Single molecule spectroscopy simulation

The information about the existence of the multiple intermediate conformational states involving the enzymatic active complex formation and a detailed characterization of the energy landscape (Fig. 24.7) of the complex formation process cannot be obtained either by only an ensemble-averaged experiment, only a single-molecule experiment, or a solely computational approach. The combined approach demonstrated here is essential to achieve the potential of both single-molecule spectroscopy and MD simulations for studies of slow enzymatic reactions and protein conformational change dynamics. 

In this chapter, we review important concepts regarding vibrational spectroscopy with the STM. First, the basis of the technique will be introduced, together with some of the most relevant results produced up to date. It will be followed by a short description of experimental issues. The third section introduces theoretical approaches employed to simulate the vibrational excitation and detection processes. The theory provides a molecular-scale view of excitation processes, and can foresee the role of various parameters such as molecular symmetry, adsorption properties, or electronic structure of the adsorbate. Finally, we will describe current approaches to understand quenching dynamics via internal molecular pathways, leading to several kinds of molecular evolution. This has been named single-molecule chemistry. 

Fig. 2.3. (A) Illustration of the crystal structure of p-terphenyl, with a single substitutional impurity of pentacene. (B) Single molecules of pentacene in p-terphenyl detected by FM-Stark optical absorption spectroscopy, (a-c) Simulated traces for absorption, FM and FM-Stark, respectively. The W -shaped structure in the center of trace (d) is the absorption from a single pentacene molecule, acquired multiple times to show repeatability, (e) Average of traces in (d) with expected hneshape. Trace (f) is the signal from a region of the spectrum with no molecules, while trace (g) is a region with many molecules showing SFS. For details, see [3,26]...

At about the same time as this work was published, Znamenskiy and Kobrak simulated the absorption spectrum of betaine-30, a commonly used solvatochromic probe molecule, in [C4inim][PF6]. They investigated the interactions responsible for the solvatochromic shift. Because this shift is used experimentally to assess solvent polarity, the calculations can thus provide a direct window into the nature of polarity in ionic Hquid systems. To conduct the study, a single molecule of betaine-30 was immersed in a Hquid containing 200 ion pairs. Twelve independent 1-ns runs were then carried out, and from that the absorption spectrum was computed. They observe two distinct time scales one on subpicosecond time scales and one that is on the order of 100 ps. This result is consistent with previous simulation studies as well as time-resolved fluorescence spectroscopy experiments. Although the actual absorption spectra computed do not agree quantitatively with experimental results, the qualitative features do. 

Solvation of DNA bases/base pairs is of fundamental importance to biological processes as they take place in aqueous media. The effect of hydration on neutral bases or base pairs has been addressed using quantum chemical methods [106-112] as well as molecular dynamics (MD) simulations [113, 114], It is known that unlike the gas phase, dipole bound anions do not exist in condensed environments because such diffuse states are destabilized in the aqueous phase [115]. The drastic change in the nature of excess electron binding in the presence of water molecules with uracil has been observed experimentally by Bowen and co-workers [95b] using negative electron photoelectron spectroscopy (PES). They observed that even with a single water molecule the dipole bound state of uracil anion in gas phase... 

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