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Carbohydrate Research 351 (2012) 26–34
Contents lists available at SciVerse ScienceDirect
Carbohydrate Research
journal homepage: www.elsevier .com/locate /carres
Radical mediated deoxygenation of inositol benzylidene acetals:conformational analysis, DFT calculations, and mechanism
Bharat P. Gurale a, Kumar Vanka b, Mysore S. Shashidhar a,⇑a Division of Organic Chemistry, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, Indiab The Division of Physical Chemistry, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
a r t i c l e i n f o a b s t r a c t
Article history:Received 11 November 2011Received in revised form 5 January 2012Accepted 5 January 2012Available online 13 January 2012
Keywords:DeoxygenationDFTInositolMechanismRadicalXanthate
0008-6215/$ - see front matter � 2012 Elsevier Ltd. Adoi:10.1016/j.carres.2012.01.001
⇑ Corresponding author. Tel.: +91 20 2590 2055; faE-mail address: [email protected] (M.S. Sh
Xanthates of 1,3-benzylidene acetal derivatives of myo- and neo-inositols undergo dideoxygenationunder Barton-McCombie conditions, as a result of intramolecular abstraction of the benzylidene acetalhydrogen and subsequent cleavage of the acetal ring. Scrutiny of structure of these bicyclic inositol deriv-atives shows that although the conformation of the two rings can vary depending on the configuration ofthe inositol ring and the phase in which the molecules are present, both the xanthates lead to the forma-tion of the same dideoxyinositol. DFT calculations on these molecular systems suggest that neo-inositolderivatives undergo conformational change prior to radical formation while myo-inositol derivativesundergo conformational change subsequent to radical formation, during the deoxygenation reaction. Alow barrier for intramolecular hydrogen transfer supports the extreme facility of this deoxygenationreaction.
� 2012 Elsevier Ltd. All rights reserved.
R1OOO
OBnOBnOC(S)SMe
Ph
H R1OOBz
OBnOBn
OO
BnO
BnOOBn
OC(S)SMe
Ph
H
1
3
5
2
1
3 5
2
R14 Bn5 PMB
BnOOH
OBnOBn
HO
myo-
neo-
R11 Bn2 PMB
a
ab, a
1. Introduction
Cyclohexane polyols—tetrols, pentols, and hexols, collectivelyreferred to as cyclitols form an important and interesting classamong organic compounds due to their biological significance.1–8
Naturally occurring cyclitols have been used as starting materialsfor the synthesis of natural products,9–15 scaffolds for the construc-tion of metal ion complexing agents16–18 and the preparation ofmolecular crystals that possess unusual properties.19–21 Conse-quently, different synthetic approaches were developed for thepreparation of cyclitols starting from benzene, quinic acid, carbohy-drates, and naturally occurring inositols.22–30 Use of theoretical cal-culations to rationalize the relative reactivity of inositol hydroxylgroups have been attempted.31–35 However, reports on the conver-sion of inositols to other cyclitols via deoxygenation are scarce.36–38
Deoxygenation of alcohols via their xanthates is a versatile methodfor the removal of hydroxyl groups in small molecules.39,40 We hadpreviously reported41 a novel route to the synthesis of a deoxy aswell as a dideoxy inositol from a single monoxanthate derivativeof myo-inositol (Scheme 1). This reaction gave the same productirrespective of the configuration of the starting xanthate (myo- orneo-).
ll rights reserved.
x: +91 20 2590 2629.ashidhar).
Deoxygenation of the epimeric (at the 1,3-benzylidene acetalcarbon atom—shown as dark circle in Scheme 2) xanthates 7–942 under similar radical deoxygenation conditions yielded thecorresponding mono-deoxygenated derivatives exclusively since
36
Scheme 1. Deoxygenation of xanthates 1–3. Conformation of the molecules 1–3depicted is based on X-ray crystallography.41,42 Reagents and conditions: (a)toluene, AIBN, n-Bu3SnH, 80–94%; (b) aq acid.
