Natural selection based on coordination chemistry: computational assessment of [4Fe–4S]-maquettes with non-coded amino acids

Cysteine is the only coded amino acid in biology that contains a thiol functional group. Deprotonated thiolate is essential for anchoring iron–sulfur ([Fe–S]) clusters, as prosthetic groups to the protein matrix. [Fe–S] metalloproteins and metalloenzymes are involved in biological electron transfer, radical chemistry, small molecule activation and signalling. These are key metabolic and regulatory processes that would likely have been present in the earliest organisms. In the context of emergence of life theories, the selection and evolution of the cysteine-specific R–CH 2 –SH side chain is a fascinating question to confront. We undertook a computational [4Fe–4S]-maquette modelling approach to evaluate how side chain length can influence [Fe–S] cluster binding and stability in short 7-mer and long 16-mer peptides, which contained either thioglycine, cysteine or homocysteine. Force field-based molecular dynamics simulations for [4Fe–4S] cluster nest formation were supplemented with density functional theory calculations of a ligand-exchange reaction between a preassembled cluster and the peptide. Secondary structure analysis revealed that peptides with cysteine are found with greater frequency nested to bind preformed [4Fe–4S] clusters. Additionally, the presence of the single methylene group in cysteine ligands mitigates the steric bulk, maintains the H-bonding and dipole network, and provides covalent Fe–S(thiolate) bonds that together create the optimal electronic and geometric structural conditions for [4Fe–4S] cluster binding compared to thioglycine or homocysteine ligands. Our theoretical work forms an experimentally testable hypothesis of the natural selection of cysteine through coordination chemistry.

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A New Phase of the Na+ Ion Conductor Na3PS4

10.26434/chemrxiv.8003717.v1 ◽

2019 ◽

Author(s):

Theodosios Famprikis ◽

James Dawson ◽

François Fauth ◽

Emmanuelle Suard ◽

Benoit Fleutot ◽

...

Keyword(s):

Solid Electrolytes ◽

Density Functional ◽

Density Functional Theory Calculations ◽

Orthorhombic Crystal ◽

Orthorhombic Crystal Structure ◽

Ion Conductor ◽

Solid State Batteries ◽

Density Analysis ◽

Two Phases ◽

Dynamics Simulations

<div> Solid electrolytes are crucial for next‑generation solid‑state batteries and Na3PS4 is one of the most promising Na+ conductors for such applications. At present, two phases of Na3PS4 have been identified and it had been thought to melt above 500 °C. In contrast, we show that it remains solid above this temperature and transforms into a third polymorph, γ, exhibiting superionic behavior. We propose an orthorhombic crystal structure for γ‑Na3PS4 based on scattering density analysis of diffraction data and density functional theory calculations. We show that the Na+ superionic behavior is associated with rotational motion of the thiophosphate polyanions pointing to a rotor phase, based on ab initio molecular dynamics simulations and supported by high‑temperature synchrotron and neutron diffraction, thermal analysis and impedance spectroscopy. These findings are of importance for the development of new polyanion‑based solid electrolytes. </div>

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Graphene adlayer growth between nonepitaxial graphene and Ni(111) substrate: a promising theoretical scheme

Physical Chemistry Chemical Physics ◽

10.1039/d0cp04667a ◽

2020 ◽

Author(s):

Lijuan Meng ◽

Jinlian Lu ◽

Yujie Bai ◽

Lili Liu ◽

Tang Jingyi ◽

...

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Chemical Vapor Deposition ◽

Molecular Dynamics Simulations ◽

Vapor Deposition ◽

Density Functional ◽

Chemical Vapor ◽

Density Functional Theory Calculations ◽

Functional Theory ◽

Dynamics Simulations

Understanding the fundamentals of chemical vapor deposition bilayer graphene growth is crucial for its synthesis. By employing density functional theory calculations and classical molecular dynamics simulations, we have investigated the...

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Molecular Insights into Cage Occupancy of Hydrogen Hydrate: A Computational Study

Processes ◽

10.3390/pr7100699 ◽

2019 ◽

Vol 7 (10) ◽

pp. 699 ◽

Cited By ~ 2

Author(s):

Ma ◽

Zhong ◽

Liu ◽

Zhong ◽

Yan ◽

...

