Comparison of ab initio and DFT electronic structure methods for peptides containing an aromatic ring: effect of dispersion and BSSE

We establish that routine B3LYP and MP2 methods give qualitatively wrong conformations for flexible organic systems containing pi systems and that recently developed methods can overcome the known inadequacies of these methods. This is illustrated for a molecule (a conformer of the Tyr-Gly dipeptide) for which B3LYP/6-31+G(d) and MP2/6-31+G(d) geometry optimizations yield strikingly different structures [Mol. Phys. 2006, 104, 559-570]: MP2 predicts a folded "closed-book" conformer with the glycine residue located above the tyrosine ring, whereas B3LYP predicts a more open conformation. By employing different levels of theory, including the local electron correlation methods LMP2 (local MP2) and LCCSD(T0) (local coupled cluster with single, double, and noniterative local triple excitations) and large basis sets (aug-cc-pVnZ, n=D, T, Q), it is shown that the folded MP2 minimum is an artifact caused by large intramolecular BSSE (basis set superposition error) effects in the MP2/6-31+G(d) calculations. The B3LYP functional gives the correct minimum, but the potential energy apparently rises too steeply when the glycine and tyrosine residues approach each other, presumably due to missing dispersion effects in the B3LYP calculations. The PWB6K and M05-2X functionals, designed to give good results for weak interactions, remedy this to some extent. The reduced BSSE in the LMP2 calculations leads to faster convergence with increasing basis set quality, and accurate results can be obtained with smaller basis sets as compared to canonical MP2. We propose LMP2 as a suitable method to study interactions with pi-electron clouds.     

Carbenoxolone induced depression of rhythmogenesis in the pre-Bötzinger Complex

Background

Carbenoxolone (CBX), a gap junction uncoupler, alters the functioning of the pre-Bötzinger Complex (preBötC), a central pattern generating neuronal network important for the production of respiratory rhythm in mammals. Even when isolated in a 1/2 mm-thick slice of medulla oblongata from neonatal mouse the preBötC continues producing periodic bursts of action potentials, termed population bursts that are thought to be important in generating various patterns of inspiration, in vivo. Whether gap junction communication contributes to preBötC rhythmogenesis remains unresolved, largely because existing gap junction uncouplers exert numerous non-specific effects (e.g., inhibition of active transport, alteration of membrane conductances). Here, we determined whether CBX alters preBötC rhythmogenesis by altering membrane properties including input resistance (R_in), voltage-gated Na⁺ current (I_Na), and/or voltage-gated K⁺ current (I_K), rather than by blocking gap junction communication. To do so we used a medullary slice preparation, network-level recordings, whole-cell voltage clamp, and glycyrrhizic acid (GZA; a substance used as a control for CBX, since it is similar in structure and does not block gap junctions).

Results

Whereas neither of the control treatments [artificial cerebrospinal fluid (aCSF) or GZA (50 μM)] noticeably affected preBötC rhythmogenesis, CBX (50 μM) decreased the frequency, area and amplitude of population bursts, eventually terminating population burst production after 45–60 min. Both CBX and GZA decreased neuronal R_in and induced an outward holding current. Although neither agent altered the steady state component of I_K evoked by depolarizing voltage steps, CBX, but not GZA, increased peak I_Na.

Conclusion

The data presented herein are consistent with the notion that gap junction communication is important for preBötC rhythmogenesis. By comparing the effects of CBX and GZA on membrane properties our data a) demonstrate that depression of preBötC rhythmogenesis by CBX results from actions on another variable or other variables; and b) show that this comparative approach can be used to evaluate the potential contribution of other non-specific actions (e.g., Ca⁺⁺ conductances or active transport) of CBX, or other uncouplers, in their alteration of preBötC rhythmogenesis, or the functioning of other networks.

     

Phase diversity with undersampled systems via superresolution preprocessing

Phase diversity algorithms allow a wavefront to be reconstructed from through-focus measurements of a point source or extended scene. These algorithms have traditionally been limited to systems that are Nyquist sampled. Many optical systems for remote sensing applications are designed to be undersampled, however. One approach to phase diversity with undersampled systems is to employ superresolution techniques to first create properly sampled scenes. This is demonstrated experimentally for a point object, but is applicable to extended scenes as well.     

