Title

Structures and Energetics of B- and Y-Ions in Peptoid Fragmentation

Poster Number

16A

Lead Author Major

Pre-Pharmacy

Lead Author Status

Junior

Format

Poster Presentation

Faculty Mentor Name

Jianhua Ren

Faculty Mentor Email

jren@pacific.edu

Faculty Mentor Department

Chemistry

Graduate Student Mentor Name

Yuntao Zhang

Graduate Student Mentor Email

y_zhang15@u.pacific.edu

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

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Apr 27th, 10:00 AM Apr 27th, 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.