Bifurcation in Rotational Spectra of Nonlinear AB2_2 Molecules

A classical microscopic theory of rovibrational motion at high angular momenta in symmetrical non-linear molecules AB$_2$ is derived within the framework of small oscillations near the stationary states of a rotating molecule. The full-dimensional analysis including stretching vibrations has confirmed the existence of the bifurcation predicted previously by means of the rigid-bender model. The formation of fourfold energy clusters has already been experimentally verified for H$_2$Se and it has been demonstrated in fully-dimensional quantum mechanical calculations using the MORBID computer program. We show in the present work that apart from the level clustering, the bifurcation produces physically important effects including molecular symmetry-breaking and a transition from the normal mode to the local mode limit for the stretching vibrations due to rovibrational interaction. The application of the present theory with realistic molecular potentials to the H$_2$Te, H$_2$Se and H$_2$S hydrides results in predictions of the bifurcation points very close to those calculated previously. However for the lighter H$_2$O molecule we find that the bifurcation occurs at higher values of the total angular momentum than obtained in previous estimations. The present work shows it to be very unlikely that the bifurcation in H$_2$O will lead to clustering of energy levels. This result is in agreement with recent variational calculations.Comment: latex, 19 pages including 2 figures provided as *.uu fil

Calculating energy levels of isomerizing tetra-atomic molecules. II. The vibrational states of acetylene and vinylidene

A general, full-dimensional computational method for the accurate calculation of rotationally and vibrationally excited states of tetra-atomic molecules is further developed. The resulting computer program may be run in serial and parallel modes and is particularly appropriate for molecules executing wide-amplitude motions and isomerizations. An application to the isomerizing acetylene∕vinylidene system is presented. Large-scale calculations using a coordinate system based on orthogonal satellite vectors have been performed in six dimensions and vibrational term values and wave functions for acetylene and vinylidene states up to ≈23000cm−1 above the potential minimum have been determined. This has permitted the characterization of acetylene and vinylidene states at and above the isomerization barrier. These calculations employ more extensive vibrational basis sets and hence consider a much higher density of states than in any variational calculations reported hitherto for this system. Comparison of the calculated density of states with that determined empirically suggests that our calculations are the most realistic achieved for this system to date. Indeed more states have been converged than in any previous study of this system. Calculations on lower lying excited states of acetylene based on HC–CH diatom-diatom coordinates give nearly identical results to those based on orthogonal satellite vectors. Comparisons are also made with calculations based on HH–CC diatom-diatom coordinates

Calculating energy levels of isomerizing tetra-atomic molecules. I. The rovibrational bound states of Ar2HF

A general, six-dimensional computational method for the accurate calculation of rotationally and vibrationally excited states of tetra-atomic molecules is developed. The resulting program is particularly appropriate for molecules executing wide-amplitude motions and isomerizations. An application to the Ar2HF van der Waals trimer is presented in which the HF intramolecular stretching coordinate is separated out adiabatically and is not treated explicitly. Vibrational term values up to about 100 cm−1 with absolute convergence to better than 0.1 cm−1 are reported. These calculations employ more extensive vibrational basis sets and hence consider a much higher density of states than hitherto. States that sample Ar–Ar–HF linear configurations and approach Ar–HF–Ar linear configurations are characterized for the first time. Results for total angular momentumJ=0 and 1 provide the first accurate calculations of rotational constants for this system. The rotational constants for the HF bending states of Ar2HF in the ground and first vibrationally excited states of the HF monomer are in good agreement with experiment, confirming the accuracy of the potential used in this work

Structural insight into the membrane targeting domain of the Legionella deAMPylase SidD

AMPylation, the post-translational modification with adenosine monophosphate (AMP), is catalyzed by effector proteins from a variety of pathogens. Legionella pneumophila is thus far the only known pathogen that, in addition to encoding an AMPylase (SidM/DrrA), also encodes a deAMPylase, called SidD, that reverses SidM-mediated AMPylation of the vesicle transport GTPase Rab1. DeAMPylation is catalyzed by the N-terminal phosphatase-like domain of SidD. Here, we determined the crystal structure of full length SidD including the uncharacterized C-terminal domain (CTD). A flexible loop rich in aromatic residues within the CTD was required to target SidD to model membranes in vitro and to the Golgi apparatus within mammalian cells. Deletion of the loop (??loop) or substitution of its aromatic phenylalanine residues rendered SidD cytosolic, showing that the hydrophobic loop is the primary membrane-targeting determinant of SidD. Notably, deletion of the two terminal alpha helices resulted in a CTD variant incapable of discriminating between membranes of different composition. Moreover, a L. pneumophila strain producing SidD??loop phenocopied a L. pneumophila ??sidD strain during growth in mouse macrophages and displayed prolonged co-localization of AMPylated Rab1 with LCVs, thus revealing that membrane targeting of SidD via its CTD is a critical prerequisite for its ability to catalyze Rab1 deAMPylation during L. pneumophila infection