scholarly journals Validation by Molecular Dynamics of the Major Components of Sugarcane Vinasse, On a Surface of Calcium Carbonate (Calcite)

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2353
Author(s):  
Oscar Eduardo Rojas Álvarez ◽  
María Inés Nicolás Vázquez ◽  
Jose Oñate-Garzón ◽  
Carlos A. Arango
Keyword(s):  
Molecular Dynamics ◽  
Calcium Carbonate ◽  
Hydrogen Bonds ◽  
Crystalline Structure ◽  
Sugar Cane ◽  
Significant Proportion ◽  
Protein Component ◽  
Glycerol Molecule ◽  
Carbonate Group ◽  
Sugar Cane Vinasse

There is ongoing interest in the alcohol industry to significantly reduce and/or add value to the liquid residue, vinasse, produced after the distillation and rectification of ethanol from sugar cane. Vinasse contains potassium, glycerol, and a protein component that can cause environmental issues if improperly disposed of. Currently, some industries have optimized their processes to reduce waste, and a significant proportion of vinasse is being considered for use as an additive in other industrial processes. In the manufacture of cement and asphalt, vinasse has been used in the mixtures at low concentrations, albeit with some physical and mechanical problems. This work is the first molecular approximation of the components of the sugar cane vinasse in an industrial context, and it provides atomic details of complex molecular events. In the current study, the major components of sugar cane vinasse, alone or complexed on the surface of calcium carbonate, were modeled and simulated using molecular dynamics. The results showed that the protein component, represented by the mannoprotein Mp1p, has a high affinity for forming hydrogen bonds with potassium and glycerol in the vinasse. Additionally, it provides atomic stability to the calcium carbonate surface, preserving the calcite crystalline structure in the same way potassium ions interact with the carbonate group through ion–dipole interactions to improve the cohesion of the modeled surface. On the contrary, when the glycerol molecule interacts with calcium carbonate using more than two hydrogen bonds, it triggers the breakdown of the crystalline structure of calcite expanding the ionic pair.

scholarly journals Sensitivity of Intra- and Intermolecular Interactions of Benzo[h]quinoline from Car–Parrinello Molecular Dynamics and Electronic Structure Inspection

2021 ◽  
Vol 22 (10) ◽  
pp. 5220
Author(s):  
Jarosław J. Panek ◽  
Joanna Zasada ◽  
Bartłomiej M. Szyja ◽  
Beata Kizior ◽  
Aneta Jezierska
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Quantum Effects ◽  
Potential Of Mean Force ◽  
Probability Density Distribution ◽  
Donor And Acceptor ◽  
Nuclear Quantum Effects ◽  
Vibrational Features

The O-H...N and O-H...O hydrogen bonds were investigated in 10-hydroxybenzo[h]quinoline (HBQ) and benzo[h]quinoline-2-methylresorcinol complex in vacuo, solvent and crystalline phases. The chosen systems contain analogous donor and acceptor moieties but differently coupled (intra- versus intermolecularly). Car–Parrinello molecular dynamics (CPMD) was employed to shed light onto principle components of interactions responsible for the self-assembly. It was applied to study the dynamics of the hydrogen bonds and vibrational features as well as to provide initial geometries for incorporation of quantum effects and electronic structure studies. The vibrational features were revealed using Fourier transformation of the autocorrelation function of atomic velocity and by inclusion of nuclear quantum effects on the O-H stretching solving vibrational Schrödinger equation a posteriori. The potential of mean force (Pmf) was computed for the whole trajectory to derive the probability density distribution and for the O-H stretching mode from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling and nuclear quantum effects. The electronic structure changes of the benzo[h]quinoline-2-methylresorcinol dimer and trimers were studied based on Constrained Density Functional Theory (CDFT) whereas the Electron Localization Function (ELF) method was applied for all systems. It was found that the bridged proton is localized on the donor side in both investigated systems in vacuo. The crystalline phase simulations indicated bridged proton-sharing and transfer events in HBQ. These effects are even more pronounced when nuclear quantization is taken into account, and the quantized Pmf allows the proton to sample the acceptor area more efficiently. The CDFT indicated the charge depletion at the bridged proton for the analyzed dimer and trimers in solvent. The ELF analysis showed the presence of the isolated proton (a signature of the strongest hydrogen bonds) only in some parts of the HBQ crystal simulation. The collected data underline the importance of the intramolecular coupling between the donor and acceptor moieties.

scholarly journals Curcumin Inhibits the Primary Nucleation of Amyloid-Beta Peptide: A Molecular Dynamics Study

Biomolecules ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1323
Author(s):  
Irini Doytchinova ◽  
Mariyana Atanasova ◽  
Evdokiya Salamanova ◽  
Stefan Ivanov ◽  
Ivan Dimitrov
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Amyloid Beta ◽  
Amyloid Plaques ◽  
Amyloid Beta Peptide ◽  
Aβ Peptides ◽  
Amyloid Peptides ◽  
Primary Nucleation ◽  
Beta Peptide ◽  
Good Agreement

