Browse
Submit Data
Databases
API
Help

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Reduced Acid Dissociation of Amino-Acids at the Surface of Water.

ABSTRACT: We use surface-specific intensity vibrational sum-frequency generation and attenuated total reflection spectroscopy to probe the ionization state of the amino-acids l-alanine and l-proline at the air/water surface and in the bulk. The ionization state is determined by probing the vibrational signatures of the carboxylic acid group, representing the nondissociated acid form, and the carboxylate anion group, representing the dissociated form, over a wide range of pH values. We find that the carboxylic acid group deprotonates at a significantly higher pH at the surface than in the bulk.

SUBMITTER: Strazdaite S

PROVIDER: S-EPMC5355887 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Reduced Acid Dissociation of Amino-Acids at the Surface of Water.

Strazdaite Simona S Meister Konrad K Bakker Huib J HJ

Journal of the American Chemical Society 20170306 10

We use surface-specific intensity vibrational sum-frequency generation and attenuated total reflection spectroscopy to probe the ionization state of the amino-acids l-alanine and l-proline at the air/water surface and in the bulk. The ionization state is determined by probing the vibrational signatures of the carboxylic acid group, representing the nondissociated acid form, and the carboxylate anion group, representing the dissociated form, over a wide range of pH values. We find that the carbox ...[more]

PMID: 28177623

Similar Datasets

Water-Assisted Homolytic Dissociation of Propyne on a Reduced Ceria Surface.

Project description:The emergence of ceria (CeO2 ) as an efficient catalyst for the selective hydrogenation of alkynes has attracted great attention. Intensive research effort has been devoted to understanding the underlying catalytic mechanism, in particular the H2 -CeO2 interaction. Herein, we show that the adsorption of propyne (C3 H4 ) on ceria, another key aspect in the hydrogenation of propyne to propene, strongly depends on the degree of reduction of the ceria surface and hydroxylation of the surface, as well as the presence of water. The dissociation of propyne and the formation of methylacetylide (CH3 CC-) have been identified through the combination of infrared reflection absorption spectroscopy (IRAS) and DFT calculations. We demonstrate that propyne undergoes heterolytic dissociation on the reduced ceria surface by forming a methylacetylide ion on the oxygen vacancy site and transferring a proton to the nearby oxygen site (OH group), while a water molecule that competes with the chemisorbed methylacetylide at the vacancy site assists the homolytic dissociation pathway by rebounding the methylacetylide to the nearby oxygen site.

| S-EPMC7187185 | biostudies-literature

Identification of bacterial lipo-amino acids: origin of regenerated fatty acid carboxylate from dissociation of lipo-glutamate anion.

Project description:The identification of bacterial metabolites produced by the microbiota is a key point to understand its role in human health. Among them, lipo-amino acids (LpAA), which are able to cross the epithelial barrier and to act on the host, are poorly identified. Structural elucidation of few of them was performed by high-resolution tandem mass spectrometry based on electrospray combined with selective ion dissociations reach by collision-induced dissociation (CID). The negative ions were used for their advantages of yielding only few fragment ions sufficient to specify each part of LpAA with sensitivity. To find specific processes that help structural assignment, the negative ion dissociations have been scrutinized for an LpAA: the N-palmitoyl acyl group linked to glutamic acid (C16Glu). The singular behavior of [C16Glu-H]¯ towards CID showed tenth product ions, eight were described by expected fragment ions. In contrast, instead of the expected product ions due to CONH-CH bond cleavage, an abundant complementary dehydrated glutamic acid and fatty acid anion pair were observed. Specific to glutamic moiety, they were formed by a stepwise dissociation via molecular isomerization through ion-dipole formation prior to dissociation. This complex dissociated by partner splitting either directly or after inter-partner proton transfer. By this pathway, surprising regeneration of deprotonated fatty acid takes place. Such regeneration is comparable to that occurred from dissociation to peptides containing acid amino-acid. Modeling allow to confirm the proposed mechanisms explaining the unexpected behavior of this glutamate conjugate.

| S-EPMC8894203 | biostudies-literature

Water-Soluble Blue Fluorescent Nonconjugated Polymer Dots from Hyaluronic Acid and Hydrophobic Amino Acids.

