A novel set of ss-N-biaryl ether sulfonamide hydroxamates as potential MMPs inhibitors: Molecular dynamics simulations and molecular properties evaluation

Matrix metalloproteinases (MMPs) constitute a family of zinc-dependent proteases involved in the extracellular matrix degradation. MMP-2 and MMP9 are overexpressed in several human cancer types, including melanoma, thus the development of new compounds to inhibit MMPs' activity is desirable. Molecular dynamic simulation and molecular properties calculations were performed on a set of novel beta-N-biaryl ether sulfonamide-based hydroxamates, reported as MMP-2 and MMP-9 inhibitors, for providing data to develop an exploratory analysis. Thermodynamic, electronic, and steric descriptors have significantly discriminated highly active from moderately and less active inhibitors of MMP-2 whereas apparent partition coefficient at pH 1.5 was also significant for the MMP-9 data set. Compound 47 was considered an outlier in all analysis, indicating the presence of a bulky substituent group in R3 is crucial to this set of inhibitors for the establishment of molecular interactions with the S1 subsite of both enzymes, but there is a limit. (C) 2012 Wiley Periodicals, Inc.

Photodynamic Efficiency of Cationic meso-Porphyrins at Lipid Bilayers: Insights from Molecular Dynamics Simulations

Porphyrin derivatives have applications as photoactive drugs in photodynamic therapy. However, little is known about their interactions with phospholipid membranes at the molecular level. We employed molecular dynamics simulations to model the binding between a series of cationic meso-(N-methyl-4-pyridinium)phenylporphyrins and anionic phosphatidylglycerol lipid bilayers. This was done in the presence of molecular oxygen within the membrane. The ability of various porphyrins to cause photodamage was quantified in terms of their immersion depth and degree of exposition to a higher oxygen concentration inside the membrane. Simulations showed that the photodynamic efficiency could be improved as the number of hydrophobic phenyl substituents attached to the porphyrinic ring increased. In the specific case of porphyrins containing two hydrophobic and two charged substituents, the cis isomer was significantly more efficient than the trans. These results correlate well with previous experimental observations. They highlight the importance of both the total charge and amphiphilicity of the photosensitizer for its performance in photodynamic therapy.

Influence of Molecular Dynamics on the Dielectric Properties of Poly(9,9-di-n-octylfluorene-alt-benzothiadiazole) -Based Devices

This paper uses Nuclear Magnetic Resonance (NMR) and Differential Scanning Calorimetry (DSC) techniques to study the molecular relaxations and phase transitions in poly(9,9-di-n-octylfluorene-alt-benzothiadiazole) (F8BT), which has been extensively studied as the active thin film in organic devices. Besides the identification of the glass transition, beta relaxation and crystal-to-crystal phase transition, we correlate such phenomena with dielectric and transport mechanisms in diodes with F8BT as the active layer. The beta relaxation has been assigned to a transition at about 210 K measured by H-1 and C-13 solid state NMR, and can be attributed to local motions in the side chains. The glass transition has been detected by DSC and H-1 NMR. Dielectric spectroscopy (DS) carried out at low frequencies on diodes made from F8BT show two peaks which are coincident with the above transitions. This allowed us to correlate the electrical changes in the film with the onset of specific molecular motions. In addition, DS indicates a third peak related with a crystal-to-crystal phase transition. Finally, these transitions were correlated with changes in the carrier mobility recorded in thin films and published recently.

Effect of the thermostat in the molecular dynamics simulation on the folding of the model protein chignolin

Molecular dynamics simulations of the model protein chignolin with explicit solvent were carried out, in order to analyze the influence of the Berendsen thermostat on the evolution and folding of the peptide. The dependence of the peptide behavior on temperature was tested with the commonly employed thermostat scheme consisting of one thermostat for the protein and another for the solvent. The thermostat coupling time of the protein was increased to infinity, when the protein is not in direct contact with the thermal bath, a situation known as minimally invasive thermostat. In agreement with other works, it was observed that only in the last situation the instantaneous temperature of the model protein obeys a canonical distribution. As for the folding studies, it was shown that, in the applications of the commonly utilized thermostat schemes, the systems are trapped in local minima regions from which it has difficulty escaping. With the minimally invasive thermostat the time that the protein needs to fold was reduced by two to three times. These results show that the obstacles to the evolution of the extended peptide to the folded structure can be overcome when the temperature of the peptide is not directly controlled.

