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Study of thermodynamic and NMR properties of some cyclohexane derivatives

Article  in  Journal of the Chilean Chemical Society · January 2011

DOI: 10.4067/S0717-97072011000400021

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J. Chil. Chem. Soc., 56, Nº 4 (2011)

“STUDY OF THERMODYNAMIC AND NMR PROPERTIES OF SOME CYCLOHEXANE DERIVATIVES”

LORENA A. GERLI C.*(1), M. PAULINA SALAS(1) , J. GUILLERMO CONTRERAS*(2)

1
Facultad de Ciencias, Universidad Católica de la Santísima Concepción, P.O.Box 297, Concepción, Chile.
2
Facultad de Ciencias Químicas, Universidad de Concepción, P.O.Box 160-C, Concepción, Chile.
(Received: April 15, 2011 - Accepted: September 7, 2011)

ABSTRACT

The preferential conformations of a series of six–membered saturated heterocycles containing oxygen and sulfur atoms, 4-alkyl-6-methyl-1,3-dithiane, with
alkyl=methyl, ethyl, propyl, isobuthyl, terbuthyl have been studied by means of ab-initio theoretical methods. The chair conformation is the most stable structure
found for all compounds studied here, likewise in its counterparts: cyclohexane, dithiane, and dioxane. The structures show anomalous effects of the chemical
shifts, in C2 and C5, due to a s C-S → s* C-Hec hyperconjugative interaction. They are also affected by normal Perlin effect in C2, where C2-Hec coupling
constants are larger than C2-Hax.

Keywords: 4-alkyl-6-methyl-1,3-dithiane; conformational analysis, NMR

INTRODUCTION conclusive with the factors involved in preferential conformations of this

type of molecules. Therefore, the present work aims to study conformational
The chemical properties of a compound depend on its geometry, i.e. on equilibrium of heterocycles containing atoms such as sulfur and oxygen.
its atomic position in space. For many molecules this position does not remain Consequently, the notorious distortion in the zone corresponding to S1-O3-
constant but may change easily depending on various factors such as: steric, C4-C6 of 1,3-thioxane, unusual from a structural point of view, makes it
dipole-dipole, and van der Waals interactions, amongst others1,2. Long time suitable to study the effects of alkyl double substitution on carbons 4 and 6 of
ago it was suggested that molecules such as cyclohexane might change its the ring (Fig.1)
geometry, but just in mid-last century this idea was experimentally proved3.
These studies leed to call such as structures Conformations which means
any geometry that a molecule might take by simple rotation of single bonds.
Another term deriving from above is conformer which describes conformations
with a life time long enough to build up real chemical species. Moreover, this
conformation corresponds to a minimum energy in the potential energy surface
of the molecule4. According to Boltzmann distribution, conformers are in
equilibrium with each other. The proportion in which each one is found in a
system consisting of a large number of molecules of the same type, depends
on its relative energy regarding the other conformers and on the system
temperature. Every conformer has unique and slightly different properties.
In a large group of molecules, where several conformers exists, each one of Figure 1: 1.3-thioxane chair conformation.
them will contribute to the system properties proportional to the number of
molecules in such conformation. Accordingly, the most stable conformer will In 4,6-dialkyl-1,3-thioxane, 1,3-dioxane and 1,3-dithiane synthesis, cis and
contribute to the system properties the most. When a conformational analysis is trans isomers are produced14,15,16 . In addition, in 1,3-thioxane, each isomeric
conducted, physical properties: density, dipole moment, solubility and energetic form is made of position isomers due to the non-equivalence of the heteroatoms.
contents as well as chemical properties (relative reactivity) of conformers can Accordingly, Cis- 4,6-dialkyl-1,3-thioxane isomers (eq-eq or ax-ax) were
be predicted, thus conformational analysis completes the structural analysis of studied by means of ab-initio theoretical methods. Geometry optimization has
a molecule, i.e. the description of connectivity, configuration and conformation been carried out for all species with their corresponding substituent (methyl,
of the atoms making the ring system. Understanding the factors that govern ethyl, propyl, iso-butyl, tert-butyl. Bond distances, angles and corresponding
conformational preferences and interactions in six-remembered heterocyclics energies were determined. The structures found, in all cases, correspond
has been the subject of considerable scientific interest5,6. The chair conformation to minima in the hipersurface of the potential energy, since no imaginary
of cyclohexane has been compared to other hetercycles such as thioxanes7. frequencies were found after vibrational frequencies calculations. The Natural
Cyclohexane is a cyclic hydrocarbon with no angle or torsional strain. The Bond Orbitals (NBO) analyses were performed to derive population analysis17
lack of strain is easily explained since carbon –carbon bond angles are 109º. in an attempt to explain the stereo-electronic effects in these of molecules.
Nevertheless, if cyclohexane were flat, it would have a considerable torsional Since NMR is one of the most efficient tool used in experimental methods18-19,
strain due to the eclipse of its 12 carbon-hydrogen bonds. Cyclohexane adopts to determine the molecular and electronic structure, theoretically-simulated
a three-dimensional structure known as the chair conformation, in which no RMN spectra were calculated for all species aiming to obtain their chemical
H-H eclipse exists, therefore, torsional strain does not exist since all C-H bonds shifts and coupling constants, and see whether the calculated structures suffer
are warped. During the past few years a number of conformational studies of any abnormal effect in their chemical shifts and/or either normal or reverse
cyclic molecules containing sulfur and oxygen, have been carried out, being Perlin effect which might be affecting their chemical shifts and bond lengths.
heterocycles the most important compounds in chemistry for many years8. Accordingly, the analysis of NBO and NMR calculations will be focused on 2,
Understanding their conformations and structures along with their governing 4, 5 and 6 either equatorial or axial carbon-hydrogen bonds.
interactions is of considerable interest to different areas of chemistry9, since
these structures are present in many molecules such as alkaloids, carbohydrates, MATERIAL AND METHODS
insecticides and plant growth regulator. It is also a that participates in natural Optimizations of the studied structures, were performed at HF20, B3LYP21
drug production10. Numerous methods and techniques have been developed in and MP222 level by using 6-31G** base and Gaussian 0323-24 program, Once
order to observe the effect of many substituents and their equatorial or axial geometry optimizations occured, (HF/6-31G**) frequency calculations were
preference 11. Many studies have provided conformational energy, differences done in order to ensure that the resulting structures correspond to a minimum
calculated using proper potential functions. They contribute significantly to energy conformation. Thermodynamic properties of the structures were
the qualitative understanding of forces and interactions determining not only obtained from frequency calculations.
conformations but also reactivity of substituted cyclohexane 12 for a range of Energies were derived from MP2 geometry calculations with a
substituent groups13-14. 6-311++G** flexible base, that includes polarization and diffusion functions
Experimental and theoretical data of 1,3-dioxane derivatives are not very Method) calculations done at HF level and with a 6-311+G** base.

