4.5 Article

A Consistent Picture of the Proton Release Mechanism of oNBA in Water by Ultrafast Spectroscopy and Ab Initio Molecular Dynamics

Journal

JOURNAL OF PHYSICAL CHEMISTRY B
Volume 115, Issue 5, Pages 1075-1083

Publisher

AMER CHEMICAL SOC
DOI: 10.1021/jp109053r

Keywords

-

Funding

  1. Swiss National Science Foundation [200021-124463/1]
  2. Swiss National Science Foundation (SNF) [200021_124463] Funding Source: Swiss National Science Foundation (SNF)

Ask authors/readers for more resources

With a combination of transient pump probe IR spectroscopy and ab initio molecular dynamics, the controversial pico- and nanosecond steps of the o-nitrobenzaldehyde (oNBA) photoreaction have been investigated in aqueous solution. In this way, the measured reaction kinetics have been complemented with an atomistic picture of the reactive events as obtained with unbiased simulations in explicit solvent. Our results allow for a detailed description of the oNBA proton photorelease, a process of fundamental importance and relevant to the use of oNBA as a proton cage in many experiments. In a first step, a stable ketene intermediate is formed on a subpicosecond time scale. This intermediate reacts in a solvent assisted way with an OH transfer to produce nitrosobenzoic acid with a characteristic time of 7 ps, Finally, in permitting pH conditions, this product molecule dissociates a carboxyl proton with a 21 ns time constant. The particular combination of theory and experiment employed in this work appears to be sufficiently general and powerful to find widespread application in the study of ultrafast reactive systems.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.5
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

Article Polymer Science

Ionomer-coated filtration membranes as an alternative to ion-exchange membranes for demineralization by electrodialysis

Sabita Kadel, Francesco Deboli, Veronique Perreault, Mateusz L. Donten, Laurent Bazinet

Summary: This study focuses on fabricating cation-coated filtration membranes with crosslinked polyethyleneimine on porous substrates as a cost-effective alternative to commercial anion-exchange membranes. Despite lower ionic conductance compared to AMX, the membranes exhibit similar electrochemical behavior. CCFMs show potential for industrial application in electrodialysis demineralization processes.

JOURNAL OF POLYMER SCIENCE (2022)

Article Biochemistry & Molecular Biology

Signal Propagation Within the MCL-1/B-IM Protein Complex

Philipp J. Heckmeier, Jeannette Ruf, David Buhrke, Brankica G. Jankovic, Peter Hamm

Summary: The protein MCL-1 is essential in regulating apoptosis in various cancers by binding to BIM according to an induced fit mechanism, leading to a cascade of structural rearrangements across a wide range of time scales.

JOURNAL OF MOLECULAR BIOLOGY (2022)

Review Chemistry, Multidisciplinary

Using azobenzene photocontrol to set proteins in motion

Olga Bozovic, Brankica Jankovic, Peter Hamm

Summary: Controlling protein activity with azobenzene photoswitches is a powerful tool to manipulate biological function, allowing changes in binding affinities, control of allostery, and initiation of out-of-equilibrium processes. By combining the potency of azobenzene photoswitching with transient spectroscopic techniques, researchers can reveal the order of events and experimentally observe biomolecular interactions in real time, providing insights into the dynamic nature of proteins.

NATURE REVIEWS CHEMISTRY (2022)

Article Chemistry, Physical

Low-frequency anharmonic couplings in bromoform revealed from 2D Raman-THz spectroscopy: From the liquid to the crystalline phase

Seyyed Jabbar Mousavi, Arian Berger, Peter Hamm, Andrey Shalit

Summary: In this study, two-dimensional Raman-THz spectroscopy was used to investigate the crystalline structure of bromoform. The results showed that the cross peaks in the crystalline sample were sharper and could be assigned to specific vibrational modes. The frequency positions of these cross peaks corresponded to the intramolecular bending modes in the Raman dimension and the lattice modes in the THz dimension. This work expands the applicability of this spectroscopic technique to solid samples and provides new experimental evidence for the coupling between intra- and intermolecular vibrational modes.

JOURNAL OF CHEMICAL PHYSICS (2022)

Article Engineering, Chemical

A versatile chemistry platform for the fabrication of cost-effective hierarchical cation and anion exchange membranes

Francesco Deboli, Bart Van der Bruggen, Mateusz L. Donten

Summary: This work presents a versatile chemistry platform for the fabrication of hierarchical cation and anion exchange membranes (hCEMs and hAEMs) with tuneable transport properties. The hierarchical ion exchange membranes were made by coating and UV crosslinking an acrylic ionomer on top of a PVC-SiO2 porous substrate. The properties and performance of the membranes were found to be dependent on the coating crosslinking density, with higher crosslinking density resulting in better selectivity and performance.

DESALINATION (2022)

Article Chemistry, Multidisciplinary

Structure, Organization, and Heterogeneity of Water-Containing Deep Eutectic Solvents

Kai Toepfer, Andrea Pasti, Anuradha Das, Seyedeh Maryam Salehi, Luis Itza Vazquez-Salazar, David Rohrbach, Thomas Feurer, Peter Hamm, Markus Meuwly

Summary: This study investigates the spectroscopy and structural dynamics of a deep eutectic mixture with varying water content using 2D IR and THz spectroscopy. Molecular dynamics simulations accurately describe the dependence of spectroscopic signatures on water content. The results demonstrate that the combination of structure-sensitive spectroscopies and molecular dynamics simulations provides molecular-level insights into the heterogeneity of such mixtures.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2022)

Article Multidisciplinary Sciences

Vibrational couplings between protein and cofactor in bacterial phytochrome Agp1 revealed by 2D-IR spectroscopy

