Article
Chemistry, Multidisciplinary
Henrik R. Larsson, Markus Schroder, Richard Beckmann, Fabien Brieuc, Christoph Schran, Dominik Marx, Oriol Vendrell
Summary: This study reveals that the interplay between proton transfer and water wagging in the protonated water dimer is more complex and sensitive to subtle energetic changes than previously thought. By comparing infrared spectra obtained with two highly accurate potential energy surfaces and conducting highly accurate state-resolved quantum simulations, the researchers discovered previously overlooked low-intensity satellite peaks in the experimental spectrum and mechanistically assigned them.
Article
Chemistry, Physical
Richard Beckmann, Rafal Topolnicki, Dominik Marx
Summary: This article investigates the effects of interactions between different numbers of helium atoms and protonated acetylene on its structure and dynamics. The results show that microsolvation by helium significantly affects the structure of C2H3+, and solvation becomes increasingly isotropic after adding six or more helium atoms. This study provides a basis for further exploration of the effects of tagging on the structure of flexible molecules.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Biochemistry & Molecular Biology
Maximilian Theiss, Merten Grupe, Tilman Lamparter, Maria Andrea Mroginski, Rolf Diller
Summary: The deactivation processes of photoexcited phycocyanobilin (PCB) in methanol were studied using UV/Vis and mid-IR femtosecond transient absorption spectroscopy, supported by density-functional theory calculations. Significant insights into the molecular structures and dynamics were gained, allowing a better understanding of the chromophore protonation/deprotonation processes associated with electronic and structural dynamics. The PCB photocycle is proposed to be closed by a long living, fluorescent species resembling the PCBC conformer.
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Jake A. Tan, Jer-Lai Kuo
Summary: In this study, the structures and spectral features of protonated noble gas clusters were investigated using a first principles approach. It was found that protonated noble gas monomers and dimers have a linear structure, while the trimers can have a T-shaped or linear structure. Additionally, interesting spectral features such as progression bands and Fermi resonance interactions were observed.
Article
Chemistry, Physical
Ivo S. Vinklarek, Andriy Pysanenko, Eva Pluharova, Michal Farnik
Summary: The uptake of water, methanol, and ethanol on nanometer-size clusters of polyaromatic hydrocarbons (PAHs) was studied, and it was found that water molecules exhibited the lowest uptake probability, about 30% lower than those for methanol and ethanol.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Summer L. Sherman, Kaitlyn C. Fischer, Etienne Garand
Summary: In this study, we investigated the conformational and isomeric populations in gas-phase protonated tripeptides using infrared predissociation spectroscopy. The results showed that the position of the methyl side-chain has a significant impact on the 3-D structure of the peptide, and the exact amino acid sequence determines the structural populations. These changes in structural populations can be explained by the electron-donating effect of the methyl side-chain.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Article
Chemistry, Physical
Dongbo Mi, Junqiang Xu, Yunpeng Zhang, Tenggao Zhu, Jiewen Ouyang, Xiaofeng Dong, Konstantin Chingin
Summary: Protonated water-hydrogen clusters [H+(H2O)(n)center dot m(H-2)] can be produced at room temperature through the association of protonated water clusters H+(H2O)(n) with H-2 gas, without any cooling necessary. A proposed mechanism for the formation of the protonated water-hydrogen complexes.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Yuri Ito, Mizuhiro Kominato, Yuji Nakashima, Keijiro Ohshimo, Fuminori Misaizu
Summary: The infrared photodissociation of protonated water clusters with an Ar atom was studied using an imaging technique to analyze their vibrational dynamics. The dynamics of each OH stretching vibration was observed through the selective photoexcitation of different cluster sizes and modes. The translational energy distributions of the photofragments were compared between different excited states, revealing different relaxation processes for H3O+-Ar and H+(H2O)(2)-Ar clusters.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Chih-Kai Lin, Qian-Rui Huang, Ying-Cheng Li, Ha-Quyen Nguyen, Jer-Lai Kuo, Asuka Fujii
Summary: Infrared predissociation spectroscopy was used to record the intriguing vibrational features of solvated protonated methanol between 2400-3800 cm(-1). The positions of OH stretching modes absorption bands are sensitive to solvation environments, with changes in these environments leading to changes in vibrational features. Theoretical analyses based on ab initio anharmonic algorithm not only reproduce experimentally observed features, but also elucidate the magnitudes of couplings and interplay between two mechanisms, providing convincing assignments of spectral patterns.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Optics
Henry Tan, Jasper J. Cadusch, Jiajun Meng, Kenneth B. Crozier
Summary: This study optimized filter design through simulations and genetic algorithms to achieve better identification of liquid and gaseous chemicals. The results showed that classifiers trained with optimized filter sets outperformed those trained with evenly spaced and handpicked filters targeting absorption bands of specific chemicals.