Molecular Dynamics Investigations of PRODAN in a DLPC Bilayer

Molecular dynamics computer simulations have been performed to identify preferred positions of the fluorescent probe PRODAN in a fully hydrated DLPC bilayer in the fluid phase. In addition to the intramolecular charge-transfer first vertical excited state, we considered different charge distributions for the electronic ground state of the PRODAN molecule by distinct atomic charge models corresponding to the probe molecule in vacuum as well as polarized in a weak and a strong dielectric solvent (cyclohexane and water). Independent on the charge distribution model of PRODAN, we observed a preferential orientation of this molecule in the bilayer with the dimethylamino group pointing toward the membrane's center and the carbonyl oxygen toward the membrane's interface. However, changing the charge distribution model of PRODAN, independent of its initial position in the equilibrated DLPC membrane, we observed different preferential positions. For the ground state representation without polarization and the in-cyclohexane polarization, the probe maintains its position close to the membrane's center. Considering the in-water polarization model, the probe approaches more of the polar headgroup region of the bilayer, with a strong structural correlation with the choline group, exposing its oxygen atom to water molecules. PRODAN's representation of the first vertical excited state with the in-water polarization also approaches the polar region of the membrane with the oxygen atom exposed to the bilayer's hydration shell. However, this model presents a stronger structural correlation with the phosphate groups than the ground state. Therefore, we conclude that the orientation of the PRODAN molecule inside the DLPC membrane is well-defined, but its position is very sensitive to the effect of the medium polarization included here by different models for the atomic charge distribution of the probe.

Characterization of suramin binding sites on the human group IIA secreted phospholipase A(2) by site-directed mutagenesis and molecular dynamics simulation

Suramin is a polysulphonated naphthylurea with inhibitory activity against the human secreted group IIA phospholipase A(2) (hsPLA2GIIA), and we have investigated suramin binding to recombinant hsPLA2GIIA using site-directed mutagenesis and molecular dynamics (MD) simulations. The changes in suramin binding affinity of 13 cationic residue mutants of the hsPLA2GIIA was strongly correlated with alterations in the inhibition of membrane damaging activity of the protein. Suramin binding to hsPLA2GIIA was also studied by MD simulations, which demonstrated that altered intermolecular potential energy of the suramin/mutant complexes was a reliable indicator of affinity change. Although residues in the C-terminal region play a major role in the stabilization of the hsPLA2GIIA/suramin complex, attractive and repulsive hydrophobic and electrostatic interactions with residues throughout the protein together with the adoption of a bent suramin conformation, all contribute to the stability of the complex. Analysis of the h5PLA2GIIA/suramin interactions allows the prediction of the properties of suramin analogues with improved binding and higher affinities which may be candidates for novel phospholipase A(2) inhibitors. (C) 2012 Elsevier Inc. All rights reserved.

Applying many-body expansion aiming to make ab in initio molecular dynamics more efficient

In this present work we present a methodology that aims to apply the many-body expansion to decrease the computational cost of ab initio molecular dynamics, keeping acceptable accuracy on the results. We implemented this methodology in a program which we called ManBo. In the many-body expansion approach, we partitioned the total energy E of the system in contributions of one body, two bodies, three bodies, etc., until the contribution of the Nth body [1-3]: E = E1 + E2 + E3 + …EN. The E1 term is the sum of the internal energy of the molecules; the term E2 is the energy due to interaction between all pairs of molecules; E3 is the energy due to interaction between all trios of molecules; and so on. In Manbo we chose to truncate the expansion in the contribution of two or three bodies, both for the calculation of the energy and for the calculation of the atomic forces. In order to partially include the many-body interactions neglected when we truncate the expansion, we can include an electrostatic embedding in the electronic structure calculations, instead of considering the monomers, pairs and trios as isolated molecules in space. In simulations we made we chose to simulate water molecules, and use the Gaussian 09 as external program to calculate the atomic forces and energy of the system, as well as reference program for analyzing the accuracy of the results obtained with the ManBo. The results show that the use of the many-body expansion seems to be an interesting approach for reducing the still prohibitive computational cost of ab initio molecular dynamics. The errors introduced on atomic forces in applying such methodology are very small. The inclusion of an embedding electrostatic seems to be a good solution for improving the results with only a small increase in simulation time. As we increase the level of calculation, the simulation time of ManBo tends to largely decrease in relation to a conventional BOMD simulation of Gaussian, due to better scalability of the methodology presented. References [1] E. E. Dahlke and D. G. Truhlar; J. Chem. Theory Comput., 3, 46 (2007). [2] E. E. Dahlke and D. G. Truhlar; J. Chem. Theory Comput., 4, 1 (2008). [3] R. Rivelino, P. Chaudhuri and S. Canuto; J. Chem. Phys., 118, 10593 (2003).

