| Literature DB >> 25984602 |
Abstract
Conformational/tautomeric transformations for X=CH-CH=Y structures (X = CH2, O, NH and Y = NH) have been studied in the gas phase, in dichloromethane and in aqueous solutions. The paper is a continuation of a former study where s-cis/s-trans conformational equilibria were predicted for analogues. The s-trans conformation is preferred for the present molecules in the gas phase on the basis of its lowest internal free energy as calculated at the B97D/aug-cc-pvqz and CCSD(T)CBS (coupled-cluster singles and doubles with non-iterative triples extrapolated to the complete basis set) levels. Transition state barriers are of 29-36 kJ/mol for rotations about the central C-C bonds. In solution, an s-trans form is still favored on the basis of its considerably lower internal free energy compared with the s-cis forms as calculated by IEF-PCM (integral-equation formalism of the polarizable continuum dielectric solvent model) at the theoretical levels indicated. A tetrahydrate model in the supermolecule/continuum approach helped explore the 2solute-solvent hydrogen bond pattern. The calculated transition state barrier for rotation about the C-C bond decreased to 27 kJ/mol for the tetrahydrate. Considering explicit solvent models, relative solvation free energies were calculated by means of the free energy perturbation method through Monte Carlo simulations. These calculated values differ remarkably from those by the PCM approach in aqueous solution, nonetheless the same prevalent conformation was predicted by the two methods. Aqueous solution structure-characteristics were determined by Monte Carlo. Equilibration of conformers/tautomers through water-assisted double proton-relay is discussed. This mechanism is not viable, however, in non-protic solvents where the calculated potential of mean force curve does not predict remarkable solute dimerization and subsequent favorable orientation.Entities:
Keywords: FEP/MC; IEF-PCM/B97D/aug-cc-pvqz; IEF-PCM/CCSD(T)/ CBS; s-cis/s-trans equilibrium; tautomerization mechanism
Mesh:
Substances:
Year: 2015 PMID: 25984602 PMCID: PMC4463675 DOI: 10.3390/ijms160510767
Source DB: PubMed Journal: Int J Mol Sci ISSN: 1422-0067 Impact factor: 5.923
Scheme 12-Propene-1-imine (1–4); 2-imino acetaldehyde (5–8); 2-amino ketene (9). Letters t and c stand for the s-trans and s-cis conformations, respectively, letters A and S stand for CCNH anti and syn orientations respectively. The heavy atoms are nearly or entirely coplanar. Remarkable deviation from planarity was found for structure (9). For detailed geometric data, see Supplementary Information (Table S1 and Figure S1a–d).
Scheme 21,2-Ethane diimine (10–15); 2-amino imino-ketene (16); 1,2-diamino acetylene (17). For t, c, A and S codes, see Scheme 1. The heavy atoms are nearly or entirely coplanar. Remarkable deviations from planarity was found for structures (16) and (17). For detailed geometric data, see Supplementary Information (Table S1 and Figure S1a–d).
Relative energy/free energy components for tautomeric/conformational isomers a.
| Structures in Schemes | Gas | Dichloromethane | Water | |||||
|---|---|---|---|---|---|---|---|---|
| ΔEgint | ΔGgth | ΔEsint | ΔGsth | ΔGsolv | ΔEsint | ΔGsth | ΔGsolv | |
| CH2=CH–CH=NH ( | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
| TS ( | 113.9 | −9.9 b | 111.5 | −10.1 b | 7.8 | 110.3 | −10.3 b | 10.3 |
| 123.2 c | ||||||||
| CH2=CH–CH=NH ( | 2.7 | −0.2 | 2.9 | −0.5 | −1.8 | 2.9 | −0.5 | −2.0 |
| 3.1 c | 3.8 c | −2.1 d | 3.7 c | −2.3 d | ||||
| TS ( | ||||||||