David Buhrke, Norbert Michael, Peter Hamm

Summary: Phytochromes are commonly found photoreceptor proteins that undergo secondary structure refolding in response to chromophoric group photoisomerization. Two-dimensional infrared absorption spectroscopy is used to study the photoreaction of bacterial phytochrome Agp1, showing that dipole coupling between the chromophore and the tongue region plays a role in stabilizing the protein in the light-activated state.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Chemistry, Physical

Low-frequency anharmonic couplings in crystalline bromoform: Theory

Beliz Sertcan, Seyyed Jabbar Mousavi, Marcella Iannuzzi, Peter Hamm

Summary: Theoretical calculations of low-frequency anharmonic couplings in the beta-phase of crystalline bromoform were conducted based on density functional theory quantum chemistry calculations. The dominant role of electrical anharmonicity in the 2D Raman-THz response of both crystalline and liquid bromoform was revealed. The difference in relative cross-peak intensities between intramolecular and intermolecular modes in bromoform can be explained by the C-3v symmetry of bromoform along with orientational averaging.

JOURNAL OF CHEMICAL PHYSICS (2023)

Article Chemistry, Physical

MCL-1 promiscuity and the structural resilience of its binding partners

Philipp J. J. Heckmeier, Jeannette Ruf, Brankica G. G. Jankovic, Peter Hamm

Summary: The study investigates the interaction between the allosteric protein MCL-1 and its natural inhibitors PUMA, BIM, and NOXA. Photoswitchable versions of MCL-1/PUMA and MCL-1/NOXA were designed, and the protein response was studied using transient infrared spectroscopy. Partial alpha-helical unfolding was observed in all cases, with varying timescales, suggesting a BH3-only-specific structural resilience in MCL-1's binding pocket.

JOURNAL OF CHEMICAL PHYSICS (2023)

Article Multidisciplinary Sciences

Addendum: Sensing the allosteric force

Brankica Jankovic, Olga Bozovic, Peter Hamm

NATURE COMMUNICATIONS (2023)

Review Chemistry, Multidisciplinary

Breaking Barriers in Ultrafast Spectroscopy and Imaging Using 100 kHz Amplified Yb-Laser Systems

Paul M. Donaldson, Greg M. Greetham, Chris T. Middleton, Bradley M. Luther, Martin T. Zanni, Peter Hamm, Amber T. Krummel

Summary: Ultrafast spectroscopy and imaging have become essential tools for scientists in various fields. The commercialization of advanced spectrometers, such as transient absorption spectrometers and vibrational sum frequency generation spectrometers, has made these measurements available to non-experts in ultrafast spectroscopy. The shift to new Yb-based lasers offers exciting new possibilities in the chemical and physical sciences, with higher efficiency and improved noise characteristics.

ACCOUNTS OF CHEMICAL RESEARCH (2023)

Article Chemistry, Physical

Versatile Femtosecond Laser Synchronization for Multiple-Timescale Transient Infrared Spectroscopy

Jan Helbing, Peter Hamm

Summary: This article introduces several ways to electronically synchronize different types of amplified femtosecond laser systems using a single freely programmable electronics hardware. These methods allow for rapid probing of a wide range of timescales in a single transient absorption experiment without the need to move any delay stage. The approach is versatile and can synchronize different lasers, such as a Ti:Sa amplifier and a 100 kHz Yb-laser system. The time-resolution in the transient experiment ranges from 1 to 3 ps, depending on the method.

JOURNAL OF PHYSICAL CHEMISTRY A (2023)

Article Chemistry, Multidisciplinary

Transient 2D IR Spectroscopy and Multiscale Simulations Reveal Vibrational Couplings in the Cyanobacteriochrome Slr1393-g3

David Buhrke, Yigal Lahav, Aditya Rao, Jeannette Ruf, Igor Schapiro, Peter Hamm

Summary: In this study, the researchers explored a cyanobacteriochrome called Slr1393-g3, which can switch between red-absorbing and green-absorbing forms. They used advanced IR spectroscopic methods to track the intermediates during the photocycle and discovered a new intermediate with distinct spectroscopic features. Additionally, they measured the vibrational couplings and structural disorder in these intermediate states using stationary and transient 2D IR experiments. Anharmonic QM/MM calculations were also performed to predict the spectra and suggest structural changes of the intermediates.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2023)

Article Chemistry, Physical

Hydration dynamics and IR spectroscopy of 4-fluorophenol

Seyedeh Maryam Salehi, Silvan Kaeser, Kai Toepfer, Polydefkis Diamantis, Rolf Pfister, Peter Hamm, Ursula Rothlisberger, Markus Meuwly

Summary: In this work, the structural dynamics and infrared spectroscopy of para-fluorophenol and phenol in the gas phase and in water were investigated using a combination of experiment and molecular dynamics simulations. The study found that the CF group of para-fluorophenol is highly hydrophobic, which is particularly relevant for applications in pharmaceutical chemistry.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2022)

Article Chemistry, Physical

Flexible to rigid: IR spectroscopic investigation of a rhenium-tricarbonyl-complex at a buried interface

Kerstin T. Oppelt, Laurent Severy, Mirjam Utters, S. David Tilley, Peter Hamm

Summary: This study investigated the solid-liquid interface of a rhenium-tricarbonyl complex embedded in a zirconium oxide layer deposited by atomic layer deposition (ALD) using time-resolved and steady state infrared spectroscopy. The research revealed correlations between the thickness of the ALD layer and the spectroscopic response of the system. A transition from flexible to rigid molecular environment, as well as limitations to ligand exchange and excited state quenching on the embedded complexes, were observed when the ALD layer matched the height of the molecules.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2021)

No Data Available