Biomedical subjects

N Arul Murugan

Publications and source records attributed to N Arul Murugan.

7 recordsLinked to original sources

PubMed2005

Orientational melting and reorientational motion in a cubane molecular crystal: a molecular simulation study.

Detailed molecular simulations are carried out to investigate the effect of temperature on orientational order in cubane molecular crystal. We report a transition from an orientationally ordered to an orientationally disordered plastic crystalline phase in the temperature range 425-450 K. This is similar to the experimentally reported transition at 395 K. The nature of this transition is first order and is associated with a 4.8% increase in unit cell volume that is comparable to the experimentally reported unit cell volume change of 5.4% (Phys. Rev. Lett. 1997, 78, 4938). An orientational order parameter, eta(T), has been defined in terms of average angle of libration of a molecular 3-fold axis and the orientational melting has been characterized by using eta(T). The orientational melting is associated with an anomaly in specific heat at constant pressure (C(P)) and compressibility (kappa). The enthalpy of transition and entropy of transition associated with this orientational melting are 20.8 J mol(-1) and 0.046 J mol(-1) K(-1), respectively. The structure of crystalline as well as plastic crystalline phases is characterized by using various radial distribution functions and orientational distribution functions. The coefficient of thermal expansion of the plastic crystalline phase is more than twice that of the crystalline phase.

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PubMed2005

What does pressure decide to cook with orientationally disordered plastic phase of cubane: an orientational glass or crystal?

The effect of pressure on the structure and reorientational motion of molecules in orientationally disordered (OD) crystalline phase of cubane has been investigated in detail using variable shape molecular simulations in constant-pressure constant-temperature ensemble. Complete orientational ordering occurs at a pressure of 1.0 GPa and the OD phase transforms to an orientationally ordered phase at this pressure. The transition is associated with a kink in the variation of structural parameters such as cell parameters, unit-cell volume, and interaction energy. This transition is also associated with an anomaly in specific heat. Above this transition pressure, the structural quantities display only smaller changes with further increase in pressure. The structure of high-pressure orientationally ordered (HPOO) phase has been characterized using radial distribution functions and orientational distribution function. From detailed analysis of the structure of HPOO phase we conclude that it is isostructural with low-temperature orientationally ordered phase. The OD phase has four times larger compressibility than the HPOO phase.

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PubMed2005

High-pressure study of adamantane: variable shape simulations up to 26 GPa.

We report simulations of adamantane by carefully combining ab initio and empirical approaches to enable simulations with internal degrees of freedom on crystalline adamantane up to a pressure of 26 GPa. Two sets of simulations, assuming the adamantane molecule as a rigid (RB) and flexible body (FB), have been carried out as a function of pressure up to 26 GPa to understand changes in the crystal structure as well as molecular structure. The flexible body simulations have been performed by including 6 lowest frequency internal modes (obtained from DFT calculations performed with Gaussian98) out of the total of 72. The calculated variation in c/a and V/V(0) from the RB and FB calculations as a function of pressure have been compared with the experimental curve. Other relevant thermodynamic and structural properties reported are the radial distribution functions, deviation in the position of a given type of atom with respect to its position at standard pressure, delta(s), cell parameters, volume, and energy. With an increase in pressure, three additional peaks are seen to develop gradually at three different pressures in the center of mass (com)-com radial distribution function (rdf). We attribute these changes to structural transformations (probably second-order phase transitions) which is consistent with the three phase transitions reported by Vijayakumar et al. for adamantane in the pressure range of 1 atm-15 GPa. Our simulations also show that these additional peaks in the rdf's are associated with the differences between opposite and parallel spin neighbors of Greig and Pawley as well as the crystallographic directional dependence of intermolecular distances in the first three shells of the neighbors. Also, the structural quantities from the RB calculation show considerable deviation from the FB calculation for pressures greater than 5 GPa, which suggests that the rigid body assumption for molecules may not be valid above this pressure.

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PubMed2005

Temperature-induced dynamical conformational disorder in 4-vinyl benzoic acid molecular crystals: a molecular simulation study.

