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35 results for “hydrogen bond”
Dynamics of terminal fraying-peeling and hydrogen bonds dictate the sequential vs co-operative melting pathways of nanoscale DNA and PNA triplexes
<div>##################################################################################################</div> <div> </div> <div>The simulation dataset used for the analysis reported in the manuscript titled -</div> <div> </div> <div> "Dynamics of terminal fraying-peeling and hydrogen bonds dictate the sequential vs co-operative melting pathways of nanoscale DNA and PNA triplexes."</div> <div> by Sandip Mandal, Krishna N. Ganesh, and Prabal K. Maiti*</div> <div> </div> <div> </div> <div>*E-mail: maiti@iisc.ac.in</div> <div>Center for Condensed Matter Theory, Department of Physics,</div> <div>Indian Institute of Science, Bangalore 560012, India</div> <div> </div> <div>##################################################################################################</div> <div> </div> <div>Packages required:</div> <div> Visual Molecular Dynamics (VMD)</div> <div> xmgrace</div> <div> numpy</div> <div> matplotlib</div> <div> scipy</div> <div> tleap/xleap</div> <div> AMBER</div> <div> CPPTRAJ</div> <div> MMGBSA</div> <div> Gaussian09 for partial charge calculation of the PNA protonated cytosine residues</div> <div> </div> <div>##################################################################################################</div> <div> </div> <div> </div> <div>Contents:</div> <div> </div> <div>The First main directory contains three folders and a README file--</div> <div>(1)PNA_DNA_PNA_Triplex</div> <div> (2)DNA_DNA_DNA_Triplex</div> <div>(3)Sequence_Dependence</div> <div>(4)README file</div> <div> </div> <div> </div> <div>##################################################################################################</div> <div> </div> <div> </div> <div>1. PNA_DNA_PNA_Triplex directory contains sub-directory for Protonated PNA-DNA-PNA triplexes simulation data, such as ---</div> <div>(a) Setup_files</div> <div>(b) Results</div> <div> </div> <div> </div> <div>(a)Setup_files:</div> <div>It contains input coordinates (PDP_18bp_PP.pdb, Protonated_PNA_DNA_PNA.inpcrd ..), topology files, and files required to build to complete </div> <div>system for simulation including library files for non-standard PNA residues and tleap script for the system setup.</div> <div> </div> <div>(b)Results: --folder contains simulation data and analysis scripts for Protonated PNA-DNA-PNA triplexes -----</div> <div> </div> <div>(a)Simulation Trajectories ( It contains simualtion trajectories for three independent trial runs named run1, run2, and run3)</div> <div>(b)RMSD</div> <div>(c)Hbond (hydrogen bonding)</div> <div>(d)Stiffness </div> <div>(e)Free Energy Landscape (FEL)</div> <div>(f)PCA (Principal Component Analysis)</div> <div>(g)Simulation Movies for the Protonated PNA-DNA-PNA triplex</div> <div> </div> <div> </div> <div>##################################################################################################</div> <div> </div> <div> </div> <div>2. DNA_DNA_DNA_Triplex directory contains sub-directory for Protonated DNA-DNA-DNA triplexes simulation data, such as ---</div> <div> (a) Setup_files</div> <div> (b) Results</div> <div> </div> <div> </div> <div>(a)Setup_files :</div> <div>It contains input coordinates (DDD_18bp_Protonated_NAB.pdb, 18bp_Protonated_NAB.inpcrd ...) and files required to build to complete</div> <div>system for simulation, including amber input files in the "Sander-Input-files" subdirectory, a script to run the simulation in a GPU clusters, and a leap script for the system setup.