Far-infrared conformer-specific signatures of small aromatic molecules of biological importance

67 Pages·2016·5.83 MB·English

by  Vasyl Yatsyna

UNIVERSITY OF GOTHENBURG
LICENTIATE THESIS
Far-infrared conformer-specific
signatures of small aromatic
molecules of biological
importance
Author:
Vasyl YATSYNA
Supervisor: Examiner:
Doc. Vitali Prof. Dag
ZHAUNERCHYK HANSTORP
Athesissubmittedinfulfillmentoftherequirements
fortheLicentiatedegree
atthe
DepartmentofPhysics
UniversityofGothenburg
31stAugust,2016

iii
Abstract
Far-infraredconformer-specificsignaturesofsmallaromatic
moleculesofbiologicalimportance
byVasyl YATSYNA
Ourunderstandingofmanybiologicalprocessesrequiresknowl-
edge about biomolecular structure and weak intra- and inter-
molecular interactions (e.g. hydrogen bonding). Both molecu-
lar structure and weak interactions can be directly studied by
far-infrared(orTHz)spectroscopy,whichprobeslow-frequency
molecularvibrations. InthisthesisIpresenttheresultsofexperi-
mentalandtheoreticalinvestigationsoffar-infraredvibrations
insmallaromaticmoleculesofbiologicalrelevance. Toenablea
directcomparisonwiththeory,far-infraredspectroscopywasper-
formedinthegasphasewithaconformer-selectiveIR-UVion-dip
technique. Thefar-infraredspectraofmoleculescontainingapep-
tide(-CO-NH-)linkrevealedthatthelow-frequencyAmideIV-VI
vibrationsarehighlysensitivetothestructureofthepeptidemoi-
ety,themolecularbackbone,andtheneighboringintra-andinter-
molecularhydrogenbonds. Thestudyoffar-infraredspectraof
phenolderivativesidentifiedvibrationsthatallowdirectprob-
ing of strength of hydrogen-bonding interaction, and a size of
aringclosedbythehydrogenbond. Furthermore,benchmark-
ingtheoryagainsttheexperimentaldataidentifiedadvantages
and disadvantages of conventional frequency calculations for
thefar-infraredregionperformedwithabinitioanddensityfunc-
tionaltheory. Forexample,theconventionalapproacheswerenot
abletoreproducestronglyanharmonicvibrationssuchasamino-
inversioninaminophenol. Instead,adouble-minimumpotential
model was used for this vibration, and successfully described
theexperimentalspectraofaminophenol. Theresultspresented
inthisthesiscanassisttheinterpretationoffar-infraredspectra
ofmorecomplexbiomolecules,pushingforwardlow-frequency
vibrationalspectroscopyforefficientstructuralanalysisandthe
studiesofweakinteractions.
Keywords: low-frequencyvibrations,far-IRspectroscopy,hy-
drogen bonding, anharmonic vibrations, second-order vibra-
tionalperturbationtheory

