated desorption of Na and K atoms from silicates are proposed, thus providing new insight on the generation of the tenuous Na and K atmosphere of the Moon.

Enhancing learning beyond the classroom: blogging and other social networking tools

Blogging has become one of the key ingredients of the so-called socials networks. This phenomenon has indeed invaded the world of education. Connections between people, comments on each other posts, and assessment of innovation are usually interesting characteristics of blogs related to students and scholars. Blogs have become a kind of new form of authority, bringing about (divergent) discussions which lead to creation of knowledge. The use of blogs as an innovative, educational tool is not at all new. However, their use in universities is not very widespread yet. Blogging for personal affairs is rather commonplace, but blogging for professional affairs – teaching, research and service, is scarce, despite the availability of ready-to-use, free tools. Unfortunately, Information Society has not reached yet enough some universities: not only are (student) blogs scarcely used as an educational tool, but it is quite rare to find a blog written by University professors. The Institute of Computational Chemistry of the University of Girona and the Department of Chemistry of the Universitat Autònoma de Barcelona has joined forces to create “InnoCiència”, a new Group on Digital Science Communitation. This group, formed by ca. ten researchers, has promoted the use of blogs, twitters. wikis and other tools of Web 2.0 in activities in Catalonia concerning the dissemination of Science, like Science Week, Open Day or Researchers’ Night. Likewise, its members promote use of social networking tools in chemistry- and communication-related courses. This communication explains the outcome of social-network experiences with teaching undergraduate students and organizing research communication events. We provide live, hands-on examples and interactive ground to show how blogs and twitters can be used to enhance the yield of teaching and research. Impact of blogging and other social networking tools on the outcome of the learning process is very depending on the target audience and the environmental conditions. A few examples are provided and some proposals to use these techniques efficiently to help students are hinted