Introduction
In this experiment, you will model the effect of hydrogen bonding on the spectra and other physical properties of donors and acceptors. In particular, you will calculate the structure and properties of an amino acid and its zwitterion, alone and in the presence of a single water molecule, using semiempirical (AM1) (1) and density functional theory (DFT) (2) calculations through Gaussian (3).
The role of the solvent in biochemical processes is a subject receiving much attention. Gas phase spectroscopists are attaching water molecules to amino acids and monitoring the change in the spectrum that results from the formation of such a complex. (4) Theoreticians are determining the number of water molecules necessary for a complex to exhibit the behavior observed in solution. (5) Aqueous glycine is almost completely zwitterionic, whereas gas phase glycine is almost exclusively neutral. (6) You will use semiempirical calculations to predict the vibrational frequencies of each, the relative conformational energies, conformational barriers, and will construct possible water-amino acid complexes, determining the above properties for these as well.
You may find this software package to be useful in your other IR and hydrogen bonding reports.
Procedure
The Chemistry Department has Gaussview and Gaussian available on the workstation
in the NMR Laboratory. The laboratory instructor will demonstrate how to build
molecules with this system and then assign each student an amino acid. Build a
structure that closely resembles what you believe to be the optimal structure
for the amino acid. Once the molecule is built, optimize the geometry. The
program will automatically vary the structure of your molecule, determining the
AM1 energy as a function of geometry until an energy minimum is found. Once you
have found an energy minimum, calculate the vibrational spectrum of your
molecule. If the vibrational spectrum yields one or more negative frequencies
(these are actually imaginary
frequencies), you have not found a true minimum. Examine the vibrational modes
in question, alter the molecule accordingly, and repeat the above procedure
until all vibrational frequencies are positive (real). Rebuild the
molecule as a zwitterion (you will need to let the program know that it needs
to “allow ions”), and optimize the structure using the above
procedure.
Once you have modeled the neutral and zwitterionic forms of your amino acid, build a complex between each compound and a single water molecule. It will take some understanding of hydrogen bonding to place the water in a location that may lead to an efficient optimization. Optimize as above. You will also need to calculate the geometry and spectrum of water alone. Repeat the entire procedure using DFT (B3LYP/6-31++g(d,p)).
Calculations
Tabulate the energies and vibrational frequencies of the amino acid, zwiterion, water, and complexes. How does the presence of water influence the energy difference between the neutral and zwitterionic form? Explain shifts in the vibrational spectra between the two molecules. Does complexation influence the spectrum?
References
(1). “AM1: A New General Purpose Quantum Mechanical Molecular Model.” M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, and J. J. P. Stewart, Journal of the American Chemical Society, 1985, 107, 3902-3909; J. J. P. Stewart Journal of Computational Chemistry, 1989, 10, 209-220 .
(2). Becke, A. D. Journal of Chemical Physics, 1993, 98, 5648; Lee, C.; Yang, W.; Parr, R. G. Physical Review B, 1988, 37, 785.
(3). Gaussian 03, Revision C.02,
M. J. Frisch, G.
W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A.
Montgomery, Jr., T. Vreven,
K. N. Kudin, J.
C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M.
Cossi, G. Scalmani, N. Rega,
G. A. Petersson,
H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida,
T. Nakajima, Y. Honda, O. Kitao,
H. Nakai, M.
Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, C. Adamo, J. Jaramillo,
R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J.
W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J.
Dannenberg,
V. G.
Zakrzewski,
J. B. Foresman,
J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov,
G. Liu, A. Liashenko, P. Piskorz,
I. Komaromi, R.
L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M.
Challacombe, P. M. W. Gill,
B. Johnson, W.
Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, Gaussian, Inc.,
(4). “Laser Spectroscopy of Jet-Cooled Biomolecules
and Their Water-Containing Clusters:
(5). “Hydration of Valine-Cation Complexes in the Gas Phase: On the Number of Water Molecules Necessary to Form a Zwitterion.” Rebecca A. Jockusch, Andrew S. Lemoff, and Evan R. Williams, Journal of Physical Chemistry A, 2001, 105, 10929-10942.
(6). “Solvent Effects on Glycine. I. A Supermolecule Modeling of Tautomerization via Intramolecular Proton Transfer” Buelent Balta and Viktorya Aviyente, Journal of Computational Chemistry, 2003, 24, 1789-1802.