N-butane, conformation

S. Flumbel, S. Sieber and K. Morokuma, The IMOMO method Integration of different levels of molecular orbital approximations for geometry optimization of large systems test for n-butane conformation and s(n)2 reaction RC1 + C1, J. Chem. Phys., 105 (1996) 1959-1967. 

Table 2. Grid Coordinates for Carbon Atoms in Staggered n-Butane Conformers ...

Conformational free energy simulations are being widely used in modeling of complex molecular systems [1]. Recent examples of applications include study of torsions in n-butane [2] and peptide sidechains [3, 4], as well as aggregation of methane [5] and a helix bundle protein in water [6]. Calculating free energy differences between molecular states is valuable because they are observable thermodynamic quantities, related to equilibrium constants and... 

Figure 4-18 The Potential Energy for Rotation of n-Butane About its Central Bond Axis. The anti conformer in the center is slightly lower in energy than the two gauche conformers.

Ethanediol, like n-butane, exists as an equilibrium mixture of two distinct conformers anti (OCCO dihedral angle = 180°) and gauche (OCCO dihedral angle 60°). 

Examine space-filling models for the two conformers and identify any likely unfavorable nonbonded interactions. Based on steric effects, which conformer would you anticipate would be the more stable Compare energies of anti-1,2-ethanediol and gauche-1,2-ethanediol to see if you are correct. Is this the same ordering of conformer energies as seen for n-butane (see Chapter 5, Problem 3)7... 

The number (nj) of the cross ct conjugations of the trios of a C-C bond and two antiperiplanar C-H bonds is important for the stabilities of alkanes. The cross conjugation number (nj) of an alkane is defined as that of the conformer where the longest C-C chain has trans a zigzag structure. For example, there are three cross conjugations (n = 3) in isobutene and none in n-butane (n = 0) (Scheme 27). Isobutane is more stable than n-butane [34, 35]. 

A further example is given by consideration of the preferred conformation of anti n-butane. This system is isoconjugate to trans 2,3-dimethyl-butadiene or trans 2,3-divinylbutadiene. Now, trans 2,3-dimethyl-butadiene is expected to have the conformation shown below. 

Accordingly, the predicted conformation of anti n-butane is the one shown below. 

FIGURE 2.7 (a) potential energy profile illustrating the potential energy changes associated with rotation around a C-C bond of ethane (b) Newman projections of designated conformers of n-butane. 

The more common case is, as depicted in the above diagram, where the energy of the products is lower than that of the reactants. This kind of reaction is said to be exothermic, and the difference in stabilities of reactant and product is simply the difference in their energies. For example, the reaction of gauche n-butane to anti n-butane is exothermic, and the difference in stabilities of the two conformers is simply the difference in their energies (0.9 kcal/mol or 3.8 kJ/mol). 

A similar situation is found in the structure of putrescine diphosphate " (a model system for amine-nucleic acid interactions) which divides into layers of HjPOJ anions bridged by protonated putrescine (1,4-diamino-n-butane) cations. In a real biological system (yeast phenylalanine transfer RNA) phosphate residues are found to be enveloped by the polyamine spermine [NH2(CH2)jNH(CH2)4NH(CH2)jNH2] which again adopts a linear, nonchelating conformation. ... 

A significant issue widi modem force fields is that it can be difficult to simultaneously address both generality and suitability for use in condensed-phase simulations. For example, the MMFF94 force field is reasonably robust for gas-phase conformational analysis over a broad range of chemical functional groups, but erroneously fails to predict a periodic box of n-butane to be a liquid at —0.5 °C (Kaminski and Jorgensen 1996). The OPLS force field, on the other hand, is very accurate for condensed-phase simulations of molecules over which it is defined, but it is an example of a force field whose parameterization is limited primarily to functionality of particular relevance to biomolecules, so it is not obvious how to include arbitrary solutes in the modeling endeavor. 

A slightly more complicated case than ethane is that of a 1,2-disubstituted ethane (YCH2—CH2Y or YCHj—CH2X),197 such as n-butane, for which there are four extremes a fully staggered conformation, called anti, trans, or antiperiplanar another staggered con-... 

The configuration-bias Monte Carlo (CB-MC) technique (112) has also been extensively applied to characterize the sorption of alkanes, principally in silicalite (111, 156, 168-171) but also in other zeolites (172-174). Smit and Siepmann (111, 168) presented a thorough study of the energetics, location, and conformations of alkanes from n-butane to n-dodecane in silicalite at room temperature. A loading of infinite dilution was simulated, based on a united-atom model of the alkanes and a zeolite simulation box of 16 unit cells. Potential parameters were very similar to those used in the MD study of June et al. (85). As expected, the static properties (heat of adsorption, Henry s law coefficient) determined from the CB-MC simulations are therefore in close agreement with the values of June et al. The... 

LH-and 13C-NMR spectra are consistent with the twin-chair conformation 169 for trans-decahydroisoquinoline, and 13C-NMR spectroscopy gives AG° 5go of 0.37 kcal mol -1 (70% N-inside conformation 170) for the cis-decahydroisoquinoline equilibrium 170 171,82 reflecting the difference between a gauche-butane and a gauche-propylamine interaction. The 3-methyl-cis-decahydroisoquinolines prefer the equatorial methyl conformations 172 and 173.82... 

This last study is quite interesting because it permits an evaluation of the anomeric effect for the nitrogen atom. Conformer 91 with the axial N-methyl group should be less stable than conformer 92 by approximately 1.3 kcal/mol on the basis of steric effects (one gauche form of n-butane, =0.9 kcal/mol and one gauche form of CHj — N - CHj-0, =0.4 kcal/mol). The second anomeric effect caused by the equatorial orientation of the nitrogen electron pair in 91 must compensate for the steric effect. An approximate value of 1.3 kcal/mol must therefore be taken for that electronic effect, a value close to that estimated for the oxygen atom of the acetal function. 

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