Project description:Fluorescent polymers have been increasingly investigated to improve their water solubility and biocompatibility to enhance their performance in drug delivery and theranostic applications. However, the environmentally friendly synthesis and dual functionality of such systems remain a challenge due to the complicated synthesis of conventional fluorescent materials. Herein, we generated a novel blue fluorescent polymer dot through chemical conjugation of hydrophobic amino acids to hyaluronic acid (HA) under one-pot green chemistry conditions. These nonconjugated fluorescent polymer dots (NCPDs) are water soluble, nontoxic to cells, have high fluorescence quantum yield, and can be used for in vitro bioimaging. HA-derived NCPDs exhibit excitation wavelength-dependent fluorescent properties. In addition, the NCPDs also show enhanced doxorubicin loading and delivery in naive and drug-resistant breast cancer cells in 2D and 3D tumor cellular systems. These results demonstrate the potential for successful synthetic scale-up and applications for HA-derived NCPDs.

| S-EPMC8296014 | biostudies-literature

Oxygen production from dissociation of Europa's water-ice surface.

Project description:Jupiter's moon Europa has a predominantly water-ice surface that is modified by exposure to its space environment. Charged particles break molecular bonds in surface ice, thus dissociating the water to ultimately produce H2 and O2, which provides a potential oxygenation mechanism for Europa's subsurface ocean. These species are understood to form Europa's primary atmospheric constituents. Although remote observations provide important global constraints on Europa's atmosphere, the molecular O2 abundance has been inferred from atomic O emissions. Europa's atmospheric composition had never been directly sampled and model-derived oxygen production estimates ranged over several orders of magnitude. Here, we report direct observations of H2+ and O2+ pickup ions from the dissociation of Europa's water-ice surface and confirm these species are primary atmospheric constituents. In contrast to expectations, we find the H2 neutral atmosphere is dominated by a non-thermal, escaping population. We find 12 ± 6 kg s-1 (2.2 ± 1.2 × 1026 s-1) O2 are produced within Europa's surface, less than previously thought, with a narrower range to support habitability in Europa's ocean. This process is found to be Europa's dominant exogenic surface erosion mechanism over meteoroid bombardment.

| S-EPMC11111413 | biostudies-literature

Topological Water Network Analysis Around Amino Acids.

Project description:Water molecules play a key role in protein stability, folding, function and ligand binding. Protein hydration has been studied using free energy perturbation algorithms. However, the study of protein hydration without free energy calculation is also an active field of research. Accordingly, topological water network (TWN) analysis has been carried out instead of free energy calculation in the present work to investigate hydration of proteins. Water networks around 20 amino acids in the aqueous solution were explored through molecular dynamics (MD) simulations. These simulation results were compared with experimental observations. Water molecules from the protein data bank structures showed TWN patterns similar to MD simulations. This work revealed that TWNs are effected by the surrounding environment. TWNs could provide valuable clues about the environment around amino acid residues in the proteins. The findings from this study could be exploited for TWN-based drug discovery and development.

| S-EPMC6681432 | biostudies-literature

Breakdown of chiral recognition of amino acids in reduced dimensions.

Project description:The homochirality of amino acids in living organisms is one of the great mysteries in the phenomena of life. To understand the chiral recognition of amino acids, we have used scanning tunnelling microscopy to investigate the self-assembly of molecules of the amino acid tryptophan (Trp) on Au(111). Earlier experiments showed only homochiral configurations in the self-assembly of amino acids, despite using a mixture of the two opposite enantiomers. In our study, we demonstrate that heterochiral configurations can be favored energetically when L- and D-Trp molecules are mixed to form self-assembly on the Au surface. Using density functional theory calculations, we show that the indole side chain strongly interacts with the Au surface, which reduces the system effectively to two-dimension, with chiral recognition disabled. Our study provides important insight into the recognition of the chirality of amino acid molecules in life.

| S-EPMC7527561 | biostudies-literature

Charge State Dependence of Amino Acid Propensity at Water Surface: Mechanisms Elucidated by Molecular Dynamics Simulations.