</div> <div> </div> <div>(b)Results --folder contains simulation data and analysis scripts for-----</div> <div> </div> <div> (a)Simulation Trajectories ( It contains simulation trajectory for three independent trial runs named run1, run2, and run3)</div> <div> (b)RMSD</div> <div> (c)Hydrogen bonding</div> <div> (d)Stiffness</div> <div> (e)Free Energy Landscape</div> <div> (f)PCA</div> <div> (g)Simulation Movies for the Protonated DNA-DNA-DNA triplex</div> <div> </div> <div> </div> <div>##################################################################################################</div> <div> </div> <div>3. Sequence_Dependence directory contains sub-directory for triplexes with all TAT base triples simualtion data, such as ---</div> <div> (A) DNA_DNA_DNA_with_all_TAT_sequence</div> <div> (B) PNA_DNA_PNA_with_all_TAT_sequence</div> <div> </div> <div>(A)Sub-directory contains simulation data for DNA-DNA-DNA triplexes with 18 TAT base triples (no protonated cytosine residues) ---</div> <div>(a)Set_up_files</div> <div>(b)Trajectory</div> <div>(c)RMSD</div> <div>(d)Hbond</div> <div> </div> <div> </div> <div>(B)Sub-directory contains simulation data for PNA-DNA-PNA triplexes with 18 TAT base triples (no protonated cytosine residues) ---</div> <div> (a)Set_up_files</div> <div> (b)Trajectory</div> <div> (c)RMSD</div> <div> (d)Hbond</div> <div> </div> <div>##################################################################################################</div> <div> </div> <div> </div> <div>The trajectories are sampled at 1 ns intervals (since the full trajectory dumped at 10 ps interval, will take huge dataspace) in each trajectory file:</div> <div>(a)The first frame corresponds to the structure immediately after 5 ns NPT equilibriation.</div> <div>(b)The next 200 frames are from the production run, at 1 to 200 ns.</div> <div> </div> <div> </div> <div>References:</div> <div>The DNA-DNA-DNA and PNA-DNA-PNA models were constructed using NAB code [1].</div> <div>System preparation with water and ions are done with the help of tleap/xleap [2].</div> <div>All simulation runs are conducted in AMBER2020 [3].</div> <div>For visualization we have used VMD [4].</div> <div> </div> <div>[1] T. J. Macke and D. A. Case, Modeling unusual nucleic acid structures, 1998</div> <div>[2] D. R. Roe and T. E. Cheatham III, Journal of chemical theory and computation, 2013, 9, 3084–3095</div> <div>[3]D. A. Case, H. M. Aktulga, K. Belfon, I. Ben-Shalom, S. R.Brozell, D. S. Cerutti, T. E. Cheatham III, V. W. D. Cruzeiro,T. A. Darden, R. E. Duke et al., Amber 2021, University of California, San Francisco, 2021</div> <div>[4] Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 14(1), 33-38 (1996).</div>
Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion
<p>KGS conformational ensembles of 100 substates from sampling ADK starting from the open conformation (PDB ID 4ake). Hydrogen bonds were included at thresholds of -1, -2, and -4 kcal/mol. Hydrogen bond network constraint relaxation was set to 1e-10 (nullspace floppy modes) and 1e-2 (kinematic flexibility modes)</p>
Intermolecular hydrogen bond ruptured by graphite with different lamellar number
<p>Intermolecular hydrogen bonds are formed through the electrostatic attraction between the hydrogen nucleus on a strong polar bond and high electronegative atom with an unshared pair of electrons and a partial negative charge. It affects the physical and chemical properties of substances. Based on this, we presented a physical method to modulate intermolecular hydrogen bonds for not changing the physical-chemical properties of materials. The graphite and graphene is added into the glycerol respectively by being used as a viscosity reducer in this paper. The samples are characterized by Raman and <sup>1</sup>H-NMR. Results show that intermolecular hydrogen bonds are adjusted by graphite or graphene. The rheology of glycerol is reduced to varying degrees. TEM and computer simulation show that the spatial limiting action of graphite or graphene is the main cause of breaking the intermolecular hydrogen bond network structure. We hope this work reveals the potential interplay between nanomaterials and hydroxyl liquids, which will contribute to the field of solid-liquid coupling lubrication.</p>
Data supporting "Atomistic Insights into Hydrogen-Bonded Supramolecular Capsule Assembly Dynamics"