922 e-mail: loregerli@ucsc.cl

 J. Chil. Chem. Soc., 56, Nº 4 (2011)

Both NMR data of protons in gaseous phase and solution and calculations was reported that the s C-C/s C-H → s* C-O hyperconjuntive effect would
to obtain coupling constants were obtained with B3LYP geometry and by using destabilize the di-equatorial conformer favoring axial double substitution.
6-311+G** base. Additionally, to the stereoelectronic effect the conformer destabilization takes
place by increasing the electron density of substituents. Frequency calculations
RESULTS AND DISCUSSION at HF geometry were performed in order to obtain thermodynamic properties.
If DG values (table 2), are observed isomeric reactions 11↔21; 12↔22;
13↔23; 14↔24 y 15↔25 where substituents corresponding to equatorial
Torsion angles of atoms in the middle part of the chair in 1,3-dioxane, group R2, isomer I, are those energetically favored. This is attributed to a clear
1,3-dithiane and cyclohexane (C6, C1, C3 and C4) are studied. It is observed reduction of 1,3-diaxiales steric factors and to a nuclear repulsion reduction
that it has a value of 0.0 degrees (table 1), while the torsion angle in the lower because Isomer I substituent groups are equatorially located.
and upper part of the chair (C2, C1, C6 and C5) is 56°, 58° y 55° for these
compounds, respectively. Table 2: Thermodynamic Data for cis A series. (kcal/mol).
Table 1: Geometry Optimization at HF/6-31G** level for cyclohexane, Interconversion Reactiona,b
DH DG %II
dioxane, dithiane and thioxane. 11A→21A 19,13 19,25 0
Cyclohexane Dioxane Dithiane Thioxane 12A→22A 19,02 19,20 0
Bond length (Å) 13A→23A 19,39 19,25 0
X1a-C2 1.532 1.385 1.810 1.817 14A→24A 21,51 22,53 0
C2-X3a 1.532 1.385 1.810 1.386 15A→25A 22,50 23,52 0
C4-C5 1.532 1.524 1.529 1.525
C5-C6 1.532 1.524 1.529 1.528 a) DH and DG in Kcal/mol.
b) Calculated energies at MP2/6-311++G** level.
Bond angles (º) The nuclear repulsion difference between isomers I and II (Structures)
X1a-C2-X3a 111.5 112.4 115.2 113.1 with size increases so the difference achieve a value of ca. 80 Kcal/mol, when
C2-X3a-C4 111.5 112.8 99.4 114.5 the substituents is ter-butyl.
C2-X1-C6 111.5 112.8 99.4 96.5 These structures are also affected by hyperconjuntive interactions that
contribute to their stabilization. The interactions that contribute the most are:
X3a-C4-C5 111.5 110.0 114.3 112.5 LP O → σ* C4 – R1, followed by LP O → σ* C4 – C5, Interactions LP S →
X1a-C6-C5 111.5 110.0 114.3 111.3 σ* C6 – R2 y LP S → σ* C5 – C6 also contributes to isomer I stabilization at
Torsional angles (º) a lesser extend (figure 2).
C5-C4-X3a-C2 54.8 56.0 57.6 65.1
C5-C6-X1a-C2 54.7 56.0 57.6 50.1
C4-C6-X1a-X3a 0.0 0.0 0.0 0.9

