More Like this

1. 1D 1 H NMR as a Tool for Fecal Metabolomics

   https://doi.org/10.1002/cpch.83  

   Ganobis, Caroline M. ; Al‐Abdul‐Wahid, M. Sameer ; Renwick, Simone ; Yen, Sandi ; Carriero, Charley ; Aucoin, Marc G. ; Allen‐Vercoe, Emma ( August 2020 , Current Protocols in Chemical Biology)

   Metabolomic studies allow a deeper understanding of the processes of a given ecological community than nucleic acid–based surveys alone. In the case of the gut microbiota, a metabolic profile of, for example, a fecal sample provides details about the function and interactions within the distal region of the gastrointestinal tract, and such a profile can be generated in a number of different ways. This unit elaborates on the use of 1D¹H NMR spectroscopy as a commonly used method to characterize small‐molecule metabolites of the fecal metabonome (meta‐metabolome). We describe a set of protocols for the preparation of fecal water extraction, storage, scanning, measurement of pH, and spectral processing and analysis. We also compare the effects of various sample storage conditions for processed and unprocessed samples to provide a framework for comprehensive analysis of small molecules from stool‐derived samples. © 2020 Wiley Periodicals LLC

   Basic Protocol 1: Extracting fecal water from crude fecal samples

   Alternate Protocol 1: Extracting fecal water from small crude fecal samples

   Basic Protocol 2: Acquiring NMR spectra of metabolite samples

   Alternate Protocol 2: Acquiring NMR spectra of metabolite samples using Bruker spectrometer running TopSpin 3.x

   Alternate Protocol 3: Acquiring NMR spectra of metabolite samples by semiautomated process

   Basic Protocol 3: Measuring sample pH

   Support Protocol 1: Cleaning NMR tubes

   Basic Protocol 4: Processing raw spectra data

   Basic Protocol 5: Profiling spectra

   Support Protocol 2: Spectral profiling of sugars and other complex metabolites

    

   more » « less
2. 31 P NMR Evidence for Peroxide Intermediates in Lipid Emulsion Photooxidations: Phosphine Substituent Effects in Trapping

   https://doi.org/10.1111/php.12810  

   Mohapatra, Prabhu P. ; Chiemezie, Callistus O. ; Kligman, Arina ; Kim, Michele M. ; Busch, Theresa M. ; Zhu, Timothy C. ; Greer, Alexander ( September 2017 , Photochemistry and Photobiology)

   Intralipid is a lipid emulsion used in photodynamic therapy (PDT) for its light scattering and tissue‐simulating properties. The purpose of this study is to determine whether or not Intralipid undergoes photooxidation, and we have carried out an Intralipid peroxide trapping study using a series of phosphines [2′‐dicyclohexylphosphino‐2,6‐dimethoxy‐1,1′‐biphenyl‐3‐sulfonate, 3‐(diphenylphosphino)benzenesulfonate, triphenylphosphine‐3,3′,3′′‐trisulfonate and triphenylphosphine]. Our new findings are as follows: (1) An oxygen atom is transferred from Intralipid peroxide to the phosphine traps in the dark, after the photooxidation of Intralipid. 3‐(Diphenylphosphino)benzenesulfonate is the most suitable trap in the series owing to a balance of nucleophilicity and water solubility. (2) Phosphine trapping and monitoring by³¹PNMRare effective in quantifying the peroxides in H₂O. An advantage of the technique is that peroxides are detected in H₂O; deuteratedNMRsolvents are not required. (3) The percent yield of the peroxides increased linearly with the increase in fluence from 45 to 180 J cm⁻²based on our trapping experiments. (4) The photooxidation yields quantitated by the phosphines and³¹PNMRare supported by the direct¹HNMRdetection using deuteratedNMRsolvents. These data provide the first steps in the development of Intralipid peroxide quantitation afterPDTusing phosphine trapping and³¹PNMRspectroscopy.

