Structures and Energetics of B- and Y-Ions in Peptoid Fragmentation
Poster Number
16A
Format
Poster Presentation
Faculty Mentor Name
Jianhua Ren
Faculty Mentor Department
Chemistry
Graduate Student Mentor Name
Yuntao Zhang
Graduate Student Mentor Department
Chemistry
Abstract/Artist Statement
In this research enterprise, the conformations and energetics of fragments from multiple peptoids were investigated using high-level computational methods. Peptoids are a new class of man-made polymers that mimic the structure and function of peptides, which are the building blocks of proteins. Unlike peptides, peptoids are not susceptible to degradation by proteases, due to their vital, minor structural differences with peptides and the high specificity of protease proteins. Its rigidity and complexity has made peptoids one of the most promising peptide-mimicking strategies. However, there are no efficient, reliable peptoid sequencing techniques to promptly determine a peptoid’s structure presently. To solve this problem, better understanding of peptoid fragmentation needs to be obtained; computational studies are the most feasible way.
In these theoretical studies, fragments were built, optimized, and analyzed using two molecular modeling programs, Spartan ’14 and Gaussian ’09. Using different starting structures based on chemistry intuition, the conformational space was extensively examined through multiple algorithms including molecular mechanic and Monte Carlo simulations. Sequential geometry optimization and energy calculations at higher levels of theory allow for determination of the low-energy peptoid fragment conformations.
Based on the energies of the most stable conformations, Y-ions are favored for longer peptoids, while less favored for shorter peptoids, when fragmenting in the middle of the peptoids. The enthalpy differences between the Y- and B-ion channels (∆HY - ∆HB) are -4.6, -1.2, 3.1, 9.3, and 4.3 kcal/mol, respectively, for two-, four-, six-, eight-, and ten-residue peptoids. Longer Y-ions are favored due to multiple hydrogen bonding interactions, while in shorter Y-ions, less hydrogen bonds are available to accommodate the concentrated charge. Compared to the increasing charge compensation in longer Y-ions, the stabilization effects of the oxazolone ring remain constant among B-ions with varying lengths.
Location
DeRosa University Center Ballroom
Start Date
27-4-2018 10:00 AM
End Date
27-4-2018 12:00 PM
Structures and Energetics of B- and Y-Ions in Peptoid Fragmentation
DeRosa University Center Ballroom
In this research enterprise, the conformations and energetics of fragments from multiple peptoids were investigated using high-level computational methods. Peptoids are a new class of man-made polymers that mimic the structure and function of peptides, which are the building blocks of proteins. Unlike peptides, peptoids are not susceptible to degradation by proteases, due to their vital, minor structural differences with peptides and the high specificity of protease proteins. Its rigidity and complexity has made peptoids one of the most promising peptide-mimicking strategies. However, there are no efficient, reliable peptoid sequencing techniques to promptly determine a peptoid’s structure presently. To solve this problem, better understanding of peptoid fragmentation needs to be obtained; computational studies are the most feasible way.
In these theoretical studies, fragments were built, optimized, and analyzed using two molecular modeling programs, Spartan ’14 and Gaussian ’09. Using different starting structures based on chemistry intuition, the conformational space was extensively examined through multiple algorithms including molecular mechanic and Monte Carlo simulations. Sequential geometry optimization and energy calculations at higher levels of theory allow for determination of the low-energy peptoid fragment conformations.
Based on the energies of the most stable conformations, Y-ions are favored for longer peptoids, while less favored for shorter peptoids, when fragmenting in the middle of the peptoids. The enthalpy differences between the Y- and B-ion channels (∆HY - ∆HB) are -4.6, -1.2, 3.1, 9.3, and 4.3 kcal/mol, respectively, for two-, four-, six-, eight-, and ten-residue peptoids. Longer Y-ions are favored due to multiple hydrogen bonding interactions, while in shorter Y-ions, less hydrogen bonds are available to accommodate the concentrated charge. Compared to the increasing charge compensation in longer Y-ions, the stabilization effects of the oxazolone ring remain constant among B-ions with varying lengths.