Electronic Transitions of Protonated and Deprotonated Amino Acids in Aqueous Solution in the Region 145-300 nm Studied by Attenuated Total Reflection Far-Ultraviolet Spectroscopy
The Journal of Physical Chemistry A (Impact Factor: 2.69). 03/2013; 117(12). DOI: 10.1021/jp4008416
The electronic transitions of 20 naturally occurring amino acids in aqueous solution were studied with attenuated total reflection far-ultraviolet (ATR-FUV) spectroscopy in the region from 145 to 300 nm. From the measured ATR spectra of sample solutions, the FUV absorption spectra attributed to the amino acids were separated from the intense solvent absorption by using a modified Kramers-Kronig transformation method. The FUV absorption spectra of the amino acids reflect the protonated states of the backbone and side-chain structures. The contributions of the side-chains to the spectra were also examined from the difference spectra subtracting the corresponding Gly spectrum from each spectrum. The observed spectra were compared mostly with the electronic transition studies of the molecular fragments of the amino acids in gas phase. The FUV spectra of the amino acids exhibited the intra- and inter-molecular electronic interactions of the solute-solute as well as the solute-solvent, and those are essential factors to elucidate UV photochemical processes of the amino acids in aqueous solution.
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ABSTRACT: This article presents a time dependent density functional theory (TDDFT) implementation to propagate the Kohn-Sham equations in real time, including the effects of a molecular environment through a Quantum-Mechanics Molecular-Mechanics (QM-MM) hamiltonian. The code delivers an all-electron description employing Gaussian basis functions, and incorporates the Amber force-field in the QM-MM treatment. The most expensive parts of the computation, comprising the commutators between the hamiltonian and the density matrix-required to propagate the electron dynamics-, and the evaluation of the exchange-correlation energy, were migrated to the CUDA platform to run on graphics processing units, which remarkably accelerates the performance of the code. The method was validated by reproducing linear-response TDDFT results for the absorption spectra of several molecular species. Two different schemes were tested to propagate the quantum dynamics: (i) a leap-frog Verlet algorithm, and (ii) the Magnus expansion to first-order. These two approaches were confronted, to find that the Magnus scheme is more efficient by a factor of six in small molecules. Interestingly, the presence of iron was found to seriously limitate the length of the integration time step, due to the high frequencies associated with the core-electrons. This highlights the importance of pseudopotentials to alleviate the cost of the propagation of the inner states when heavy nuclei are present. Finally, the methodology was applied to investigate the shifts induced by the chemical environment on the most intense UV absorption bands of two model systems of general relevance: the formamide molecule in water solution, and the carboxy-heme group in Flavohemoglobin. In both cases, shifts of several nanometers are observed, consistently with the available experimental data.The Journal of Chemical Physics 04/2014; 140(16):164105. DOI:10.1063/1.4871688 · 2.95 Impact Factor
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