Rajul Ranjan Choudhury

Structural changes during the unfolding of Bovine serum albumin in the presence of urea: A small-angle neutron scattering study

The native form of serum albumin is the most important soluble protein in the body plasma. In order to investigate the structural changes of Bovine serum albumin (BSA) during its unfolding in the presence of urea, a small-angle neutron scattering (SANS) study was performed. The scattering curves of dilute solutions of BSA with different concentrations of urea in D2O at pH 7.2 ± 0.2 were measured at room temperature. The scattering profile was fitted to a prolate ellipsoidal shape (a, b, b) of the protein witha = 52.2 Å andb = 24.2 Å. The change in the dimensions of the protein as it unfolds was found to be anisotropic. The radius of gyration of the compact form of the protein in solution decreased as the urea concentration was increased.

The role of the double-well potential seen by the amino group in the ferroelectric phase transition in triglycine sulfate

The two most important molecular movements which bring about the order–disorder ferroelectric phase transition in the hydrogen-bonded ferroelectric triglycine sulfate (TGS) are the swinging of the amino group (−NH3+) of one of its three glycine ions, namely GI, and the tunnelling of hydrogen in the hydrogen bond between its other two glycine ions, GII and GIII (GII–H–GIII). The potential function for bent hydrogen bonds is used along with the structural parameters of the TGS crystal to model the double-well potential (U) seen by the amino group (−NH3+) of GI in TGS. The ferroelectric phase transition in TGS is investigated from the point of view of the double-well instability. Results obtained are in good agreement with those obtained earlier using the Ising-type theoretical model. Correlation between the two crucial molecular movements in TGS, namely swinging of the −NH3+ group of GI and tunnelling of hydrogen in the hydrogen bond GII–H–GIII of TGS, is established.

Hydrogen bonding in oxalic acid and its complexes: A database study of neutron structures

The basic result of carboxylic group that the oxygen atom of the -OH never seems to be a hydrogen bond acceptor is violated in the cases, namely urea oxalic acid and bis urea oxalic acid complexes, where the hydroxyl oxygen atom is an acceptor of a weak N—H… O hydrogen bond. The parameters of this hydrogen bond, respectively in these structures are: hydrogen acceptor distance 2.110 Å and 2.127 Å and the bending angle at hydrogen, 165.6° and 165.8°. The bond strength around the hydroxyl oxygen is close to 1.91 valence units, indicating that it has hardly any strength left to form hydrogen bonds. These two structures being highly planar, force the formation of this hydrogen bond. As oxalic acid is the common moiety, the structures of the two polymorphs, α-oxalic acid and β-oxalic acid, also were looked into in terms of hydrogen bonding and packing.

Low-barrier hydrogen bonds in proteins

Hydrogen bonding interactions are one of the most important chemical interactions among materials, especially biological materials, which help confer specificity, which is crucial for their efficient functioning. Recently, low-barrier hydrogen bonds (LBHBs) have been proposed to play a critical role in enzyme catalysis. In this review, tools to identify LBHBs are described, along with analyses of neutron crystal structures of small molecules to identify geometric parameters characteristic of LBHBs, which are assumed to be characterized by dynamic disorder along the hydrogen bond (H-bond) of the bonding hydrogen atom. The analysis of protein structures determined by neutron diffraction indicates that LBHBs are found to occur in both active site and non-active site regions of a protein. Moreover, very short H-bonds are observed in the vicinity of folding cores identified through nuclear magnetic resonance studies on two proteins, SUMO-1 and HIV-1 protease. This observation suggests that LBHBs may also be important in the context of folding of proteins.

Zinc (tris) thiourea sulphate (ZTS): A single crystal neutron diffraction study

The crystal structure of ZTS has been determined by neutron diffraction with a finalR-value of 0.026. Using the structural parameters, the contributions from the structural groups to the linear optical susceptibility and linear electro-optic coefficients have been evaluated. Results showed a significant contribution from the hydrogen bonds in the structure.