Molecular dynamics of poly(Ethylene Glycol) intercalated in clay, studied using 13C solid-state NMR

In this study, Cross-Polarization Magic-angle Spinning CP/MAS, 2D Exchange, Centerband-Only Detection of Exchange (CODEX), and Separated-Local-Field (SLF) NMR experiments were used to study the molecular dynamics of poly(ethylene glycol) (PEG) inside Hectorite/PEG intercalation compounds in both single- and double-layer configurations. The results revealed that the overall amplitude of the motions of the PEG chain in the single-layer configuration is considerably smaller than that observed for the double-layer intercalation compound. This result indicates that the effect of having the polymer chain interacting with both clay platelets is to produce a substantial decrease in the motional amplitudes of those chains. The presence of these dynamically restricted segments might be explained by the presence of anchoring points between the clay platelets and the PEG oxygen atoms, which was induced by the Na+ cations. By comparing the PEG motional amplitudes of the double-layered nanocomposites composed of polymers with different molecular weights, a decrease in the motional amplitude for the smaller PEG chain was observed, which might also be understood using the presence of anchoring points.

Computer simulation study of collective dynamics in the glass former Ca(NO3)(2)center dot 4H(2)O

Time correlation functions of current fluctuations were calculated by molecular dynamics (MD) simulations in order to investigate sound waves of high wavevectors in the glass-forming liquid Ca(NO3)(2)center dot 4H(2)O. Dispersion curves, omega(k), were obtained for longitudinal (LA) and transverse acoustic (TA) modes, and also for longitudinal optic (LO) modes. Spectra of LA modes calculated by MD simulations were modeled by a viscoelastic model within the memory function framework. The viscoelastic model is used to rationalize the change of slope taking place at k similar to 0.3 angstrom(-1) in the omega(k) curve of acoustic modes. For still larger wavevectors, mixing of acoustic and optic modes is observed. Partial time correlation functions of longitudinal mass currents were calculated separately for the ions and the water molecules. The wavevector dependence of excitation energies of the corresponding partial LA modes indicates the coexistence of a relatively stiff subsystem made of cations and anions, and a softer subsystem made of water molecules. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4751548]

Interactions between 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid and gamma-Al2O3 (100) surface calculated by density functional theory

The main aim of this work is to investigate the 1-butyl-3-methylimidazolium tetrafluoroborate ([C4C1Im]+[BF4]-) ionic liquid (IL) adsorption on the gamma-Al2O3 (100) by density functional theory calculations to try to rationalize the adsorption as an electrostatic phenomenon. Optimized geometries and interaction energies of IL one-monolayer on the gamma-Al2O3 were obtained on high surface coverage (one cationanion pair per 94.96 nm2). A study of dispersion force was made to estimate its contribution to the adsorption. Overall, the process is ruled by electrostatic interaction between ions and surface. Adsorption of the anion [BF4]- and cation [C4C1Im]+ was also studied by Bader charge analysis and charge density difference for supported and unsupported situations. It is suggested that the IL ions have their charges maintained with significant anion cloud polarization inward to the acid aluminum sites. (c) 2012 Wiley Periodicals, Inc.

Electronic Properties of Water in Liquid Environment. A Sequential QM/MM Study Using the Free Energy Gradient Method

There is a continuous search for theoretical methods that are able to describe the effects of the liquid environment on molecular systems. Different methods emphasize different aspects, and the treatment of both the local and bulk properties is still a great challenge. In this work, the electronic properties of a water molecule in liquid environment is studied by performing a relaxation of the geometry and electronic distribution using the free energy gradient method. This is made using a series of steps in each of which we run a purely molecular mechanical (MM) Monte Carlo Metropolis simulation of liquid water and subsequently perform a quantum mechanical/molecular mechanical (QM/MM) calculation of the ensemble averages of the charge distribution, atomic forces, and second derivatives. The MP2/aug-cc-pV5Z level is used to describe the electronic properties of the QM water. B3LYP with specially designed basis functions are used for the magnetic properties. Very good agreement is found for the local properties of water, such as geometry, vibrational frequencies, dipole moment, dipole polarizability, chemical shift, and spin-spin coupling constants. The very good performance of the free energy method combined with a QM/MM approach along with the possible limitations are briefly discussed.

