scholarly journals Terahertz Absorption Properties of Two Solid Amino Acids and Their Aqueous Solutions

2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Ping Ye ◽  
Guoyang Wang ◽  
Yizhou Yang ◽  
Qinghao Meng ◽  
Jiahui Wang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Aqueous Solutions ◽  
Density Functional ◽  
Basis Set ◽  
Molecular Vibration ◽  
Absorption Properties ◽  
Future Studies ◽  
Terahertz Absorption ◽  
The Time Domain

A new type of embedded cyclic olefin copolymer microfluidic chip was designed and combined with terahertz (THz) technology to study the effects of glycine and arginine on the THz wave absorption characteristics. This study aims to understand the interactions between solid amino acid molecules and between amino acid and water molecules and to determine the changes in their microstructure. By observing the intensity of the time domain spectra in the range of 0.2–2.6 THz, we found that, as the concentration of glycine and arginine increased, the THz transmission gradually decreased. It can be inferred that the molecular structure and quantity of different amino acids have different influence on the hydrogen bond, which affects the absorption coefficient in solution. It was also found that the terahertz technique is able to identify the solid amino acid species better, and it can also perform some species identification for liquid amino acids. These results provide a reference for future studies on the terahertz absorption properties of amino acid samples. Moreover, Gaussian16 software was used to calculate the terahertz spectra using the density functional theory, B3LYP functional, and 6-31G basis set. Additionally, Gaussian View6 video software provided the frequency values, molecular vibration modes of the theoretical absorption peaks of glycine, arginine, and its aqueous solutions in the frequency range of 0.2–2.6 THz, which offers theoretical support for future studies.

Apparent molar heat capacities and volumes of some aqueous solutions of aliphatic amino acids at 288.15, 298.15, 313.15, and 328.15 K

1994 ◽  
Vol 72 (2) ◽  
pp. 362-368 ◽  
Author(s):  
Andrew W. Hakin ◽  
Michelle M. Duke ◽  
Sheri A. Klassen ◽  
Robert M. McKay ◽  
Kathryn E. Preuss
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Aqueous Solutions ◽  
Equilibrium Constants ◽  
Heat Capacities ◽  
Apparent Molar Volumes ◽  
Protein Chemistry ◽  
Standard State ◽  
Apparent Molar Heat Capacities ◽  
Molar Volumes

The thermodynamics of amino acid systems are key to the understanding of protein chemistry. We have found that many previous studies of the apparent molar volumes and heat capacities of aqueous solutions of amino acids were conducted at the standard temperature of 298.15 K. This does not allow for the fact that most biological processes occur at temperatures removed from this standard condition.In an attempt to address this imbalance we have measured densities and heat capacities for aqueous solutions of glycine, L-alanine, L-serine, and L-threonine at 288.15, 298.15, 313.15, and 328.15 K using a Picker flow microcalorimeter. Apparent molar volumes and heat capacities, and the associated standard state partial molar properties have been calculated. Constant pressure variations of revised Helgeson, Kirkham, and Flowers equations have been fitted to calculated standard state volumes and heat capacities over the temperature range 288.15 to 328.15 K. These equations may be used to estimate standard state volumes and heat capacities, and hence equilibrium constants, for aqueous amino acid systems at higher temperatures.

The volumetric and thermochemical properties of aqueous solutions of L-valine, L-leucine, and L-isoleucine at 288.15, 298.15, 313.15, and 328.15 K

1994 ◽  
Vol 72 (6) ◽  
pp. 1489-1494 ◽  
Author(s):  
Michelle M. Duke ◽  
Andrew W. Hakin ◽  
Robert M. McKay ◽  
Kathryn E. Preuss
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Aqueous Solutions ◽  
Constant Pressure ◽  
Heat Capacities ◽  
Thermochemical Properties ◽  
Acid System ◽  
Standard State ◽  
Apparent Molar Heat Capacities ◽  
Fitting Procedures

