Debamalya Banerjee

Gadolinium tagging for high-precision measurements of 6 nm distances in protein assemblies by EPR

Double electron-electron resonance (DEER) distance measurements of a protein complex tagged with two Gd(3+) chelates developed for rigid positioning of the metal ion are shown to deliver outstandingly accurate distance measurements in the 6 nm range. The accuracy was assessed by comparison with modeled distance distributions based on the three-dimensional molecular structures of the protein and the tag and further comparison with paramagnetic NMR data. The close agreement between the predicted and experimentally measured distances opens new possibilities for investigating the structure of biomolecular assemblies. As an example, we show that the dimer interface of rat ERp29 in solution is the same as that determined previously for human ERp29 in the single crystal.

ESR evidence for 2 coexisting liquid phases in deeply supercooled bulk water

Using electron spin resonance spectroscopy (ESR), we measure the rotational mobility of probe molecules highly diluted in deeply supercooled bulk water and negligibly constrained by the possible ice fraction. The mobility increases above the putative glass transition temperature of water, Tg = 136 K, and smoothly connects to the thermodynamically stable region by traversing the so called “no mans land” (the range 150–235 K), where it is believed that the homogeneous nucleation of ice suppresses the liquid water. Two coexisting fractions of the probe molecules are evidenced. The 2 fractions exhibit different mobility and fragility; the slower one is thermally activated (low fragility) and is larger at low temperatures below a fragile-to-strong dynamic cross-over at ≈225 K. The reorientation of the probe molecules decouples from the viscosity below ≈225 K. The translational diffusion of water exhibits a corresponding decoupling at the same temperature [Chen S-H, et al. (2006) The violation of the Stokes–Einstein relation in supercooled water. Proc Natl Acad Sci USA 103:12974–12978]. The present findings are consistent with key issues concerning both the statics and the dynamics of supercooled water, namely the large structural fluctuations [Poole PH, Sciortino F, Essmann U, Stanley HE (1992) Phase behavior of metastable water. Nature 360:324–328] and the fragile-to-strong dynamic cross-over at ≈228 K [Ito K, Moynihan CT, Angell CA (1999) Thermodynamic determination of fragility in liquids and a fragile-to-strong liquid transition in water. Nature 398:492–494].

Confinement in silicon nanowires: Optical properties

The blueshift of the optical absorption edge along with the intense red photoluminescence (PL) peak has been observed from micron-long crystalline silicon nanowires prepared by pulsed-laser vaporization of heated Si (mixed with metal catalyst) targets. Previous studies on the confinement in silicon nanostructures resulted in a dispute regarding the application of theoretical models to explain their optical properties. Based on the microstructure a phenomenological confinement model, incorporating the nanowire diameter distribution is used, which is found to describe the optical properties including the shape of absorption spectra, the band gap, and the PL peak position of the Si nanowires very well.

The interplay between the solid effect and the cross effect mechanisms in solid state ¹³C DNP at 95 GHz using trityl radicals.

The (13)C solid state Dynamic Nuclear Polarization (DNP) mechanism using trityl radicals (OX63) as polarizers was investigated in the temperature range of 10-60K. The solutions used were 6M (13)C urea in DMSO/H2O (50% v/v) with 15 mM and 30 mM OX63. The measurements were carried out at ∼3.5 T, which corresponds to Larmor frequencies of 95 GHz and 36 MHz for the OX63 and the (13)C nuclei, respectively. Measurements of the (13)C signal intensity as a function of the microwave (MW) irradiation frequency yielded (13)C DNP spectra with temperature dependent lineshapes for both samples. The maximum enhancement for the 30 mM sample was reached at 40K, while that of the 15 mM sample at 20-30K. Furthermore, the lineshapes observed showed that both the cross effect (CE) and the solid effect (SE) DNP mechanisms are active in this temperature range and that their relative contribution is temperature dependent. Simulations of the spectra with the relative contributions of the CE and SE mechanisms as a fit parameter revealed that for both samples the CE contribution decreases with decreasing temperature while the SE contribution increases. In addition, for the 15 mM sample the contributions of the two mechanisms are comparable from 20K to 60K while for the 30 mM the CE dominates in this range, as expected from the higher concentration. The steep decrease of the CE contribution towards low temperatures is however unexpected. The temperature dependence of the OX63 longitudinal relaxation, DNP buildup times and (13)C spin lattice relaxation times did not reveal any obvious correlation with the DNP temperature dependence. A similar behavior of the CE and SE mechanism was observed for (1)H DNP with the nitroxide radical TEMPOL as a polarizer. This suggests that this effect is a general phenomenon involving a temperature dependent competition between the CE and SE mechanisms, the source of which is, however, still unknown.