Article
Chemistry, Physical
Arman Nejad, Xiang Li, Tianxin Zhu, Yun Liu, Chuanxi Duan
Summary: This study presents the first high-resolution measurements of the jet-cooled laser absorption spectrum of (HCOOH)3. The analysis of the C-O stretching fundamentals provides vibration-rotation parameters and discusses the mechanisms of vibrational predissociation and intramolecular vibrational redistribution. The prospects of further high-resolution measurements or isotope substitution experiments are discussed to reveal the mode-specificity of broadening mechanisms.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
A. J. Barclay, A. R. W. McKellar, N. Moazzen-Ahmadi
Summary: This study provides experimental evidence for the structural information of the first solvation shell of carbon dioxide in argon clusters, and discovers possible low-frequency vibrational modes, posing a challenge for cluster theory.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Multidisciplinary
John H. Hack, James P. Dombrowski, Xinyou Ma, Yaxin Chen, Nicholas H. C. Lewis, William B. Carpenter, Chenghan Li, Gregory A. Voth, Harold H. Kung, Andrei Tokmakoff
Summary: The molecular structure and behavior of water confined in aluminosilicate zeolite pores is essential for understanding zeolite acid chemistry under hydrous conditions. By using a combination of ultrafast two-dimensional infrared spectroscopy and ab initio molecular dynamics, this study was able to characterize the hydrogen-bonding network within highly hydrated zeolite HZSM-5 pores. Results indicated that the excess charge is detached from the zeolite and resides near the more highly coordinated water molecules in the cluster.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Inorganic & Nuclear
Chun-Han Lu, Yi-Ting Tsai, Tzong-Liang Tsai, Ting-Shan Chan, Xuejie Zhang, Chun Che Lin
Summary: In this study, a white phosphor-based near-infrared (NIR) lighting material with high internal quantum efficiency and wide spectral range was developed. By designing a NIR ceramic device, dental problems such as caries and tooth calcification can be effectively detected.
INORGANIC CHEMISTRY
(2022)
Article
Chemistry, Physical
Shuo Yang, Zhaojun Zhang, Dong H. Zhang
Summary: This study presents a full-dimensional ab initio potential energy surface (PES) and dipole moment surface (DMS) for the ammonia dimer (NH3)2. The PES was fitted using the fundamental invariant neural network method and accurately predicted the dissociation energy of two NH3 monomers.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Matteo Accorsi, Markus Tiemann, Leon Wehrhan, Lauren M. Finn, Ruben Cruz, Max Rautenberg, Franziska Emmerling, Joachim Heberle, Bettina G. Keller, Joerg Rademann
Summary: This study reports the discovery and investigation of pentafluorophosphato amino acids as novel phosphotyrosine biomimetics. Experimental and computational methods were used to demonstrate that these novel biomimetics have significantly enhanced binding affinity to the protein tyrosine phosphatase PTP1B, suggesting their potential value in drug molecule development.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Kenichi Ataka, Janina Drauschke, Valentina Stulberg, Beate Koksch, Joachim Heberle
Summary: The pH low insertion peptide (pHLIP) is a pH-sensitive cell penetrating peptide that undergoes conformational changes from a coil to an alpha-helix in response to pH. It has potential applications in drug delivery and visualization of acidic tissues. In this study, the pH-induced insertion and folding processes of pHLIP into a lipid bilayer were examined using surface-enhanced infrared absorption spectroscopy. The results showed that the peptide forms a partially helical structure at slightly acidic pH and undergoes further reorientation and insertion into the membrane at lower pH. The formation of alpha-helical structure and complete secondary structure occurs at pH 5.3. Analysis of the vibrational bands suggests the involvement of specific amino acid groups in the conformational changes of pHLIP in different pH states.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2022)
Article
Chemistry, Physical
Luiz Schubert, Pit Langner, David Ehrenberg, Victor A. Lorenz-Fonfria, Joachim Heberle
