Dataset Information

Stoichiometric analysis of competing intermolecular hydrogen bonds using infrared spectroscopy.

ABSTRACT: We quantitatively analyze multiple hydrogen bonds in mixtures of two monomers: urethane dimethacrylate (UDMA) and triethylene glycol-divinylbenzyl ether (TEG-DVBE). The carbonyl stretching band in infrared (IR) absorption spectra is deconvoluted into free and hydrogen-bonded carbonyl groups. The amounts of the sub-components are determined for 21 mixture compositions and initially analyzed using a simple stoichiometric model (based on one dominant hydrogen acceptor group per monomer species) for the equilibrium state of hydrogen bond formation. However, our in-depth stoichiometric analysis suggests that at least two UDMA acceptor groups (carbonyl and alkoxy oxygens) and one TEG-DVBE acceptor group (ether oxygen) contribute to intermolecular hydrogen bonding interactions. This finding is further supported by a quantitative analysis of the hydrogen bonding effect on the N-H stretching band. Moreover, the equilibrium constants of these hydrogen bond formations confirm that the interassociation between UDMA and TEG-DVBE is non-negligible in comparison to the UDMA selfassociations. Such quantitative information on intermolecular interactions provides insight into the effect of hydrogen bonding on the copolymerization kinetics of these monomer mixtures.

SUBMITTER: Ryu IS

PROVIDER: S-EPMC6205508 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Stoichiometric analysis of competing intermolecular hydrogen bonds using infrared spectroscopy.

Ryu Ian Seungwan IS Liu Xiaohui X Jin Ying Y Sun Jirun J Lee Young Jong YJ

RSC advances 20180627 42

We quantitatively analyze multiple hydrogen bonds in mixtures of two monomers: urethane dimethacrylate (UDMA) and triethylene glycol-divinylbenzyl ether (TEG-DVBE). The carbonyl stretching band in infrared (IR) absorption spectra is deconvoluted into free and hydrogen-bonded carbonyl groups. The amounts of the sub-components are determined for 21 mixture compositions and initially analyzed using a simple stoichiometric model (based on one dominant hydrogen acceptor group per monomer species) for ...[more]

PMID: 30386590

Similar Datasets

Project description:Time-resolved Fourier transform infrared (FTIR) spectroscopy is a powerful tool to elucidate label-free the reaction mechanisms of proteins. After assignment of the absorption bands to individual groups of the protein, the order of events during the reaction mechanism can be monitored and rate constants can be obtained. Additionally, structural information is encoded into infrared spectra and can be decoded by combining the experimental data with biomolecular simulations. We have determined recently the infrared vibrations of GTP and guanosine diphosphate (GDP) bound to Gαi1, a ubiquitous GTPase. These vibrations are highly sensitive for the environment of the phosphate groups and thereby for the binding mode the GTPase adopts to enable fast hydrolysis of GTP. In this study we calculated these infrared vibrations from biomolecular simulations to transfer the spectral information into a computational model that provides structural information far beyond crystal structure resolution. Conformational ensembles were generated using 15 snapshots of several 100 ns molecular-mechanics/molecular-dynamics (MM-MD) simulations, followed by quantum-mechanics/molecular-mechanics (QM/MM) minimization and normal mode analysis. In comparison with other approaches, no time-consuming QM/MM-MD simulation was necessary. We carefully benchmarked the simulation systems by deletion of single hydrogen bonds between the GTPase and GTP through several Gαi1 point mutants. The missing hydrogen bonds lead to blue-shifts of the corresponding absorption bands. These band shifts for α-GTP (Gαi1-T48A), γ-GTP (Gαi1-R178S), and for both β-GTP/γ-GTP (Gαi1-K46A, Gαi1-D200E) were found in agreement in the experimental and the theoretical spectra. We applied our approach to open questions regarding Gαi1: we show that the GDP state of Gαi1 carries a Mg2+, which is not found in x-ray structures. Further, the catalytic role of K46, a central residue of the P-loop, and the protonation state of the GTP are elucidated.

Project description:Intra- and intermolecular interactions have been explored in selected N-oxide derivatives: 2-(N,N-dimethylamino-N-oxymethyl)-4,6-dimethylphenyl (1) and 5,5'-dibromo-3-diethylaminomethyl-2,2'-biphenol N-oxide (2). Both compounds possess intramolecular hydrogen bonding, which is classified as moderate in 1 and strong in 2, and resonance-assisted in both cases. Density Functional Theory (DFT) in its classical formulation as well as Time-Dependent extension (TD-DFT) were employed to study proton transfer phenomena. The simulations were performed in the gas phase and with implicit and explicit solvation models. The obtained structures of the studied N-oxides were compared with experimental data available. The proton reaction path was investigated using scan with an optimization method, and water molecule reorientation in the monohydrate of 1 was found upon the proton scan progress. It was found that spontaneous proton transfer phenomenon cannot occur in the electronic ground state of the compound 1. An opposite situation was noticed for the compound 2. The changes of nucleophilicity and electrophilicity upon the bridged proton migration were analyzed on the basis of Fukui functions in the case of 1. The interaction energy decomposition of dimers and microsolvation models was investigated using Symmetry-Adapted Perturbation Theory (SAPT). The simulations were performed in both phases to introduce polar environment influence on the interaction energies. The SAPT study showed rather minor role of induction in the formation of homodimers. However, it is worth noticing that the same induction term is responsible for the preference of water molecules' interaction with N-oxide hydrogen bond acceptor atoms in the microsolvation study. The Natural Bond Orbital (NBO) analysis was performed for the complexes with water to investigate the charge flow upon the polar environment introduction. Finally, the TD-DFT was applied for isolated molecules as well as for microsolvation models showing that the presence of solvent affects excited states, especially when the N-oxide acceptor atom is microsolvated.

Dataset Information

Stoichiometric analysis of competing intermolecular hydrogen bonds using infrared spectroscopy.

Publications

Stoichiometric analysis of competing intermolecular hydrogen bonds using infrared spectroscopy.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets