Investigation of temperature dependence of vibrational modes in a heme protein model compound using a self -consistent harmonic approximation
Abstract
Biologically significant heme protein model compounds are studied via normal mode analysis using both a conventional harmonic approach and a self consistent harmonic approximation (SCHA) approach in order to model anharmonicities. The SCHA calculation allows us to investigate and predict the temperature dependence of vibrational modes and bond amplitudes---something that no other theoretical method can accomplish without either prohibitive computational cost or unreasonable and non-physical results such as premature bond dissociation or conformational change. Considering temperature dependence of dynamics is important as most biological compounds perform their functions at temperatures (room temperature) much greater than those used during experimental spectroscopic measurements (usually liquid nitrogen or liquid helium temperatures). Our findings indicate that an increase in temperature will selectively amplify certain bond amplitudes in a, complex fashion that is not possible to predict from geometry, bond strengths or standard normal mode frequencies and amplitudes. In the end, intuition is in some sense verified by finding that the most amplified motions tend to be rotational motions of groups which are weakly bound and weakly coupled to the rest of the molecule---such as phenyl groups at the heme periphery. From both standard normal mode and SCHA calculations, density of states is obtained and compared with experimental density of states arising from a novel experimental technique called nuclear resonance vibrational spectroscopy (NRVS). Standard harmonic parameters are calculated and refined to match experimental data in Fe(OEP)Cl and Fe(TPP)NO(1-MeIm). Fe(TPP)NO(1-MeIm) is further modeled by use of a set of anharmonic interatomic potentials. Use of these potentials in a SCHA calculation allows prediction of the temperature dependence of the vibrational spectrum which compares favorably with experimental data.
Degree
Ph.D.
Advisors
Prohofsky, Purdue University.
Subject Area
Molecular physics|Condensed matter physics
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