O
OC(S)SMe
OR1O
OBnOBn
Ph
H O
OC(S)SMe
OBnO
OBnBnO
PhHHH
H
nOe
H HnOe
nOe
3CCR11BC Bn2BC PMB
Chart 1. Results of 2D NMR spectroscopy of xanthates 1–3.41,42
a
R17 Bn8 PMB
9
OO
R1OBnO
OBn
OC(S)SMePh
H OO
R1OBnO
OBn
PhH
OO
BnOBnO
OBnOC(S)SMe
PhH
myo-
neo-
R110 Bn11 PMB
a
Scheme 2. Deoxygenation of epimeric xanthates 7–9. Conformation of the mole-cules 8, 9 depicted is based on X-ray crystallography.42 Reagents and conditions: (a)toluene, AIBN, n-Bu3SnH, 80–94%.
O OC(S)SMeOR1O
OBnBnO
Ph
HO
OC(S)SMeOR1O
OBnBnO
PhH
O
OC(S)SMe
OBnO
OBnBnO
PhH
3CC 3CB
O
OC(S)SM
OBnO
OBnBnO
PhH
H
OO
R1O
BnOOBn
PhH
H5
OO
R1O
BnOOBn
PhHH
5
Radicals
R11CC Bn2CC PMB
myo-xanthates
neo-xanthate
R11CB Bn2CB PMB
R112CC Bn13CC PMB
R112CB Bn13CB PMB
H
Scheme 3. Possible conformations of the xanthates 1–3 and the radicals generated fconformation of the inositol and the acetal rings, respectively.
B. P. Gurale et al. / Carbohydrate Research 351 (2012) 26–34 27
intramolecular (acetal) hydrogen abstraction is sterically forbid-den in the C5-radicals produced from the xanthates 7–9. Theseresults established that formation of the dideoxy myo-inositolderivative involved intramolecular hydrogen abstraction and sub-sequent cleavage of the 1,3-benzylidene acetal in the radical ini-tially formed.
The xanthates 1 and 2 are derived from myo-inositol, while 3is derived from neo-inositol; myo- and neo-xanthates vary in con-figuration at the carbon (C5, according to the numbering of theinositol ring) carrying the xanthate moiety. A comparison of thestructure of the xanthates 1–3 and 7–9 shows that the relativeconformation of the inositol and the acetal rings can vary amongthese bicyclic inositol derivatives. Such variations could haveimplications on the course and mechanism of these deoxygen-ation reactions. Although the conformations of the xanthatesshown in Scheme 1 were established by X-ray crystallography,it does not imply that these are the reactive conformations norminimum energy conformations nor does it imply that these con-formations exist in solution, exclusively. In order to gain insightinto these possibilities and the associated reaction mechanism,we have examined the conformation of the xanthates by DFT cal-culations and computed the geometry of the transition state forthe intramolecular hydrogen transfer. Results of these investiga-tions form the subject of the present article.
2. Results and discussion
Single crystal X-ray crystallographic data of the xanthates 1–3showed that the conformation of the myo-xanthates 141 and 242
and the neo-xanthate 3 in their crystals are as shown in Scheme 1.NMR spectroscopy of the same compounds (Chart 1) revealed thatsolution state conformation of the myo-xanthates 1 and 2 is
O
OC(S)SMe
OR1O
OBnOBn
Ph
H
3BC
e
O
MeS(S)CO
OBnO
OBnOBn
PhH
H
3BB
O
OC(S)SMe
OR1O
OBnOBn
Ph
H
O
MeS(S)CO
OBnO
OBnOBn
Ph
H
H
OO
R1OOBnOBn
PhH
H5
OO
R1OOBnOBn
PhH
H5
R11BC Bn2BC PMB
R11BB Bn2BB PMB
R112BC Bn13BC PMB
R112BB Bn13BB PMB
H
rom them. The suffixes to compound numbers indicate the chair (C) or boat (B)
O
OC(S)SMe
OR1O
OBnOBn
PhH
5
OO
R1O
BnOOBn
OC(S)SMe
PhH
5Path AOR
OO
R1O
BnOOBn
OC(S)SMePh
H
5
Path B
OO
R1O
OBnOBn
PhH
5OO
R1O
BnOOBn
PhH.