The amyloid plaques are a key hallmark of neurodegenerative diseases such as Alzheimer’s disease and Parkinson’s disease. Amyloidogenesis is a complex long-lasting multiphase process starting with the formation of nuclei of amyloid peptides: a process assigned as a primary nucleation. Curcumin (CU) is a well-known inhibitor of the aggregation of amyloid-beta (Aβ) peptides. Even more, CU is able to disintegrate preformed Aβ firbils and amyloid plaques. Here, we simulate by molecular dynamics the primary nucleation process of 12 Aβ peptides and investigate the effects of CU on the process. We found that CU molecules intercalate among the Aβ chains and bind tightly to them by hydrogen bonds, hydrophobic, π–π, and cation–π interactions. In the presence of CU, the Aβ peptides form a primary nucleus of a bigger size. The peptide chains in the nucleus become less flexible and more disordered, and the number of non-native contacts and hydrogen bonds between them decreases. For comparison, the effects of the weaker Aβ inhibitor ferulic acid (FA) on the primary nucleation are also examined. Our study is in good agreement with the observation that taken regularly, CU is able to prevent or at least delay the onset of neurodegenerative disorders.

WHICH IS THE PROTON-SHUTTLE IN ISOXANTHOPTERIN DEAMINASE? QM/MM MD UNDERSTANDING

2013 ◽  
Vol 12 (08) ◽  
pp. 1341002 ◽  
Author(s):  
XIN ZHANG ◽  
MING LEI
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Glutamic Acid ◽  
Active Site ◽  
Nucleophilic Attack ◽  
Zinc Ions ◽  
Initial Model ◽  
Dynamics Simulations

The deamination process of isoxanthopterin catalyzed by isoxanthopterin deaminase was determined using the combined QM(PM3)/MM molecular dynamics simulations. In this paper, the updated PM3 parameters were employed for zinc ions and the initial model was built up based on the crystal structure. Proton transfer and following steps have been investigated in two paths: Asp336 and His285 serve as the proton shuttle, respectively. Our simulations showed that His285 is more effective than Aap336 in proton transfer for deamination of isoxanthopterin. As hydrogen bonds between the substrate and surrounding residues play a key role in nucleophilic attack, we suggested mutating Thr195 to glutamic acid, which could enhance the hydrogen bonds and help isoxanthopterin get close to the active site. The simulations which change the substrate to pterin 6-carboxylate also performed for comparison. Our results provide reference for understanding of the mechanism of deaminase and for enhancing the deamination rate of isoxanthopterin deaminase.

scholarly journals Car–Parrinello and path integral molecular dynamics study of the intramolecular hydrogen bonds in the crystals of benzoylacetone and dideuterobenzoylacetone

2014 ◽  
Vol 16 (42) ◽  
pp. 23026-23037 ◽  
Author(s):  
Piotr Durlak ◽  
Zdzisław Latajka
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Path Integral ◽  
Molecular Crystal ◽  
Short Hydrogen Bond ◽  
Deuterated Analogue ◽  
Dynamics Simulations ◽  
Intramolecular Hydrogen

The dynamics of the intramolecular short hydrogen bond in the molecular crystal of benzoylacetone and its deuterated analogue are investigated using ab initio molecular dynamics simulations.

scholarly journals Ultrastructure of the earthworm calciferous gland. A preliminary study

2009 ◽  
Vol 15 (S3) ◽  
pp. 25-26
Author(s):  
J. Méndez ◽  
J. B. Rodríguez ◽  
R. Álvarez-Otero ◽  
M. J. I. Briones ◽  
L. Gago-Duport
Keyword(s):  
Calcium Carbonate ◽  
Crystalline Structure ◽  
Concentrated Suspension ◽  
Earthworm Species ◽  
Preliminary Study

AbstractThe earthworm species belonging to the Lumbricidae family (Annelida, Oligochaeta) posses a complex oesophageal organ known as “calciferous gland” which secretes a concentrated suspension of calcium carbonate. Previous studies have demonstrated the non-crystalline structure of this calcareous fluid representing an interesting example of biomineralisation.