v
List of Papers
Thisthesisisbasedonthefollowingpapers,whicharereferred
tointhetextbytheirRomannumerals.
I Aminophenolisomersunraveledbyconformer-specific
far-IRactionspectroscopy
VasylYatsyna, DaniëlJ.Bakker,RaimundFeifel,AnoukM.
Rijs,andVitaliZhaunerchyk
Phys. Chem. Chem. Phys.,2016,18,6275-6283
II Far-infrared Amide IV-VI spectroscopy of isolated 2-
and4-MethylAcetanilide
VasylYatsyna,DaniëlJ.Bakker,RaimundFeifel,AnoukM.
Rijs,andVitaliZhaunerchyk
J.Chem. Phys.,acceptedforpublication(August26,2016)
III Far-Infrared Signatures of Hydrogen Bonding in Phe-
nolDerivatives
DaniëlJ.Bakker,AtzePeters,VasylYatsyna, VitaliZhauner-
chyk,andAnoukM.Rijs
J.Phys. Chem. Lett.,2016,7(7),pp. 1238–1243
All the papers included in the thesis are the result of team
workandinternationalcollaboration. Mypositionintheauthor
listsreflectstheamountofworkontherespectivepapers. Inthe
caseswhenIaminthefirstpositionoftheauthorlist,Ihadthe
mainresponsibilitiesforthepaper,includingexperimentaldata
analysis,quantumchemicalcalculationsandmanuscriptprepara-
tion. MycontributionforthepaperIIIincludedexperimentaland
theoreticalstudiesperformedforethylvanillinconformers,dis-
cussionofthemethodsandresults,andtakingpartinmanuscript
preparation.
vi
Also,duringmyPhDIhaveauthoredthefollowingpapers,
buttheyarenotincludedinthisthesis,beingoutofscopeofthe
currenttopic:
1 Infraredactionspectroscopyoflow-temperatureneutral
gas-phasemoleculesofarbitrarystructure
VasylYatsyna, Daniël J. Bakker, Raimund Feifel, Anouk M.
Rijs,andVitaliZhaunerchyk
Phys. Rev. Lett,acceptedforpublication(August10,2016)
2 NEXAFSandXPSstudiesofnitrosylchloride
LucaSchio,CuiLi,SusannaMonti,PeterSalén,VasylYatsyna,
RaimundFeifel, MicheleAlagia, RobertRichter, StefanoFal-
cinelli, Stefano Stranges, Vitali Zhaunerchyk and Vincenzo
Carravetta
Phys. Chem. Chem. Phys.,2015,17,9040-9048
3 CompletedissociationbranchingfractionsandCoulomb
explosion dynamics of SO induced by excitation of O 1s
2
pre-edgeresonances
PeterSalén,VasylYatsyna,LucaSchio,RaimundFeifel,Mag-
nusafUgglas,RobertRichter,MicheleAlagia,StefanoStranges,
andVitaliZhaunerchyk
J.Chem. Phys.,2015,143,134302
4 Experimental and theoretical XPS and NEXAFS studies
ofN-methylacetamideandN-methyltrifluoroacetamide
CuiLi,PeterSalén,VasylYatsyna,LucaSchio,RaimundFeifel,
RichardSquibb,MagdalenaKamin´ska,MatsLarsson,Robert
Richter,MicheleAlagia,StefanoStranges,SusannaMonti,Vin-
cenzoCarravettaandVitaliZhaunerchyk
Phys. Chem. Chem. Phys.,2016,18,2210-2218
5 NEXAFSspectroscopyandsite-specificfragmentationof
N-methylformamide,N,N-dimethylformamide,andN,N-di-
methylacetamide
PeterSalén,VasylYatsyna,LucaSchio,RaimundFeifel,Robert
Richter,MicheleAlagia,StefanoStrangesandVitaliZhauner-
chyk
J.Chem. Phys.,2016,144,244310
vii
Contents
Abstract iii
ListofPapers v
1 Introduction 1
1.1 Far-infraredmolecularvibrationsandtheirimpor-
tance . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 MolecularstructuralanalysisbasedonIRspectra
andquantum-chemicalcalculations . . . . . . . . 2
1.3 Computationalspectroscopy: treatmentofanhar-
monicvibrations . . . . . . . . . . . . . . . . . . . 5
1.3.1 Quantumchemicalcomputationsingeneral 5
1.3.2 Treatmentofvibrationalanharmonicity . . 6
1.4 Molecularsystemsinvestigated . . . . . . . . . . . 7
1.4.1 Aminophenolisomers . . . . . . . . . . . . 7
1.4.2 MethylAcetanilidemoleculeasapeptide
model . . . . . . . . . . . . . . . . . . . . . 8
1.4.3 Phenol derivatives with intra-molecular
hydrogenbonding . . . . . . . . . . . . . . 9
2 Methods 11
2.1 Experimentalsetup . . . . . . . . . . . . . . . . . . 11
2.2 Supersonic-jetcooling . . . . . . . . . . . . . . . . 14
2.3 REMPIspectroscopy . . . . . . . . . . . . . . . . . 17
2.4 IR-UVion-dipspectroscopy . . . . . . . . . . . . . 20
2.5 Freeelectronlaserasatoolforinfrared
actionspectroscopy . . . . . . . . . . . . . . . . . . 21
2.6 Computational: frequencycalculationsand
VPT2approach . . . . . . . . . . . . . . . . . . . . 23
2.6.1 Doubleharmonicapproximation . . . . . . 23
2.6.2 Second-ordervibrationalperturbationthe-
ory(VPT2) . . . . . . . . . . . . . . . . . . . 24
viii
3 ResultsandDiscussions 25
3.1 Far-infraredstudiesofaminophenol
isomers . . . . . . . . . . . . . . . . . . . . . . . . . 25
3.2 AmideIV-VIspectroscopyforpeptidestructural
analysis: thecaseofMethylAcetanilides . . . . . . 30
3.3 Directprobingofhydrogenbondsbyfar-infrared
spectroscopy . . . . . . . . . . . . . . . . . . . . . . 33
4 ConclusionsandOutlook 37
4.1 General . . . . . . . . . . . . . . . . . . . . . . . . . 37
4.2 Conformer-andisomer-selectivityoffar-infrared
vibrations. . . . . . . . . . . . . . . . . . . . . . . . 38
4.3 PerformanceofVPT2foranharmonictreatmentof
far-infraredvibrations . . . . . . . . . . . . . . . . 38
4.4 Outlookandfutureperspectives . . . . . . . . . . 39
Sammanfattning 42
Acknowledgements 43
Bibliography 45
ix
List of Abbreviations
IR InfraRed
FIR Far-InfraRed
UV UltraViolet
TOF Time-Of-Flight
He Helium
Ar Argon
Xe Xenon
FEL FreeElectronLaser
FELIX FreeElectronLaserforInfraredeXperiments
HF Hartree-Fock
MD MolecularDynamics
DFT DensityFunctionalTheory
REMPI ResonanceEnhancedMulti-PhotonIonization
VPT2 Second-orderVibrationalPerturbationTheory