Study of the torsional potential energies of 2-methylpropane, n-butane, and 2-methylbutane with high-level ab initio calculations

Hafezi, Mohammad; Sharif, Farhad

doi:10.1016/j.theochem.2007.02.034

Cited by 15 publications

(11 citation statements)

References 30 publications

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“…63,73,77 Unlike experimental estimates, ab initio calculated energy differences for the rotational barriers of n-butane indicate that the cis barrier is significantly higher compared with the t/g barrier. 72,73 For example, Smith and Jaffe employed CCSD(T)/ cc-pVTZ//MP2/6-311g(2df,p) level of theory, resulting in values of 13.85 AE 0.42 kJ mol À1 for the t/g barrier and 22.93 AE 0.42 kJ mol À1 for the cis barrier. 73 There is also some evidence that there is a small reduction in the t/g barrier compared to n-butane with increasing chain length.…”

Section: Optimization Of Torsional Potentialsmentioning

confidence: 99%

“…These suggest that the t/g and cis barriers are comparable in energy, with one estimate giving values of 15.15 and 16.56 kJ mol À1 for the t/g and cis barriers respectively. 72,73 The torsional energy about the dihedral C-C-C-C in n-butane involves 1-4 interactions between the methyl groups and it is therefore expected that the torsional energy about single bonds in longer n-alkanes may result in different values for the gauche energy and the rotational barriers. 73 There are indications from experiment that the gauche energy is slightly lower in longer n-alkanes compared to n-butane.…”

Section: Pccp Papermentioning

confidence: 99%

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Optimization of the GAFF force field to describe liquid crystal molecules: the path to a dramatic improvement in transition temperature predictions

Boyd

Wilson

2015

Phys. Chem. Chem. Phys.

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The physical properties and phase transitions of thermotropic liquid crystals are highly sensitive to small changes in chemical structure. However, these changes are challenging to model, as both the phase diagram and mesophase properties obtained from fully atomistic simulations are strongly dependent on the force field model employed, and the current generation of chemical force fields has not proved accurate enough to provide reliable predictions of transition temperatures for many liquid crystals. This paper presents a strategy for improving the nematic clearing point, TNI, in atomistic simulations, by systematic optimization of the General Amber Force Field (GAFF) for key mesogenic fragments. We show that with careful optimization of the parameters describing a series of liquid crystal fragment molecules, it is possible to transfer these parameters to larger liquid crystal molecules and make accurate predictions for nematic mesophase formation. This new force field, GAFF-LCFF, is used to predict the nematic-isotropic clearing point to within 5 °C for the nematogen 1,3-benzenedicarboxylic acid,1,3-bis(4-butylphenyl)ester, an improvement of 60 °C over the standard GAFF force field.

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Section: Optimization Of Torsional Potentialsmentioning

confidence: 99%

Section: Pccp Papermentioning

confidence: 99%

Optimization of the GAFF force field to describe liquid crystal molecules: the path to a dramatic improvement in transition temperature predictions

Boyd

Wilson

2015

Phys. Chem. Chem. Phys.

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“…In nbutane, the experimental value is 3.62 kcal/mol 19 with calculated values being 3.49 20 and 3.31kcal/mol 21,22 . In their work, Mirkin et al found a good agreement between experimental values and MP2/6-31G* rotational barriers which were relatively larger than HF/6-31G* or HF/6-31G ones 18,23 . Concerning 2,3-DMH, the onedimensional rotation from A leads to the following conformational changes: Around C2C3 bond:…”

Section: Hmentioning

confidence: 82%

Theoretical and Spectroscopic investigations of conformations, rotational barriers and scaled vibrations of 2,3-dimethyl hexane

Aboulmouhajir¹,

Mouatarif²,

Hachim³

et al. 2017

Mediterr.J.Chem.,

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The 2,3-dimethyl hexane conformational isomerism has been investigated in detail, based on HF, Post-HF and DFT calculations at different basis set. The effect of size of basis, ZPE, thermal contributions, electronic correlation and optimization methods on the conformational stability was discussed. The rotational barriers from the most stable conformer to the lowest energy secondary conformers and their correspondent inversion barriers at both HF and MP2 methods using 6-31G* basis set have also been approached. A normal mode calculation of the most and less-stable conformers using a scaled ab initio force field in terms of non-redundant local symmetry coordinates have been made to elucidate the conformational dependence of the vibrational spectra.

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“…Gauche conformations are 0.628 kcal/mol higher in energy than the trans conformation. Moreover, the trans-gauche barrier is 3.303 kcal/mol, while the cis barrier which results in eclipsed methyl groups is 5.460 kcal/mol (Hafezi and Sharif, 2007). Such a potential energy surface favors the global minimum energy anti or trans -conformation (torsion angle = 180°), thus biasing the population towards more extended conformations.…”

Section: Discussionmentioning

confidence: 99%

Lipid bilayer molecular dynamics study of lipid-derived agonists of the putative cannabinoid receptor, GPR55

Kotsikorou

Lynch

Abood

et al. 2011

Chemistry and Physics of Lipids

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Both L-α-lysophosphatidylinositol (LPI) and 2-arachidonoyl-sn-glycero-3-phosphoinositol (2-AGPI) have been reported to activate the putative cannabinoid receptor, GPR55. Recent microsecond time-scale molecular dynamics (MD) simulations and isothiocyanate covalent labeling studies have suggested that a transmembrane helix 6/7 (TMH6/7) lipid pathway for ligand entry may be necessary for interaction with cannabinoid receptors. Because LPI and 2-AGPI are lipid-derived ligands, conformations that each assumes in the lipid bilayer are therefore likely important for their interaction with GPR55. We report here the results of 70 ns NAMD molecular dynamics (MD) simulations of LPI and of 2-AGPI in a fully hydrated bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). These simulations are compared with a 70ns simulation of the cannabinoid CB1 receptor endogenous ligand, N-arachidonoylethanolamine (anandamide, AEA) in a POPC bilayer. These simulations revealed that (1) LPI and 2-AGPI sit much higher in the bilayer than AEA, with inositol headgroups that can at times be solvated completely by water; (2) the behavior of the acyl chains of AEA and 2-AGPI are similar in their flexibilities in the bilayer, while the acyl chain of LPI has reduced flexibility; and (3) both 2-AGPI and LPI can adopt a tilted headgroup orientation by hydrogen bonding to the phospholipid phosphate/glycerol groups or via intramolecular hydrogen bonding. This tilted head group conformation (which represents over 40% of the conformer population of LPI (42.2±3.3%) and 2-AGPI(43.7±1.4%) may provide a low enough profile in the lipid bilayer for LPI and 2-AGPI to enter GPR55 via the putative TMH6/7 entry port.

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Study of the torsional potential energies of 2-methylpropane, n-butane, and 2-methylbutane with high-level ab initio calculations

Cited by 15 publications

References 30 publications

Optimization of the GAFF force field to describe liquid crystal molecules: the path to a dramatic improvement in transition temperature predictions

Optimization of the GAFF force field to describe liquid crystal molecules: the path to a dramatic improvement in transition temperature predictions

Theoretical and Spectroscopic investigations of conformations, rotational barriers and scaled vibrations of 2,3-dimethyl hexane

Lipid bilayer molecular dynamics study of lipid-derived agonists of the putative cannabinoid receptor, GPR55

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