Ab initio and experimental studies of the large-amplitude motion in BF2OH

The ground state rotational spectrum of BF2OH was measured under high resolution by microwave Fourier transform spectroscopy (FTMW), and the small torsional splitting could be resolved for several lines. This splitting was analyzed using a phenomenological model previously developed for HNO3 [Coudert and Perrin, J. Mol. Spectrosc. 1995, 172, 352] and with the help of the geometries of the stationary points calculated ab initio. The torsional splitting was also calculated using the results of the calculations for the ground vibrational state, for the excited OH torsional states 91 and 92, and for the excited BOH bending state 41, and a satisfactory agreement with available experimental data was found.     

Why are some ML2 molecules (M = Ca, Sr, Ba; L = H, F, Cl, Br) bent while others are linear? Implications of the pseudo Jahn-Teller effect

The unexpected bent geometries of some alkaline earth dihalides and dihydrides, ML(2) (M = Ca, Sr, Ba; L = H, F, Cl, Br) have been explained in the literature using various models that attribute the effect to different phenomena like covalency, metal core polarization, sd-hybridization, and electron pair repulsion. We employ (based on first principles) the pseudo Jahn-Teller effect, as the only source of instability of high-symmetry configurations in nondegenerate states, to analyze the origin of the geometry of these systems and show that this approach explains all of their main structural features, including the topology of the Laplacian of the electron density and the vibrational frequencies. The main contribution to the distortion of the linear configuration is due to the pseudo Jahn-Teller mixing by bending of the sigma(u) HOMO formed by the ligand orbitals with the unoccupied pig orbitals of the metal (with main d(xz) and d(yz) character), resulting in new covalency which stabilizes the bent configuration. We show that the model approaches to the problem, mentioned above, are either restricted particular cases of the pseudo Jahn-Teller interaction, or they yield very small contributions to the instability that do not explain the origin of the bending. All of our conclusions are supported by high-quality ab initio calculations.     

Pseudo Jahn-Teller origin of cis-trans and other conformational changes. The role of double bonds

Based on the pseudo Jahn-Teller effect (PJTE) theory, an approach is developed to rationalize and predict the conformations and conformational changes in molecular systems with a common pattern, a double bond. It is shown that starting with the high-symmetry geometry of the environment (in many cases D(2d)), the double bond descends from an e(2) electronic configuration (e is a twofold degenerate MO) which produces a variety of PJT distortions, the main of which is the rotational (b(1)) transformation D(2d) → D(2h) accompanied by the formation of the double bond. Further PJT interactions with higher energy E-states may trigger additional distortions which in D(2h) symmetry are classified as in-plane (e(i)) cis and trans, and out-of-plane (e(o)) chair and boat. The realization of these conformations depends on the positions of the excited E-states and the PJTE parameter values. The two emerging PJTE problems, ((3)A(2) + (3)E(1) + (3)E(2)) ? (e(i) + e(o)) and ((1)A(1) + (1)B(1) + (1)B(2) + (1)E(1) + (1)E(2)) ? (b(1) + e(i) + e(o)), are formulated in the matrix form and provide a general picture of the ground and excited adiabatic potential energy surfaces. Following this scheme in combination with ab initio calculations, the possible conformations and conformational transitions are analyzed for several specific systems including (in increasing complexity) N(2)H(2), C(2)H(4), N(2)(NH(2))(2) and N(2)(C(6)H(5))(2) (azobenzene). The family of molecular systems with a double bond is vast, but the importance of the PJT approach developed here is also in its general validity as it can be applied to any other systems.     

Pathogen identification using mass spectrometry in the clinical microbiology laboratory

The recent application of Matrix-assisted Laser Desorption/Ionization Time-of-Flight and Polymerase Chain Reaction Electrospray Ionization Quadrupole Time-of-Flight mass spectrometry approaches to microbial identification has initiated a revolution in the clinical microbiology lab. The commercial application of these technologies to pathogen identification has only begun in the last five years, and already new potentially life-saving applications of these technologies are rapidly identifying organisms that in the past have proven notoriously difficult to identify. In this review, we will provide a brief historical perspective on how these developments arose, describe why they are being successfully applied now and provide an overview of current approaches. Using examples involving clinical isolates of Staphylococcus aureus, a perspective on future use and developments of mass spectrometry in the identification of microbial organisms is provided.     