Keyword(s):

Molecular Dynamics ◽

Hydrogen Storage ◽

Molecular Dynamics Simulations ◽

Density Functional ◽

Storage Capacity ◽

Computational Study ◽

Density Functional Theory Calculations ◽

Hydrogen Storage Capacity ◽

Large Cage ◽

Dynamics Simulations

Density functional theory calculations and molecular dynamics simulations were performed to investigate the hydrogen storage capacity in the sII hydrate. Calculation results show that the optimum hydrogen storage capacity is ~5.6 wt%, with the double occupancy in the small cage and quintuple occupancy in the large cage. Molecular dynamics simulations indicate that these multiple occupied hydrogen hydrates can occur at mild conditions, and their stability will be further enhanced by increasing the pressure or decreasing the temperature. Our work highlights that the hydrate is a promising material for storing hydrogen.

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High-pressure and high-temperature physical properties of LiF studied by density functional theory calculations and molecular dynamics simulations

Journal of Physics and Chemistry of Solids ◽

10.1016/j.jpcs.2018.01.037 ◽

2018 ◽

Vol 116 ◽

pp. 209-215 ◽

Cited By ~ 5

Author(s):

Xiao-Wei Sun ◽

Zi-Jiang Liu ◽

Wei-Long Quan ◽

Ting Song ◽

Rabah Khenata ◽

...

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

High Pressure ◽

High Temperature ◽

Physical Properties ◽

Molecular Dynamics Simulations ◽

Density Functional ◽

Density Functional Theory Calculations ◽

Functional Theory ◽

Dynamics Simulations

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Characterization of acetylated histidine b1-ion structure: A competition between oxazolone and side chain imidazole moiety

European Journal of Mass Spectrometry ◽

10.1177/1469066718756801 ◽

2018 ◽

Vol 24 (3) ◽

pp. 261-268 ◽

Cited By ~ 2

Author(s):

Kranthikumar Yadav ◽

J Laxmikanth Rao ◽

R Srinivas ◽

R Nagaraj ◽

MV Jagannadham

Keyword(s):

Density Functional ◽

Density Functional Theory Calculations ◽

Mass Spectrometric Study ◽

Research Area ◽

Side Chain ◽

Oxazolone Structure ◽

Post Translational Modifications ◽

Tandem Mass Spectrometric ◽

Oxazolone Ring

The detection of post-translational modifications of proteins is an important comprehensive research area. Over the years, proteomic studies involving protein acetylation have attracted a great deal of attention. In the present study, we have focussed on the acetylation of histidine and the intrinsic stability of b1-ion of oxazolone ring and/or with side chain imidazole bicyclic product. The formation of oxazolone structure may occur when an amino moiety undergoes acetylation reaction and when it is present in the vicinity of the side chain imidazole moiety. Tryptic peptides generated from the proteins of Acenitobacter radioresistens MMC5-containing N-terminal histidine were explored in a standard proteomic workflow. Formation of [Formula: see text] ion with an oxazolone ring in these peptides has been supported by a tandem mass spectrometric study of a synthetic peptide and density functional theory calculations. The results obtained from this study have implications in understanding the fragmentation of the peptides generated in the proteomic workflows.

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The Role of SiH3 Diffusion in Determining the Surface Smoothness of Plasma-Deposited Amorphous Si Thin Films: An Atomic-Scale Analysis

MRS Proceedings ◽

10.1557/proc-862-a3.2 ◽

2005 ◽

Vol 862 ◽

Author(s):

Mayur S. Valipa ◽

Tamas Bakos ◽

Eray S. Aydil ◽

Dimitrios Maroudas

Keyword(s):

Thin Films ◽

Density Functional ◽

Activation Barrier ◽

Density Functional Theory Calculations ◽

Atomic Scale ◽

Functional Theory ◽

Weak Adsorption ◽

Dynamics Simulations ◽

Hydrogenated Amorphous

AbstractDevice-quality hydrogenated amorphous silicon (a-Si:H) thin films grown under conditions where the SiH3 radical is the dominant deposition precursor are remarkably smooth, as the SiH3 radical is very mobile and fills surface valleys during its diffusion on the a-Si:H surface. In this paper, we analyze atomic-scale mechanisms of SiH3 diffusion on a-Si:H surfaces based on molecular-dynamics simulations of SiH3 radical impingement on surfaces of a-Si:H films. The computed average activation barrier for radical diffusion on a-Si:H is 0.16 eV. This low barrier is due to the weak adsorption of the radical onto the a-Si:H surface and its migration predominantly through overcoordination defects; this is consistent with our density functional theory calculations on crystalline Si surfaces. The diffusing SiH3 radical incorporates preferentially into valleys on the a-Si:H surface when it transfers an H atom and forms a Si-Si backbond, even in the absence of dangling bonds.

