Annalisa
Vigorito
,
Camilla
Calabrese
,
Ettore
Paltanin
,
Sonia
Melandri
and
Assimo
Maris
*
Dipartimento di Chimica G. Ciamician, Università degli Studi di Bologna, Via Selmi 2, 40126 Bologna, Italy. E-mail: assimo.maris@unibo.it; Tel: +39 051 2099502
First published on 22nd November 2016
The conformational space of antioxidant dihydrolipoic acid has been explored through the investigation of its pharmacophore, 1,3-propanedithiol. Five of the possible 25 non-equivalent isomers (namely: gGGg′, gGGg, g′AGg, gAGg and g′AGg′) were observed in the 59.6–74.4 GHz frequency region using free-jet absorption rotational spectroscopy. Furthermore, for three of them, the 34S mono-substituted isotopologues were also detected in natural abundance. Theoretical simulations show that the balance of steric and electronic intramolecular interactions arises on a shallow conformational potential energy surface and suggest that in polar solvents the flexibility of the dithiol chain is greater than that in the isolated phase.
Since the difference in electronegativity between S and H is small, the SH bond presents low polarity and shows hydrogen bonds weaker than those formed by the OH bond; on the other hand, sulphydryl groups can react forming sulfur–sulfur (–S–S–) covalent linkages, as in the case of proteins, where disulfide bonds formed between cysteine residues play an active role in their molecular folding and stability. Actually, the thiol/disulfide pair is a redox couple, with the following oxidation reaction: 2 –SH ↔ –S–S– + 2H+ + 2e−, and it is precisely this feature that makes it essential in several biochemical processes, involving both macromolecules containing cysteine residues and relatively small molecules, such as tripeptide glutathione1 (γ-Glu–Cys–Gly) and dihydrolipoic acid, which act as reducing agents. In particular, dihydrolipoic acid (DHLA hereafter, Fig. 1) is one of the most powerful cellular antioxidants (reduction potential −0.32 V).2 The oxidation of DHLA to lipoic acid involves the 1,3-propanedithiol terminal chain (13PDT hereafter, Fig. 1) which, thanks to the formation of an intramolecular disulfide bridge, becomes the 1,2-dithiolane cycle.3,4
Fig. 1 Sketch of dihydrolipoic acid (IUPAC: 6,8-dimercaptooctanoic acid) and 1,3-propanedithiol with the numbering of atoms and the torsional angles used in the text. |
Due to the high polarizability of the sulfur atom, thiols coordinate metals that behave as soft Lewis acids, and this is the reason why, since ancient times, they have also been known as mercaptans, that is, mercury capturers. Furthermore, the thiol-metal binding affinity is of relevance in biological systems: for instance metallothionein proteins are able to bind both physiological and xenobiotic heavy metals through the disulfide binding of their cysteine residues;5 iron–sulfur clusters constitute the active site of iron–sulfur proteins,6 and the already mentioned glutathione and DHLA create stable metal-sulfides.7,8 In particular, it has been evidenced that the bi-dentate 13PDT tail of DHLA efficiently acts as a metal chelator agent. Moreover, differently from other molecules, DHLA is able to cross the blood–brain barrier and for this reason it can be used as a drug to mobilize metal atoms attached to the brain cells towards the blood stream.3
Interested in the widespread biological activity of DHLA, we focused our attention on its structural features. Since DHLA contains a relatively long substituted alkyl chain, it is characterized by high torsional flexibility and its conformational space is described by nine dihedral angles giving rise to 39 = 19683 possible rotamers. As the full exploration of this space is a huge task, we based the present study on the conformational preferences of 13PDT, which represents the pharmacophoric group of DHLA. We used the high resolution of millimeter wave spectroscopy to obtain detailed structural information on the different conformations present in the cold and isolated environment of a free jet expansion. The experimental results were then rationalized and explained through a thorough and extensive comparison with theoretical calculations obtained under the same isolated conditions or in the simulated aqueous environment.