Molecular dynamics models and thermodynamic characteristics of hydrogen bonds in 1,2-ethanediol

2017 ◽  
Vol 91 (6) ◽  
pp. 1056-1063 ◽  
Author(s):  
T. M. Usacheva ◽  
V. I. Zhuravlev ◽  
N. V. Lifanova ◽  
V. K. Matveev
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Thermodynamic Characteristics ◽  
Dynamics Models

Influence of a Combined Low Dosage Gas Hydrate Inhibitor on Methane Hydrate Surface

2014 ◽  
Vol 1008-1009 ◽  
pp. 300-306
Author(s):  
Cui Ping Tang ◽  
Dong Liang Li ◽  
De Qing Liang
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Gas Hydrate ◽  
Methane Hydrate ◽  
Md Simulation ◽  
Side Group ◽  
Large Space ◽  
Surface Molecules ◽  
Low Dosage

According to analysis of the gas hydrate cage and structure of the inhibitor and simulation of molecular dynamics, the interaction between GHI1 and hydrates was discussed. The structure analysis indicated the side group of PVP can insert into the open hydrate cage, and force the hydrate growing along the polymer chain, which results in a large space resistance and inhibits gas hydrate agglomerating. The results of MD simulation show GHI1 can damage the surface cage in hydrate lattice; the hydrogen and oxygen in GHI1 can form hydrogen bonds respectively with oxygen and hydrogen in hydrates, which makes the surface molecules of the cages unstable and distorts the cages; Synergist diethylene glycol ether increases strength and range of length of hydrogen bond.

scholarly journals The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

2013 ◽  
Vol 9 ◽  
pp. 118-134 ◽  
Author(s):  
Jutta Erika Helga Köhler ◽  
Nicole Grczelschak-Mick
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Hydrogen Bonds ◽  
Md Simulations ◽  
Benzene Molecule ◽  
Glucose Unit ◽  
Hand Orientation ◽  
Different Temperatures ◽  
Dynamics Simulations ◽  
The Right

Four highly ordered hydrogen-bonded models of β-cyclodextrin (β-CD) and its inclusion complex with benzene were investigated by three different theoretical methods: classical quantum mechanics (QM) on AM1 and on the BP/TZVP-DISP3 level of approximation, and thirdly by classical molecular dynamics simulations (MD) at different temperatures (120 K and 273 to 300 K). The hydrogen bonds at the larger O2/O3 rim of empty β-CDs prefer the right-hand orientation, e.g., O3-H…O2-H in the same glucose unit and bifurcated towards …O4 and O3 of the next glucose unit on the right side. On AM1 level the complex energy was −2.75 kcal mol−1 when the benzene molecule was located parallel inside the β-CD cavity and −2.46 kcal mol−1 when it was positioned vertically. The AM1 HOMO/LUMO gap of the empty β-CD with about 12 eV is lowered to about 10 eV in the complex, in agreement with data from the literature. AM1 IR spectra displayed a splitting of the O–H frequencies of cyclodextrin upon complex formation. At the BP/TZVP-DISP3 level the parallel and vertical positions from the starting structures converged to a structure where benzene assumes a more oblique position (−20.16 kcal mol−1 and −20.22 kcal mol−1, resp.) as was reported in the literature. The character of the COSMO-RS σ-surface of β-CD was much more hydrophobic on its O6 rim than on its O2/O3 side when all hydrogen bonds were arranged in a concerted mode. This static QM picture of the β-CD/benzene complex at 0 K was extended by MD simulations. At 120 K benzene was mobile but always stayed inside the cavity of β-CD. The trajectories at 273, 280, 290 and 300 K certainly no longer displayed the highly ordered hydrogen bonds of β-CD and benzene occupied many different positions inside the cavity, before it left the β-CD finally at its O2/O3 side.

scholarly journals Molecular Dynamics Simulations for Effects of Fluoropolymer Binder Content in CL-20/TNT Based Polymer-Bonded Explosives

Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 4876
Author(s):  
Shenshen Li ◽  
Jijun Xiao
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Correlation Function ◽  
Binding Energy ◽  
Hydrogen Bonds ◽  
Bond Length ◽  
Pair Correlation Function ◽  
Pair Correlation ◽  
Binder Content ◽  
Polymer Bonded Explosives

In order to better understand the role of binder content, molecular dynamics (MD) simulations were performed to study the interfacial interactions, sensitivity and mechanical properties of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane/2,4,6-trinitrotoluene (CL-20/TNT) based polymer-bonded explosives (PBXs) with fluorine rubber F2311. The binding energy between CL-20/TNT co-crystal (1 0 0) surface and F2311, pair correlation function, the maximum bond length of the N–NO2 trigger bond, and the mechanical properties of the PBXs were reported. From the calculated binding energy, it was found that binding energy increases with increasing F2311 content. Additionally, according to the results of pair correlation function, it turns out that H–O hydrogen bonds and H–F hydrogen bonds exist between F2311 molecules and the molecules in CL-20/TNT. The length of trigger bond in CL-20/TNT were adopted as theoretical criterion of sensitivity. The maximum bond length of the N–NO2 trigger bond decreased very significantly when the F2311 content increased from 0 to 9.2%. This indicated increasing F2311 content can reduce sensitivity and improve thermal stability. However, the maximum bond length of the N–NO2 trigger bond remained essentially unchanged when the F2311 content was further increased. Additionally, the calculated mechanical data indicated that with the increase in F2311 content, the rigidity of CL-20/TNT based PBXs was decrease, the toughness was improved.

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