Densities and volumetric heat capacities have been measured for aqueous solutions of L-valine, L-leucine, and L-isoleucine at 288.15, 298.15, 313.15, and 328.15 K. These data have been used to calculate apparent molar volumes, [Formula: see text] and apparent molar heat capacities, [Formula: see text] which in turn have been used to obtain standard state volumes, [Formula: see text] and standard state heat capacities, [Formula: see text] for each aqueous amino acid system. Helgeson, Kirkham, and Flowers equations, for neutral organics in water, have been used to model the calculated standard state volumes and heat capacities of the amino acids as a function of temperature at constant pressure. The results of our fitting procedures may be used to predict the behaviour of [Formula: see text] and [Formula: see text] for the selected amino acid systems outside of the temperature range utilised in this investigation.

scholarly journals Breakdown of chiral recognition of amino acids in reduced dimensions

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yongchan Jeong ◽  
Hyo Won Kim ◽  
JiYeon Ku ◽  
Jungpil Seo
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Self Assembly ◽  
Density Functional ◽  
Chiral Recognition ◽  
Density Functional Theory Calculations ◽  
The Self ◽  
Reduced Dimensions ◽  
Tunnelling Microscopy ◽  
Living Organisms

Abstract 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.

An autoradiographical study of amino acid and nucleoside incorporation during the cell cycle of Amoeba proteus

1981 ◽  
Vol 51 (1) ◽  
pp. 219-228
Author(s):  
K.I. Mills ◽  
L.G. Bell
Keyword(s):  
Cell Cycle ◽  
Amino Acids ◽  
Amino Acid ◽  
Rna Synthesis ◽  
Thymidine Incorporation ◽  
Tritiated Thymidine ◽  
Amoeba Proteus ◽  
Macromolecular Synthesis ◽  
Future Studies ◽  
Specific Proteins

The incorporation of tritiated thymidine, uridine and leucine, into the acid-precipitable material of DNA. RNA and proteins, respectively, was studied by autoradiography throughout the cell cycle of Amoeba proteus. DNA synthesis occupied the first 17 h of the cycle (57 h long) and 2 peaks between 0.5 and 9.13 h accounted for the majority of the thymidine incorporation. RNA synthesis was represented by a series of peak uridine grain counts, the 3 major peaks occurring at 10, 26–27 and 47–48 h. The incorporation of leucine also followed a pattern of peaks and dips, the main peaks occurring 1–2 h after the major increases in uridine incorporation. The fraction of label present over the nucleus decreased during the cell cycle, and this was probably due to a lowered incorporation of the leucine label by proteins synthesized in the cytoplasm and destined to become nuclear proteins. The incorporation patterns of 6 amino acids (arginine, aspartic acid, leucine, lysine, serine and valine) were studied individually during 3 periods of the cell cycle: 0-10 h (S phase); 20–30 h (early G2); and 40–50 h (mid-late G2). Variations in the intensity and timings of the incorporation maxima of the amino acids were observed, although the timings of increased grain counts of some of the amino acids frequently coincided. “Unique” incorporation peaks (i.e. only observed in one of the amino acids studied) possibly indicate the synthesis of phase-specific proteins. The amino acid and nucleoside incorporation profiles presented in this paper will enable the results obtained from future studies on amoebae to be related to the macromolecular synthesis patterns.

How to fragment a polypeptide? An ab initio computational study of pair interactions between amino acids and ligand-amino acids in proteins

2011 ◽  
Vol 76 (5) ◽  
pp. 605-618
Author(s):  
Vojtěch Klusák ◽  
Petr Dobeš ◽  
Jiří Černý ◽  
Jiří Vondrášek
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Ab Initio ◽  
Building Blocks ◽  
Basis Set ◽  
Single Amino Acid ◽  
Amino Acid Side Chain ◽  
Protein Chain ◽  
The Stability ◽  
Dispersion Term