Summary: Mid-IR spectroscopy is used to investigate protein reactions. In this study, quantum-cascade-laser-based dual-comb spectroscopy is used to probe protein conformational changes and protonation events by a single-shot experiment. The feasibility of QCL-based infrared spectroscopy in monitoring irreversible reactions is demonstrated.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Multidisciplinary Sciences
Sandra Mous, Guillaume Gotthard, David Ehrenberg, Saumik Sen, Tobias Weinert, Philip J. M. Johnson, Daniel James, Karol Nass, Antonia Furrer, Demet Kekilli, Pikyee Ma, Steffen Bruenle, Cecilia Maria Casadei, Isabelle Martiel, Florian Dworkowski, Dardan Gashi, Petr Skopintsev, Maximilian Wranik, Gregor Knopp, Ezequiel Panepucci, Valerie Panneels, Claudio Cirelli, Dmitry Ozerov, Gebhard F. X. Schertler, Meitian Wang, Chris Milne, Joerg Standfuss, Igor Schapiro, Joachim Heberle, Przemyslaw Nogly
Summary: By combining time-resolved crystallography, spectroscopy, and multiscale simulations, we have elucidated the molecular mechanism and structural dynamics of a chloride-pumping rhodopsin throughout the transport cycle. We identified transient anion-binding sites, provided evidence for the use of light energy in the pumping mechanism, and discovered molecular gates that ensure unidirectional transport. These findings reveal key mechanistic features that enable finely controlled chloride transport across the cell membrane in this light-powered chloride ion pump.
Article
Biochemistry & Molecular Biology
Mariafrancesca La Greca, Jheng-Liang Chen, Luiz Schubert, Jacek Kozuch, Tim Berneiser, Ulrich Terpitz, Joachim Heberle, Ramona Schlesinger
Summary: This study reports the spectroscopic characterization of a light-driven proton pump rhodopsin (UmRh1) from the smut pathogen Ustilago maydis. The impact of the auxin hormone indole-3-acetic acid on UmRh1 pump activity was also investigated. An easy pumping activity test was established to probe the ability of UmRh1 to pump protons out of living yeast cells.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Federico Baserga, Antreas Vorkas, Fucsia Crea, Luiz Schubert, Jheng-Liang Chen, Aoife Redlich, Mariafrancesca La Greca, Julian Storm, Sabine Oldemeyer, Kirsten Hoffmann, Ramona Schlesinger, Joachim Heberle
Summary: This study investigates the interaction between membrane proteins and the lipid bilayer by analyzing changes in lipid vibrational bands. The results show that the activation of membrane proteins leads to structural changes and perturbs the lipidic environment. Isotopologue analysis also reveals changes in the collective state of lipids.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Thomas Hohmann, Suvrat Chowdhary, Kenichi Ataka, Jasmin Er, Gesa Heather Dreyhsig, Joachim Heberle, Beate Koksch
Summary: A new class of peptide-based fluoropolymers composed of fluorinated aliphatic amino acids has been designed. The structural characterization revealed the effects of fluorine-induced alterations and unique formation of PPII structures. Various techniques were employed to examine the insertion and folding processes into lipid vesicles. The degree of fluorination affects the alpha-helical content while partitioning into lipid bilayers. The enzymatic degradability of fluorinated peptides was also studied, showing that all sequences can be degraded despite the degree of fluorination. These fluoropeptides with enzyme-degradable features will be crucial for the future development of fluorinated peptide-based biomaterials.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Yingliang Liu, Aditya S. Chaudhari, Aditi Chatterjee, Prokopis C. Andrikopoulos, Alessandra Picchiotti, Mateusz Rebarz, Miroslav Kloz, Victor A. Lorenz-Fonfria, Bohdan Schneider, Gustavo Fuertes
Summary: A broadband dual transient visible absorption (visTA)/femtosecond stimulated Raman spectroscopy (FSRS) set-up was developed to monitor the complete excited-state dynamics of flavin mononucleotide (FMN) in solution and embedded in bacterial light-oxygen-voltage (LOV) photoreceptor EL222. The set-up covers a wide range of time delays and Raman shifts, providing valuable information on short-lived conformationally excited states. Additional dynamical events were found in the low-frequency Raman region below 1000 cm(-1).