a)X1 and X3= C, O o S for cyclohexane, dioxane, dithiane and

thioxane. X3= O for thioxane.

Therefore the chair structure of 1,3-dithiane is slightly warped due to the

larger sulfur atomic ratio when compared to oxygen and carbon25. On the other
hand, the (S1-O3-C4-C6) central torsional angle in 1,3 thioxane is 2°, whereas
cyclohexane has a torsion angle of 0°. Consequently, it is observed that the chair
conformation is much more twisted, and the dihedral angles in the upper and
lower part of the structure are different. In fact, when the heterocycle contains
oxygen or sulfur, the dihedrals are 50° and 65o, respectively. Therefore, the
regular chair structure found in dioxane, dithane and cyclohexane show
notorious deviations. In addition, differences in size, electronegativity and
polarization associated with oxygen and sulfur are reflected in the structure,
conformation and reactivity of thioxane. Moreover, estereoelectric26 effects
cause significant changes on chemical shifts and coupling constants in the 1H
and 13C NMR spectra of these structures. Wolfe et al.27, proposed the term Figure 2: Relevant Hyperconjuntive Interactions in isomer Cis of
“Perling Effect” to indicate that C-H bonds affected by anomeric interactions isomer II are conformationally limited due to an important 1,3-diaxial
are longer and weaker and their coupling constants smaller. However, steric hindrance as both substituents are axially located making 1,3-diaxial
Juaristi et al.28,29, reported the existence of “Inverse Perlin Effect” in 1,3 repulsion of HaxC2-RaxC6, HaxC2-RaxC4 increase and become energetically
dithiane showing that the longest bond has the highest coupling constant. The unstable. The 1H-NMR data for these species, chemical shifts (d) and coupling
same author reported abnormalities in chemical shifts of 1H-NMR of 1,3- constants (J) are given in table 3. In figure 3 the chemical shifts of axial and
diheterociclohexane30 arguing that stereolectronic interactions cause anomalous equatorial protons of the structures under study are plotted. From table 3, it can
chemical shifts of C2 in 1,3-dithiane and in C5 in 1,3-dioxane. Specifically C-S be inferred that Hax and Hec chemical shifts are different depending on the
s → s* C-Heq hyperconjugative interaction which was proposed as a result extension of the shielding which can be higher than H shift of TMS the more
of an increase of C2-Heq bond electronic density for high-filed shifts of H(2eq) vulnerable is the H in their midst.
and a low-field shift for H(2ax). Since stereoelectronic effects can arise in “2 Thus, it is observed that both axial and equatorial protons of carbon 2 are
orbitals-2 electrons” interactions between an electronic couple of a bonding or the most unshielded (Figure 3). Protons at carbon 5 are the more protected
non-bonding orbital and an antibonding orbital, those compounds with strong axial protons and thereby the most shielded. Chemical shifts for axial protons
anomeric effect are expected to be suitable example for searching significant of carbon 4 and 6 decreased being proton of carbon 6 more shielded which
departures of proportionality between the s-character of the bond and its indicates that sulfur atom would be protecting it. The higher electron density
corresponding coupling constant31. The influence of this type of interactions around a proton the higher is shielding and the smaller is the chemical shift.
causes changes in energy, geometry, atomic charges, bond order, among
other properties. An effective method to identify and explain stereolectronic
interactions is the analysis known as NBO “natural bond orbital analysis”,
developed by Weinhold et al32. Kleinpeter et al33 carried out a similar study
using trans-1,4-di-substituted cyclohexane by analyzing the -O-COCX3 bond
for CX3= Me, Et, iso-Pr, ter-Bu, CF3, CH2Cl, thus changing its polarization. It

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J. Chil. Chem. Soc., 56, Nº 4 (2011)

