Dynamics and fragmentation mechanism of (CHCH)Pt(CH) on SiO surfaces.

The interaction of trimethyl(methylcyclopentadienyl)platinum(IV) ((CHCH)Pt(CH)) molecules on fully and partially hydroxylated SiO surfaces, as well as the dynamics of this interaction were investigated using density functional theory (DFT) and finite temperature DFT-based molecular dynamics simulations. Fully and partially hydroxylated surfaces represent substrates before and after electron beam treatment and this study examines the role of electron beam pretreatment on the substrates in the initial stages of precursor dissociation and formation of Pt deposits. Our simulations show that on fully hydroxylated surfaces or untreated surfaces, the precursor molecules remain inactivated while we observe fragmentation of (CHCH)Pt(CH) on partially hydroxylated surfaces.

Temperature-dependent conformational dynamics of cytochrome c: Implications in apoptosis.

Heat, electric shock, and burn injuries induce apoptosis by releasing cytochrome c (cyt-c) from mitochondria and by subsequently activating the death protease, caspases-3. During apoptosis, cyt-c undergoes changes in the secondary structure that have been suggested to increase its peroxidase activity. Information about these structural changes will provide better understanding of the apoptotic mechanism.

Investigation of structural dynamics of Thrombocytopenia Cargeeg mutants of human apoptotic cytochrome c: A molecular dynamics simulation approach.

Naturally occurring mutations to cytochrome c (cyt-c) have been identified recently in patients with mild autosomal dominant thrombocytopenia (low platelet levels), which yield cyt-c mutants with enhanced apoptotic activity. However, the molecular mechanism underlying this low platelet production and enhanced apoptosis remain unclear. Therefore, an attempt is made herein for the first time to investigate the effects of mutations of glycine 41 by serine (G41S) and tyrosine 48 by histidine (Y48H) on the conformational and dynamic changes of apoptotic (Fe) cyt-c using all atom molecular dynamics (MD) simulations in explicit water solvent.

Effects of different solvents on the conformations of apoptotic cytochrome c: Structural insights from molecular dynamics simulation.

Cytochrome c (cyt-c) upon binding with cardiolipin acquires peroxidase activity and is strictly connected to the pathogenesis of many human diseases including neurodegenerative and cardiovascular diseases. Interaction of cyt-c with cardiolipin mimics partial unfolding/conformational changes of cyt-c in different solvent environments. Dynamic pictures of these conformational changes of cyt-c are crucial in understanding their physiological roles in mitochondrial functions.

Dynamics of tungsten hexacarbonyl, dicobalt octacarbonyl, and their fragments adsorbed on silica surfaces.

Tungsten and cobalt carbonyls adsorbed on a substrate are typical starting points for the electron beam induced deposition of tungsten or cobalt based metallic nanostructures. We employ first principles molecular dynamics simulations to investigate the dynamics and vibrational spectra of W(CO)6 and W(CO)5 as well as Co2(CO)8 and Co(CO)4 precursor molecules on fully and partially hydroxylated silica surfaces. Such surfaces resemble the initial conditions of electron beam induced growth processes.

Giant pressure-induced volume collapse in the pyrite mineral MnS2.

Dramatic volume collapses under pressure are fundamental to geochemistry and of increasing importance to fields as diverse as hydrogen storage and high-temperature superconductivity. In transition metal materials, collapses are usually driven by so-called spin-state transitions, the interplay between the single-ion crystal field and the size of the magnetic moment. Here we show that the classical S = 5/2 mineral hauerite (MnS2) undergoes an unprecedented (ΔV ~ 22%) collapse driven by a conceptually different magnetic mechanism.

Comparative structural and conformational studies on H43R and W32F mutants of copper-zinc superoxide dismutase by molecular dynamics simulation.

Recently, mutations in copper-zinc superoxide dismutase (SOD1) have been linked to familial amyotrophic lateral sclerosis (fALS), a progressive neurodegenerative disease involving motor neuron loss, paralysis and death. It is mainly due to protein misfolding and aggregation resulting from the enhanced peroxidase activity of SOD1 mutants. In this study, we have carried out a 20 ns molecular dynamics simulation for wild type (WT), H43R and W32F mutated SOD1's dimer and compared their structure and conformational properties by extracting several quantitative properties from the trajectory to understand the pathology of fALS disease.

Spontaneous dissociation of Co(2)(CO)(8) and autocatalytic growth of Co on SiO(2): A combined experimental and theoretical investigation.

We present experimental results and theoretical simulations of the adsorption behavior of the metal-organic precursor Co(2)(CO)(8) on SiO(2) surfaces after application of two different pretreatment steps, namely by air plasma cleaning or a focused electron beam pre-irradiation. We observe a spontaneous dissociation of the precursor molecules as well as autodeposition of cobalt on the pretreated SiO(2) surfaces. We also find that the differences in metal content and relative stability of these deposits depend on the pretreatment conditions of the substrate.

Theoretical investigation of quinone metabolites of dopamine interaction with DNA--insights into toxicological effects.

Dopamine (3,4-dihydroxyphenylethylamine, DA), an important neurotransmitter, exists in the cell bodies of the dopaminergic neurons of the substantia nigra. Oxidation of DA to its quinone and subsequent reaction with Adenine and Guanine in DNA result in the formation of depurinating adducts, thus causing DNA damage. In this article, we investigate the interaction of quinone metabolites of dopamine (DMQ) with models representing the structure of DNA using dispersion corrected density functional theory with an aim to evaluate the associated structural changes in DNA upon their interaction.