Search results for "Molecules"
showing 10 items of 1147 documents
Unfolding dynamics of small peptides biased by constant mechanical forces
2018
We show how multi-ensemble Markov state models can be combined with constant-force equilibrium simulations. Besides obtaining the unfolding/folding rates, Markov state models allow gaining detailed insights into the folding dynamics and pathways through identifying folding intermediates and misfolded structures. For two specific peptides, we demonstrate that the end-to-end distance is an insufficient reaction coordinate. This problem is alleviated through constructing models with multiple collective variables, for which we employ the time-lagged independent component analysis requiring only minimal prior knowledge. Our results show that combining Markov state models with constant-force simu…
Noise driven translocation of short polymers in crowded solutions
2008
In this work we study the noise induced effects on the dynamics of short polymers crossing a potential barrier, in the presence of a metastable state. An improved version of the Rouse model for a flexible polymer has been adopted to mimic the molecular dynamics by taking into account both the interactions between adjacent monomers and introducing a Lennard-Jones potential between all beads. A bending recoil torque has also been included in our model. The polymer dynamics is simulated in a two-dimensional domain by numerically solving the Langevin equations of motion with a Gaussian uncorrelated noise. We find a nonmonotonic behaviour of the mean first passage time and the most probable tran…
Global stability of protein folding from an empirical free energy function
2013
The principles governing protein folding stand as one of the biggest challenges of Biophysics. Modeling the global stability of proteins and predicting their tertiary structure are hard tasks, due in part to the variety and large number of forces involved and the difficulties to describe them with sufficient accuracy. We have developed a fast, physics-based empirical potential, intended to be used in global structure prediction methods. This model considers four main contributions: Two entropic factors, the hydrophobic effect and configurational entropy, and two terms resulting from a decomposition of close-packing interactions, namely the balance of the dispersive interactions of folded an…
CO-releasing binuclear rhodium complexes as inhibitors of nitric oxide generation in stimulated macrophages.
2013
Nontoxic CO-releasing dirhodium complexes act as inhibitors of NO in stimulated macrophage cells, suggesting that novel antiinflammatory treatments could involve the use of these types of binuclear complexes.
Design and synthesis of pironetin analogue/colchicine hybrids and study of their cytotoxic activity and mechanisms of interaction with tubulin
2014
We here report the synthesis of a series of 12 hybrid molecules composed of a colchicine moiety and a pironetin analogue fragment. The two fragments are connected through an ester-amide spacer of variable length. The cytotoxic activities of these compounds and their interactions with tubulin have been investigated. Relations between the structure and activity are discussed. Since the spacer is not long enough to permit a simultaneous binding of the hybrid molecules to the colchicine and pironetin sites on tubulin, a further feature investigated was whether these molecules would interact with the latter through the pironetin end (irreversible covalent binding) or through the colchicine end (…
Mono-, di- and tri-nuclear Ni(II) complexes of N-, O-donor ligands: structural diversity and reactivity
2002
A series of mono-, di- and tri-nuclear Ni(II) complexes of N, O-donating molecules possessing ---H2C---NH--- and ---HC=N--- moieties have been synthesized and characterized and the structures have been determined by single crystal X-ray diffraction. All these exhibited interesting molecular packing in their crystal lattices. Di-nuclear complexes were found to be cleaved in pyridine to result in mononuclear ones with additional coordinations being provided by pyridine. Di-nuclear complexes were found to form urea adducts as demonstrated based on absorption and vibrational studies.
Electronic structure and energy decomposition analyses as a tool to interpret the redox potential ranking of naphtho-, biphenyl- and biphenylenequino…
2016
By calling on modelling approaches we have performed a comparative study on the redox properties of various naphtho-, biphenyl- and biphenylene-quinone isomers. These different compounds exhibit as a whole a redox potential range between 2.09 and 2.90 V vs. Li+/Li. A specific methodology was used to decrypt the interplay among isomerism, aromaticity and antiaromaticity modifications and the stabilization/destabilization effects due to other molecular components on this key electrochemical feature for electrode materials of batteries. In particular, energy decomposition analysis, within the Quantum Theory of Atoms in Molecules, along with the electron and electron spin population changes upo…
endo-Functionalized molecular tubes : selective encapsulation of neutral molecules in non-polar media
2016
Four endo-functionalized molecular tubes with urea/thiourea groups in the deep cavities have been synthesized, and their binding ability to neutral molecules studied. Very high binding affinity and selectivity have been achieved, which are rationalized by invoking the shape and electrostatic complementarity and dipole alignment.
Activation of the Cyano Group at Imidazole via Copper Stimulated Alcoholysis
2019
Reactions of 4,5-dicyano-1-methylimidazole with CuX2 (X = Cl, Br) in alcohol solvents (ethanol and methanol) resulted in the formation of Cu(II) carboximidate complexes [CuCl2(5- cyano-4-C(OEt)N-1-methylimidazole)(EtOH)] (1), [Cu2(µ
Polarization Force Fields for Peptides Implemented in ECEPP2 and MM2
2000
Abstract The empirical conformational energy program for peptides (ECEPP2) and molecular mechanics (MM2) have been used for the simulation of the For-Gly-NH2 backbone. I propose two different methods for the calculation of the polarization energy term: the polarization procedure by non-interacting induced dipoles (NID) which assumes scalar isotropic point polarizabilities and the polarization scheme by interacting induced dipoles (ID) which calculates tensor effective anisotropic point polarizabilities (method of Applequist). I present a comparative study of ECEPP2 and MM2 + polarization. I discuss molecular mechanics results including the total energy differences, partitional analyses of t…