| (95.4°, 96.0°, 96.3°) e | 35.5 | −3.5 b | 35.4 | −3.0 b | −0.6 | 35.5 | −3.0 b | −0.9 |
| (96.1°) | 29.3 c | |||||||
| CH2=CH–CH=NH ( | 13.4 | −2.4 | 14.3 | −4.0 b,f | 1.3 | 13.0 | −4.0 b,f | 2.2 |
| 11.4 c | 10.1 c | 2.6 d | 9.7 c | 3.2 d | ||||
| CH2=CH–CH=NH ( | 15.1 | −2.8 b | 16.1 | −2.3 b | −8.7 | 15.1 | −2.5 b | −1.4 |
| 13.1 c | −0.9 d | |||||||
| O=CH–CH=NH ( | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
| O=CH–CH=NH ( | 2.9 | −0.5 | 3.5 | 0.2 | −1.3 | 3.8 | 0.0 | −2.0 |
| TS ( | ||||||||
| (87.3°, 88.2°, 88.4°) e | 29.1 | −3.4 b | 29.9 | −3.0 b | −3.3 | 30.4 | −3.0 b | −4.5 |
| (89.2°) | 30.8 | |||||||
| O=CH–CH=NH ( | 7.8 | −0.1 | 8.0 | 1.0 | 0.4 | 8.2 | 0.4 | 0.2 |
| 7.8 c | 9.6 c | −1.9 d | 10.5 c | −3.0 d | ||||
| O=CH–CH=NH( | 23.1 | −5.4 d | 26.8 | −3.6 b | −10.6 | 29.0 | −3.3 b | −14.9 |
| 24.4 | 32.5 c | −16.2 d | 36.1 c | −22.3 d | ||||
| O=C=CH–NH2 ( | 20.8 | −1.0 | 19.7 | 7.4 | 19.4 | −0.8 b | 8.2 | |
| 35.1 | 32.0 c | 9.2 d | 31.4 c | 10.3 d | ||||
| HN=CH–CH=NH ( | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
| HN=CH–CH=NH ( | 4.6 | −2.3 b | 5.8 | −2.9 b | −3.4 | 6.5 | −3.0 b | −4.8 |
| 6.2 c | 8.7 c | −2.7 b | −5.0 d | 9.8 c | −2.9 b | −6.8 d | ||
| TS ( | ||||||||
| (92.7o, 93.2o, 93.4°) e | 32.6 | −3.6 b | 34.3 | −2.8 b | −5.2 | 35.2 | −3.0 b | −7.2 |
| (93.6°) | 31.3 | |||||||
| HN=CH–CH=NH ( | 11.8 | −2.8 b | 13.0 | −3.3 b | −1.5 | 13.6 | −4.1 b | −2.3 |
| 10.6 c | 13.9 c | −4.5 d | 15.3 c | −6.2 d | ||||
| HN=CH–CH=NH ( | 6.9 | −1.1 | 7.8 | −1.4 | −3.6 | 8.2 | −1.7 | −4.8 |
| 9.4 c | 11.6 c | −4.9 d | 12.6 c | −7.1 d | ||||
| HN=CH–CH=NH ( | 16.1 | 16.7 | −0.9 b | −3.0 | 17.0 | −2.2 b | −4.0 | |
| 20.8 c | −5.7 d | 21.7 c | −7.2 d | |||||
| TS ( | ||||||||
| (86.3°, -, 93.5°) e | 35.2 | −4.0 b | 38.3 | −3.8 b | −9.8 | |||
| (83.6o) | 32.3 | |||||||
| HN=CH–CH=NH ( | 28.8 | 33.3 | −4.7 b | −12.8 | 36.2 | −5.4 b | −18.5 | |
| 36.7 c | −17.4 c | 40.8 c | −24.4 d | |||||
| HN=C=CH–NH2 ( | 49.2 | 49.8 | 0.1 | 50.2 | −7.5 g | −0.8 | ||
| 64.0 c | ||||||||
| H2N–C≡C–NH2 ( | 98.6 | −7.4 g | 99.2 | −2.6 | 99.2 | −5.0 g | −4.0 | |
a Values in kJ/mol. For structure numbers in parentheses, see Scheme 1 and Scheme 2. Geometries were optimized at the B97D/aug-cc-pvtz and MP2/aug-cc-pvtz levels in the indicated environment. ΔEint and ΔGsolv values (upper rows) from B97D/aug-cc-pvqz single point calculations; b –RT ln2 = −1.7 kJ/mol is included in ΔGth for the entropy of mixing for the TS antipodes or for a symmetry number of 2 for the reference structure; c CCSD(T)CBS//MP2/aug-cc-pvtz energies; d MP2/aug-cc-pvtz value; e Values in parentheses for a TS (transition state) stand for the X=C–C=N torsion angles increasing in the gas, CH2Cl2, and water series (X = CH2, O, NH). The energy/free energy parameters are provided with respect to the corresponding data of the CH2CHCHNH (1), OCHCHNH (5) and NHCHCHNH (10) conformers, respectively; f A small imaginary frequency for the lowest energy out-of-plane torsion remained through the energy minimization even using the analytical second derivative optimization. ΔGsth was estimated by using the corresponding water frequency (65 cm−1), for which the normal coordinate was extremely similar. For all other water vibrations, the frequencies and the normal coordinates were very similar and deviated by 2–4 cm−1 for the low-frequency vibrations. The largest deviation has been found at 6 cm−1 above 2000 cm−1; and g −2RT ln2 = −3.4 kJ/mol is included in the ΔGth because of the rotational symmetry number of 2 for the reference tAA (9) form with C2h symmetry and due to the entropy of mixing for antipodes. TS: transition state.