Measurements of the decay KL-->e+ e- gamma

The E799-II (KTeV) experiment at Fermilab has collected 83 262 K(L)-->e+ e- gamma(gamma) events above a background of 79 events. We measure a decay width, normalized to the K(L)-->pi0pi0pi(D)0 (pi0-->gammagamma, pi0-->gammagamma, pi(D0-->e+ e- gamma(gamma)) decay width, of Gamma(K(L)-->e+e-gamma(gamma))/Gamma(K(L)-->pi0pi0pi(D)0)=(1.3302+/-0.0046(stat)+/-0.0102(syst)) x 10(-3). We also measure parameters of two K(L)gamma*gamma form factor models. In the Bergstr?m-Massó-Singer parametrization, we find Calpha(K*)= -0.517 +/- 0.030(stat) +/- 0.022(syst). We separately fit for the first parameter of the D'Ambrosio-Isidori-Portolés model and find alpha(DIP)= -1.729 +/- 0.043(stat) +/- 0.028(syst).     

Low-frequency wind noise correlation in microphone arrays

A three-axis orthogonal microphone array with ten sensors in each arm has been used to study wind noise in the frequency range from 0.05 to 50 Hz. Simultaneous measurements were made of the three components of the varying wind velocity. Measurements have been made for wind speeds from 4 to 7 m/s at three different sites. The frequency-dependent correlation of the wind noise over a range of wind velocities and atmospheric and environmental conditions in the downwind direction varies as exp(-3.2X)cos(27piX). For the crosswind and vertical directions, the correlation decays approximately as exp(-7Y), where X is the separation in wavelengths in the downwind direction and Y is this separation in the crosswind or vertical direction. Over a limited range of wave numbers, the power density spectra of the varying wind velocity varied as the wave number to the -(5/3) power and the pressure spectra as the -(7/3) power.     

Search for the rare decay K(L)-->pi(0)e(+)e(-)

The KTeV/E799 experiment at Fermilab has searched for the rare kaon decay K(L)-->pi(0)e(+)e(-). This mode is expected to have a significant CP violating component. The measurement of its branching ratio could support the standard model or could indicate the existence of new physics. This Letter reports new results from the 1999-2000 data set. One event is observed with an expected background at 0.99+/-0.35 events. We set a limit on the branching ratio of 3.5x10(-10) at the 90% confidence level. Combining with the previous result based on the data set taken in 1997 yields the final KTeV result: BR(K(L)-->pi(0)e(+)e(-))<2.8x10(-10) at 90% C.L.     

Time-resolved studies of single quantum dots in magnetic fields

We present time-resolved and time-integrated spectroscopy of single InAs quantum dots grown in a GaAs matrix. We observe a number of interesting features in the spectra, including the zero field splitting of exciton and biexciton lines due to quantum dot asymmetry. By the application of an in-plane magnetic field, the normally optically active and inactive exciton states become mixed, enabling us to optically probe the normally inaccessible ‘dark’ states. Time resolved measurements on the mixed states show decay times several times longer than the exciton lifetime at zero field, which we show to be consistent with a dark exciton lifetime orders of magnitude longer than that for bright exciton.     

Mid-infrared luminescence from coupled quantum dots and wells

Coupled nanostructures have been developed in the InAs/InSb/GaSb materials system in order to extend the emission wavelength further into the infrared, beyond 2 μm. The samples studied consist of a single narrow InAs quantum well grown below a layer of InSb quantum dots in a GaSb matrix, in which the coupling has been altered by changing the thickness of a GaSb spacer layer. The overall transition energy of the combined dot–well system is generally reduced with respect to the dots and well only but the dependence on spacer thickness is more complex than that expected from a simple envelope function model.     

Waiting times: Positive and negative results on the Wyner-Ziv problem

Asymptotic properties of the waiting timeW _k (x,y) until an initial segment of lengthk of a sample pathx of an ergodic finite-alphabet process is seen in an independently chosen sample pathy are discussed. Wyner and Ziv have shown that for irreducible Markov chains, (1/k) logW _k (x,y) converges in probability to the entropyH of the process. In this paper, almost sure convergence toH is established for the somewhat larger class of functions of irreducible Markov chains and convergence in probability toH is established for weak Bernoulli processes. A stationary coding of an i.i.d. process is constructed for which there is a subsequencek(n) such that (1/k(n) logW _k(n )(x,y), converges in probability to +. Positive and negative results for the case when only approximate matches are required are also obtained.Partially supported by NSF Grant DMS-9024240.From 9/1 to 12/1 earch year: Mathematies Institute, POB 127, 1364 Budapest, Hungary. 011-361-1-177-175. At other times: Department of Mathematics, University of Toledo, Toledo, Ohio 43606, (419) 537-2069.