Conformations of amino acids characterized by theoretical spectroscopy

96 Pages·2014·12.29 MB·English

Conformations of amino acids
characterized by theoretical
spectroscopy
Hongbao Li
Doctoral Thesis in Theoretical Chemistry and Biology
School of Biotechnology
Royal Institute of Technology
Stockholm, Sweden 2014
Conformations of amino acids
characterized by theoretical spectroscopy
Thesis for Philosophy Doctor degree
Department of Theoretical Chemistry and Biology
School of Biotechnology
Royal Institute of Technology
Stockholm, Sweden 2014
⃝c Hongbao Li, 2014
ISBN 978-91-7595-175-1
ISSN 1654-2312
TRITA-BIO Report 2014:11
Printed by Universitetsservice US-AB
Stockholm, Sweden, 2014
献给我的家人
To my family

Abstract
Amino acids are the basic building blocks of proteins. The determination
of their structures plays an important role in correctly describing the functions
of the proteins. This thesis is devoted to theoretical studies on the potential
energy surface of amino acids, in particular the infrared and soft X-ray spectral
fingerprints of their most stable conformers.
The stable structures of amino acids can be explored by different methods.
We have used a full space systematic search strategy to determine the poten-
tial energy surface of deprotonated arginine and revealed several new conformers.
With that, the calculated thermodynamic parameters are finally in good agree-
ment with their experimental counterparts. We have also proposed a molecular
fragment based step-by-step strategy to search for the most stable conformers of
large biomolecules. The high efficiency and good accuracy of this strategy have
been firmly illustrated by the modeling of several polypeptides.
Infrared (IR) spectroscopy has become one of the most applied techniques to
characterizethestructuresofgas-phaseaminoacids. Adirectcomparisonbetween
experimental and calculated infrared spectra provides an efficient way to describe
the conformation exchanges of the amino acids. It is found that the conformers
of an amino acid are not always necessary to reach the thermal equilibrium under
certain experimental conditions. The local minima could be responsible for the
appearance of the measured spectra. This important point has been highlighted
by the calculations of deprotonated tyrosine and cysteine, as well as the arginine.
The near-edge X-ray absorption fine structure (NEXAFS) spectra and X-ray
photoelectron spectra (XPS) have also been simulated for neutral, deprotonated
and protonated arginine. The influences of intra-, and intermolecular hydrogen
bonds on the electronic structure of the arginine have been carefully examined. It
issuggestedthattheXPSiscapableofdistinguishingthecanonicalandzwitterinic
isomers of arginine, and works much better than any other tools available.
Preface
The work presented in this thesis was conducted at the Department of Theoretical
Chemistry and Biology, School of Biotechnology, Royal Institute of Technology,
Stockholm (Sweden) and Hefei National Laboratory for Physical Sciences at the
Microscale, University of Science and Technology of China, Hefei (P. R. China).
List of papers included in the thesis
Paper 1. Local structures and chemical properties of deprotonated arginine,
Hongbao Li, Zijing Lin and Yi Luo.
Chin. J. Chem. Phys. 2012, 25, 681.
Paper 2. A fragment based step-by-step strategy for determining the most
stable conformers of biomolecules,
Hongbao Li, Zijing Lin and Yi Luo,
Chem. Phys. Lett. submitted.
Paper 3. Gas-phase IR spectroscopy of deprotonated amino acids: Global or
Local minima?,
Hongbao Li, Zijing Lin and Yi Luo,
Chem. Phys. Lett. 2014, 598, 86.
Paper 4. The role of dimerization on the structure transformation of arginine
in gas phase,
Hongbao Li, Zijing Lin and Yi Luo.
Chem. Phys. Lett. submitted.
Paper 5. First-principles study on core-level spectroscopy of arginine in gas
and solid phases,
Hongbao Li, Weijie Hua, Zijing Lin and Yi Luo,
J. Phys. Chem. B 2012, 116, 12641.
vii
List of related papers not included in the thesis
Paper 1. Theoretical spectroscopic studies on chemical and electronic struc-
tures of arginylglycine,