Phase transition in triglycine family of hydrogen bonded ferroelectrics: An interpretation based on structural studies

Using the crystal structure, a comprehensive interpretation of the origin of ferroelectricity in the hydrogen bonded triglycine family of crystals is given. Our detailed analysis showed that the instability of nitrogen double well potential plays a driving role in the mechanism of the ferroelectric transitions in these crystals.

Influence of N?H?O hydrogen bonds on the structure and properties of (K1?x(NH4)xH2PO4) proton glasses: a?single crystal neutron diffraction study

It has been known for quite some time now that proton dynamics plays a key role in the structural ferroelectric (FE)/antiferroelectric (AFE) phase transition in the crystals belonging to the potassium dihydrogen phosphate crystal family. Mixed crystals belonging to this family having the composition M(1-x)(NW(4))(x)W(2)AO(4), where M = K, Rb, Cs, W = H, D, and A = P, As, exhibit proton glass behavior due to frustration between FE and AFE ordering; these proton glasses do not undergo any structural phase change but retain their room temperature structure down to very low temperatures. Single crystal neutron diffraction investigations of four mixed crystals with composition (K(1-x)(NH(4))(x)H(2)PO(4)), where x = 0.0, 0.29, 0.67 1.0, were undertaken with the intention to investigate the effect of the local structural deviations on the overall average structure of the crystals and correlate these structural changes to the presence or absence of a structural phase transition in these crystals. Hydrogen bonding is shown to play a key role in the changing nature of the mixed crystals as the composition varies from the potassium rich ferroelectric region to the proton glass region to the ammonium rich antiferroelectric region.

Pressure induced structural phase transition in triglycine sulfate and triglycine selenate

To elucidate the cause of destruction of ferroelectricity with pressure in triglycine sulfate and triglycine selenate, we have investigated these compounds with the help of Raman measurements as well as first principles total energy and structural optimization calculations. Our results show that, beyond the critical pressures, the loss of ferroelectricity in these compounds is due to the conformational change in one of the three glycine ions of these crystals. Our studies suggest that pressure induced phase transition might be of displacive nature unlike the temperature induced ferroelectric phase transition in these crystals which is known to be of order-disorder type.

Ferroelectric phase transition in triglycine selenate: an interpretation based on its structure and its comparison with triglycine sulphate

Triglycine selenate (TGSe) is a hydrogen-bonded ferroelectric, which undergoes a structural phase transition at T c  = 295 K. It is isomorphous to triglycine sulphate (TGS) which is a very well studied order–disorder ferroelectric extensively used in infrared detection. The crucial molecular unit from the point of view of ferroelectric phase transition in these crystals is the group of one of the three glycine ions GI, which has two equivalent positions in an asymmetric unit. This group gets disordered between its two equivalent positions for temperatures above T c . The potential energy of this group as a function of the distance between its equivalent positions was modelled, and the phase transition in TGSe was interpreted using “the coupled anharmonic oscillator model” of ferroelectrics proposed by Y. Onodera. Similarities as well as differences between the ferroelectric phase transition in TGS and TGSe are discussed.

Mechanism of order–disorder phase transition in phenanthrene crystals: an interpretation based on the rotational potential energy surface for a phenanthrene molecule in a phenanthrene crystal

Crystals of phenanthrene undergo an order–disorder phase change at 72°C. High temperature phase was found to be disordered with two possible molecular positions. In order to understand the fundamental mechanism of the phase transition, we have modeled the molecular movement within the phenanthrene crystal and estimated the rotational potential energy surface for a phenanthrene molecule, as it undergoes this flip-flop motion. The situation in phenanthrene crystal is explained by a model where the molecules exhibit large amplitude librations having been trapped in the potential wells. Fluctuations in the orientation of the neighboring molecules result in changes in the shape of the potential well and consequently giving rise to angular motions of molecules with large amplitude. The calculations show that the two minima of the potential energy surface are not equivalent, as a result, the occupancy of the two possible molecular positions will not be the same, hence the space group of the disorder phase will remain P21 and not change to P21/a.