To determine reasonably which amino acid side chain contributes significantly to the stability of a protein or to the stability of a protein–ligand complex is not a straightforward task. We suggest a partial but systematic solution of the problem by a specific fragmentation of a protein chain into blocks of single amino acid side chains with their corresponding backbone part. For such systems of building blocks, we have calculated the stabilisation/interaction energies by means of correlated ab initio calculations. We have shown that a reasonable way to treat an amino-acid residue composing the protein is to break the homonuclear C–C bond between the Cα atom and the C(O) carboxyl carbon. The reference data obtained by the RI-MP2 method with the cc-pVDZ basis set were compared with RIDFT, RIDFT augmented by the dispersion term, SCC-DFTB-D and Hartree–Fock calculations. The results clearly show the failure of those methods lacking an appropriate treatment of the correlation energy. The DFT methods augmented by the empirical dispersion term on the other hand describe the interaction in good agreement with the reference method.

scholarly journals Modern diversification of the amino acid repertoire driven by oxygen

2017 ◽  
Vol 115 (1) ◽  
pp. 41-46 ◽  
Author(s):  
Matthias Granold ◽  
Parvana Hajieva ◽  
Monica Ioana Toşa ◽  
Florin-Dan Irimie ◽  
Bernd Moosmann
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Chemical Reactivity ◽  
Protein Biosynthesis ◽  
Building Blocks ◽  
Peroxyl Radicals ◽  
Basis Set ◽  
Universal Genetic Code ◽  
Amino Acid Properties

All extant life employs the same 20 amino acids for protein biosynthesis. Studies on the number of amino acids necessary to produce a foldable and catalytically active polypeptide have shown that a basis set of 7–13 amino acids is sufficient to build major structural elements of modern proteins. Hence, the reasons for the evolutionary selection of the current 20 amino acids out of a much larger available pool have remained elusive. Here, we have analyzed the quantum chemistry of all proteinogenic and various prebiotic amino acids. We find that the energetic HOMO–LUMO gap, a correlate of chemical reactivity, becomes incrementally closer in modern amino acids, reaching the level of specialized redox cofactors in the late amino acids tryptophan and selenocysteine. We show that the arising prediction of a higher reactivity of the more recently added amino acids is correct as regards various free radicals, particularly oxygen-derived peroxyl radicals. Moreover, we demonstrate an immediate survival benefit conferred by the enhanced redox reactivity of the modern amino acids tyrosine and tryptophan in oxidatively stressed cells. Our data indicate that in demanding building blocks with more versatile redox chemistry, biospheric molecular oxygen triggered the selective fixation of the last amino acids in the genetic code. Thus, functional rather than structural amino acid properties were decisive during the finalization of the universal genetic code.

scholarly journals Ketene and Ammonia Forming Acetamide in the Interstellar Medium

2020 ◽  
Vol 14 (1) ◽  
Author(s):  
Akash Kothari ◽  
Linglan Zhu ◽  
Jon Babi ◽  
Natalie Galant ◽  
Anita Rágyanszki ◽  
...  
Keyword(s):  
Amino Acids ◽  
Interstellar Medium ◽  
Density Functional ◽  
Reaction Pathway ◽  
Building Blocks ◽  
Peptide Bond ◽  
Product Formation ◽  
Basis Set ◽  
Peptide Bonds ◽  
Dense Molecular Cloud

Background: Peptide bonds are among the fundamental building blocks of life, polymerizing amino acids to form proteins that make up the structural components of living cells and regulate biochemical processes. The detection of glycine by NASA in comet Wild 2 in 2009 suggests the possibility of the formation of biomolecules in extraterrestrial environments through the interstellar medium. Detected in the dense molecular cloud Sagittarius B2, acetamide is the largest molecule containing a peptide bond and is hypothesized to be the precursor to all amino acids; as such, viability of its formation is of important biological relevance. Methods: Under a proposed mechanism of ammonia and ketene reactants, which have also been detected in dense molecular clouds in the ISM, the reaction pathway for the formation of acetamide was modelled using quantum chemical calculations in Gaussian16, using Austin-Frisch-Petersson functional with dispersion density functional theory at a 6-31G(d) basis set level of theory to optimize geometries and determine the thermodynamic properties for the reaction. Stability of the reactants, transition states, and products were examined to establish a reasonable mechanism. Conclusion: Product formation of acetamide was found to be highly exergonic and exothermic with a low energy barrier, suggesting a mechanism that is viable in the extreme density and temperature conditions found in ISM.

scholarly journals The Surface Composition of Amino Acid - KCl Solutions is pH-Dependent

