elucidating the effects of amide side chain interactions in flexible biomolecules v. alvin shubert,...
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Elucidating the effects of amide side chain interactions in flexible biomolecules
V. Alvin Shubert, Esteban E. Baquero, Jasper R. Clarkson, Timothy S. ZwierDepartment of Chemistry, Purdue University
West Lafayette, IN 47907
M. J. TubergenDepartment of Chemistry, Kent State University
IntroductionPrevious studies on the single conformation IR and UV spectroscopy and dynamics of conformational isomerization.
Tryptamine Melatonin N-acetyl tryptophan methyl
amide NATMAAbove studies have led us to custom build molecules with different types of flexibility built in.
p-methoxyphenethylacetamide 2-phenoxyethylacetamide O-(acetamidoethyl)-N-acetyltyramine
MPEAmide POEA OANAT
O N
O
N
O
O N
O
ON
O
RI03
59th MSS, WG02
Introduction
Doubly substituted molecules
• Two branches to potential energy surface (PES)– Can branches be decoupled?
– What types of chains allow for interchain interactions (e.g. H-bonding)?
– What types of chains hinder interchain interactions?
• Dynamics studies– Breaking H-bonds
– Put energy into one chain, observe effects on other chain
N-(2-phenylethyl)-acetamide
N,N’-(1,4-phenylenedi-2,1-ethanediyl)bis acetamide
1,4-phenylenebis(oxy)bis-N-methylpropanamide-
2,2’-[1,4-phenylenebis(oxy)]bis-ethanamide
3,3’-(1,4-phenylenedi)bis-(N-methylpropanamide)
O-(acetamidoethyl)-N-acetyltyramine
1,4 (N-methylpropanamide-N’-ethylacetamide)benzene
N-methyl-benzenepropanamide
3-phenoxy-N-methylpropanamide
2-phenoxyethylacetamide
NH
O
R
NH
R
O
NH
OR
O
NH
O
OR
Molecules under study
What types of low energy conformations will be formed for double chain molecules?
• How does the presence of the second chain affect the conformational preferences of the first chain and vice versa?
• Given n low energy structures for one chain and m for the other, might expect nXm conformations.
• However, this assumes two things:– Chains do not asymmetrize the benzene ring– Chains are non interacting
• Since chains do asymmetrize the benzene ring,# of conformations expected = nXmX # of spectroscopically distinct orientations
• If chains do interact, this may lead to structures containing individual chain conformations that were high energy in single chain molecules.
The number of possible conformations gets very large very fast.
Disconnectivity Diagrams
-44.0
-40.0
-36.0
-32.0
-28.0
-24.0
-20.0
-16.0
Energy (kcal/mol)
ON
OO N
O
O N
O
N
O
POEA
OANAT
MPEAmide
-415.0
-410.0
-405.0
-400.0
-395.0
-390.0
-385.0
-380.0
-375.0
-370.0
-365.0
-360.0
-355.0
-350.0
-89.0
-85.0
-81.0
-77.0
-73.0
-69.0
-65.0
-61.0
OPTIM.2.3 and Disconnect, David J. Wales, Cambridge University
Experimental methodsResonant 2 photon ionization (R2PI): Records spectra in mass selective fashion
Biomolecule* (S1)
Biomolecule (S0)
Biomolecule+ + e-
Hol
e-bu
rn
Pro
be
Conformer A Conformer B
Hol
e-bu
rn
Pro
be
UV Source fixed: Provides selectivity IR Source tuned
R2PI: Electronic SpectrumResonant ion dip infrared spec-troscopy (RIDIRS): Conforma-
tion specific IR spectrum
UV-UV Hole-burning: Conformation specific electronic spectrum
Computational methodsSearch for lowest energy structures
1. Draw molecule in MacroModel, use conformation search.
2. Sift through structures found by MacroModel (Typically > 500).
3. Use unique structures as starting structures for optimizations using Gaussian03. Optimize at B3LYP/6-311+G* level of theory.
4. Using Gaussian03 and optimized structures, calculate infrared frequencies and intensities.
800
600
400
200
0
Infr
are
d Inte
nsi
ty (
KM
/mole
)
3500300025002000150010005000Frequency (cm
-1)
R2PI and UV-UV hole-burning spectra of OANAT
• Six conformations resolved to date.
• Four conformations (C,D,E,F) have origins within 85 cm-1 of 35,630 cm-1.
• Two conformations (A,B) are red shifted by more than 1000 cm-
1 from the other four.
3.5
3.0
2.5
2.0
1.5
1.0
0.5
0.0
Ion
inte
nsity
36400362003600035800356003540035200350003480034600photon energy (cm
-1)
HB at 34,536.4 cm-1
(also origin)
HB at 34,539.3 cm-1
(also origin)
HB at 35,549.2 cm-1
(also origin)
HB at 35,607.5 cm-1
(also origin)
HB at 35,631.6 cm-1
(origin at 35,622.05 cm-1
)
HB at 35,711.1 cm-1
(also origin)
R2PI of OANAT
A
BC
D
E
F
RIDIR spectra in amide NH stretch region
• RIDIR spectra indicate three classes of conformations for OANAT.
