scholarly journals Density functional theory-based investigation of HCN and NH3 formation mechanisms during phenylalanine pyrolysis

RSC Advances ◽  
2020 ◽  
Vol 10 (47) ◽  
pp. 28431-28436
Author(s):  
Baizhong Sun ◽  
Chuanqun Liu ◽  
Deyong Che ◽  
Hongpeng Liu ◽  
Shuai Guo
Keyword(s):  
Amino Acids ◽  
Density Functional Theory ◽  
Density Functional ◽  
Nitrogen Transfer ◽  
Formation Mechanisms ◽  
Functional Theory ◽  
Nh3 Formation

As sludge pyrolysis produces large amounts of toxic NH3 and HCN, many works have studied nitrogen transfer during this process, commonly employing amino acids as models of sludge protein.

scholarly journals Predicting Core Level Photoelectron Spectra of Amino Acids Using Density Functional Theory

2020 ◽  
Vol 11 (6) ◽  
pp. 2256-2262
Author(s):  
Jo M. Pi ◽  
Martina Stella ◽  
Nathalie K. Fernando ◽  
Aaron Y. Lam ◽  
Anna Regoutz ◽  
...  
Keyword(s):  
Amino Acids ◽  
Density Functional Theory ◽  
Density Functional ◽  
Core Level ◽  
Photoelectron Spectra ◽  
Functional Theory

Adsorption characteristics of amino acids on graphene and germanene using dispersion-corrected density functional theory

2021 ◽  
Vol 127 ◽  
pp. 114498
Author(s):  
Azadeh Ayatollahi ◽  
Mahmood Rezaee Roknabadi ◽  
Mohammad Behdani ◽  
Nasser Shahtahmassebi ◽  
Biplab Sanyal
Keyword(s):  
Amino Acids ◽  
Density Functional Theory ◽  
Density Functional ◽  
Functional Theory ◽  
Adsorption Characteristics

Experimental and Theoretical Study of the First Vanadocene(IV) Complexes of α-Amino Acids Prepared from Vanadocene Dichloride

2004 ◽  
Vol 69 (4) ◽  
pp. 811-821 ◽  
Author(s):  
Jaromír Vinklárek ◽  
Hana Paláčková ◽  
Jan Honzíček
Keyword(s):  
Amino Acids ◽  
Density Functional Theory ◽  
Density Functional ◽  
Theoretical Study ◽  
Model Systems ◽  
Amino Groups ◽  
Aqueous Methanol ◽  
Functional Theory ◽  
Elemental Analyses ◽  
Vanadocene Dichloride

The first bioinorganic vanadocene(IV) complexes of α-amino acids ([Cp2V(aa)]Cl, Cp = η5-C5H5, aa = glycine, L-alanine, L-valine) were prepared by reaction of vanadocene dichloride ([Cp2VCl2]) and α-amino acids in aqueous methanol. Analogous cationic complexes with PF6- counterions were obtained by metathetical reactions of the chloride precursors with KPF6. These compounds are of great interest as model systems for the vanadocene moiety binding to proteins. All complexes have been characterized by elemental analyses and IR, Raman and EPR spectroscopies. On the basis of EPR spectra, a chelate in all the studied complexes was proposed, formed by the carboxylato and amino groups. This structure has also been confirmed by density functional theory (DFT) calculations.

scholarly journals Investigating 3,4-Bis(3-Nitrofurazan-4-Yl)furoxan Detonation with a Rapidly Tuned Density Functional Tight Binding Model

2021 ◽  
Author(s):  
Rebecca Lindsey ◽  
Sorin Bastea ◽  
Nir Goldman ◽  
Laurence E. Fried
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Tight Binding ◽  
Computational Cost ◽  
Formation Mechanisms ◽  
Extreme Conditions ◽  
Clear Understanding ◽  
Molecular Materials ◽  
Functional Theory ◽  
Complete Combustion

<p>Carbon rich materials lacking sufficient oxygen to undergo complete combustion have long been known to produce nanocarbon condensates of utility to industries spanning nanomedicine to quantum computing, when subject to strong shockwaves. However, the associated extreme conditions (e.g. 1000s of K and 10s of GPa) and rapid system evolution (e.g. 10s of ps) has precluded a clear understanding of early time phenomena giving way to carbon condensate formation. The semi-quantum density functional theory tight binding (DFTB) simulation method is ideal for studying chemistry on these timescales, offering much of the predictive power of density functional theory (DFT) at a fraction of the computational cost. However available parameterizations are not designed for application to organic molecular materials under extreme conditions.</p><p><i>Here, we describe a new machine learning (ML) approach for rapidly tuning DFTB models to simulate molecular materials under extreme conditions and demonstrate its application to modeling of 3,4-bis(3-nitrofurazan-4-yl)furoxan (i.e. DNTF), which has recently been shown to produce liquid carbon nanodroplets upon detonation that subsequently solidify into graphitic nano-onions</i>. We investigate early shockwave-driven decomposition chemistry to determine (1) major chemical kinetics steps, (2) the DNTF shock equation of state, and (3) implications of (1) and (2) for the DNTF nanocarbon formation mechanisms. We find evolution to be characterized by release of CO<sub>2</sub>, N<sub>2</sub>, and CO, as well as large C<i><sub>x</sub></i>N<i><sub>y</sub></i>O<i><sub>z</sub></i> species that are likely to be precursors to the experimentally observed carbon nano onions. Moreover, we find O purification (i.e. via CO<sub>2</sub> elimination) more rapid than that of N (i.e. via N<sub>2</sub> elimination), consistent with the experimentally observed N-containing species entrainment within the carbon condensates. Ultimately, we find the present developed ML-driven DFTB tuning approach well suited to the study of chemistry under extreme conditions, by providing a means of achieving long-timescale simulation with DFT-accuracy.</p><p> </p>

scholarly journals Density-functional theory study of gramicidin A ion channel geometry and electronic properties

2013 ◽  
Vol 10 (89) ◽  
pp. 20130547 ◽  
Author(s):  
Milica Todorović ◽  
David R. Bowler ◽  
Michael J. Gillan ◽  
Tsuyoshi Miyazaki
Keyword(s):  
Amino Acids ◽  
Density Functional Theory ◽  
Ion Channel ◽  
Ground State ◽  
Density Functional ◽  
Gramicidin A ◽  
Linear Scaling ◽  
Side Chains ◽  
Functional Theory ◽  
Ground State Geometry

Understanding the mechanisms underlying ion channel function from the atomic-scale requires accurate ab initio modelling as well as careful experiments. Here, we present a density functional theory (DFT) study of the ion channel gramicidin A (gA), whose inner pore conducts only monovalent cations and whose conductance has been shown to depend on the side chains of the amino acids in the channel. We investigate the ground state geometry and electronic properties of the channel in vacuum, focusing on their dependence on the side chains of the amino acids. We find that the side chains affect the ground state geometry, while the electrostatic potential of the pore is independent of the side chains. This study is also in preparation for a full, linear scaling DFT study of gA in a lipid bilayer with surrounding water. We demonstrate that linear scaling DFT methods can accurately model the system with reasonable computational cost. Linear scaling DFT allows ab initio calculations with 10 000–100 000 atoms and beyond, and will be an important new tool for biomolecular simulations.

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