Article
Biochemistry & Molecular Biology
Aditya S. Chaudhari, Aditi Chatterjee, Catarina A. O. Domingos, Prokopis C. Andrikopoulos, Yingliang Liu, Inger Andersson, Bohdan Schneider, Victor A. Lorenz-Fonfria, Gustavo Fuertes
Summary: Photoreceptors containing the LOV domain respond to blue light by exciting their FMN chromophore, but the mechanism and kinetics of dark-state recovery are not well understood. This study used genetic code expansion technology to incorporate CNF at specific positions of the bacterial transcription factor EL222 and identified CNF31 and CNF35 as indicators of monomer/oligomer and caged/decaged equilibria. Time-resolved spectroscopy experiments revealed four dynamical events during the lit-to-dark transition, including rearrangements around the A'alpha helix interface, FMN-cysteinyl adduct scission, folding of alpha-helices, and relaxation of residue CNF151. These findings highlight the importance of characterizing all parts of a protein and suggest a key role for the N-terminal A'alpha extension of the LOV domain in controlling EL222 photocycle length.
Article
Chemistry, Physical
Luiz Schubert, Jheng-Liang Chen, Tobias Fritz, Florina Marxer, Pit Langner, Kirsten Hoffmann, Ana P. Gamiz-Hernandez, Ville R. I. Kaila, Ramona Schlesinger, Joachim Heberle
Summary: Directional ion transport across biological membranes is vital for cellular processes, and understanding the molecular mechanism of vectorial ion transport is crucial. In this study, the protonation steps in the light-driven inward proton pump were tracked, revealing key proton release sites and shedding light on the molecular determinants of proton translocation.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Maryam Saliminasab, Yoichi Yamazaki, Alyssa Palmateer, Andrew Harris, Luiz Schubert, Pit Langner, Joachim Heberle, Ana-Nicoleta Bondar, Leonid S. Brown
Summary: Microbial rhodopsins are a group of light-activated retinal-binding membrane proteins that perform various functions. This study reports on a new group of sensory rhodopsins that show similarities to proton pumps but interact with transducers in a similar manner to haloarchaeal sensory rhodopsins. The sensory rhodopsins in this group have unique amino acid residues, including a tyrosine in place of a carboxyl counterion. Experimental data, bioinformatics sequence analyses, and structural modeling suggest that the tyrosine/aspartate complex counterion contributes to a complex water-mediated hydrogen-bonding network.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Elena Buhl, Tom Resler, Rebecca Lam, Marvin Asido, Ernst Bamberg, Ramona Schlesinger, Christian Bamann, Joachim Heberle, Josef Wachtveitl
Summary: The study reveals the correlation between channel opening of CrChR2 and retinal isomerization, photocycle, and protein channel activity. The photocycle of the R120H variant is intact despite deficient channel activity. Analysis of the amide I mode shows impairment of the ultrafast protein response after retinal excitation.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Maria Walter, Luiz Schubert, Joachim Heberle, Ramona Schlesinger, Aba Losi
Summary: In this study, time-resolved photoacoustics (PA) was used to explore the energy landscape and volumetric changes of transient species formed after photoexcitation in biological photoreceptors. PA experiments were performed on several channelrhodopsins, revealing important parameters and providing insights into their protonation dynamics and energy levels.
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES
(2023)