SCN as a local probe of protein structural dynamics DOI
Sena Aydin, Seyedeh Maryam Salehi, Kai Töpfer

et al.

The Journal of Chemical Physics, Journal Year: 2024, Volume and Issue: 161(5)

Published: Aug. 2, 2024

The dynamics of lysozyme is probed by attaching -SCN to all alanine residues. one-dimensional infrared spectra exhibit frequency shifts in the position maximum absorption 4 cm-1, which consistent with experiments different solvents and indicates moderately strong interactions vibrational probe its environment. Isotopic substitution 12C → 13C leads a redshift -47 agrees quantitatively for CN-substituted copper complexes solution. low-frequency, far-infrared part protein contains label-specific information difference when compared wild type protein. Depending on labels, local structural changes are observed. For example, introducing label at Ala129 breaking α-helical structure concomitant change spectrum. Finally, hydration SCN-labeled residues as function time can be related reorientation label. It concluded that potentially useful probing dynamics, both high-frequency (CN-stretch)

Language: Английский

Theory of frequency fluctuation of intramolecular vibration in solution phase: Application to C–N stretching mode of organic compounds DOI
Naoki Negishi, Daisuke Yokogawa

The Journal of Chemical Physics, Journal Year: 2025, Volume and Issue: 162(10)

Published: March 10, 2025

We formulate frequency fluctuations of intramolecular vibrations a solute by exploring the fluctuation electrostatic potential solvents. present numerical methodology for estimating fluctuations; is based on reference interaction site model self-consistent field with constrained spatial electron density distribution, theoretical solvation fields classical statistic mechanics. By applying theory to C–N stretching several nitrile compounds, our estimated scale and bandwidth shift changing solvent kinds reproduced experimental data. Furthermore, we regard standard deviation as multiple random variables analyzing fluctuations. Our results reveal that dominant almost parallel vibrational axis. In addition, become spatially nonuniform solvents form stronger hydrogen bonds solute. The development confirms nonuniformity crucial

Language: Английский

Citations

1
Evaluating aliphatic CF, CF2, and CF3 groups as vibrational Stark effect reporters DOI
Rubén Cruz, Kenichi Ataka, Joachim Heberle

et al.

The Journal of Chemical Physics, Journal Year: 2024, Volume and Issue: 160(20)

Published: May 28, 2024

Given the extensive use of fluorination in molecular design, it is imperative to understand solvation properties fluorinated compounds and impact C-F bond on electrostatic interactions. Vibrational spectroscopy can provide direct insights into these interactions by using stretching [v(C-F)] as an electric field probe through vibrational Stark effect (VSE). In this work, we explore VSE three basic patterns aliphatic fluorination, i.e., mono-, di-, trifluorination CF, CF2, CF3 groups, respectively, compare their response well-studied aromatic v(C-F). Magnitudes (i.e., tuning rates) orientations difference dipole vectors v(C-F)-containing normal modes were determined density functional theory a dynamics (MD)-assisted solvatochromic analysis model solvents varying polarity. We obtain rates 0.2-0.8 cm-1/(MV/cm), with smallest largest sensitivities for CFaliphatic CF3,aliphatic, respectively. While average fields oriented along main symmetry axis CFn, thus its static dipole, rate tilted up 87° potentially enabling map electrostatics multiple dimensions. discuss influence conformational heterogeneity spectral shifts point out importance multipolar and/or polarizable MD force describe molecules. The implications work are relevance studies molecules found pharmaceuticals, peptides, proteins.

Language: Английский

Citations

5
Interplay between static and dynamic disorder: Contrasting effects on dark state population inside a cavity DOI
Robert F. Catuto, Hsing-Ta Chen

The Journal of Chemical Physics, Journal Year: 2025, Volume and Issue: 162(20)

Published: May 22, 2025

Strong light–matter interactions between molecules and quantized electromagnetic fields inside an optical cavity open up novel possibilities, although inevitably influenced by disorder, inherent attribute of realistic molecular systems. Here, we explore the steady-state response emitters within a lossy cavity, with focus on combined effects static dynamic disorders, as frequently observed in solution-phase experiments. By analyzing transmission spectra, energy change, dark state population, uncover contrasting disorders population its interplay polariton states. We find that Rabi splitting exhibits inversion increasing disorder strength, where maximum is determined disorders. Furthermore, identify state-induced linewidth narrowing, revealing mechanism distinct from motional narrowing induced frequency fluctuations. These mechanistic insights highlight critical role states, establishing foundation for future developments chemistry strong coupling spectroscopy.

Language: Английский

Citations

0
Hydrogen Bond Blueshifts in Nitrile Vibrational Spectra Are Dictated by Hydrogen Bond Geometry and Dynamics DOI Creative Commons
Jacob M. Kirsh, Jacek Kozuch

JACS Au, Journal Year: 2024, Volume and Issue: 4(12), P. 4844 - 4855

Published: Dec. 5, 2024

Vibrational Stark effect (VSE) spectroscopy has become one of the most important experimental approaches to determine strength noncovalent, electrostatic interactions in chemistry and biology quantify their influence on structure reactivity. Nitriles (C≡N) have been widely used as VSE probes, but application complicated by an anomalous hydrogen bond (HB) blueshift which is not encompassed within framework. We present empirical model describing HB terms H-bonding geometry, i.e., a function distance angle with respect C≡N group. This obtained comparing vibrational observables from density functional theory electrostatics polarizable AMOEBA force field, it provides physical explanation for underlying multipolar Pauli repulsion contributions. Additionally, we compare predicted blueshifts results find our useful, direct framework analyze geometry rigid HBs, such proteins or chemical frameworks. In contrast, nitriles highly dynamic environments like protic solvents are no longer solely geometry; this consequence motional narrowing, demonstrate simulating IR spectra. Overall, when dynamics accounted for, excellent correlation found between observed blueshifts. includes different types donors, suggesting that general can aid understanding wherever be implemented.

Language: Английский

Citations

2
SCN as a local probe of protein structural dynamics DOI
Sena Aydin, Seyedeh Maryam Salehi, Kai Töpfer

et al.

The Journal of Chemical Physics, Journal Year: 2024, Volume and Issue: 161(5)

Published: Aug. 2, 2024

The dynamics of lysozyme is probed by attaching -SCN to all alanine residues. one-dimensional infrared spectra exhibit frequency shifts in the position maximum absorption 4 cm-1, which consistent with experiments different solvents and indicates moderately strong interactions vibrational probe its environment. Isotopic substitution 12C → 13C leads a redshift -47 agrees quantitatively for CN-substituted copper complexes solution. low-frequency, far-infrared part protein contains label-specific information difference when compared wild type protein. Depending on labels, local structural changes are observed. For example, introducing label at Ala129 breaking α-helical structure concomitant change spectrum. Finally, hydration SCN-labeled residues as function time can be related reorientation label. It concluded that potentially useful probing dynamics, both high-frequency (CN-stretch)

Language: Английский

Citations

1