Vibrational spectroscopic map, vibrational spectroscopy, and intermolecular interaction

CR Baiz, B Błasiak, J Bredenbeck, M Cho… - Chemical …, 2020 - ACS Publications
Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and
studies of functional materials. Over the past decade, various coherent nonlinear vibrational …

Water dynamics in the hydration shells of biomolecules

D Laage, T Elsaesser, JT Hynes - Chemical Reviews, 2017 - ACS Publications
The structure and function of biomolecules are strongly influenced by their hydration shells.
Structural fluctuations and molecular excitations of hydrating water molecules cover a broad …

Watching proteins wiggle: mapping structures with two-dimensional infrared spectroscopy

A Ghosh, JS Ostrander, MT Zanni - Chemical reviews, 2017 - ACS Publications
Proteins exhibit structural fluctuations over decades of time scales. From the picosecond
side chain motions to aggregates that form over the course of minutes, characterizing protein …

Phosphonomethyl oligonucleotides as backbone-modified artificial genetic polymers

C Liu, C Cozens, F Jaziri, J Rozenski… - Journal of the …, 2018 - ACS Publications
Although several synthetic or xenobiotic nucleic acids (XNAs) have been shown to be viable
genetic materials in vitro, major hurdles remain for their in vivo applications, particularly …

Magnesium contact ions stabilize the tertiary structure of transfer RNA: electrostatics mapped by two-dimensional infrared spectra and theoretical simulations

J Schauss, A Kundu, BP Fingerhut… - The Journal of Physical …, 2020 - ACS Publications
Ions interacting with hydrated RNA play a central role in defining its secondary and tertiary
structure. While spatial arrangements of ions, water molecules, and phosphate groups have …

Probing the hydrogen-bonding environment of individual bases in DNA duplexes with isotope-edited infrared spectroscopy

RJ Fick, AY Liu, F Nussbaumer, C Kreutz… - The Journal of …, 2021 - ACS Publications
Measuring the strength of the hydrogen bonds between DNA base pairs is of vital
importance for understanding how our genetic code is physically accessed and recognized …

[HTML][HTML] Perspective: Structure and ultrafast dynamics of biomolecular hydration shells

D Laage, T Elsaesser, JT Hynes - Structural Dynamics, 2017 - pubs.aip.org
The structure and function of biomolecules can be strongly influenced by their hydration
shells. A key challenge is thus to determine the extent to which these shells differ from bulk …

Polarization-and wavelength-dependent surface-enhanced Raman spectroscopy using optically anisotropic rippled substrates for sensing

D Gkogkou, B Schreiber, T Shaykhutdinov, HK Ly… - Acs …, 2016 - ACS Publications
Anisotropic Ag nanoparticle arrays were created by metal evaporation on rippled silicon
templates for sensing of molecules with surface-enhanced Raman spectroscopy. Our results …

Probing the local structure and dynamics of nucleotides using vibrationally enhanced alkynyl stretching

T Dong, P Yu, J Zhao, J Wang - Physical Chemistry Chemical Physics, 2022 - pubs.rsc.org
Monitoring the site-specific local structure and dynamics of polynucleotides and DNA is
important for understanding their biological functions. However, structurally characterizing …

C–B–A test of DNA force fields

IA Strelnikov, NA Kovaleva, AP Klinov, EA Zubova - ACS omega, 2023 - ACS Publications
The DNA duplex may be locally strongly bent in complexes with proteins, for example, with
polymerases or in a nucleosome. At such bends, the DNA helix is locally in the …