Characterization of the stable structures was done using standard geometry full-optimizations followed by calculations of the analytical second derivatives. The computations were run applying second-order Møller–Plesset (MP2) perturbation theory12,13 in combination with both Pople's 6-311++G(d,p)14,15 and Peterson and Dunning's aug-cc-pVTZ16,17 triple-valence basis sets. Internal rotation pathways were explored varying the involved dihedral angles by regular steps, whereas all the other internal coordinates were freely optimized. For this purpose only the less computationally demanding Pople's basis set was utilized. Finally, in order to simulate the effect of a polar solvent, both the minima and the internal motion pathways were investigated using a polarizable continuum model18 at the same levels of calculation as for the isolated phase. All quantum mechanical computations were performed using the Gaussian 09 (revision D.01) quantum chemistry package.19 Molecular graphics images were produced using the freely available UCSF Chimera20 and Gmolden21 packages.
Conf. | Γ irr | n | MP2/6-311++G(d,p) | MP2/aug-cc-pVTZ | ||||||
---|---|---|---|---|---|---|---|---|---|---|
ΔE0 | ΔE0,aq | A e/Be/Ce (MHz) | |μa/b/c| (D) | ΔE0 | ΔE0,aq | A e/Be/Ce (MHz) | |μa/b/c| (D) | |||
a Minimum not reached: during the optimization process, the aGG′a species relaxes to the aGG′g′ species. | ||||||||||
gGGg | C 2 | 2 | 0 | 39 | 5842/1439/1332 | 0/2.8/0 | 43 | 0 | 5658/1491/1364 | 0/2.7/0 |
gGGg′ | C 1 | 4 | 17 | 107 | 5204/1606/1423 | 0.9/1.9/0.5 | 0 | 14 | 5164/1633/1440 | 0.9/1.9/0.4 |
aGGg′ | C 1 | 4 | 235 | 366 | 5141/1657/1466 | 1.2/1.3/0.7 | 187 | 233 | 5138/1672/1478 | 1.0/1.2/0.7 |
g′GGg′ | C 2 | 2 | 263 | 258 | 5618/1482/1348 | 0/0.8/0 | 178 | 123 | 5488/1532/1381 | 0/1.1/0 |
aGGg | C 1 | 4 | 302 | 348 | 6001/1417/1330 | 0.2/1.5/1.0 | 336 | 287 | 5749/1485/1375 | 0.1/1.8/0.9 |
aGGa | C 2 | 2 | 658 | 653 | 6460/1348/1292 | 0/0.0/0 | 640 | 557 | 5923/1464/1379 | 0/0.8/0 |
g′AGg | C 1 | 4 | 151 | 100 | 8769/1105/1035 | 0.4/2.0/0.2 | 280 | 131 | 8742/1113/1040 | 0.5/2.0/0.0 |
gAGg | C 1 | 4 | 217 | 149 | 8944/1090/1030 | 0.7/1.0/0.9 | 333 | 173 | 8821/1101/1037 | 0.8/1.1/0.7 |
gAGg′ | C 1 | 4 | 308 | 219 | 9290/1078/1016 | 0.4/0.6/0.3 | 401 | 217 | 9123/1090/1025 | 0.4/0.7/0.4 |
g′AGg′ | C 1 | 4 | 310 | 183 | 9125/1093/1021 | 0.1/1.5/1.3 | 399 | 189 | 9048/1101/1027 | 0.2/1.6/1.2 |
aAGg | C 1 | 4 | 457 | 431 | 9190/1098/1032 | 0.3/0.4/0.1 | 505 | 390 | 9014/1110/1043 | 0.4/0.7/0.3 |