Project description:Atmospheric aerosols contain a variety of compounds, among them free amino acids and salt ions. The pH of the aerosol droplets depends on their origin and environment. Consequently, compounds like free amino acids found in the droplets will be at different charge states, since these states to a great extent depend on the surrounding pH condition. In droplets of marine origin, amino acids are believed to drive salt ions to the water surface and a pH-dependent amino acid surface propensity will, therefore, indirectly affect many processes in atmospheric chemistry and physics such as for instance cloud condensation. To understand the surface propensity of glycine, valine, and phenylalanine at acidic, neutral, and basic pH, we used molecular dynamics (MD) simulations to investigate them at three different charge states in water. Their respective surface propensities were obtained by the means of a potential of mean force (PMF) in an umbrella sampling approach. Glycine was found to have no preference for the surface, while both valine and phenylalanine showed high propensities. Among the charge states of the surface-enriched ones, the cation, representing the amino acids at low pH, was found to have the highest affinity. Free energy decomposition revealed that the driving forces depend strongly on the nature of the amino acid and its charge state. In phenylalanine, the main factor was found to be a substantial entropy gain, likely related to the side chain, whereas in valine, hydrogen bonding to the functional groups leads to favorable energies and, in turn, affects the surface propensity. A significant gain in water-water enthalpy was seen for both valine and phenylalanine.

| S-EPMC8279654 | biostudies-literature

Electron capture dissociation, electron detachment dissociation, and collision-induced dissociation of polyamidoamine (PAMAM) dendrimer ions with amino, amidoethanol, and sodium carboxylate surface groups.

Project description:Here, we investigate the effect of the structure (generation) and nature of the surface groups of different polyamidoamine (PAMAM) dendrimers on electron-mediated dissociation, either electron capture dissociation (ECD) or electron detachment dissociation (EDD), and compare the fragmentation with that observed in collision-induced dissociation (CID). ECD and EDD of the PAMAM dendrimers resulted in simple mass spectra, which are straightforward to interpret, whereas CID produced complex mass spectra. The results show that electron-mediated dissociation (ECD and EDD) of PAMAM dendrimers does not depend on the nature of the surface group but tends to occur within the innermost generations. CID of the PAMAM dendrimers showed a strong dependence on the nature of the surface group and occurred mostly in the outer generation. The results demonstrate the potential utility of ECD and EDD as a tool for the structural analysis of PAMAM dendrimers.

| S-EPMC2571976 | biostudies-literature

Branched chain amino acids impact health and lifespan indirectly via amino acid balance and appetite control

Project description:Elevated branched chain amino acids (BCAAs) are associated with obesity and insulin resistance. How long-term dietary BCAAs impact late-life health and lifespan is unknown. Here, we show that when dietary BCAAs are varied against a fixed, isocaloric macronutrient background, long-term exposure to high BCAA diets led to hyperphagia, obesity and reduced lifespan. These effects were not due to elevated BCAA per se or hepatic mTOR activation, but rather the shift in balance between dietary BCAAs and other AAs, notably tryptophan and threonine. Increasing the ratio of BCAAs to these AAs resulted in hyperphagia and was linked to central serotonin depletion. Preventing hyperphagia by calorie restriction or pair-feeding averted the health costs of a high BCAA diet. Our data highlight a role for amino acid quality in energy balance and show that health costs of chronic high BCAA intakes were not due to intrinsic toxicity; rather, to hyperphagia driven by AA imbalance.

2019-03-11 | GSE114855 | GEO

Solubility of the Proteinogenic ?-Amino Acids in Water, Ethanol, and Ethanol-Water Mixtures.

Project description:The addition of organic solvents to ?-amino acids in aqueous solution could be an effective method in crystallization. We reviewed the available data on the solubility of ?-amino acids in water, water-ethanol mixtures, and ethanol at 298.15 K and 0.1 MPa. The solubility of l-alanine, l-proline, l-arginine, l-cysteine, and l-lysine in water and ethanol mixtures and the solubility of l-alanine, l-proline, l-arginine, l-cysteine, l-lysine, l-asparagine, l-glutamine, l-histidine, and l-leucine in pure ethanol systems were measured and are published here for the first time. The impact on the solubility of amino acids that can convert in solution, l-glutamic acid and l-cysteine, was studied. At lower concentrations, only the ninhydrin method and the ultraperfomance liquid chromatography (UPLC) method yield reliable results. In the case of ?-amino acids that convert in solution, only the UPLC method was able to discern between the different ?-amino acids and yields reliable results. Our results demonstrate that ?-amino acids with similar physical structures have similar changes in solubility in mixed water/ethanol mixtures. The solubility of l-tryptophan increased at moderate ethanol concentrations.

| S-EPMC5846082 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data