OO
R1O
BnOOBn
Ph
H
5..
OO
BnOBnO
OBn
OC(S)SMe
PhH O
OBnO
BnOOBn
OC(S)SMe
PhH
5
neo-xanthate 3CB3CC
Path B
Path A
OO
R1O
BnOOBn
Ph .
4 or 5
R11BC Bn2BC PMB
R11CC Bn2CC PMB
R11CB Bn2CB PMB
R112BC Bn13BC PMB
R112CC Bn13CC PMB
R112CB Bn13CB PMB
R114a Bn14b PMB
a
n-Bu3SnH
a a
aa
R1OOBz
OBnOBn.
R115a Bn15b PMB
Scheme 4. Plausible pathways for the intramolecular abstraction of hydrogen by the radical initially generated from xanthates 1–3. Reagents and conditions: (a) toluene,AIBN, n-Bu3SnH, 80–94%.
28 B. P. Gurale et al. / Carbohydrate Research 351 (2012) 26–34
perhaps the same as that in their crystals but the neo-xanthate 3does not maintain the same conformation in solution. Hence thepossibility that these xanthates exist in more than one conforma-tion in solution cannot be ruled out. Four possible conformationsof the xanthates 1–3 and conformation of the radicals generatedfrom them are shown in Scheme 3 (same radical—12, is generatedfrom xanthates 1 and 3).
Intramolecular abstraction of the acetal hydrogen in the radi-cals generated at the C5-carbon from the xanthates 1–3 appearslikely only in one of the conformations (12CC/13CC) depicted forthe radicals 12 and 13 in Scheme 3. However, since experimentallywe obtain the dideoxy inositol derivative 4 (or 5) as the only prod-uct, on treatment of the xanthates 1–3 with tributyltinhydride,either the starting xanthates or the intermediate radicals must beundergoing conformational change prior to intramolecularabstraction of the benzylidene acetal hydrogen, leading to the for-mation of the same radical (in which intramolecular hydrogenabstraction is facile). Hence, one can visualize two different pathsfor the deoxygenation reaction (Scheme 4), leading to the forma-tion of the dideoxy inositols 4 and 5. Path A, in which conforma-tional change of the xanthate precedes formation of the radical(in which intramolecular hydrogen abstraction is facile) and PathB, in which the initially generated radicals from myo- and neo-xan-thates undergo a change in conformation before intramolecularhydrogen abstraction. Since all the three xanthates 1–3 give thesame dideoxy derivative in high yield, the reaction must be pro-ceeding via a common radical intermediate. Since experimentscannot distinguish between Path A and Path B, we performedDFT calculations to see the relative facilities of the two paths lead-ing to the formation of the dideoxy derivative 4 and 5.
Results obtained from geometrical optimization studies (DFTcalculations), showed that the relative stabilities of the conforma-tions of the myo-xanthates are in the order 1BC > 1CC > 1CB and2BC > 2CB > 2CC (Fig. 1). Although the relative order of stabilityfor the conformers of 1 and 2 is different, the most stable con-former for both the xanthates has the boat–chair conformation.For the neo-xanthate the order of relative stabilities for the threedifferent conformations was 3CC > 3CB > 3BC. During these DFTcalculations we found that for all the xanthates the conformationin which both the rings are in the boat form are least stable andinherently flip over to one of the three conformations in which atleast one ring has the chair conformation. It is interesting to notethat while the conformation of the myo-xanthate in its crystals is1BC (most stable conformation according to DFT calculations) theconformation of the neo-xanthate in its crystals is 3CB (which isnot the most stable conformation according to DFT calculations).This difference in the conformation of the neo-xanthate betweenthe crystalline state and that predicted by geometrical optimiza-tion could be due to lattice interactions in the crystal, since the dif-ference in stability between 3CB and 3CC is not large. It isinteresting to note that 3CC is the conformation (or one of the con-formations present in solution) suggested by NMR spectroscopy inchloroform solution. The change in conformation of the xanthate 3on going from crystalline state to the solution state at ambienttemperature also suggests that these conformational changes donot involve high energy barriers. The order of relative stabilities(predicted by DFT calculations) for the three different conforma-tions for the radical generated from 1 or 3 is in the order12CC > 12BC > 12CB and for the radical generated from 2 is in theorder 13CC > 13BC > 13CB (Fig. 2). The geometry of the inositol ring
Figure 1. Results of the geometrical optimization for xanthates 1–3.