gAGa | C 1 | 4 | 469 | 427 | 9118/1115/1043 | 1.5/1.5/0.0 | 555 | 429 | 8950/1126/1051 | 1.4/1.4/0.1 |
g′AGa | C 1 | 4 | 469 | 404 | 9525/1091/1021 | 1.2/2.3/0.9 | 556 | 407 | 8870/1134/1052 | 1.1/2.3/1.0 |
aAGg′ | C 1 | 4 | 607 | 503 | 8961/1125/1045 | 0.0/0.2/1.3 | 610 | 432 | 9347/1100/1031 | 0.1/0.1/1.4 |
aAGa | C 1 | 4 | 767 | 735 | 9370/1124/1045 | 1.2/0.7/1.0 | 764 | 649 | 9141/1136/1058 | 1.1/0.9/1.2 |
gAAg | C 2 | 2 | 159 | 3 | 14531/897/865 | 0/0.5/0 | 369 | 127 | 14746/896/865 | 0/0.7/0 |
gAAg′ | C s | 2 | 207 | 0 | 14547/896/864 | 0/0.5/1.3 | 408 | 129 | 14772/895/865 | 0/0.7/1.3 |
aAAg | C 1 | 4 | 462 | 310 | 14396/908/872 | 0.7/1.7/0.8 | 591 | 356 | 14455/911/875 | 0.6/1.7/0.7 |
aAAa | C 2v | 1 | 804 | 655 | 14209/921/879 | 0/2.8/0 | 816 | 602 | 14129/928/886 | 0/2.7/0 |
gGG′g | C 1 | 4 | 923 | 958 | 4637/1755/1361 | 1.0/2.0/0.3 | 890 | 807 | 4604/1802/1387 | 1.1/2.1/0.2 |
aGG′g | C 1 | 4 | 1184 | 1158 | 4601/1817/1381 | 1.8/2.2/1.0 | 1145 | 1001 | 4531/1884/1410 | 1.6/2.4/0.9 |
g′GG′g | C 1 | 2 | 1200 | 1182 | 4741/1727/1358 | 0.9/2.0/0.8 | 1122 | 1007 | 4685/1779/1384 | 0.9/2.2/0.7 |
gGG′g′ | C 1 | 2 | 1272 | 1170 | 4549/1860/1420 | 0.4/2.8/0.7 | 1229 | 1053 | 4525/1915/1451 | 0.3/2.8/0.6 |
aGG′g′ | C 1 | 4 | 1473 | 1215 | 4504/1920/1440 | 0.7/2.8/0.1 | 1441 | 1105 | 4488/1962/1462 | 0.6/2.8/0.0 |
aGG′a | C 1 | 2 | 1800 | 1474 | 4542/1912/1439 | 0.5/2.5/1.1 | 1752 | —a | 4604/1914/1456 | 0.6/2.4/1.1 |
Since conformational relaxation processes through low energy barriers (around 400 cm−1) are common in Ar expansions,30 the presence of other conformers was checked using a lighter carrier gas, He instead of Ar, and the g′AGg′ species was then detected. Measured transition lines were fitted31 to Watson's S-reduced semirigid asymmetric rotor Hamiltonian (Ir representation)32 achieving the spectroscopic parameters summarized in Table 2. The conformational assignment was further confirmed by the values of the spatial coordinates of the S atoms, obtained from the experimental rotational constants of normal and isotopic species using Kraitchman's substitution method (rs).33 The equilibrium (re) ab initio predictions are compared to the rs structure in Fig. 3 and Table 3. Although a direct comparison between ab initio structures (referring to the equilibrium geometry) and experimental data (related to the ground vibrational state) must be considered with care, it is worth noting that the rotational constants and the substitution coordinates are better reproduced by Pople's basis set instead of the more extended Dunning's one.