    

   more » « less
3. Enabling materials informatics for 29Si solid-state NMR of crystalline materials

   https://doi.org/10.1038/s41524-020-0328-3  

   Sun, He ; Dwaraknath, Shyam ; Ling, Handong ; Qu, Xiaohui ; Huck, Patrick ; Persson, Kristin A. ; Hayes, Sophia E. ( May 2020 , npj Computational Materials)

   Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for obtaining precise information about the local bonding of materials, but difficult to interpret without a well-vetted dataset of reference spectra. The ability to predict NMR parameters and connect them to three-dimensional local environments is critical for understanding more complex, long-range interactions. New computational methods have revealed structural information available from²⁹Si solid-state NMR by generating computed reference spectra for solids. Such predictions are useful for the identification of new silicon-containing compounds, and serve as a starting point for determination of the local environments present in amorphous structures. In this study, we have used 42 silicon sites as a benchmarking set to compare experimentally reported²⁹Si solid-state NMR spectra with those computed by CASTEP-NMR and Vienna Ab Initio Simulation Program (VASP). Data-driven approaches enable us to identify the source of discrepancies across a range of experimental and computational results. The information from NMR (in the form of an NMR tensor) has been validated, and in some cases corrected, in an effort to catalog these for the local spectroscopy database infrastructure (LSDI), where over 10,000²⁹Si NMR tensors for crystalline materials have been computed. Knowledge of specific tensor values can serve as the basis for executing NMR experiments with precision, optimizing conditions to capture the elements accurately. The ability to predict and compare experimental observables from a wide range of structures can aid researchers in their chemical assignments and structure determination, since the computed values enables the extension beyond tables of typical chemical shift (or shielding) ranges.

    

   more » « less
4. Origin of the 29 Si NMR chemical shift in R 3 Si–X and relationship to the formation of silylium (R 3 Si + ) ions

   https://doi.org/10.1039/D0DT02099K  

   Huynh, Winn ; Conley, Matthew P. ( November 2020 , Dalton Transactions)

   null (Ed.)

   The origin in deshielding of 29 Si NMR chemical shifts in R 3 Si–X, where X = H, OMe, Cl, OTf, [CH 6 B 11 X 6 ], toluene, and O X (O X = surface oxygen), as well as i Pr 3 Si + and Mes 3 Si + were studied using DFT methods. At the M06-L/6-31G(d,p) level of theory the geometry optimized structures agree well with those obtained experimentally. The trends in 29 Si NMR chemical shift also reproduce experimental trends; i Pr 3 Si–H has the most shielded 29 Si NMR chemical shift and free i Pr 3 Si + or isolable Mes 3 Si + have the most deshielded 29 Si NMR chemical shift. Natural localized molecular orbital (NLMO) analysis of the contributions to paramagnetic shielding ( σ p ) in these compounds shows that Si–R (R = alkyl, H) bonding orbitals are the major contributors to deshielding in this series. The Si–R bonding orbitals are coupled to the empty p-orbital in i Pr 3 Si + or Mes 3 Si + , or to the orbital in R 3 Si–X. This trend also applies to surface bound R 3 Si–O X . This model also explains chemical shift trends in recently isolated t Bu 2 SiH 2 + , t BuSiH 2 + , and SiH 3 + that show more shielded 29 Si NMR signals than R 3 Si + species. There is no correlation between isotropic 29 Si NMR chemical shift and charge at silicon. 

   more » « less
5. Metal Ion Sensing by BAPTA: Investigation Using 1H NMR Spectroscopy

   https://doi.org/10.47611/jsrhs.v11i4.3515  

   Adoni, Sunayna ; Mologu, Trivikram ; Igumenova, Tatyana ( November 2022 , Journal of Student Research)

   Many  biological  macromolecules  rely  on  metal  ions  to  maintain  structural  integrity  and  control  their  regulatory  function. In biological fluids, detection and identification of metal ions requires sensitive analytical tools with clear readouts.  In  this  work,  we  sought  to  investigate  the  potential  of  solution  Nuclear  Magnetic  Resonance  (NMR)  spectroscopy to analyze metal ion solutions and mixtures. To enable 1H NMR detection, we prepared the complexes of  eight  metal  ions  with  the  chelating  agent,  1,2-bis(o-aminophenoxy)ethane-N,N,N′,N′-tetraacetic  acid  (BAPTA).  The 1H NMR spectra were collected for BAPTA samples as a function of metal ion concentrations. The analysis of NMR data revealed that all metal ions with a notable exception of Mg2+ bind BAPTA with high affinities and form complexes with 1:1 metal-to-chelator stoichiometry. Both methylene and aromatic regions of the BAPTA 1H NMR spectra  experience  significant  changes  upon  the  metal  ion  complex  formation.  We  identified  the  spectroscopic  signatures  of  trivalent  and  paramagnetic  ions  and  demonstrated  that  the  binary  Zn2+/Pb2+  metal  ion  mixture  can  be  successfully analyzed by NMR. We conclude that complexation with BAPTA followed by the 1H NMR analysis is a sensitive method to detect and identify both nutritive and xenobiotic metal ions.

    

   more » « less