On the Treatment of Conformational Flexibility when Using Residual Dipolar Couplings for Structure Determination

Abstract

The determination of the three-dimensional structure of organic and biomolecular compounds by NMR spectroscopy usually involves the measurement of 3 J coupling constants, [1] NOEs, [2] and cross-correlated relaxation [3] to obtain information about dihedral angles, distances, and projection angles, respectively. If interconversion of conformers takes place and is fast on the NMR time scale, NMR spectroscopic parameters for flexible parts of the molecule are motionally averaged. This effect is one of the main complications in the structure determination of nonrigid molecules and often prohibits the determination of the relative configuration of organic compounds.It has been shown that residual dipolar couplings (RDCs) can yield information complementary to that obtained from 3 J coupling constants and NOE parameters also for organic compounds [4][5][6][7][8][9][10] and enable the assignment of relative configurations even in the presence of a limited degree of motion. [11][12][13][14][15] The problem of the joint treatment of an unknown configuration and conformational averaging when residual dipolar couplings are used in structure determination has scarcely been tackled. Herein two approaches are discussed, and it is shown that even conformer populations can be obtained from experimentally determined RDCs.The example chosen for illustration is a five-memberedring compound investigated recently by some of us. The amethylene-g-butyrolactone had been synthesized as single diastereoisomer, [16] the relative configuration of which (trans, denoted 1, or cis, denoted 2) was unknown and could not be determined by using conventional NMR spectroscopic parameters.[11] By using RDCs, however, it was possible to assign the relative configuration as trans (Scheme 1).[11]The number of ring conformers of 1 is restricted to two, denoted A and B in the following. These conformers are envelope conformations, one with C2 below (A) and one with C2 above (B) the almost planar arrangement of the remaining ring atoms (see also Figure SI1 in the Supporting Information).[17] In the previous study, [11] we used the transition structure between A and B as a crude approximation of the average ring conformation of 1. Additionally, we fitted the structures of the two rigid conformers to the RDC data by using one order tensor [18,19] each. By using this method we were able to assign the relative configuration as trans.[20]However, we did not attempt to extract information concerning the populations of the two conformers (p A and p B ), which was therefore one subject of the current investigation.The direct (residual) dipolar coupling D IS between spins I and S, with magnetogyric ratios g I and g S , is given by Equation (1): [9,21] ISis the dipole-dipole coupling constant (in Hz), V IS is the angle between the interspin vector and the external magnetic field, and r IS is the interspin distance (which corresponds to the bond length for directly bound nuclei). The angular brackets indicate that the RDCs are averaged over both molecular tumbling ...

Challenge of Large-Scale Motion for Residual Dipolar Coupling Based Analysis of Configuration: The Case of Fibrosterol Sulfate A

“…25,30,31 Hence, we determined the alignment tensor for each main conformer individually according to Eq.3 and Eq.4, as mentioned in the Methodology section. Note that only the product of population and alignment tensor can be derived from the experimentally measured RDCs 54 and the two unknown parameters cannot be separated unless additional information either on the population of each conformer in the ensemble or the relative sizes of the alignment tensors for each conformer are obtained from independent sources.…”

“…Note that only the product of population and alignment tensor can be derived from the experimentally measured RDCs 54 and the two unknown parameters cannot be separated unless additional information either on the population of each conformer in the ensemble or the relative sizes of the alignment tensors for each conformer are obtained from independent sources. In a previous study on α-methylene-γ-butyrolactone, 31 this problem was solved assuming that the magnitude of the alignment tensors was the same for the two conformers in the ensemble. This is not, however, a valid assumption for fibrosterol sulfate A since the degree of alignment induced by extended or collapsed structures are expected to be very different.…”

Determining the Stereochemistry of Molecules from Residual Dipolar Couplings (RDCs)

“…If enough data are available, it is straightforward to find the correct configuration by comparing the quality of the fit. This method has been used only for the determination of relative configurations on two compounds so far, γ -butyrolactone 4 36 and fibrosterol 5 37 below.…”

“…For one compound, it was investigated whether one could introduce an approximation to solve this mutual dependence. 36 It turned out to be possible to assume a very similar magnitude of orientation for both underlying conformers.…”

Structural Discrimination in Small Molecules by Accurate Measurement of Long‐Range Proton–Carbon NMR Residual Dipolar Couplings

“…Although residual dipolar couplings (RDCs) are widely used in macromolecular structural studies by NMR, [1] they also are proving to be very powerful for the constitutional, [2] configurational, [3–9] and conformational analysis [10–11] of small molecules. Before RDCs were available, the determination of the 3D structure of small molecules by solution NMR was principally achieved on the basis of parameters such as NOE and 3 J coupling constants.…”