gGGg | Parent | 34S1 = 34S5 | |
---|---|---|---|
a Standard error in parentheses in the units of the last digit. b Values in squared brackets are fixed to the parent species ones. c Number of transitions. d Root mean square deviation of the fit. e Yes (y) or no (n) observation of a-, b-, and c-type transitions, respectively. f Minimum and maximum J quantum numbers for the observed rotational transitions. | |||
A 0 (MHz) | 5815.075(9)a | 5774.18(3) | |
B 0 (MHz) | 1437.049(4) | 1402.80(2) | |
C 0 (MHz) | 1325.975(5) | 1294.99(2) | |
D J (kHz) | 1.666(5) | 1.62(2) | |
D JK (kHz) | −19.151(9) | −18.9(1) | |
D K (kHz) | 71.9(1) | 71.7(5) | |
d 1 (kHz) | −0.3640(6) | [0.3640]b | |
d 2 (kHz) | −0.0148(2) | [−0.0148] | |
N | 45 | 19 | |
RMSd (kHz) | 50 | 53 | |
a/b/ce | n/y/n | n/y/n | |
J min–Jmaxf | 5–23 | 5–14 |
gGGg′ | Parent | 34S1 | 34S5 |
---|---|---|---|
A 0 (MHz) | 5364.435(3) | 5323.76(1) | 5329.96(1) |
B 0 (MHz) | 1543.221(3) | 1507.18(2) | 1505.478(9) |
C 0 (MHz) | 1382.752(3) | 1351.53(1) | 1350.551(9) |
D J (kHz) | 2.082(6) | 2.06(1) | 2.053(9) |
D JK (kHz) | −18.596(4) | −18.29(6) | −18.43(6) |
D K (kHz) | 53.85(3) | 53.6(2) | 53.9(2) |
d 1 (kHz) | −0.5320(5) | 0.54(3) | −0.498(9) |
d 2 (kHz) | −0.0229(2) | — | −0.024(2) |
H J (Hz) | −0.047(5) | — | — |
N | 97 | 27 | 30 |
RMSd (kHz) | 42 | 52 | 43 |
a/b/ce | y/y/y | n/y/n | n/y/n |
J min–Jmaxf | 5–24 | 5–15 | 5–17 |
g′AGg | Parent | 34S1 | 34S5 |
---|---|---|---|
A 0 (MHz) | 8767.42(2) | 8741.83(2) | 8682.972(2) |
B 0 (MHz) | 1100.891(4) | 1070.453(5) | 1075.142(5) |
C 0 (MHz) | 1029.212(5) | 1002.296(5) | 1005.547(5) |
D J (kHz) | 0.205(4) | [0.205] | [0.205] |
D JK (kHz) | −4.95(1) | [−4.95] | [−4.95] |
D K (kHz) | 71.8(6) | 76.6(6) | [71.8] |
d 1 (kHz) | −0.0296(6) | [−0.0296] | [−0.0296] |
N | 49 | 18 | 16 |
RMSd (kHz) | 35 | 47 | 39 |
a/b/ce | n/y/n | n/y/n | n/y/n |
J min–Jmaxf | 3–24 | 3–14 | 3–13 |
Fig. 3 The observed conformers of 13PDT (re) showing their principal axis system and the substitution coordinates of the S atoms (rs, indicated as red points). |
a | b | c | |||
---|---|---|---|---|---|
a Constain's errors34 expressed in units of the last decimal digit. b From MP2/6-311++G(d,p) geometries. c From MP2/aug-cc-pVTZ geometries. d Imaginary value. | |||||
gGGg | S1 | r s | 2.0858(9)a | 0.550(3) | 0.15(1) |
r e | 2.087 | −0.545 | −0.153 | ||
r e | 2.041 | −0.562 | −0.155 | ||
S5 | r s | 2.0858(9) | 0.550(3) | 0.15(1) | |
r e | −2.087 | −0.545 | 0.153 | ||
r e | −2.041 | −0.562 | 0.155 | ||
gGGg′ | S1 | r s | 1.9892(2) | 0.592(3) | 0.17(1) |
r e | 1.947 | −0.603 | −0.174 | ||
r e | 1.927 | −0.607 | −0.173 | ||
S5 | r s | 2.0377(8) | 0.542(3) | 0.168(9) | |
r e | −1.993 | −0.557 | 0.175 | ||
r e | −1.975 | −0.561 | 0.175 | ||
g′AGg | S1 | r s | 2.5786(6) | 0.282(6) | 0.10(2) |
r e | 2.573 | 0.285 | −0.103 | ||
r e | 2.566 | 0.284 | −0.102 | ||
S5 | r s | 2.3669(7) | 0.543(3) | i0.02(8)d | |
r e | −2.367 | 0.540 | −0.037 | ||
r e | −2.354 | 0.544 | −0.035 |
Information encoded in the measured spectral intensities was then analyzed. First the predicted μb:μc ratios were confirmed for all detected rotamers. Then, the relative intensities of the Q-branch lines of the gGGg′, gGGg and g′AGg conformers provided a direct indication of the population's distribution at the rotational levels, which is consistent with a temperature of 5–7 K. Finally, from the observed intensity values weighted on both the structural degeneracy and the square values of the calculated dipole moment components, the conformational relative abundances could be estimated as gGGg′:gGGg:g′AGg:gAGg:g′AGg′ = 13:9:6:2:0 in Ar and 13:9:3:2:1 in He expansion. These values are in qualitative agreement with the predictions derived by the calculated relative energies (MP2/aug-cc-pVTZ 13.0:5.2:3.0:2.3:1.6 and MP2/6-311++g(d,p) 13.0:7.1:6.4:4.5:2.8) and reveal that in Ar expansion the conformational relaxation of g′AGg′ onto g′AGg takes place. Other conformers of 13PDT were expected to be observed considering their theoretical abundances, but they were not detected. The lack of observation of the higher-energy GG and AG rotamers can be explained considering both the values of the electric dipole moment components (as in the case of gAGg′) and the relaxation to lower-energy conformers in the supersonic jet. Regarding the most stable conformers of the AA species, the reason for their non-disclosure is ascribed to the low values of the electric dipole moment components.