<p>The archive contains 2 folders:<br> <br> 1. input, that contains all the input files for the GROMACS run (gromacs_input folder), PLUMED metadynamics (plumed_metad folder), and PLUMED analysis and reweighting (plumed_analysis folder).<br> 2. trajectories, that contains the trajectories of the 2 µs metadynamics run for both resorcinarene and pyrogallolarene assemblies. There are both the trajectories with (saved every 100 ps) and without solvent (saved every ps). </p>
Intermolecular hydrogen bond ruptured by graphite with different lamellar number
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Semiconductor Porous Hydrogen-Bonded Organic Frameworks Based on Tetrathiafulvalene Derivatives
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Rational Design of 7-Azaindole-Based Robust Microporous Hydrogen-Bonded Organic Framework for Gas Sorption
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The physicochemical and thermal properties of deep eutectic solvent with different hydrogen bond donor (alpha hydroxy acid and polyol)
<p><span>Deep eutectic solvents (DESs) are a novel class of solvents that have gathered interest due to their unique properties particularly in its application of biomass fractionation. It is critical to study its properties from an engineering standpoint because of its importance in mass transfer, fluid mechanics, modelling, simulation and equipment design. The comparison of physicochemical and thermal properties of DESs has not been thoroughly investigated, particularly when a different functional group, such as alpha hydroxy acid (lactic acid, LA) or polyol (glycerol, Gly), is used as the hydrogen bond donor (HBD). Furthermore, understanding how molar ratios affect properties is crucial since they may be fine-tuned to meet the needs of specific applications. Thus, the purpose of this study is to determine the physicochemical properties (viscosity, density, refractive index and pH) and the thermal properties (freezing point and decomposition temperature) of DESs with different HBD functional groups (LA and Gly) at various molar ratios (1:2–1:10). The HBD's functional groups and molar ratio change significantly impacted the properties due to hydrogen bonding sites and strength, alkyl chain length and molecular weight and electrostatic and dispersion interactions. The correlation between DESs molar ratios and properties is not always linearly due to eutectic phenomena.</span></p>
Data from: Intramolecular hydrogen bonds in 1,4-dihydropyridine derivatives
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Data from: Contribution of hydrogen bonds to paper strength properties
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Footprinting SHAPE-eCLIP reveals transcriptome-wide hydrogen bonds at RNA-protein interfaces
GEO Series GSE149767. Homo sapiens. 40 samples. Type: Other; Third-party reanalysis.
Data files for the publication "Charge transfer across C-H---O hydrogen bonds stabilizes oil droplets in water"
<p>This dataset includes text/dat files for all the data included in the manuscript " Charge transfer across C-H---O hydrogen bonds stabilizes oil droplets in water".</p>
Hexafluorophosphate-Triggered Hydrogen Isotope Exchange (HIE) in Fluorinated Environments: A Platform for the Deuteration of Aromatic Compounds via Strong Bond Activation
<p>The data set contains DFT with the program package ORCA to calculate the free enthalpy of the reaction for the hydrolysis of PF6-activated with hexafluoroisopropanol (HFIP) and reaction barriers with the help of nudged elastic band (NEB) calculation. The data in Simulated_IR contains DFT optimization and frequency calculations performed using Gaussian16 package.</p>
Data Set : Role of intramolecular hydrogen bonding on photoelectron circular dichroism: the diastereoisomers of 1-Amino-2-Indanol
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Data files for the publication "Dissecting the hydrogen bond network of water: charge transfer and nuclear quantum effects"
<p>This dataset includes text/dat files for all the data included in the manuscript "Dissecting the hydrogen bond network of water: charge transfer and nuclear quantum effects".</p>
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