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

Murugan, N.; Hugosson, Håkan Wilhelm

doi:10.1039/b805505j

Cited by 6 publications

(7 citation statements)

References 23 publications

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“…The inter-and intra-molecular interactions for the trans-1,2-dichloroethylene molecule were described using the GAFF force field [25,26]. The simulations were carried out for the temperature range 200-350 K in the NPT ensemble, therefore allowing the box size to change, and the total time scale of each simulation run was 40-50 ns [27,28]. As can be seen in Fig.…”

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Microscopic structures and dynamics of high- and low-density liquidtrans-1,2-dichloroethylene

et al. 2010

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We present a study of the dynamics and structural changes for trans-1,2-dichloroethylene between high-and low-density liquids using neutron-scattering techniques ͑diffraction, small-angle neutron scattering, and time of flight spectroscopy͒ and molecular-dynamics simulations. We show that changes in the short-range ordering of molecules goes along with a change in the molecular dynamics: both structure and dynamics of the highdensity liquid are more cooperative than those of the low-density liquid. The microscopic mechanism underlying the cooperative motions in the high-density liquid has been found to be related to the backscattering of molecules due to a strong correlation of molecular ordering. Classical thermodynamics establishes the existence of one unique liquid state for any material, i.e., there is only a liquid phase characterized by its density given the thermodybamic coordinates pressure and temperature. Nevertheless, recent experimental results and molecular-dynamics ͑MD͒ simulations suggest that, even for one-component systems, several liquid phases can appear with an associated liquid-liquid phase transition ͑LLPT͒. A noticeable number of cases has been found for atomic liquids, the best-known example concerning liquid phosphorus, 1,2 where the LLPT appears as a transition between thermodynamically stable phases with strong structural changes. 3 As far as molecular liquids are concerned, the number of experimental evidences for LLPT is still rather scarce and comprises only a limited number of compounds such as triphenyl phosphite 4 and n-butanol. 5 According to the so-called two order parameter theories that propose an explanation for the LLPT, liquids must be described not only by their density but also by an additional order parameter accounting for changes in the molecular arrangement. [6][7][8] The LLPT can end in a liquid-liquid critical point between a high-density liquid ͑HDL͒ and a low-density liquid ͑LDL͒. However, changes in the dynamics with an associated change in structural features can also be explained by a singularity-free scenario. 9 In the latter case, changes in both dynamics and structure from a HDL to a LDL also take place at the point where the isobaric heat capacity C P has a maximum, but no critical point or LLPT are observed at nonzero temperature.An early work on trans-1,2-dichloroethylene ͑T melt = 223 K͒ suggested the existence of a LLPT at T t = 247 K Ͼ T melt based on a small jump in density ͑less than 0.06%͒ as well as in the compressibility and a clear discontinuity on the spin-lattice relaxation time T 1 . 10,11 The observed changes in T 1 were tentatively related to a lack of freedom of the molecular rotation in the HDL, not present in the LDL. The change in the dynamics of this substance between both liquids was thereafter also supported by discontinuities in the viscosity measurements and the slope of the rotational relaxation time 12 and by the absorbance, frequency, and linewidth of several infrared vibrational spectroscopy bands. 13 Concerning structural rela...

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Microscopic structures and dynamics of high- and low-density liquidtrans-1,2-dichloroethylene

et al. 2010

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“…19,20 The simulations were carried out for the temperature range 200-350 K in the NPT ensemble, therefore allowing the box size to change, and the total time of each simulation run was 40-50 ns. 21,22 This simulation is the same as that used in Ref. 15 for the preliminary analysis of the short-range order in liquid TDCE.…”

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confidence: 99%

Differences in first neighbor orientation behind the anomalies in the low and high density trans-1,2-dichloroethene liquid

Rovira-Esteva

Murugan

Pardo

et al. 2012

The Journal of Chemical Physics

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Trans-1,2-dichloroethene (HClC=CClH) has several structural and dynamic anomalies between its low- and high-density liquid, previously found through neutron scattering experiments. To explain the microscopic origin of the differences found in those experiments, a series of molecular dynamics simulations were performed. The analysis of molecular short-range order shows that the number of molecules in the first neighbor shell is 12 for the high-density liquid and 11 for the low-density one. It also shows that the angular position of the center of mass of the first neighbor is roughly the same although the molecular orientation is not. In both liquids the first neighbor and its reference molecule arrange mainly in two configurations, each being the most probable in one of the liquids. First neighbors in the configuration that predominates in the high-density liquid tend to locate themselves closer to the reference molecule, an evidence that they are more strongly bonded. This arrangement facilitates a better packing of the rest of molecules in the first neighbor shell so that on average an additional molecule can be included, and is proposed to be the key in the explanation of all the observed anomalies in the characteristics of both liquids.

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“…The atomic charges for the asparagine were adopted from the fit to reproduce electrostatic potential obtained from HF/6-31G* level calculations using the CHELPG procedure as implemented in the Gaussian09 software . We have employed the GAFF force-field for asparagine as the applicability of this force field to model the structural and dynamical properties of organic molecules have been demonstrated in many earlier research reports. − Moreover, a GAFF force-field for chloroform and TIP3P model for water were used in these simulations. The MD simulations were carried out in an orthorhombic box containing asparagine and solvents.…”

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confidence: 99%

Solvent Polarity-Induced Conformational Unlocking of Asparagine

2012

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Classical and Car-Parrinello molecular dynamics simulations are performed to study the solvent effect on the conformational distribution of asparagine. Conformational populations obtained from the simulations in gas phase and in nonpolar chloroform solvent are in agreement with the most probable single conformation of asparagine in the gas phase measured in recent laser ablation with molecular beam Fourier transform microwave spectroscopy experiments. We rationalize that intramolecular hydrogen bonding and dipole-dipole interactions between carbonyl groups dictate such a conformational locking to a single asparagine conformer. The solvent polarity induced interlocking or intermolecular hydrogen bonding with water solvent molecules destabilizes the (NH···O═C) bonding between side chain and terminal groups of asparagine, while not essentially affecting the (NH···O═C) intramolecular hydrogen bondings within the side chain nor within the terminal groups. Such a conformational unlocking or cage effect is observed in asparagine within aqueous solution. We observed a spontaneous conversion of neutral to zwitterionic isomer of asparagine in aqueous solution, which is in agreement with interpretation of Raman spectroscopy results. Using Møller-Plesset second order perturbation theory, we show that a tautomeric shift from neutral to zwitterionic occurs on asparagine in between DMSO and water solvents. The ramification of these findings for the conformational character of asparagine is briefly discussed.

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

Cited by 6 publications

References 23 publications

Microscopic structures and dynamics of high- and low-density liquidtrans-1,2-dichloroethylene

Microscopic structures and dynamics of high- and low-density liquidtrans-1,2-dichloroethylene

Differences in first neighbor orientation behind the anomalies in the low and high density trans-1,2-dichloroethene liquid

Solvent Polarity-Induced Conformational Unlocking of Asparagine

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