Monitoring the Site-Specific Solid-State NMR Data in Oligopeptides

The Physical Chemistry and Chemical Physics (PCCP) Section of the International Journal of Molecular Sciences in Its Publications: The First 300 Thematic Articles in the First 3 Years

The Physical Chemistry and Chemical Physics Section (PCCP Section) is one of the youngest among the sections of the International Journal of Molecular Sciences (IJMS)—the year 2021 will only mark three years since its inception [...]

Modeling the Structure of Crystalline Alamethicin and Its NMR Chemical Shift Tensors

Alamethicin (ALM) is an antimicrobial peptide that is frequently employed in studies of the mechanism of action of pore-forming molecules. Advanced techniques of solid-state NMR spectroscopy (SSNMR) are important in these studies, as they are capable of describing the alignment of helical peptides, such as ALM, in lipid bilayers. Here, it is demonstrated how an analysis of the SSNMR measurements can benefit from fully periodic calculations, which employ the plane-wave density-functional theory (PW DFT) of the solid-phase geometry and related spectral parameters of ALM. The PW DFT calculations are used to obtain the structure of desolvated crystalline ALM and predict the NMR chemical shift tensors (CSTs) of its nuclei. A variation in the CSTs of the amidic nitrogens and carbonyl carbons along the ALM backbone is evaluated and included in simulations of the orientation-dependent anisotropic 15N and 13C chemical shift components. In this way, the influence of the site-specific structural effects on the experimentally determined orientation of ALM is shown in models of cell membranes.

Parametrizing the Spatial Dependence of 1H NMR Chemical Shifts in π-Stacked Molecular Fragments

Most recently a renewed interest in several areas has arisen in factors governing the 1H NMR chemical shift (1H CS) of protons in aromatic systems. Therefore, it is important to describe how 1H CS values are affected by π-stacking intermolecular interactions. The parametrization of radial and angular dependences of the 1H CS is proposed, which is based on conventional gauge-independent atomic orbital (GIAO) calculations of explicit molecular fragments. Such a parametrization is exemplified for a benzene dimer with intermonomer vertical and horizontal distances which are in the range of values often found in crystals of organic compounds. Results obtained by the GIAO calculations combined with B3LYP and MP2 methods were compared, and revealed qualitatively the same trends in the 1H CS data. The parametrization was found to be quantitatively correct for the T-shaped benzene dimers, and its limitations were discussed. Parametrized 1H CS surfaces should become useful for providing additional restraints in the search of site-specific information through an analysis of structurally induced 1H CS changes.

Polymorphic Forms of Valinomycin Investigated by NMR Crystallography

A dodecadepsipeptide valinomycin (VLM) has been most recently reported to be a potential anti-coronavirus drug that could be efficiently produced on a large scale. It is thus of importance to study solid-phase forms of VLM in order to be able to ensure its polymorphic purity in drug formulations. The previously available solid-state NMR (SSNMR) data are combined with the plane-wave DFT computations in the NMR crystallography framework. Structural/spectroscopical predictions (the PBE functional/GIPAW method) are obtained to characterize four polymorphs of VLM. Interactions which confer a conformational stability to VLM molecules in these crystalline forms are described in detail. The way how various structural factors affect the values of SSNMR parameters is thoroughly analyzed, and several SSNMR markers of the respective VLM polymorphs are identified. The markers are connected to hydrogen bonding effects upon the corresponding (13C/15N/1H) isotropic chemical shifts of (CO, Namid, Hamid, Hα) VLM backbone nuclei. These results are expected to be crucial for polymorph control of VLM and in probing its interactions in dosage forms.