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We present simulations on vibrational ladder climbing in carboxy-hemoglobin. Motivated by recent experiments, we study the influence of different realistic pump probe parameters. To allow for a direct comparison with experimental results, transient absorption spectra obtained by a weak probe pulse following the strong, shaped pump pulse are calculated. The influence of the protein fluctuations is taken into account using a recently developed microscopic model. This model consists of a quantum Hamiltonian describing the CO vibration in carboxy-hemoglobin, together with a fluctuating potential, which is obtained by electronic structure calculation based on a large number of protein configurations. Using realistic pulse parameters, vibrational excitations to very high-lying states are possible, in qualitative agreement with experimental observations.

The carboxylate side chains of Asp and Glu have significant coupling with the amide states of the backbone of the Villin headpiece. In two-dimensional spectroscopy, cross peaks are observed between these side chains and the main amide-I band. To model the absorption of the side chains, the electric field variations of vibrational frequencies of a carboxylic acid group (neutral form, CH(3)-COOH) and a carboxylate group (ionized form, CH(3)-COO(-)) are parametrized by means of density functional theory calculations. Simulations indicate that the side chains significantly couple to only one or two amide-I modes out of all of the amino acid residues which makes them useful as spectroscopic markers, providing information about the local structural behavior of the protein. Both experiment and simulations show that the cross peaks between the carboxylate and the amide-I bands are significantly diminished above the melting temperature.

In this paper, we present a theoretical approach to construct a fluctuating quantum model of the CO vibration in heme-CO proteins and its interaction with external laser fields. The methodology consists of mixed quantum-classical calculations for a restricted number of snapshots, which are then used to construct a parametrized quantum model. As an example, we calculate the infrared absorption spectrum of carboxy-hemoglobin, based on a simplified protein model, and found the absorption linewidth in good agreement with the experimental results. [ABSTRACT FROM AUTHOR]