Extensive molecular simulations are carried out as a function of temperature to understand and quantify the conformational disorder in molecular crystals of 4-vinyl benzoic acid. The conformational disorder is found to be dynamic and associated with a flip-flop motion of vinyl groups. The population of minor conformer is less than 3% up to 300 K and is 13.2% at 350 K and these results are consistent with the experimental observations. At still higher temperatures, the population of minor conformer increases up to 25%. The evolution of structure at both molecular and unit-cell level of the molecular crystal as a function of temperature has been characterized by various quantities such as radial distribution functions, average cell parameters, volume, and interaction energies. The van't Hoff plot shows a nonlinear behavior at lower temperatures as it has been reported recently by Ogawa and co-workers in the case of stilbene, azobenzene, and N-(4-methylbenzylidene)-4-methylaniline molecular crystals. A set of rigid body simulations were also carried out to quantify the effect of conformational disorder on structural quantities such as unit-cell volume and interaction energy. The anomalous shrinkage of vinyl C=C bond length as a function of temperature has been explained by combining the results of simulations and a set of constrained optimizations using ab initio electronic structure calculations for various molecular structures differing in torsional angle.

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PubMed2005

Effect of pressure on pedal motion in stilbene molecular crystals and its dependence on the crystallographic site.

We report computer simulation of a stilbene molecular crystal as a function of pressure up to 4 GPa. Molecular structure and the crystal structure of stilbene have been characterized by calculating the radial distribution function and dihedral angle distribution, features associated with pedal motion and cell parameters. Results suggest that the population of minor conformer at site 2 disappears altogether above 1.25 GPa. In contrast, the population of minor conformer at site 1 remains at around 12%. Pedal motion is not observed beyond a pressure of 0.8 and 1.4 GPa at site 1 and site 2, respectively. Specific heat and compressibility exhibit an anomaly around 1.25 GPa. The anomaly seems to be associated with the disappearance of pedal motion at site 2. Initially, increase in pressure leads to an increase in the magnitude of lattice energy, but beyond 0.5 GPa it decreases.

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PubMed2005

Pressure-induced ordering in adamantane: a Monte Carlo simulation study.

Isothermal-isobaric ensemble Monte Carlo simulation of adamantane has been carried out with a variable shape simulation cell. The low-temperature crystalline phase and the room-temperature plastic crystalline phases have been studied employing the modified Williams potential. We show that at room temperature, the plastic crystalline phase transforms to the crystalline phase on increase in pressure. Further, we show that this is the same phase as the low-temperature ordered tetragonal phase of adamantane. The high-pressure ordered phase appears to be characterized by a slightly larger shift of the first peak toward a lower value of r in C-C, C-H, and H-H radial distribution functions as compared to the low-temperature tetragonal phase. The coexistence curve between the crystalline and plastic crystalline phase has been obtained approximately up to a pressure of 4 GPa.

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PubMed2005

Pressure induced orientational ordering in p-terphenyl.

Three different interaction potentials existing in the literature along with a model proposed here have been used to model p-terphenyl under standard conditions. Of these, the model that predicts the room-temperature crystal structure well has been used to understand the behavior of p-terphenyl under pressure. Lattice parameters show good agreement with the X-ray diffraction values reported by Puschnig et al. (Puschnig, P.; Heimel, G.; Weinmeier, K.; Resel, R.; Ambrosch-Draxl, C. High Pressure Res. 2002, 22, 105). The nonplanar structure of p-terphenyl transforms to a planar structure with gradual disappearance of disorder associated with ring flipping. We show that the transformation is accompanied by a change in the potential energy profile from W-shaped to a U-shaped form, which is associated with complete planarization between 1.0 and 1.5 GPa. Our results reported here are in excellent agreement with X-ray diffraction results which also suggest the existence of a similar transition as a function of pressure in polyphenyls such as biphenyl and p-hexaphenyl. Interestingly, the amplitude of the torsional motion is largest at an intermediate pressure of 1.0 GPa. This is attributed to the rather flat potential energy landscape which occurs during the transition from W- to U-shaped potential.

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