Search results for "molecular dynamics"
showing 10 items of 1075 documents
Natural payload delivery of the doxorubicin anticancer drug from boron nitride oxide nanosheets
2019
International audience; We studied the behavior of doxorubicin (DOX; an anticancer drug) molecules loaded on a boron nitride oxide nanosheet (BNO-NS) using the density functional theory (DFT), time-dependent density functional theory (TDDFT), and molecular dynamic (MD) simulation methods. We found that DOX molecules in pi-pi or covalent interaction with BNO-NS preserve their optical properties in water. Moreover, the BNO-NS vector allowed stabilizing the DOX molecules on a cellular membrane contrary to isolated DOX that randomly moved in the solvent box without any interaction with the cell membrane. From these results, we conclude that hydrophilic BNO-NS represents a good candidate for DOX…
Direct experimental observation of mesoscopic fluorous domains in fluorinated room temperature ionic liquids
2017
Fluorinated room temperature ionic liquids (FRTILs) represent a class of solvent media that are attracting great attention due to their IL-specific properties as well as features stemming from their fluorous nature. Medium-to-long fluorous tails constitute a well-defined apolar moiety in the otherwise polar environment. Similarly to the case of alkyl tails, such chains are expected to result in the formation of self-assembled fluorous domains. So far, however, no direct experimental observation has been made of the existence of such structural heterogeneities on the nm scale. We report here the first experimental evidence of the existence of mesoscopic spatial segregation of fluorinated dom…
CO rebinding kinetics and molecular dynamics simulations highlight dynamic regulation of internal cavities in human cytoglobin
2013
Abstract: Cytoglobin (Cygb) was recently discovered in the human genome and localized in different tissues. It was suggested to play tissue-specific protective roles, spanning from scavenging of reactive oxygen species in neurons to supplying oxygen to enzymes in fibroblasts. To shed light on the functioning of such versatile machinery, we have studied the processes supporting transport of gaseous heme ligands in Cygb. Carbon monoxide rebinding shows a complex kinetic pattern with several distinct reaction intermediates, reflecting rebinding from temporary docking sites, second order recombination, and formation (and dissociation) of a bis-histidyl heme hexacoordinated reaction intermediate…
Simulations of Glassforming Network Fluids: Classical Molecular Dynamics versus Car-Parrinello Molecular Dynamics
2010
Abstract Static and dynamic Properties of molten germanium dioxide are studied by two simulation methods, classical Molecular Dynamics (MD) using the Oeffner-Elliott (OE) potential, and “ab initio” Car-Parrinello Molecular Dynamics (CPMD). While CPMD provides a (presumably) more accurate description of the local structure and the forces, it severely suffers from finite size effects when the structure beyond the first neighbor shells is considered. For glassforming fluids, the demanding equilibrium needs are a further reason, why simply MD is still preferable, when a “good” effective potential is available.
The interplay between structure and ionic motions in glasses
2003
We present research examples that demonstrate how molecular dynamics simulations of real materials have reached a high level of sophistication. For simplicity, we focus on examples taken from our own research-although many other groups have done similarly valuable work on other systems and problems.
The inhibition of glycerol permeation through aquaglyceroporin-3 induced by mercury(II)
2016
Mercurial compounds are known to inhibit water permeation through aquaporins (AQPs). Although in the last years some hypotheses were proposed, the exact mechanism of inhibition is still an open question and even less is known about the inhibition of the glycerol permeation through aquaglyceroporins. Molecular dynamics (MD) simulations of human aquaporin-3 (AQP3) have been performed up to 200 ns in the presence of Hg2+ ions. For the first time, we have observed the unbiased passage of a glycerol molecule from the extracellular to cytosolic side. Moreover, the presence of Hg2+ ions covalently bound to Cys40 leads to a collapse of the aromatic/arginine selectivity filter (ar/R SF), blocking th…
Membrane Structure of Aquaporin Observed with Combined Experimental and Theoretical Sum Frequency Generation Spectroscopy
2021
High-resolution structural information on membrane proteins is essential for understanding cell biology and for the structure-based design of new medical drugs and drug delivery strategies. X-ray diffraction (XRD) can provide angstrom-level information about the structure of membrane proteins, yet for XRD experiments, proteins are removed from their native membrane environment, chemically stabilized, and crystallized, all of which can compromise the conformation. Here, we describe how a combination of surface-sensitive vibrational spectroscopy and molecular dynamics simulations can account for the native membrane environment. We observe the structure of a glycerol facilitator channel (GlpF)…
Design, Synthesis and Biological Evaluation of 7-Chloro-9
2019
Glycogen synthase kinase-3β (GSK-3β) represents a relevant drug target for the treatment of neurodegenerative pathologies including Alzheimer’s disease. We herein report on the optimization of a novel class of GSK-3β inhibitors based on the tofacitinib-derived screen hit 3-((3R,4R)-3-((7-chloro-9H-pyrimido[4,5-b]indol-4-yl)(methyl)amino)-4-methylpiperidin-1-yl)-3-oxopropanenitrile (1). We synthesized a series of 19 novel 7-chloro-9H-pyrimido[4,5-b]indole-based derivatives and studied their structure–activity relationships with focus on the cyanoacetyl piperidine moiety. We unveiled the crucial role of the nitrile group and its importance for the activity of this compound series. A successfu…
Adsorption of the herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA) by goethite.
2014
Interaction between the goethite surface and 4-chloro-2-methylphenoxyacetic acid (MCPA) herbicide was studied using density functional theory (DFT) calculations combined with molecular dynamics (MD). The important step made here lies in the use of a periodic DFT method enabling the study of a mineral surface of different protonation states, in strong contrast with previous molecular modeling studies limited to single protonation state corresponding to the point of zero charge. Different surface OH groups and MCPA proton states were used to mimic the strong effects of pH on the outer- and inner-sphere surface complexes that are theoretically possible, together with their binding energies, an…
A topological isomer of the Au25(SR)18−nanocluster
2020
Energetically low-lying structural isomers of the much-studied thiolate-protected gold cluster Au25(SR)18− are discovered from extensive (80 ns) molecular dynamics (MD) simulations using the reactive molecular force field ReaxFF and confirmed by density functional theory (DFT). A particularly interesting isomer is found, which is topologically connected to the known crystal structure by a low-barrier collective rotation of the icosahedral Au13 core. The isomerization takes place without breaking of any Au–S bonds. The predicted isomer is essentially iso-energetic with the known Au25(SR)18− structure, but has a distinctly different optical spectrum. It has a significantly larger collision cr…