Figure 1The structures of the tetrahydrates of the s-trans species 5 and 10 and the s-cis species 8 and 15 as optimized in continuum water solvent at the IEF-PCM/B97D/aug-cc-pvtz level. The hydrogen bond parameters (from left to right) in Figure 1 are as follow. 5 tA: OCCN = 180°, the O=C, O…Hw11 (198 pm), and O…Hw21 (201 pm) bonds are coplanar, bond angles: Ow1Hw11…O = 177°, Ow2Hw21…O = 178°. The C=N, N–H and the N…Hw31 (187 pm) bonds are coplanar, H…Ow4 = 208 pm. The N…Hw31Ow3 bond angle is 177°, N–H…Ow4 = 173°. 10 tAA: NCCN = 179.9°, the N=C, N–H, and N…Hw21 (187 pm) bonds are coplanar, H…Ow1 = 209 pm. Bond angles: Ow1…H–N = 173°, Ow2Hw21…N = 177°. The C=N, N–H and the N…Hw31 (187 pm) bonds are coplanar, H…Ow4 = 208 pm. The N…Hw31Ow3 bond angle is 177°, N–H…Ow4 = 173°. 8 cA: OCCN = 23.7°, only one water—carbonyl hydrogen bond: O…Hw11 (194 pm), Ow1Hw11…O = 161°. Waters 1 and 2 form a solvent-solvent hydrogen bond with Ow1…Hw21 distance of 194 pm and Ow1…Hw21Ow2 angle of 177°. Water 2 and water 3 are also linked by a solvent-solvent hydrogen bond: Hw22…Ow3 = 187 pm and Ow2Hw22…Ow3 = 177°. The C=N, N–H and the N…Hw31 (186 pm) bonds are almost coplanar (the sum of the bond angles is 359°), H…Ow4 = 201 pm. The N…Hw31Ow3 bond angle is 178°, N–H…Ow4 = 176°. 15 cAA: NCCN = 30.5°, the N=C, N–H, and N…Hw21 (182 pm) bonds are coplanar, H…Ow1 = 207 pm. Bond angles: Ow1…H–N = 176°, Ow2Hw21…N = 177°. Water 2 and water 3 form a solvent–solvent hydrogen bond: Ow2…Hw32 = 193 pm and Ow2…Hw32Ow3 = 161°. The C=N, N–H and the N…Hw31 (190 pm) bonds are coplanar, H…Ow4 = 210 pm. The N…Hw31Ow3 bond angle is 175°, N–H…Ow4 = 172°.
B97D/aug-cc-pvtz polar atomic and net solute charges from IEF-PCM calculations a.
| Structures in Schemes | Polar Atoms | Pure Solute | Solute + 4H2O | Net Solute Charges | |
|---|---|---|---|---|---|
| Pure Solute | in Supermolecule | ||||
| O=CH–CH=NH ( | O | −0.510 | −0.340 | 0.000 | 0.268 |
| N | −0.754 | −0.495 | |||
| H | 0.419 | 0.406 | |||
| O=CH–CH=NH ( | O | −0.488 | −0.389 | 0.000 | 0.184 |
| N | −0.726 | −0.489 | |||
| H | 0.404 | 0.368 | |||
| HN=CH–CH=NH ( | H | 0.404 | 0.460 | 0.000 | 0.186 |
| N | −0.800 | −0.666 | |||
| N | −0.800 | −0.641 | |||
| H | 0.404 | 0.439 | |||
| HN=CH–CH=NH ( | H | 0.388 | 0.354 | 0.000 | 0.208 |
| N | −0.757 | −0.531 | |||
| N | −0.757 | −0.479 | |||
| H | 0.388 | 0.325 | |||
a For structure numbers in parentheses, see Scheme 1 and Scheme 2. Geometries were optimized at the IEF-PCM/B97D/aug-cc-pvtz level in aqueous solution. Charges were derived by their CHELPG fit the in-solution molecular electrostatic potentials.