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Functional stability of water wire–carbonyl interactions in an ion channel

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2001083117 ◽

2020 ◽

Vol 117 (22) ◽

pp. 11908-11915 ◽

Cited By ~ 1

Author(s):

Joana Paulino ◽

Myunggi Yi ◽

Ivan Hung ◽

Zhehong Gan ◽

Xiaoling Wang ◽

...

Keyword(s):

Hydrogen Bonding ◽

Nmr Spectroscopy ◽

Lipid Bilayers ◽

Density Functional ◽

Liquid Crystalline ◽

Density Functional Theory Calculations ◽

Bulk Water ◽

Simple Explanation ◽

Dynamics Simulations ◽

Water Hydrogen

Water wires are critical for the functioning of many membrane proteins, as in channels that conduct water, protons, and other ions. Here, in liquid crystalline lipid bilayers under symmetric environmental conditions, the selective hydrogen bonding interactions between eight waters comprising a water wire and a subset of 26 carbonyl oxygens lining the antiparallel dimeric gramicidin A channel are characterized by17O NMR spectroscopy at 35.2 T (or 1,500 MHz for1H) and computational studies. While backbone15N spectra clearly indicate structural symmetry between the two subunits, single site17O labels of the pore-lining carbonyls report two resonances, implying a break in dimer symmetry caused by the selective interactions with the water wire. The17O shifts document selective water hydrogen bonding with carbonyl oxygens that are stable on the millisecond timescale. Such interactions are supported by density functional theory calculations on snapshots taken from molecular dynamics simulations. Water hydrogen bonding in the pore is restricted to just three simultaneous interactions, unlike bulk water environs. The stability of the water wire orientation and its electric dipole leads to opposite charge-dipole interactions for K+ions bound at the two ends of the pore, thereby providing a simple explanation for an ∼20-fold difference in K+affinity between two binding sites that are ∼24 Å apart. The17O NMR spectroscopy reported here represents a breakthrough in high field NMR technology that will have applications throughout molecular biophysics, because of the acute sensitivity of the17O nucleus to its chemical environment.

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Insights into structural and dynamical features of water at halloysite interfaces probed by DFT and classical molecular dynamics simulations

Physical Chemistry Chemical Physics ◽

10.1039/c5cp05920h ◽

2016 ◽

Vol 18 (3) ◽

pp. 2164-2174 ◽

Cited By ~ 14

Author(s):

Davide Presti ◽

Alfonso Pedone ◽

Giordano Mancini ◽

Celia Duce ◽

Maria Rosaria Tiné ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Density Functional ◽

Density Functional Theory Calculations ◽

Water Molecules ◽

Functional Theory ◽

Structure And Dynamics ◽

Classical Molecular Dynamics ◽

Dynamical Features ◽

Dynamics Simulations

Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension.

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Classical Polarizable Force Field to Study Hydrated Hectorite: Optimization on DFT Calculations and Validation against XRD Data

Minerals ◽

10.3390/min8050205 ◽

2018 ◽

Vol 8 (5) ◽

pp. 205 ◽

Cited By ~ 3

Author(s):

Ragnhild Hånde ◽

Vivien Ramothe ◽

Stéphane Tesson ◽

Baptiste Dazas ◽

Eric Ferrage ◽

...

Keyword(s):

Force Field ◽

Density Functional ◽

Density Functional Theory Calculations ◽

X Ray Diffraction ◽

Electronic Density ◽

Functional Theory ◽

Polarizable Force Field ◽

Xrd Patterns ◽

The One ◽

Dynamics Simulations

Following our previous works on dioctahedral clays, we extend the classical Polarizable Ion Model (PIM) to trioctahedral clays, by considering dry Na-, Cs-, Ca- and Sr-hectorites as well as hydrated Na-hectorite. The parameters of the force field are determined by optimizing the atomic forces and dipoles on density functional theory calculations. The simulation results are validated by comparison with experimental X-ray diffraction (XRD) data. The XRD patterns calculated from classical molecular dynamics simulations performed with the PIM force field are in very good agreement with experimental results. In the bihydrated state, the less structured electronic density profile obtained with PIM compared to the one from the state-of-the-art non-polarizable force field clayFF explains the slightly better agreement between the PIM results and experiments.

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