• Two stretches seen, one from each chainIo
n in
tens
ity (
arbi
trar
y un
its)
352035003480346034403420340033803360
photon energy (cm-1
)
A
B
C
D
C
B
A
A
B
CD
E
F
OANATPOEAMPEAmide
MPEAmide
POEA
ON
O
O N
O
O N
O
N
O
OANAT
Summary of Experimental Results
• 2 major conformations for alkyl chain
• 1 major conformation for alkoxy chain
• Expected 8 conformations in OANAT, only found 6
• Two classes of conformations:– H-bonding between chains
– Independent chains• Only 3 independent chain conformations found, not 8 as expected
Interacting chains Independent chains
Computational resultsSingle chain molecules
NPEA, NMBPA, PNMP, and POEA• Generally, find few low energy structures (< 0.2 kcal/mol, relative)
(3, 2, 1, and 1, respectively)• Most significant differences seen in vibrational frequencies are those associated with the ether
linkages of PNMP and POEA
MPEAmide, NPEBA, NMPNEA, PBNMP, PBOBEA, and OANAT• Generally, find many low energy structures (6-10)• Many have non-interacting chains and can be additively constructed from conformations found for single chain
molecules• Little shift seen in vibrational frequencies compared to single chain molecules when chains are non-interacting• If chains interact (i.e. form an interchain H-bond), shifts are seen in frequencies, especially for NH and CO stretches
Double chain molecules
OCH3
Combining single chains onto one molecule: Structures
NPEA
0.000 kcal/mol
0.172 kcal/mol
NMBPA
0.000 kcal/mol
+
NMPNEA
0.283 kcal/mol
0.329 kcal/mol
0.240 kcal/mol
0.414 kcal/mol
NH
O
NH
O
NH
NH O
O
Computational resultsCombining single chains onto one molecule: Vibrational frequencies
2000
1500
1000
500
0
Infr
are
d I
nte
nsi
ty (
KM
/mo
le)
3600320028002400200016001200
Frequency (cm-1
)
NPEA (0.000 kcal/mol) + NMBPA (0.000 kcal/mol)
NPEA (0.172 kcal/mol) + NMBPA (0.000 kcal/mol)
NMPNEA (0.283kcal/mol)
NMPNEA (0.240 kcal/mol)
NMPNEA (0.329 kcal/mol)
NMPNEA (0.414 kcal/mol)NH
O
NPEA
NH
O
NMBPA
NH
NH O
O
NMPNEA
-6
-4
-2
0
2
4
6
35003480346034403420340033803360
-1.0
-0.5
0.0
0.5
ion
inte
nsi
ty (
arb
itra
ry u
nits
)
35203510350034903480
photon energy (cm-1
)
What if chains do interact? Example, OANAT
Interacting chains
Independent chains
A
B
C
D
E
F
B3LYP/6-31+G*, 6-311+G*Gaussian98 and Gaussian03
Alkyl NH · · · Alkoxy CO Alkyl CO · · · Alkoxy NH
Alkyl NH · · · Alkoxy CO
Alkyl CO · · · Alkoxy NH
NPEBA: H-bond conformation at 0.006 kcal/mol, 3 more with H-bonds at < 0.75 kcal/mol
PBNMP: Weak H-bonding in 2 conformations > 1.4 kcal/mol
PBOBEA: No conformations with H-bonds found
NMPNEA: Lowest energy conformation contains H-bond between NH of CONH and CO of NHCO
Discussion
• What types of chains lead to interactions?– NHCO ordering leads to more interaction than CONH– Alkyl chains allow interaction between chains– O connecting chain to ring hinder interaction between chains– Different orderings of amide groups on opposite chains allows for more interaction
• How does interaction effect number of conformations?– Interchain interaction tends to increase number of low energy conformations
• Best design for a molecule with two decoupled branches to PES is to use CONH ordering for amide group and use O to connect chain to ring
NH
NH
O O
NH
NH
OO
NH
NH
O
O
O NH
ONH
O O
Summary
• Six conformers of OANAT have been resolved to date• Doubly substituted molecules are more than sum of their parts – simply building
structures based on low energy conformations of single arm molecules is not adequate. Interactions between chains act to lower the energy of some chain configurations.
• Calculations are only a rough guide at our level of theory.
Future Work
• Spectra in the 1000-2000 cm-1 region• SEP and SEP hole-filling• IR hole-filling: Selective excitation of amide in each chain• Complete search for low energy conformations, disconnectivity diagrams• Build different types of chains (i.e. vary number of carbons between amide group and
chromophore, use different chromophores, and/or substitute into different positions, ortho or meta)
AcknowledgementsPeople
Prof. Timothy S. Zwier
The Zwier Group
Jasper R. Clarkson
Esteban Baquero
Tracy LeGreve
Bill James
Jaime Stearns
Talitha Selby
Josh Newby
Prof. Michael J. Tubergen
Prof. David Wales
Dr. Dave Evans
Prof. Mark Lipton
Kevin Worrel
Funding
National Science Foundation