Experimental vibrational spectroscopy (FTIR and FT-Raman) of D-tryptophan and its anharmonic theoretical studies using density functional theory

Catalytic Strategy for Chemical Analysis of Volatile Iodine with the Assistance of Machine Learning

A strategy of catalytic chemical detection (CCD) with the assistance of a machine learning (ML) approach was proposed and evaluated in this work. In the CCD method, the target analyte acts as the catalyst of the detection reaction rather than traditional reactants. The detection of a typical environmental contaminant-volatile iodine was selected as an example to establish the general routine in designing CCD. One major obstacle lies in the complex of manual selection of detection reaction, especially considering that more than 650,000 related reactions were exhibited in SciFinder database. Traditional workflow is time-consuming and material-consuming; therefore, the ML approach with descriptors directly related to CCD was employed. The reaction of indoles and aromatic aldehydes to bis(indolyl)methanes was screened out with the ML approach. After preliminary experiments, the screened reaction for iodine detection achieved desirable sensitivity, specificity, and recognizability simultaneously. The fabricated sensor devices were practicable for portable detection in real gas samples with a low concentration. This work provides a practical example of chemical analysis based on catalytic strategy and exemplifies the powerful application for the ML method in chemistry through the introduction of original descriptors.

Molecularly Imprinted Polymer-Amyloid Fibril-Based Electrochemical Biosensor for Ultrasensitive Detection of Tryptophan

A tryptophan (Trp) sensor was investigated based on electrochemical impedance spectroscopy (EIS) of a molecularly imprinted polymer on a lysozyme amyloid fibril (MIP-AF). The MIP-AF was composed of aniline as a monomer chemically polymerized in the presence of a Trp template molecule onto the AF surface. After extracting the template molecule, the MIP-AF had cavities with a high affinity for the Trp molecules. The obtained MIP-AF demonstrated rapid Trp adsorption and substantial binding capacity (50 µM mg⁻¹). Trp determination was studied using non-Faradaic EIS by drop drying the MIP-AF on the working electrode of a screen-printed electrode. The MIP-AF provided a large linear range (10 pM–80 µM), a low detection limit (8 pM), and high selectivity for Trp determination. Furthermore, the proposed method also indicates that the MIP-AF can be used to determine Trp in real samples such as milk and cancer cell media.

Silva AG, Fonseca MG, Silva-Filho EC. Clay Mineral Minerals as a Strategy for Biomolecule Incorporation: Amino Acids Approach

The potential use of amino acids by ruminal microorganisms converting them into microbial protein for ruminants makes it challenging to supplement these nutrients in an accessible form in animals' diets. Several strategies to protect amino acids from ruminal degradation were reported, producing amino acids available for the protein used in the intestine called "bypass." The intercalation of biomolecules in clay mineral minerals has gained notoriety due to its ability to support, protect, transport, physicochemical properties and non-toxicity. This study aimed to investigate the incorporation of L-lysine (Lys), L-methionine (Met), and L-tryptophan (Trp) amino acids in the clay minerals sepiolite (Sep) and Veegum® (Veg) using the adsorption method. The characterization techniques of X-ray diffraction and infrared spectroscopy indicated the presence of biomolecules in the inorganic matrices. Elemental and thermal analyzes monitored the percentages of incorporated amino acids. They showed better incorporation capacities for Veg, such as Met-Veg < Lys-Veg < Trp-Veg and Lys-Sep < Met-Sep < Trp-Sep for sepiolite, except for the incorporation of Met. Matrices provide a promising alternative for planning the administration of biomolecules, using essential amino acids as models, and may offer an alternative to improve functional diet strategies.

Electrochemical Amino Acid Sensing: A Review on Challenges and Achievements

The rapid growth of research in electrochemistry in the last decade has resulted in a significant advancement in exploiting electrochemical strategies for assessing biological substances. Among these, amino acids are of utmost interest due to their key role in human health. Indeed, an unbalanced amino acid level is the origin of several metabolic and genetic diseases, which has led to a great need for effective and reliable evaluation methods. This review is an effort to summarize and present both challenges and achievements in electrochemical amino acid sensing from the last decade (from 2010 onwards) to show where limitations and advantages stem from. In this review, we place special emphasis on five well-known electroactive amino acids, namely cysteine, tyrosine, tryptophan, methionine and histidine. The recent research and achievements in this area and significant performance metrics of the proposed electrochemical sensors, including the limit of detection, sensitivity, stability, linear dynamic range(s) and applicability in real sample analysis, are summarized and presented in separate sections. More than 400 recent scientific studies were included in this review to portray a rich set of ideas and exemplify the capabilities of the electrochemical strategies to detect these essential biomolecules at trace and even ultra-trace levels. Finally, we discuss, in the last section, the remaining issues and the opportunities to push the boundaries of our knowledge in amino acid electrochemistry even further.

Planarity and out-of-plane vibrational modes of tryptophan and tyrosine in biomolecular modeling

Tryptophan and tyrosine are amino acids that play significant roles in the folding processes of proteins at water-membrane interfaces because of their amphipathic heteroaromatic rings. Employing appropriate heteroaromatic molecular structures is essential for obtaining accurate dynamics and predictive capabilities in molecular simulations of these amino acids. In this study, molecular dynamics simulations that applied the most recent version of the CHARMM36 force field were conducted on aqueous solutions of tryptophan and of tyrosine. Geometric analysis and dynamics quantified how aromatic rings deviated from planar structures and exhibited out-of-plane fluctuations. Radial distribution functions showed possible biological significance because the extent of ring planarity slightly affected local water concentrations near aromatic rings. Instantaneous all-atom normal mode analysis (NMA) and Fourier transformation of time autocorrelation functions of out-of-plane displacements were applied to study out-of-plane vibrations of atoms in these rings. The NMA started with minimum energy configurations and then averaged over fluctuations in aqueous solution. The frequencies and frequency patterns that were obtained for tryptophan and tyrosine with CHARMM36 differed from literature reports of Raman spectra, infrared spectra, and frequencies calculated using quantum mechanics, with some out-of-plane modes found at higher frequencies. Effects of imposing improper torsion potentials and changing torsion angle force constants were investigated for all atoms in the rings of tryptophan and tyrosine. Results show that these coarse force field variations only affect planarity and out-of-plane vibrations of atoms within the rings, and not other vibrations. Although increasing improper torsion force constants reduced deviations from aromatic ring planarity significantly, it increased out-of-plane mode frequencies. Reducing torsion angle force constants (with and without improper torsions) shifted modes to lower frequencies. A combination of decreasing most torsion angle force constants for ring atoms in both amino acids and including improper torsion forces attained frequencies and frequency patterns for out-of-plane normal modes that were more similar to the literature spectra. These force field variations decreased the extents of out-of-plane vibrations within the heteroaromatic rings of tryptophan, especially around the nitrogen atom in the ring, but not within the heteroaromatic ring of tyrosine. Conclusions were unaffected by the peptide endgroup, water, or simulation ensemble.