Hongbao Li, Zijing Lin and Yi Luo,
In Manuscript.
Paper 2. Extensive conformational searches of 13 representative dipeptides
and an efficient method for dipeptide structure determinations
based on amino acid conformers,
Wenbo Yu, Xuee Xu, Hongbao Li, Rui Pang, Kun Fang and
Zijing Lin,
J. Comput. Chem. 2009, 30, 2105.
Paper 3. X-ray spectroscopy of blocked alanine in water solution from su-
permolecular and supermolecular-continuum solvation models: a
first-principles study,
Weijie Hua, Yuejie Ai, Bin Gao, Hongbao Li, Lina Xu, and Yi
Luo,
Phys. Chem. Chem. Phys. 2012, 14, 9666.
Comments on my contributions to the papers included
• I have taken the major responsibility for calculations and writ-
ing manuscripts of all the papers included in this thesis.
viii
Acknowledgments
I would like to give my acknowledgements to many people who
made this thesis possible.
First, I would like to express my sincere gratitude to my supervi-
sor, Prof. Yi Luo, for giving me the opportunity to study at KTH. I
thank him for his patience, support and encouragement on my work
and daily life. I would like to say this thesis would not be possible
without his help and guidance.
I would like to give my thanks to Prof. Zijing Lin, my supervi-
sor at University of Science and Technology of China (USTC), for
introducing me to this research field and to Prof. Yi Luo.
Many thanks to the head of the Department of Theoretical Chem-
˚
istry and Biology, Prof. Hans Agren, for creating and leading such
a wonderful environment. I have made a lot of friends in this family
and I enjoy the time being here.
I would like to thank Dr. Weijie Hua for helping me with the
X-ray programs and for the helpful discussions on my projects.
I would like to thank Dr. Bin Gao, Dr. Qiang Fu, Dr. Duan
Sai, Dr. Xing Chen, Dr. Yuejie Ai, Dr. Lili Lin and Yongfei Ji for
their help and simulating discussions on my work.
I would like to thank Dr. Ying Fu and Yaoquan Tu for their
suggestions and helps in my study and daily life.
Many thanks to the seniors in our department, Prof. Faris
Gel’mukhanov, Prof. Olav Vahtras, Prof. Boris Minaev, Dr. Zilv-
inas Rinkevicious, Dr. Marten Ahlquist and Dr. Arul Murugan for
their kindness and helps.
ix
Thank our kindly secretaries Ms. Nina Bauer, Ms. Marlene
Johnsson and Ms. Lotta Rosenfeldt for their helps in many occa-
sions.
I want to thank my college Dr. Hui Cao, Dr. Shilv Chen, Dr.
Peng Cui, Dr. Zhihui Chen, Dr. Bogdan Frecus, Dr. Kai Fu, Dr.
Qiu Fang, Dr. Li Gao, Dr. Xiaofei Li, Dr. Xin Li, Dr. Jicai Liu,
Dr. Quan Miao, Dr. Zhijun Ning, Dr. Hao Ren, Dr. Xiangjun
Shang, Dr. Xiuneng Song, Dr. Yuping Sun, Dr. Fuming Ying, Dr.
Liqun Xue, Dr. Chunze Yuan, Dr. Guangping Zhang, Dr. Feng
Zhang, Dr. Qiong Zhang, Dr. Wenhua Zhang, Dr. Ying Zhang,
Dr. Ke Zhao, Xinrui Cao, Xiao Cheng, Zuyong Gong, Wei Hu, Jing
Huang, Ignat Harczuk, Zhengzhong Kang, Guanglin Kuang, Junfeng
Li, Keyan Lian, Li Li, Xin Li, Lijun Liang, Yong Ma, Ce Song, Lu
Sun, Xianqiang Sun, Xu Wang, Yan Wang, Ying Wang and many
other current and former members of the department for their help
and friendship.
Thanks to Dr. Weijie Hua for sharing the Latex template. Spe-
cial thanks to Dr. Sai Duan, Dr. Guangjun Tian, Dr. Guangping
Zhang, Yongfei Ji and Wei Hu for their valuable suggestions to im-
prove the thesis.
I want to acknowledge the financial support (2009-2011) from
the China Scholarship Council (CSC).
Finally, I would like to thank my wife Lingling Ding and my
family for their endless love and support.
Hongbao Li
Spring 2014, Stockholm
Abbreviations
APE adiabatic proton-detachment energies
BE88 Becke exchange functional
BE binding energy
BO Born-Oppenheimer
CAD collisionally activated dissociation
DFT density functional theory
ECH equivalent core-hole approximation
FCH full core-hole approximation
FES free energy surface
ESI electrospray ionization
FAB fast stom bombardment
GGA generalized gradient approximation
HB hydrogen bond
HF Hartree-Fock
HK Hohenberg and Kohn
HWHM half-width at half-maximum
IGLO-III triple-ζ quality individual gauge for localized orbital
IP ionization potential
IR infrared
x