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

2005

J. Phys. Chem. B

Self Cite

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.

Section: Resultssupporting

confidence: 75%

Orientational Melting and Reorientational Motion in a Cubane Molecular Crystal: A Molecular Simulation Study

2005

J. Phys. Chem. B

Self Cite

“…In this kind of systems, it is thus preferable to include not only the solvent‐induced geometrical changes but also the temperature‐induced ones. There are many reports in the literature that discuss the disorder and conformational transition for the molecules even in the solid state at room temperature19, 20, and it is certainly relevant to study temperature‐induced geometrical changes for a solute also in a solute–solvent supermolecular system. Calculations of the properties for minimum energy structures are evidently acceptable when the temperature‐induced geometrical changes are insignificant for the candidate molecule, while thus for thermochromic molecules the solvent‐induced and temperature‐induced geometrical changes in a solute should be accounted for.…”

Section: Introductionmentioning

confidence: 99%

Modeling solvatochromism of Nile red in water

Int J of Quantum Chemistry

Rinkevičius

Ågren

2011

Spurred by the pioneering modeling studies of Sylvio Canuto on absorption spectra and solvatochromic shifts of organic molecules in polar and nonpolar solvents, we report in this work a computational study for the common optical dye probe Nile red (NR) to elucidate the origin of its absorption shift between gas phase and aqueous solution. The Car-Parrinello molecular dynamics (CPMD) technique is used for gas phase NR, whereas for NR in water solvent, a hybrid quantum mechanics-molecular dynamics (CPMD-QM/MM) approach has been utilized. For the configurations obtained from CPMD and CPMD-QM/MM, the absorption spectrum has been calculated using the INDO/CIS method as implemented in the ZINDO program. Different solvation shells for NR in water have been defined based on solute-all-atoms and solvent center of mass radial distribution function (g(r X−O ) rdf). The electronic excitation energies for these solvation shells were calculated in a systematic way to evaluate their individual contributions. In addition, calculations of absorption spectra were performed for NR (excluding solvent molecules) obtained from CPMD-QM/MM calculations to isolate the contribution to the solvatochromic shift just due to solvent-induced geometrical change. Interestingly, this geometrical change in NR itself contributes as much as 50 nm to the solvatochromic shift. The calculated λ max for gas phase is around 488 nm and is comparable to the values reported for NR in nonpolar solvents, whereas the inclusion of solvent molecules in the hydration shell yields a λ max of 565 nm which contributes to almost 77 nm of the solvatochromic shift. The inclusion of solvent molecules up to the fourth solvation shell in the g(r X−O ) rdf yields λ max of 596 nm which is in good agreement with the experimentally reported value 593 nm. The change in λ max due to inclusion of the fourth solvation shell is MURUGAN, RINKEVICIUS, AND ÅGREN only 1 nm, indicating that the spectrum has converged with respect to the solvent effect. Overall, this study suggests that the combined use of CPMD-QM/MM and ZINDO can be successfully used to model and to interpret solvatochromic and thermochromic behavior of NR and other organic dye molecules.

“…Cyclohexane or cyclopentane based organic compounds [1][2][3] and torsionally flexible molecules 4,5 are shown to exist in different conformational states. The relative population of different conformational states is decided by the solvents, 6,7 temperature, pressure and can also be modified by the chemical substitution of different groups.…”

Section: Introductionmentioning

confidence: 99%

Investigations into conformational transitions and solvation structure of a 7-piperidino-5,9-methanobenzo[8] annulene in water

Phys. Chem. Chem. Phys.

Hugosson

2008

Self Cite

Solvation shell structure of a 7-piperidino-5,9-methanobenzo[8] annulene (PMA) in water has been investigated in ambient conditions using both molecular dynamics (MD) and Car-Parrinello molecular dynamics (CPMD) calculations. From the MD calculations, we find that this molecule exists in three major conformational states out of which two are in twist-boat forms and one in chair form. Due to the limited time scale accessible in CPMD simulations, we have studied all the three conformational states separately using CPMD. The molecular geometry, electronic charge distribution and solvation structure for all three forms are investigated. The stability order of the chair and twist-boat conformations in water solvent has been reversed when compared to the gaseous phase results and in the case of polar aprotic solvents (J. Org. Chem., 1999, 61, 5979). From the radial distribution function, we find that the solvent density around the chair form is significantly lower, which has to be directly related to the smaller solvent accessible area for this conformation and this is in complete agreement with earlier reports. Among the findings are that the solvation shell structure around the nitrogen atom in the chair form of PMA is considerably different from the open conformational forms or the twist-boat forms. The dipole moment for the closed form is found to be significantly larger when compared to the twist-boat forms.