Table 4: Bond Length in Å of C2 and C5 axial and equatorial hydrogen’s

and coupling constants in (Hz) of cis A series.
Bond Length and Coupling Bond Length and Coupling constants
Isomer
constants H 2ax y H 2ec H 5ax y H 5ec
C2 C2 1JC2 1JC2 C5 C5 1JC5 1JC5
Δa
Hax Hec Hax Hec Hax Hec Hax Hec Δa
11A 1,087 1,080 150,6 152,5 1,9 1,086 1,089 125,7 118,9 -6,9
12A 1,089 1,080 150,6 152,5 1,9 1,085 1,089 125,7 118,2 -7,6
13A 1,087 1,080 150,6 152,5 1,8 1,084 1,089 125,8 118,2 -7,6
14A 1,087 1,080 150,5 151,9 1,5 1,087 1,087 125,2 118,5 -6,7
15A 1,087 1,080 150,5 152,1 1,5 1,084 1,085 125,7 118,2 -7,5

Δa: Perlin Effect = JC,Hec – JC,Hax

1 1

CONCLUSIONS

At least for the structures study here, ab-initio theoretical calculations

allow derive reliable geometries and energetic conformations. Moreover,
calculations such as NMR, NBO analysis, in the gas phase or solution and
Fig.3. Calculated Chemical shifts of isomer 12 cis A (R1- methyl; R2-
scanning the potential energy hypersurfaces, lead us to conclude that:
ethyl).
1) (HF, B3LYP y MP2) ab-initio methods provided results, good enough to
reach the objectives of the present work; Reasonable structures of all 4,6-dialkyl
It can be concluded that, serie cis A shows small differences between axial
– 1,3-tioxane species were obtained. “Normal” geometric parameters were
and equatorial chemical shifts of protons bounded to a single carbon atom.
derived in all cases and conformational energies, thermodynamic properties
The change from gaseous to solutions shows significant differences between
and NMR parameters of protons both in gaseous phase and solution by using
chemical shifts of H2 protons and sulfur atom protection would affect carbon
PCM method were also obtained.
6-proton more than oxygen atom affects proton at carbon 4. Chemical shifts
2) The structures of 1,3 tioxane derivatives show an upper zone , a flat
also show steroelectronic interactions which may be responsible for anomalous
middle one and a slightly flat lower zone compared to data for 1,3 dioxane.
chemical shifts as found in C2 hydrogen of 1.3-dithiane34. These parameters
Accordingly, in the upper zones an increase in the (S1-C2-O3) bond angles
can be compared with those found for cyclohexane where dHec > dHax and is
takes place. A value of ca. 113° has been obtained. In (C6-C5-C4) bond angles
reflected in longer C-Hax bonds than equatorial ones.
takes values of 115° in the lower zones and C-C-C-O and S1-C2-O3-C4 strain
Chemical shifts of cis A serie were studied and no anomalous effect in C2
angles of ca. τ ≅ 58º and 63º values were calculated, respectively.
was found as they show dHec > dHax, where Hec are displaced to low fields
3) Geometry optimization of structures under study shows similar bond
and Hax to high fields (table 3).
and angle length, with differences less than or equal to 0,02 Å.
4) Cis serie has a purely steric control due to 1.3-diaxial repulsive
Table 3: 1H- NMR parameters of calculated and experimental protons for
decreases of HaxC2-HaxC6, HaxC2-HaxC4 favoring isomers I. 12A is the
Cis 4,6-dimethyl-1,3-thioxane.(ppm).
exception since it is being affected by LPS→σ*C6-Rax, LPS→σ*C5-C6,
Nucleous H-NMR parameters
1
LPO→σ*C4-R2 and LPO→σ*C4-C5 hyperconjugative effcts.
Gas CS2a CHCl3a DMSOa Expa 5) Chemical shifts for axial protons of all estructures show that C2 protons
H2a 4,85 3,92 4,12 4,12 4,66 have longer chemical shifts than C4 and C5. Axial proton at Carbon 2 is the
most unshielded and both axial and equatorial protons of carbon 5 are the most
H2e 4,81 4,03 4,22 4,22 4,66 shielded.
H5a 1,53 0,95 1,15 1,15 1,20 6) The strcutures are affected by Normal Perlin Effect in C2 where all C2-
H5e 1,23 1,01 1,20 1,20 1,67 Hec coupling constants are higher than C2-Hax as evidenced by an increase
in C2-Hax bond length due to a C-H (s C-Hax → s*C-Hax) hyperconjuntive
H4a 3,29 2,66 1,86 2,86 2,90
interaction which would weaken this type of bond.
H6a 2,99 2,30 2,50 2,50 2,90 7) C5 would show a reverse Perlin effect, where J C5-Hax > J C5-Hec as
2J2a2e -9,39 - shown by an increase in C5 –Hec bond length.
2J5e5a -12,1 13,5
3J5a4a 8,92 11,0
ACKNOWLEDGEMENTS
3J5e4a 1,94 2,40 This work was supported by an operating grants Nº01/2011 from the
3J5a6a 9,49 11,0 Unversidad Católica de la Santisima Concepcion (Chile) and Universidad de
3J5e6a 2,51 2,80 Concepcion (Chile) Nº 208.021.027-1

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