A Dynamic Nuclear Polarization spectrometer at 95 GHz/144 MHz with EPR and NMR excitation and detection capabilities

A spectrometer specifically designed for systematic studies of the spin dynamics underlying Dynamic Nuclear Polarization (DNP) in solids at low temperatures is described. The spectrometer functions as a fully operational NMR spectrometer (144 MHz) and pulse EPR spectrometer (95 GHz) with a microwave (MW) power of up to 300 mW at the sample position, generating a MW B(1) field as high as 800 KHz. The combined NMR/EPR probe comprises of an open-structure horn-reflector configuration that functions as a low Q EPR cavity and an RF coil that can accommodate a 30-50 μl sample tube. The performance of the spectrometer is demonstrated through some basic pulsed EPR experiments, such as echo-detected EPR, saturation recovery and nutation measurements, that enable quantification of the actual intensity of MW irradiation at the position of the sample. In addition, DNP enhanced NMR signals of samples containing TEMPO and trityl are followed as a function of the MW frequency. Buildup curves of the nuclear polarization are recorded as a function of the microwave irradiation time period at different temperatures and for different MW powers.

Molecular Probe Dynamics Reveals Suppression of Ice-Like Regions in Strongly Confined Supercooled Water

The structure of the hydrogen bond network is a key element for understanding waters thermodynamic and kinetic anomalies. While ambient water is strongly believed to be a uniform, continuous hydrogen-bonded liquid, there is growing consensus that supercooled water is better described in terms of distinct domains with either a low-density ice-like structure or a high-density disordered one. We evidenced two distinct rotational mobilities of probe molecules in interstitial supercooled water of polycrystalline ice [Banerjee D, et al. (2009) ESR evidence for 2 coexisting liquid phases in deeply supercooled bulk water. Proc Natl Acad Sci USA 106: 11448–11453]. Here we show that, by increasing the confinement of interstitial water, the mobility of probe molecules, surprisingly, increases. We argue that loose confinement allows the presence of ice-like regions in supercooled water, whereas a tighter confinement yields the suppression of this ordered fraction and leads to higher fluidity. Compelling evidence of the presence of ice-like regions is provided by the probe orientational entropy barrier which is set, through hydrogen bonding, by the configuration of the surrounding water molecules and yields a direct measure of the configurational entropy of the same. We find that, under loose confinement of supercooled water, the entropy barrier surmounted by the slower probe fraction exceeds that of equilibrium water by the melting entropy of ice, whereas no increase of the barrier is observed under stronger confinement. The lower limit of metastability of supercooled water is discussed.

Fluorite and Mixed-Metal Kagome-Related Topologies in Metal–Organic Framework Compounds: Synthesis, Structure, and Properties

Two new three-dimensional metal-organic frameworks (MOFs) [Mn(2)(mu(3)-OH)(H(2)O)(2)(BTC)] x 2 H(2)O, I, and [NaMn(BTC)], II (BTC = 1,2,4-benzenetricarboxylate = trimellitate) were synthesized and their structures determined by single-crystal X-ray diffraction (XRD). In I, the Mn(4) cluster, [Mn(4)(mu(3)-OH)(2)(H(2)O)(4)O(12)], is connected with eight trimellitate anions and each trimellitate anion connects to four different Mn(4) clusters, resulting in a fluorite-like structure. In II, the Mn(2)O(8) dimer is connected with two Na(+) ions through carboxylate oxygen to form mixed-metal distorted Kagome-related two-dimensional -M-O-M- layers, which are pillared by the trimellitate anions forming the three-dimensional structure. The extra-framework water molecules in I are reversibly adsorbed and are also corroborated by powder XRD studies. The formation of octameric water clusters involving free and coordinated water molecules appears to be new. Interesting magnetic behavior has been observed for both compounds. Electron spin resonance (ESR) studies indicate a broadening of the signal below the ordering temperature and appear to support the findings of the magnetic studies.

Vitrification, relaxation and free volume in glycerol-water binary liquid mixture: Spin probe ESR studies

Glass transition and relaxation of the glycerol-water (G-W) binary mixture system have been studied over the glycerol concentration range of 5-85 mol% by using the highly sensitive technique of electron spin resonance (ESR). For the water rich mixture the glass transition,sensed by the dissolved spin probe, arises from the vitrified mesoscopic portion of the binary system. The concentration dependence of the glass transition temperature manifests a closely related molecular level cooperativity in the system. A drastic change in the mesoscopic structure of the system at the critical concentration of 40 mol is confirmed by an estimation of the spin probe effective volume in a temperature range where the tracer reorientation is strongly coupled to the system dynamics.