2020 ◽  
Author(s):  
Geethanjali Gopakumar ◽  
Isaak Unger ◽  
Clara-Magdalena Saak ◽  
Gunnar Öhrwall ◽  
Arnaldo Naves de Brito ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Aqueous Solutions ◽  
Photoelectron Spectroscopy ◽  
Surface Composition ◽  
Inorganic Ions ◽  
X Ray ◽  
Ph Dependent

The manuscript based on X-ray photoelectron spectroscopy on aqueous solutions containing KCl and different amino acids. Our analysis suggests that the presence of the inorganic ions at the surface of the liquid is strongly dependent on the pH of the solution and the type of amino acid.

Apparent molal heat capacities and volumes of amino acids in aqueous polyol solutions

1978 ◽  
Vol 56 (13) ◽  
pp. 1827-1831 ◽  
Author(s):  
Giuseppa DiPaola ◽  
Bernard Belleau
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Aqueous Solutions ◽  
Transfer Functions ◽  
Heat Capacities ◽  
Side Chains ◽  
Dilute Solutions ◽  
Flow Microcalorimeter ◽  
Regular Increase ◽  
Apparent Molal Heat Capacities

Densities (24 °C) and volumetric specific beats (25 °C) were measured for amino acids (0.05–0.5 m) containing apolar side chains in water, and in aqueous solutions of glycerol, mannitol, sorbitol, NaCl, urea, and Gu•HCl, with a flow densimeter and flow microcalorimeter respectively.The derived apparent molal quantifies and transfer functions of the amino acids in aqueous polyol solutions reveal no specificities which might explain the origin of the unique behavior of polyols in protein systems. However, the study did reveal a regular increase in the structure-making ability of the amino acid as the hydrophobicity of the side chains increased. This structure-making tendency was reduced significantly in dilute solutions of the higher polyols.

Exploring human porphobilinogen synthase metalloprotein by quantum biochemistry and evolutionary methods

Metallomics ◽  
2021 ◽  
Vol 13 (4) ◽  
Author(s):  
E D Barbosa ◽  
J X Lima Neto ◽  
D G Teixeira ◽  
K S Bezerra ◽  
V S do Amaral ◽  
...  
Keyword(s):  
Amino Acids ◽  
Density Functional ◽  
Basis Set ◽  
Functional Theory ◽  
Conserved Residues ◽  
Benchmark Analysis ◽  
Exchange Correlation ◽  
The Density Functional Theory ◽  
Porphobilinogen Synthase ◽  
Molecular Fractionation

Abstract Previous studies have shown the porphobilinogen synthase (PBGS) zinc-binding mechanism and its conservation among the living cells. However, the precise molecular interaction of zinc with the active center of the enzyme is unknown. In particular, quantum chemistry techniques within the density functional theory (DFT) framework have been the key methodology to describe metalloproteins, when one is looking for a compromise between accuracy and computational feasibility. Considering this, we used DFT-based models within the molecular fractionation with conjugate caps scheme to evaluate the binding energy features of zinc interacting with the human PBGS. Besides, phylogenetic and clustering analyses were successfully employed in extracting useful information from protein sequences to identify groups of conserved residues that build the ions-binding site. Our results also report a conservative assessment of the relevant amino acids, as well as the benchmark analysis of the calculation models used. The most relevant intermolecular interactions in Zn2+–PBGS are due to the amino acids CYS0122, CYS0124, CYS0132, ASP0169, SER0168, ARG0221, HIS0131, ASP0120, GLY0133, VAL0121, ARG0209, and ARG0174. Among these residues, we highlighted ASP0120, GLY0133, HIS0131, SER0168, and ARG0209 by co-occurring in all clusters generated by unsupervised clustering analysis. On the other hand, the triple cysteines at 2.5 Å from zinc (CYS0122, CYS0124, and CYS0132) have the highest energy attraction and are absent in the taxa Viridiplantae, Sar, Rhodophyta, and some Bacteria. Additionally, the performance of the DFT-based models shows that the processing time-dependence is more associated with the choice of the basis set than the exchange–correlation functional.

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