Using Discrete and Continuous Models to Solve Nanoporous Flow Optimization Problems

We consider using a discrete network model in combination with continuous nonlinear optimization models to solve the problem of optimizing channels in nanoporous materials. The problem and the hierarchical optimization algorithm are described in [2]. A key feature of the model is the fact that we use the edges of the finite element grid as the locations of the channels. The focus here is on the use of the discrete model within that algorithm. We develop several approximations to the relevant flow and a greedy algorithm for quickly generating a "good" tree connecting all of the nodes in the finite-element mesh to a designated root node. We also consider Metropolis-Hastings (MH) improvements to the greedy result. We consider both a regular triangulation and a Delaunay triangulation of the region, and present some numerical results.     

Lost topological (Berry) phase factor in electronic structure calculations. Example: the ozone molecule

It is shown that standard computations of electronic structures of polyatomic systems that yield the global minimum configuration and vibrational frequencies may be faulty if the symmetry of this configuration is lower than the highest possible one and the origin of this distortion, which is always due to the Jahn-Teller effect, is neglected; this may lead, in particular, to the loss of the Berry phase factor that changes the vibronic energy level spectrum and which we show to be present even when there are no apparent conical intersections. The general case and the ozone molecule are analyzed.     

Ab initio and equilibrium bond angles. Structures of HNO and H2O2

The possibility of calculating accurate ab initio bond angles is examined using a sample of 29 molecules (35 independent angles) containing only first row atoms and whose equilibrium structures are known. Three different correlated methods are compared: MP2, CCSD(T), and DFT, using the hybrid functional B3LYP. The convergence of Dunning's correlation consistent polarized valence basis sets, cc-pVnZ is also studied. It is found that the CCSD(T) method is consistently the most accurate; the DFT/B3LYP being slightly less reliable than MP2. It is shown that when convergence of the basis set is achieved (which is dependent on the kind of bonding) and when the effect of diffuse functions on electronegative atoms is taken into account, a high accuracy may be obtained: 0.03° for the median of absolute deviations or 0.07° for the mean absolute deviation. It does not exclude the possibility that the ab initio method may fail in some particular case, for instance when a large amplitude motion is involved. The MP2/cc-pVQZ method gives a mean absolute deviation of 0.22° to be compared with the 0.07° of the CCSD(T) method. To obtain these results, it was necessary to reanalyze the structure of a few molecules, particularly, a new and more accurate structure is proposed for nitroxyl, HNO and hydrogen peroxide, H₂O₂.     

Accurate ab initio gradient calculation of the structures and conformations of some boric and fluoroboric acids. Basis-set effects on angles around oxygen

Accurate geometry determinations by SCF computation are reported for BF₂H, H₂BOH, two conformers of FHBOH,F₂BOH, three conformers of HB(OH)₂, and three conformers of FB(OH)₂. The effect of adding polarization functions to the double zeta basis set is examined in detail both with respect to alteration of the computed absolute values of the structural parameters and to changes in the consistency of the computed relative values. It is shown that geometry computation should be done at a level which is adequate to produce small and constant offset values for the parameters sought, i.e. constant and predictable residual errors resulting from use of a finite basis set and neglect of electron correlation. In the rare situations when the desired chemical information is found in absolute rather than relative values of the parameters, the offset correction can be added to the computed value. In many cases, such structure evaluations are at least as reliable as those from the best experiments. For the compounds in this study, substitution of either F or OH increases the ionic character of both the B---F and B---bonds. The B---F bond is slightly more ionic than B---O. The OH group is a slightly stronger σ electron-acceptor and π electron-donor than is F.