Organotin Chemistry
Nate F. Cardarelli in Tin as a Vital Nutrient:, 2019
The higher molecular weights resulting from associaton can be detected in the gas phase by finding fragments higher than the parent molecular ion or polytin-bearing fragments in the mass spectrum, by a higher-than-parent molecular weight from colligative properties in solution, from larger nmr |1J(119Sn-13C)| or |2J(119Sn-C-1H)| spin-spin couplings in solution,10 from reduced energy ν(OC=O) modes in either the solution or solid states or from lowered tin-119m Mössbauer isomer shifts (IS) and enhanced quadrupole splittings (QS), the resolution of spectra at ambient temperatures, or from the small slope of the temperature dependence of the area under the Moss-bauer resonances in the solid state.11–14 The assumption must be made that the associated species survive transfer from the solid state to dilute solution to the gas phase. From the X-ray diffraction results come the detailed molecular and crystal structure parameters for the solid.7–9 Close intermolecular Sn···O contact distances, wider carbon-tin-carbon angles, and the suggestive juxtaposition of potentially bonded groups can help decide the coordination number at the tin-metal center and the molecularity of the solid. The X-ray data will also tell whether the original stereochemistry of the steroid has been preserved on organotin esterification.
Toward Selectively Toxic Silver Nanoparticles
Huiliang Cao in Silver Nanoparticles for Antibacterial Devices, 2017
According to Equation 12.4, the decrease in the particle size leads to a decrease in the ACN, . The coordination number concept can be useful to describe many physicochemical phenomena of various materials. It has been found that ACN determines the effective hybridisation and therefore the magnetic moment of the clusters (Datta et al. 2007). A decrease in ACN causes a transition from bulk to atomic or molecular properties (DiCenzo et al. 1988; Rao et al. 2002).
Structural Studies of Copper Proteins Using X-Ray Absorption Spectroscopy
René Lontie in Copper Proteins and Copper Enzymes, 1984
As mentioned above, the use of the imidazole group-fitting technique enhances the possibility of identifying other atoms of interest. Table 4 also lists the types and the numbers of atoms other than imidazoles identified in the curve-fitting procedure. Two interesting points are observed. First, evidence for a copper backscatterer within 4 Å was observed only in OxyHc. The lack of evidence for a copper backscatterer in half-ApoHc and in Dimer Hc is not unexpected since only one copper atom in each active site is present in the former32 and the two copper atoms in the latter have been previously calculated to be approximately 6 Å apart,33 beyond the detection limit of the EXAFS technique. The lack of evidence of a copper backscatterer in DeoxyHc is interesting since it implies a substantial rearrangement in the active-site structure during the oxygenation cycle. In fact, such conformational changes are consistent with numerous observations on oxygen binding, such as the dissociation of subunits,34,35 changes in the 250-nm band in circular dichroism,34,36 and a slow relaxation time in kinetic studies.27 Second, the change in coordination number in the Oxy-Deoxy cycle is significant. A reduction of coordination number from 4 to 2 from OxyHc to DeoxyHc is also consistent with the suggestion of substantial structural rearrangement. Such rearrangement probably involves removal of the bound dioxygen and breaking of the bridging ligand bonds. The presence of two ligands in Cu(I) is not uncommon among Cu(I) compounds.37 The unsaturation of the site in DeoxyHc may indeed serve the purpose of binding dioxygen. In half-ApoHc, an additional low Z atom was found coordinated to the Cu(I) site.31 The additional ligand is probably cyanide ion since one cyanide ion has been shown to be coordinated to a copper atom in Hc after dialysis of Hc at low cyanide ion concentrations.38
Prediction of methionine oxidation risk in monoclonal antibodies using a machine learning method
Published in mAbs, 2018
Kannan Sankar, Kam Hon Hoi, Yizhou Yin, Prasanna Ramachandran, Nisana Andersen, Amy Hilderbrand, Paul McDonald, Christoph Spiess, Qing Zhang
The remarkable accuracy of the prediction model sheds light on the mechanism of Met oxidation and susceptibility of the residues to various ROS. The important descriptors in the model are in a way related to each other. For example, residues with fewer spatial contacts with neighbors are likely more exposed to the solvent, and this property has been measured in some studies as the water coordination number (WCN).27 In turn, these residues will exhibit higher average fluctuations. Increased fluctuation of the Met residue (partly arising from exposure to solvent) will also contribute to increased susceptibility to oxidation as manifested by the importance of the features ‘anmFluc’ and ‘hnmFluc’. Fewer residue contacts, larger fluctuations and a larger solvent exposure results in a higher chance of the residue coming in contact with ROS. The observation that the hydrophobic partition of SASA (‘PhobSasaRes’) is more important than the hydrophilic partition (‘PhilSasaRes’) can be explained by the fact that the oxidation process results in the energetically favorable conversion of an exposed hydrophobic patch on Met to a hydrophilic patch in contact with water. The RF model is a perfect framework to dissociate the contributions of these descriptors and offers robust predictions.
In silico prediction of post-translational modifications in therapeutic antibodies
Published in mAbs, 2022
Shabdita Vatsa
Structure-based approaches predict PTM liabilities by using structural features correlated with enzymatic and chemical modifications.18 Common structural features include, but are not limited to, secondary structure, water coordination number (WCN), and solvent-accessible surface area (SASA).9 WCN represents the average number of water molecules within the radius of an atom;19 SASA represents the surface area of the protein that interacts with the solvent.20 Structural features such as SASA are typically extracted from crystal21 or predicted structures for antibodies.22 Alternatively, machine learning algorithms (e.g., NetSurfP) can also be used to predict structural features such as secondary structure, solvent exposure, and structural disorder for protein sequences.23
Rux largely restores lungs in Iraq PM-exposed mice, Up-regulating regulatory T-cells (Tregs)
Published in Experimental Lung Research, 2018
David Lin, Jonathan Li, Rabail Razi, Niha Qamar, Laurie Levine, Thomas Zimmerman, Sayyed A. Hamidi, Millicent Schmidt, Marc G. Golightly, Todd Rueb, Andrea Harrington, Merrill Garnett, Frank Antonawich, Steven McClain, Edmund Miller, Courtney Cox, Po Hsuan Huang, Anthony M. Szema
Ruthenium complexes have been published and identified in recent literature as anti-inflammatory and anti-cancer agents.19–25 RuX as an anti-inflammatory agent may be due to the higher coordination numbers of transition metals (ruthenium and palladium), allowing transition metal complexes to have more diverse molecular geometry, unknown to organic molecules created by carbon (coordination number 4).26 RuX's geometric versatility can allow transition metal complexes to operate in chemical spaces unreachable by organic molecules and undergo unique reactions and mechanisms, potentially serving as therapeutic alternative mediator.26 An alternative explanation for RuX as an anti-inflammatory agent can be due to α-lipoic acid as an active ingredient.26,27 α-lipoic acid with its antioxidant property allows it to interact with and terminate free radicals, potentially serving as another therapeutic alternative mediator.26,27
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