B. P. Gurale et al. / Carbohydrate Research 351 (2012) 26–34 29
in the radical 12BC (and 13BC) deviates from ‘boat’ implying thatthe boat form of the radical (as depicted in Scheme 3) is unstable.
The change in energy necessary for the myo-xanthate 1 toundergo deoxygenation via Path A is 2.8 kcal/mol while thatthrough Path B is 0.6 kcal/mol and the corresponding values forthe xanthate 2 are 5.2 kcal/mol and 0.6 kcal/mol. Since Path B re-quires lesser change in energy, the conversion of the myo-xanthatesto the dideoxy inositol proceeds via Path B. Similarly, the change in
energy necessary for the neo-xanthate 3 to undergo deoxygenationvia Path A is 2.5 kcal/mol while that through Path B is 6.3 kcal/mol.Since in this conversion, Path A requires lesser change in energy, theconversion of the neo-xanthate to the dideoxy inositol proceeds viaPath A. Hence although both the myo and neo-xanthates lead to theformation of the same product by radical deoxygenation, the prod-uct appears to be forming by two different pathways. However boththe pathways lead to the formation of the relatively stable radical
0
-22.0
-30.7
Radical 12CC
TS
Radical 15a
Ekcal/mol
-5
-10
-15
0
-20
-25
-30
-4.2
Radical 14a
+5
-35
Chart 2. A comparison of the energies of the transition state and radicals 12CC, 14aand 15a.
Figure 2. Results of the geometrical optimization for radicals (12, 13) derived from xanthates 1–3.
30 B. P. Gurale et al. / Carbohydrate Research 351 (2012) 26–34
12CC where the radical center and the benzylidene hydrogen are inclose proximity to allow the intramolecular abstraction of hydrogenand generate the benzylidene radical (which rearranges to form thedideoxy product). We have also determined the geometry andenergy of the transition state for the intramolecular abstraction ofthe benzylic hydrogen in the radical 12CC, as well as the energy ofthe radicals formed subsequent to intramolecular hydrogen transfer(Chart 2 and Fig. 3). These values reveal that the barrier for theintramolecular hydrogen transfer in 12CC is quite low (4.2 kcal/mol), which is in agreement with the experimentally observedextreme facility with which the di-deoxygenation reaction occurs.A comparison of the energies of the radicals formed subsequent tointramolecular hydrogen transfer also supports the ease of cleavageof the benzylidene acetal. The results of the DFT calculations there-fore support the sequence of events depicted (in Scheme 4) duringthe dideoxygenation reaction shown in Scheme 1.
2.1. DFT calculations on the radical deoxygenation of the 1,5-benzylidene acetal
We also subjected the xanthate derived from the 1,5-benzyli-dene acetal to radical deoxygenation to see the selectivity betweenthe deoxygenation at the C1- and C5-positions of myo-inositol. Thisis of significance since, (a) selective deoxygenation at any of thetwo positions would be of potential synthetic utility and (b)plasma radiation-induced generation of hydroxyl alkyl radicals in
solid myo-inositol led to preferential formation of radical at theC5-position (over the C1-positon), but the C1-radical was relativelymore stable than the C5-radical produced.43 Hence it was of inter-est to see the trend in stability of the radicals generated during thedideoxygenation of the xanthate carrying the unsymmetrical ben-zylidene acetal moiety. As reported earlier,41 deoxygenation of thexanthate 16 yielded the 1,5-dideoxy derivative 17 as the major
aOO
MeO
OMeOMe
PhH
H16
OC(S)SMe1 2
3
45
6MeO
OMeOMe31
17 (68%)
5
BzOMeO
OMeOMe3
5BzO
1
18 (16%)
+
Scheme 5. Deoxygenation of the xanthate 16. Reagents and conditions: (a) toluene, AIBN, n-Bu3SnH, 80–94%.
