Notes

COVID-19 mRNA vaccinations travel differential antibody Fc-functional profiles within expecting, breast feeding, along with nonpregnant women.
Untargeted metabolomics aims to quantify the complete set of metabolites within a biological system, most commonly by liquid chromatography/mass spectrometry (LC/MS). Since nearly the inception of the field, compound identification has been widely recognized as the rate-limiting step of the experimental workflow. In spite of exponential increases in the size of metabolomic databases, which now contain experimental MS/MS spectra for over a half million reference compounds, chemical structures still cannot be confidently assigned to many signals in a typical LC/MS dataset. The purpose of this Perspective is to consider why identification rates continue to be low in untargeted metabolomics. One rationalization is that many naturally occurring metabolites detected by LC/MS are true "novel" compounds that have yet to be incorporated into metabolomic databases. An alternative possibility, however, is that research data do not provide database matches because of informatic artifacts, chemical contaminants, and signal redundancies. Increasing evidence suggests that, for at least some sample types, many unidentifiable signals in untargeted metabolomics result from the latter rather than new compounds originating from the specimen being measured. The implications of these observations on chemical discovery in untargeted metabolomics is discussed.The pseudosymmetric relationship of the bacterial sialic acid, pseudaminic acid, and 3-deoxy-d-manno-oct-2-ulosonic acid (KDO) affords the hypothesis that suitably protected KDO donors will adopt the trans, gauche conformation of their side chain and consequently be highly equatorially selective in their coupling reactions conducted at low temperature. This hypothesis is borne out by the synthesis, conformational analysis, and excellent equatorial selectivity seen on coupling of per-O-acetyl or benzyl-protected KDO donors in dichloromethane at -78 °C. Mechanistic understanding of glycosylation reactions is advancing to a stage at which predictions of selectivity can be made. In this instance, predictions of selectivity provide the first highly selective entry into KDO equatorial glycosides such as are found in the capsular polysaccharides of numerous pathogenic bacteria.We present a well-parallelized local implementation of high-spin open-shell coupled cluster methods with single and double excitations (CCSD) using pair natural orbitals (PNOs). The methods are based on the spin-orbital coupled cluster theory using restricted open-shell Hartree-Fock (ROHF) reference functions. Two variants, namely PNO-UCCSD and PNO-RCCSD are implemented and compared. In PNO-UCCSD the coupled cluster amplitudes are spin-unrestricted, while in PNO-RCCSD the linear terms are spin-adapted by a spin-projection approach as described in J. Chem. Phys. 99, 5219 (1993). Near linear scaling of the computational cost with the number of correlated electrons is achieved by applying domain and pair approximations. The PNOs are spin-independent and obtained using a semicanonical spin-restricted MP2 approximation with large domains of projected atomic orbitals (PAOs). The pair approximations of our previously described closed-shell PNO-LCCSD method are carefully revised so that they are compatible to the UCCSD theory, and PNO-UCCSD or PNO-RCCSD calculations for closed-shell molecules yield exactly the same results as corresponding spin-free closed-shell PNO-LCCSD calculations. The convergence of the results with respect to the thresholds and options that control the domain and pair approximations is demonstrated. It is found that large domains are required for the single excitations in open-shell calculations in order to obtain converged results. In general, the errors of relative energies caused by the local approximations can be reduced to below 1 kcal mol-1, even for difficult cases. Presently PNO-RCCSD and PNO-UCCSD calculations for molecules with 100-200 atoms and augmented triple-ζ basis sets can be carried out in a few hours of elapsed time using ~100 CPU cores. In addition, the program is also capable of performing distinguishable cluster (PNO-RDCSD and PNO-UDCSC) calculations. The present work is a critical step in developing fully local open-shell PNO-RCCSD(T)-F12 methods.An extension of the CRYSTAL program is presented allowing for calculations of anharmonic Infrared (IR) intensities and Raman activities for periodic systems. This work is a follow up of two papers devoted to the computation of anharmonic vibrational states of solids from DFT calculations, part I description of the potential energy surface (J. Chem. Theory Comput. 15 (2019) 3755-3765) and part II implementation of the VSCF and VCI methods (J. Chem. Theory Comput. 15 (2019) 3766-3777). The approach presented here relies on the evaluation of integrals of the dipole moment and polarizability operators over anharmonic wavefunctions obtained from either VSCF or VCI calculations. With this extension, the program now allows for a more complete characterization of the vibrational spectroscopic features of solids within the density functional theory. In particular, it is able (i) to provide reliable positions and inten-sities for most intense spectral features, and (ii) to check whether a first overtone or a combi-nati (DFT exchange-correlation functional/basis set) for the electronic structure calculations on the computed spectra is discussed and found to be significant, which suggests some special care is needed for the analysis of subtle spectral features.Ultraviolet photodissociation (UVPD) has emerged as a promising tool to characterize proteins with regard to not only their primary sequences and post-translational modifications, but also their tertiary structures. In this study, three metal-binding proteins, Staphylococcal nuclease, azurin, and calmodulin, are used to demonstrate the use of UVPD to elucidate metal-binding regions via comparisons between the fragmentation patterns of apo (metal-free) and holo (metal-bound) proteins. The binding of staphylococcal nuclease to calcium was evaluated, in addition to a series of lanthanide(III) ions which are expected to bind in a similar manner as calcium. see more On the basis of comparative analysis of the UVPD spectra, the binding region for calcium and the lanthanide ions was determined to extend from residues 40-50, aligning with the known crystal structure. Similar analysis was performed for both azurin (interrogating copper and silver binding) and calmodulin (four calcium binding sites). This work demonstrates the utility of UVPD methods for determining and analyzing the metal binding sites of a variety of classes of proteins.
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