IEF-PCM and FEP/Monte Carlo relative solvation free energies, ΔGsolv a.
| For Transformation | Dichloromethane | Water | ||
|---|---|---|---|---|
| IEF-PCM | MC | IEF-PCM | MC | |
| CH2=CH–CH=NH | ||||
| 7.8 (7.8) | 5.1 ± 0.1 | |||
| −1.8 (−1.8) | −1.2 ± 0.2 | −2.0 (−2.1) | −1.6 ± 0.3 | |
| −2.1 | −2.3 | |||
| O=CH–CH=NH | ||||
| 0.4 (0.4) | 1.4 ± 0.5 | 0.2 (0.3) | 9.5 ± 0.9 | |
| −1.9 | −3.0 | |||
| −14.9 (−14.8) | −9.0 ± 0.3 | |||
| −22.3 | ||||
| 7.4 (7.4) | 5.7 ± 0.2 | 8.2 (8.2) | 14.1 ± 0.4 | |
| 9.2 | 10.3 | |||
| HN=CH–CH=NH | ||||
| −3.4 (−3.3) | −0.8 ± 0.3 | −4.8 (−4.8) | −0.1 ± 0.4 | |
| −5.0 | −6.8 | |||
| −4.8 (−4.8) | 2.6 ± 0.4 | |||
| −7.1 | ||||
| −9.8 (−9.8) | −3.1 ± 0.2 | |||
| −18.5 (−18.6) | −9.4 ± 0.4 | |||
| −24.4 | ||||
| 2.1 (2.1) | 4.5 ± 0.3 | 2.5 (2.5) | 10.2 ± 0.5 | |
| 0.4 | 0.9 | |||
a Values in kJ/mol. IEF-PCM: upper row B97D/aug-cc-pvqz (aug-cc-pvtz values in parentheses), lower row MP2/aug-cc-pvtz values.
Coordination numbers (CN) and number of hydrogen bonds (nHB) in aqueous solution a.
| Structures in Schemes | O/Ow | O/Hw | Nt/Ow | Nt/Hw | Nc/Ow | Nc/Hw | (N)Ht/Ow | (N)Hc/Ow | |
|---|---|---|---|---|---|---|---|---|---|
| CH2=CH–CH–NH ( | 3.4 | 2.0 | 0.9 | 2.3 (−3.0) c | |||||
| CH2=CH–CH–NH ( | 3.1 | 2.1 | 0.8 | 2.4 (−3.0) c | |||||
| O=CH–CH=NH ( | 1.4 | 1.3 | 2.5 | 1.3 | 1.0 | 2.9 (−3.0) | |||
| O=CH–CH=NH ( | - d | 1.1 | 2.0 | 1.0 | 0.8 | 1.4 (−3.5) c | |||
| O=CH–CH=NH ( | 1.9 | 1.5 | 2.8 | 1.3 | 1.0 | 3.0 (−3.5) | |||
| O=C=CH–NH2 ( | - d | 0.6 e | - d | 1.0 | 0.7 | 2.3 (−2.5) c | |||
| HN=CH–CH=NH ( | 2.8 | 1.5 | 0.8 | 3.9 (−3.0) | |||||
| HN=CH–CH=NH ( | 2.9, 3.1 | 1.3, 1.7 | 1.0, 1.0 | 4.4 (−3.0) | |||||
| HN=CH–CH=NH ( | 3.0 | 1.5 | 0.95 | 4.1 (−3.0) | |||||
| HN=CH–CH=NH ( | 2.1, 2.7 | 1.3, 1.0 | 0.4, 0.95 | 2.6 (−3.0) | |||||
| TS (from
| 3.2 | 1.6 | 1.0 | 4.3 (−3.0) | |||||
| HN=CH–CH=NH ( | 2.9 | 1.6 | 1.0 | 4.7 (−2.5) |
a For species 9, the nitrogen/X CN values appear with subscript “t”, for 11 and 13 coordination numbers refer to nitrogens from the left to right in Scheme 2. Integration limits: 305 pm (O/Ow), 240–255 pm (O/Hw), 325–355 pm (N/Ow), 245–260 pm (N/Hw), 235–255 pm (H/Ow); b Integration limit of the pedf in parentheses; c No resolved first peak below 350 pm; d Middle of a plateau; e End of a plateau at 225 pm; f First and second CN values for the right-hand and the left-hand side N–H atoms, respectively; and g Equivalent nitrogens in gauche position.
Scheme 3IEF-PCM/B97D/aug-cc-pvtz optimized s-trans 2-propene-imine dimer (18) in dichloromethane. N–H…N angle 157°, C=N…N=C torsion angle 41.2°. 2-diamino acetylene dimer, optimized in the gas phase (19). Schematic structure of the 2-amino imino-ketene dimer (20). 2-amino ketene dimer, optimized in dichloromethane (21). Dashed lines indicate selected interatomic distances in pm.
Figure 2Potential of mean force for the s-trans/anti dimer in dichloromethane.