Theoretical Calculations on Small Amino Acids

2000 ◽  
pp. 15-26
Author(s):  
Anne-Marie Sapse
Keyword(s):  
Amino Acids ◽  
Theoretical Calculations

scholarly journals A single-molecule electrical approach for amino acid detection and chirality recognition

2021 ◽  
Vol 7 (10) ◽  
pp. eabe4365
Author(s):  
Zihao Liu ◽  
Xingxing Li ◽  
Hiroshi Masai ◽  
Xinyi Huang ◽  
Susumu Tsuda ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Single Molecule ◽  
Theoretical Calculations ◽  
Protein Sequencing ◽  
Current Fluctuations ◽  
Point Contacts ◽  
Conductance Data ◽  
Single Molecule Junctions

One of the ultimate goals of analytic chemistry is to efficiently discriminate between amino acids. Here we demonstrate this ability using a single-molecule electrical methodology based on molecular nanocircuits formed from stable graphene-molecule-graphene single-molecule junctions. These molecular junctions are fabricated by covalently bonding a molecular machine featuring a permethylated-β-cyclodextrin between a pair of graphene point contacts. Using pH to vary the type and charge of the amino acids, we find distinct multimodal current fluctuations originating from the different host-guest interactions, consistent with theoretical calculations. These conductance data produce characteristic dwell times and shuttling rates for each amino acid, and allow accurate, statistical real-time, in situ measurements. Testing four amino acids and their enantiomers shows the ability to distinguish between them within a few microseconds, thus paving a facile and precise way to amino acid identification and even single-molecule protein sequencing.

scholarly journals Oxidation of amino acids by peracetic acid: Reaction kinetics, pathways and theoretical calculations

2018 ◽  
Vol 1 ◽  
pp. 100002 ◽  
Author(s):  
Penghui Du ◽  
Wen Liu ◽  
Hongbin Cao ◽  
He Zhao ◽  
Ching-Hua Huang
Keyword(s):  
Amino Acids ◽  
Reaction Kinetics ◽  
Peracetic Acid ◽  
Theoretical Calculations ◽  
Acid Reaction

scholarly journals Transferability and reproducibility in electron-density studies – bond-topological and atomic properties of tripeptides of the type L-alanyl-X-L-alanine

2009 ◽  
Vol 65 (4) ◽  
pp. 488-501 ◽  
Author(s):  
Simon Grabowsky ◽  
Roman Kalinowski ◽  
Manuela Weber ◽  
Diana Förster ◽  
Carsten Paulmann ◽  
...  
Keyword(s):  
Amino Acids ◽  
Electron Density ◽  
Crystal Packing ◽  
Theoretical Calculations ◽  
Data Bank ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Model Case ◽  
Atomic Properties ◽  
Chemical Effects

In the last decade three different data bank approaches have been developed that are intended to make electron-density examinations of large biologically important molecules possible. They rely on Bader's concept of transferability of submolecular fragments with retention of their electronic properties. Therefore, elaborate studies on the quantification of transferability in experiment and theory are still very important. Tripeptides of the type L-alanyl-X-L-alanine (X being any of the 20 naturally encoded amino acids) serve as a model case between amino acids and proteins. The two experimental electron-density determinations (L-alanyl-L-histidinyl-L-alanine and L-alanyl-L-phenylalanyl-L-alanine, highly resolved synchrotron X-ray diffraction data sets) performed in this study and theoretical calculations on all 20 different L-alanyl-X-L-alanine molecules contribute to a better estimation of transferability in the peptide case. As a measure of reproducibility and transferability, standard deviations from averaging over bond-topological and atomic properties of atoms or bonds that are considered equal in their chemical environments were calculated. This way, transferability and reproducibility indices were introduced. It can be shown that experimental transferability indices generally slightly exceed experimental reproducibility indices and that these larger deviations can be attributed to chemical effects such as changes in the geometry (bond lengths and angles), the polarization pattern and the neighboring sphere due to crystal packing. These effects can partly be separated from each other and quantified with the help of gas-phase calculations at optimized and experimental geometries. Thus, the degree of transferability can be quantified in very narrow limits taking into account experimental errors and chemical effects.

scholarly journals Amino acids as corrosion inhibitors for copper in acidic medium: Experimental and theoretical study

2013 ◽  
Vol 78 (12) ◽  
pp. 2069-2086 ◽  
Author(s):  
Ingrid Milosev ◽  
Jasminka Pavlinac ◽  
Milan Hodoscek ◽  
Antonija Lesar
Keyword(s):  
Amino Acids ◽  
Density Functional ◽  
Corrosion Inhibitors ◽  
Inhibition Efficiency ◽  
Theoretical Study ◽  
Theoretical Calculations ◽  
Dynamic Simulations ◽  
Protonated Forms ◽  
Dynamics Simulations ◽  
Green Corrosion Inhibitors

Experimental electrochemical methods combined with quantum chemical calculations and molecular dynamics simulations were used to investigate the possibility of use various amino acids as ?green? corrosion inhibitors for copper in 0.5 M HCl solution. Among eleven amino acids studied, cysteine achieved the highest inhibitor effectiveness reaching 52% at 10 mM concentration. Other amino acids reached achieved effectiveness less than 25%, some of them even acted as corrosion accelerators. Based on the experimental results, theoretical calculations and simulations were focused on cysteine and alanine. The electronic and reactivity parameters of their protonated forms in electrical double layer were evaluated by density functional calculations. In addition, molecular dynamic simulations were introduced to follow the adsorption behaviour of these two amino acids at the Cu(111) surface in the electrolyte solution. The results indicate that the orientation of both molecules is nearly parallel to the surface except of ammonium group which is directed away from the surface. Therefore, as the orientation of the cysteine and alanine molecules at the surface is similar, thiol functional group is responsible for superior inhibition efficiency of cysteine.

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