Order induced charge carrier mobility enhancement in columnar liquid crystal diodes

Discotic molecules comprising a rigid aromatic core and flexible side chains have been promisingly applied in OLEDs as self-organizing organic semiconductors. Due to their potentially high charge carrier mobility along the columns, device performance can be readily improved by proper alignment of columns throughout the bulk. In the present work, the charge mobility was increased by 5 orders of magnitude due to homeotropic columnar ordering induced by the boundary interfaces during thermal annealing in the mesophase. State-of-the-art diodes were fabricated using spin-coated films whose homeotropic alignment with formation of hexagonal germs was observed by polarizing optical microscopy. The photophysical properties showed drastic changes at the mesophase-isotropic transition, which is supported by the gain of order observed by X-ray diffraction. The electrical properties were investigated by modeling the current−voltage characteristics by a space-charge-limited current transport with a field dependent mobility.

Molecular and Electronic Structure of the Peptide Subunit of Geobacter sulfurreducens Conductive Phi from First Principles

The respiration of metal oxides by the bacterium Geobacter sulfurreducens requires the assembly of a small peptide (the GS pilin) into conductive filaments termed pili. We gained insights into the contribution of the GS pilin to the pilus conductivity by developing a homology model and performing molecular dynamics simulations of the pilin peptide in vacuo and in solution. The results were consistent with a predominantly helical peptide containing the conserved a-helix region required for pilin assembly but carrying a short carboxy-terminal random-coiled segment rather than the large globular head of other bacterial pilins. The electronic structure of the pain was also explored from first principles and revealed a biphasic charge distribution along the pilin and a low electronic HOMO-LUMO gap, even in a wet environment. The low electronic band gap was the result of strong electrostatic fields generated by the alignment of the peptide bond dipoles in the pilin's alpha-helix and by charges from ions in solution and amino acids in the protein. The electronic structure also revealed some level of orbital delocalization in regions of the pilin containing aromatic amino acids and in spatial regions of high resonance where the HOMO and LUMO states are, which could provide an optimal environment for the hopping of electrons under thermal fluctuations. Hence, the structural and electronic features of the pilin revealed in these studies support the notion of a pilin peptide environment optimized for electron conduction.

Agar-Based Gel Electrolyte for Electrochromic Device Application

Gel Polymer Electrolytes (GPE) based on agar and containing LiClO4 have been prepared, characterized and applied to electrochromic devices. The ionic conductivity revealed the best result of 6.5 x 10(-5) S/cm for the sample with 17 wt.% of LiClO4, which increased to 5.4 x 10(-4) S/cm at 72 degrees C. TheGPE have been used in electrochromic devices (ECD) with K-glass/WO3/GPE/CeO2-TiO2/K-glass configuration. The ECD changed transmittance values up to 30% between the colored and transparent states. The charge density measurements revealed an increase of 5.5 to 7.5 mC/cm(2) from the first to 500th cycles and then a decrease to 4.4 mC/cm(2) during the next 4500 cycles. Coloration efficiency (eta) of 25 cm(2)/C was obtained.

Site localization of Cd impurities in sapphire

By combining first-principles electronic structure calculations and existing time-differential gamma-gamma perturbed-angular-correlation experiments we studied the site localization, the local environment, and the electronic structure of Cd impurities in sapphire (alpha-Al2O3) single crystals in different charged states. The ab initio calculations were performed with the full-potential augmented plane wave plus local orbitals method and the projector augmented wave method. Comparing the calculated electric-field-gradient tensor at the Cd nuclei in the alpha-Al2O3 host lattice and the corresponding available experimental values, we have seen that it is equally possible for Cd to replace an Al atom (in a negative charge state) or to be placed in an interstitial site (in a neutral charge state). To finally address the issue of the Cd impurity localization, we performed formation energy calculations. These results have shown that Cd placed in the substitutional Al site, in the negatively charged state, is the most probable configuration.