OO
MeO
OMeOMe
PhH
H
3
16BC
OO
MeOOMe
OMe
Ph
16CC3 OC(S)SMe
OC(S)SMe
1
5
1
5
HOO
MeO OMe
OMePh
H
16CB
3
OC(S)SMe
16BB
OO
MeO
OMeOMe
Ph
H
H3 OC(S)SMe
1
51
5HnOe
OO
MeO
OMeOMe
PhH
H
3
Radical 19BC
OO
MeOOMe
OMe
PhHH
Radical 19CC
3
OO
MeO OMe
OMe
PhH
H
Radical 19CB
3
Radical 19BB
OO
MeO
OMeOMe
Ph
H
H3
Scheme 6. Possible conformations of the xanthate 16 and the radicals generated from them.
Figure 3. Results of the geometrical optimization of the transition state during the intramolecular abstraction of hydrogen in 12CC and conformation of the radicals 14a and15a. Of the hydrogens, only the migrating hydrogen atom is shown in the transition state, for clarity.
B. P. Gurale et al. / Carbohydrate Research 351 (2012) 26–34 31
product and 1,3-dideoxy derivative 18 as the minor product(Scheme 5).
Four possible conformations of the xanthates 16 (as discussedearlier for the xanthates 1–3 and radicals 12 and 13) and confor-mation of the radicals generated from them are shown in Scheme6. 2D NMR spectrum of 16 suggests that the xanthate 16 exists inthe conformation 16BC in solution. We could not obtain crystals of16 as it is a gummy solid and hence its molecular conformation inits crystals is not known.
Results of the geometrical optimization of the possible confor-mations of the xanthate 16 (Fig. 4) reveal a decreasing order of sta-bility of the three conformers, 16BC > 16CC > 16CB. As observed forthe xanthates 1 and 2, the conformation in which both the rings arein the boat form is least stable and inherently flip over to one of thethree conformations in which at least one ring has the chair confor-mation. Results on the geometrical optimization of the radicals
generated from the four possible conformers of 16 (Fig. 5) revealthe order of stability to be 19CC > 19BC > 19CB. DFT calculationsalso indicate that the conformation 19BB is very unstable and flipsover to one of the other three conformations and energy minimiza-tion of 19BC results in a conformation similar to 19CC.
A comparison of the two possible paths (Scheme 7) for the for-mation of the dideoxy inositol derivatives 17 and 18 from the xan-thate 16 supports the deoxygenation of 16 via Path B, since thechange in energy is lesser in Path B. We have assumed that 20aand 20b flip over to 20c and 20d, respectively, since the former ‘ax-ial rich’ conformations would be expected to be far less stable thanthe latter ‘equatorial rich’ conformations.
It is interesting to note that the radical formation (by cleavageof the benzylidene acetal moiety) at the C5-position is preferredover that at the C1-position of the inositol ring, as revealed bythe formation of larger proportion of the C5-deoxy derivative
Figure 4. Results of the geometrical optimization of possible conformations of the xanthate 16.
Figure 5. Results of the geometrical optimization of possible conformations of the radical generated from the xanthate 16.
a
OBz
MeOOMe
OMe
20a
3OO
MeOOMe
OMe
Ph
1
5 5 3
1
H
n-Bu3SnH
19CC
a
Path A
Path BOO
MeO
OMeOMe
PhH
H16BC
OC(S)SMe1 2
3
45
6
OO
MeO
OMeOMe
PhH
H19BC
1 23
45
6
3
OO
MeOOMe
OMe
Ph
16CC
OC(S)SMe
1
5
H
MeOOMe
OMe3
1
OBz5
20b
MeOOMe
OMe3
5BzO
1
20d
MeOOMe
OMeBzO 3
20c
5
17(16%)18
(68%)
n-Bu3SnH
3
OO
MeOOMe
OMe
Ph
1
5
20e
Ha
Scheme 7. Plausible mechanism for the deoxygenation of the xanthate 16. Reagents and conditions: (a) toluene, AIBN, n-Bu3SnH, 80–94%.
