Vibrational Spectroscopy of N₃^– in the Gas and Condensed Phase

Abstract

Azido-derivatized amino acids are potentially useful, positionally resolved spectroscopic probes for studying the structural dynamics of proteins and macromolecules in solution. To this end a computational model for the vibrational modes of N − 3 based on accurate electronic structure calculations and a reproducing kernel Hilbert space representation of the potential energy surface for the internal degrees of freedom is developed. Fully dimensional quantum bound state calculations find the antisymmetric stretch vibration at 1974 cm −1 compared with 1986 cm −1 from experiment. This mode shifts by 64 cm −1 (from the frequency distribution) and 74 cm −1 (from the IRlineshape) to the blue, respectively, compared with 61 cm −1 from experiment for N − 3 in water. The decay time of the frequency fluctuation correlation function is 1.1 ps, in good agreement with experiment (1.2 to 1.3 ps) and the full width at half maximum of the asymmetric stretch in solution is 18.5 cm −1 compared with 25.2 cm −1 from experiment. A computationally more efficient analysis based on instantaneous normal modes is shown to provide comparable, albeit somewhat less quantitative results compared to solving the 3-dimensional Schrödinger equation for the fundamental vibrations.

Cross-Correlated Motions in Azidolysozyme

“…Molecular dynamics (MD) simulations of WT and all AlaN 3 -labelled proteins were conducted using the CHARMM [19] force field. For the simulations with the multi-dimensional RKHS PES for the spectroscopic probe, a suitably interfaced with the CHARMM program [20] was employed [17]. MD simulations were performed with the TIP3P water [21] model in a cubic box of size (62.1) 3 Å 3 .…”

“…Except for the region around residue Glu35, the fluctuations for the three systems are comparable. Moreover, for some residues (9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22) for Ala92 and (45-47) for Ala47 the fluctuation is higher compared to WT, whereas for residues (30)(31)(32)(33)(34)(35)(36) and (40-43) the fluctuations reduce after attaching the label. Figure S13 bottom panel shows the corresponding RMSDs, which are ∼1.5 Å and suggest stable systems on this time scale.…”

“…Based on recent studies [16] the vibrational dynamics of N − 3 in the gas phase and in solution can be captured quantitatively [17]. Moreover, azidoalanine (AlaN 3 ) is one of the ideal labels that has been shown to be positionally sensitive to probe for local dynamics [16].…”

Tautomeric Effect of Histidine on β-Sheet Formation of Amyloid Beta 1–40: 2D-IR Simulations

“…During the numerical integration, the direct relationship between the signal and FFCF is lost (56). For example, the first term of the correlation function is an attempt to catch the shorter time dynamics related to hydrogen bonded species, such as solvent fluctuations (57,58). The remaining two terms also provide a slower dynamic property of the system.…”

Probing the Differential Dynamics of the Monomeric and Dimeric Insulin from Amide-I IR Spectroscopy

“…On each snapshot the local frequency is determined from either an instantaneous normal mode calculation or from solving the 1d or 3d nuclear Schrödinger equation. 34,36 For the latter approach, the PES is scanned along all relevant degrees of freedom, similar to the map approach. However, when solving the Schrödinger equation, choosing the reduced mass is not obvious, in particular for covalently bound probes.…”