The experimental findings confirm that the structural arrangements adopted by 13PDT are different from the 1,3-propanediol ones, as already suggested by the computational results. Due to the lower strength of the SH hydrogen bond with respect to the OH one, the conformational preferences of 13PDT arise from a balance of electronic and steric effects, whereas the intramolecular hydrogen bond interaction is the main driving force in the case of the analogue 1,3-propanediol. As a consequence, the population of 13PDT spreads on a larger number of conformers. Moreover, it should be noted that, due to the lack of a dominant interaction, the changes in the conformational relative energy values obtained at different levels of calculation are not negligible.
Fig. 4 Theoretical 2D sections of the conformational PES (cm−1) of 13PDT under isolated conditions (left side) or in a polar medium (right side). |
The investigation of the backbone internal rotation pathways is a more challenging task because, during the exploration of the PES as a function of τ2 and τ3, the rearrangement of the SH groups easily takes place, introducing additional variables to the model and thus preventing the achievement of a 2D-PES. Nevertheless, choosing a gg′ orientation of the SH groups and varying the τ2 and τ3 dihedral angles in the τ = 30°–240° range by steps of Δτ = 10°, we could obtain a 2D-PES including the gGGg′, gGAg′, gAGg′, and gAAg′ species (see left side of Fig. 4). The calculated SCCC internal rotation barriers (1100–1600 cm−1) are higher than the sulphydryl ones and are compared with the CCCC ones estimated for butane.35
In order to extrapolate these results to an environment closer to the biological one, the effect of a polar medium was simulated using a polarizable continuum model.18 The relative energy of the minima and the 2D-PESs achieved using water's dielectric constant (εr = 78.3553) are reported in Table 1 and in the right side of Fig. 4, respectively. As a general result, the 2D-PESs appear to be flattened: most of the minima are closer in energy and also the interconversion skeletal barriers decrease, indicating that in a polar solvent the torsional flexibility of 13PDT is even greater than that in the gas phase. In particular, the stabilization energies due the polar medium increase with the “anti character” of the skeletal arrangement, being 14–16 kJ mol−1 for GG, 16–17 kJ mol−1 for AG, and 17–18 kJ mol−1 for the AA species. Consequently, the gAAg and gAAg′ conformers become the most stable minima. Concerning the GG′ forms, two trends can be recognized: the stabilization energies are 19–20 kJ mol−1 if the sulfur electronic clouds face each other (aGG′a and aGG′g′) and 15–17 kJ mol−1 otherwise. However, all the GG′ conformers remain the less stable ones.
Fig. 5 X-ray diffraction structures of the DHLA ligand in different biological environments available from the Protein Data Bank using the reported PDB identifiers. |
Due to the relatively easy capability to change its conformation, the 13PDT appears to be free to adapt its shape depending on the surroundings, in order to maximize the intermolecular interactions, providing a possible rationale for the different biochemical roles played by DHLA in cellular processes.
Footnote |
† Electronic supplementary information (ESI) available: Ab initio structural parameters and energy values for all conformers, mono-dimensional sections of the bi-dimensional conformational potential energy surfaces and measured transitions used in the fit. See DOI: 10.1039/c6cp05606g |
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