TY - JOUR
T1 - A general new method for calculating the molecular nonpolar surface for analysis of LC-MS data
AU - Dhakal, Rabin
AU - Nieman, Reed
AU - Valente, Daniel C.A.
AU - Cardozo, Thiago M.
AU - Jayee, Bhumika
AU - Aqdas, Amna
AU - Peng, Wenjing
AU - Aquino, Adelia J.A.
AU - Mechref, Yehia
AU - Lischka, Hans
AU - Moussa, Hanna
N1 - Funding Information:
This work was supported by grants from NIH (1R01GM112490-06 and 1R01GM130091-02). It was funded in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brasil (CAPES) – Finance Code 001. We thank the HPCC of Texas Tech University for computer time.
Funding Information:
This work was supported by grants from NIH ( 1R01GM112490-06 and 1R01GM130091-02 ). It was funded in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brasil (CAPES) – Finance Code 001. We thank the HPCC of Texas Tech University for computer time.
Publisher Copyright:
© 2020 Elsevier B.V.
PY - 2021/3
Y1 - 2021/3
N2 - The accurate determination of the nonpolar surface area of glycans is vital when utilizing liquid chromatography/mass spectrometry (LC-MS) for structural characterization. A new approach for defining and computing nonpolar surface areas based on continuum solvation models (CS-NPSA) is presented. It is based on the classification of individual surface elements representing the solvent accessible surface used for the description of the polarized charge density elements in the CS models. Each element can be classified as polar or nonpolar according to a threshold value. The summation of the nonpolar elements then results in the NPSA leading to a very fine resolution of this surface. The further advantage of the CS-NPSA approach is the straightforward connection to standard quantum chemical methods and program packages. The method has been analyzed in terms of the contributions of different atoms to the NPSA. The analysis showed that not only atoms normally classified as nonpolar contributed to the NPSA, but at least partially also atoms next to polar atoms or N atoms. By virtue of the construction of the solvent accessible surface, atoms in the inner regions of a molecule can be automatically identified as not contributing to the NPSA. The method has been applied to a variety of examples such as the phenylbutanehydrazide series, model dextrans consisting of glucose units and biantennary glycans. Linear correlation of the CS-NPSA values with retention times obtained from liquid chromatographic separations measurements in the mentioned cases give excellent results and promise for more extended applications on a larger variety of compounds.
AB - The accurate determination of the nonpolar surface area of glycans is vital when utilizing liquid chromatography/mass spectrometry (LC-MS) for structural characterization. A new approach for defining and computing nonpolar surface areas based on continuum solvation models (CS-NPSA) is presented. It is based on the classification of individual surface elements representing the solvent accessible surface used for the description of the polarized charge density elements in the CS models. Each element can be classified as polar or nonpolar according to a threshold value. The summation of the nonpolar elements then results in the NPSA leading to a very fine resolution of this surface. The further advantage of the CS-NPSA approach is the straightforward connection to standard quantum chemical methods and program packages. The method has been analyzed in terms of the contributions of different atoms to the NPSA. The analysis showed that not only atoms normally classified as nonpolar contributed to the NPSA, but at least partially also atoms next to polar atoms or N atoms. By virtue of the construction of the solvent accessible surface, atoms in the inner regions of a molecule can be automatically identified as not contributing to the NPSA. The method has been applied to a variety of examples such as the phenylbutanehydrazide series, model dextrans consisting of glucose units and biantennary glycans. Linear correlation of the CS-NPSA values with retention times obtained from liquid chromatographic separations measurements in the mentioned cases give excellent results and promise for more extended applications on a larger variety of compounds.
KW - Analysis of LC-MS data
KW - Continuum solvation
KW - Nonpolar surface area
KW - Solvent accessible surface
UR - http://www.scopus.com/inward/record.url?scp=85099513818&partnerID=8YFLogxK
U2 - 10.1016/j.ijms.2020.116495
DO - 10.1016/j.ijms.2020.116495
M3 - Article
AN - SCOPUS:85099513818
VL - 461
JO - International Journal of Mass Spectrometry
JF - International Journal of Mass Spectrometry
SN - 1387-3806
M1 - 116495
ER -