32 B. P. Gurale et al. / Carbohydrate Research 351 (2012) 26–34
relative to the C1-deoxy derivative. This is similar to the observa-tion during the plasma radiation-induced generation of hydroxyl
alkyl radicals in solid myo-inositol wherein the formation of theC5-radical was preferred over the formation of the radical at
Figure 6. Results of the geometrical optimization of the radicals 20d and 20c.
B. P. Gurale et al. / Carbohydrate Research 351 (2012) 26–34 33
C1- and C4-positions.43 Estimation of the relative stabilities of thetwo regioisomeric radicals 20c and 20d generated by the cleavageof the benzylidene acetal, suggested negligible difference betweenthem (Fig. 6).
3. Conclusions
Analysis of the structure and conformation of inositol derivedxanthates and the radicals generated from them under Barton–McCombie conditions reveal that myo-inositol derived xanthatesand their neo-inositol analogs undergo deoxygenation by two dif-ferent pathways. During this reaction, conformational changes oc-cur in radicals derived from myo-inositol derivatives whileconformational changes occur in neo-inositol derived xanthateprior to the formation of the radical. Although the difference instability predicted between the conformers is not very large, theobserved trend in stability allows us to arrive at these interestingconclusions. These results are of relevance to other bicyclic sys-tems which could be conformationally flexible.
4. Computational details
All the density functional theory calculations were carried outusing the Turbomole suite of programs.44–46 The strategy adoptedfor the geometry optimizations is as follows: for a given geometry,a conformational search was first done using Molecular Mechanics(MM+ force field) methods as implemented in the Hyperchem47
software. The best five geometries obtained from the conforma-tional analysis were then used as input structures for the DFT calcu-lations. The conformation obtained with the lowest energy (i.e., themost stable conformation) has then been considered for the relative(DE) analysis as reported in the paper. The DFT Geometry optimiza-tions were performed using the B-P 86 functional.48,49 The elec-tronic configuration of the atoms was described by a triple-zetabasis set augmented by a polarization function (TURBOMOLE basisset TZVP).50 The resolution of identity (RI),51 along with the multi-
pole accelerated resolution of identity (marij)52 approximationswere employed for an accurate and efficient treatment of the elec-tronic Coulomb term in the density functional calculations. Solventeffects have been incorporated using the COSMO model, 44 with tol-uene (epsilon = 2.38)53 as the solvent. In the case of the radicalstructures, care was taken to ensure that the geometry optimizationof the structures, done with UHF, did not lead to spin contamination.A perusal of the total spin quantum number values from the geom-etry optimization outputs indicated that their value was different byonly about 1% from the exact value in every case, indicating the ab-sence of spin contamination. Also, all the radical structures consid-ered were assumed to be in the doublet state. For certain cases, thequartet spin state calculations were also done, and they showed thatthe resultant quartet geometries were significantly higher in energythan their doublet counterparts, thus indicating that the doublet isthe stable spin state for the radicals that have been considered inthis study. The transition state obtained for the intramolecularhydrogen transfer was confirmed to have only one negative fre-quency corresponding to the proper normal mode.
Acknowledgements
Bharat P. Gurale thanks CSIR, New Delhi, for the award of re-search fellowships. B.P.G. and K.V. acknowledge the Centre ofExcellence in Scientific Computing (COESC), Pune, for providingcomputational facilities.
Supplementary data
Supplementary data (geometry optimized colored diagrams(Figs. 1–6) and Cartesian co-ordinates (DFT data) for 1–3, 12–16,19 and 20) associated with this article can be found, in the onlineversion, at doi:10.1016/j.carres.2012.01.001.
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