Complexation of siRNA with Dendrimer: A Molecular Modeling Approach

This paper reports the structural behavior and thermodynamics of the complexation of siRNA with poly(amidoamine) (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) through fully atomistic molecular dynamics (MD) simulations accompanied by free energy calculations and inherent structure determination. We have also done simulation with one siRNA and two dendrimers (2 x G3 or 2xG4) to get the microscopic picture of various binding modes. Our simulation results reveal the formation of stable siRNA-dendrimer complex over nanosecond time scale. With the increase in dendrimcr generation, the charge ratio increases and hence the binding energy between siRNA and dendrimer also increases in accordance with available experimental measurements. Calculated radial distribution functions of amines groups of various subgenerations in a given generation of dendrimer and phosphate in backbone of siRNA reveals that one dendrimer of generation 4 shows better binding with siRNA almost wrapping the dendrimer when compared to the binding with lower generation dendrimer like G3. In contrast, two dendrimers of generation 4 show binding without siRNA wrapping the den-rimer because of repulsion between two dendrimers. The counterion distribution around the complex and the water molecules in the hydration shell of siRNA give microscopic picture of the binding dynamics. We see a clear correlation between water. counterions motions and the complexation i.e. the water molecules and counterions which condensed around siRNA are moved away from the siRNA backbone when dendrimer start binding to the siRNA back hone. As siRNA wraps/bind to the dendrimer counterions originally condensed onto siRNA (Na-1) and dendrimer (Cl-) get released. We give a quantitative estimate of the entropy of counterions and show that there is gain in entropy due to counterions release during the complexation. Furthermore, the free energy of complexation of IG3 and IG4 at two different salt concentrations shows that increase in salt concentration leads to the weakening of the binding affinity of siRNA and dendrimer.

Self-assembled flower-like nanostructures of InN and GaN grown by plasma-assisted molecular beam epitaxy

Nanosized hexagonal InN flower-like structures were fabricated by droplet epitaxy on GaN/Si(111) and GaN flower-like nanostructure fabricated directly on Si(111) substrate using radio frequency plasma-assisted molecular beam epitaxy. Powder X-ray diffraction (XRD) and scanning electron microscopy (SEM) were used to study the crystallinity and morphology of the nanostructures. Moreover, X-ray photoelectron spectroscopy (XPS) and photoluminescence (PL) were used to investigate the chemical compositions and optical properties of nano-flowers, respectively. Activation energy of free exciton transitions in GaN nano-flowers was derived to be similar to 28.5 meV from the temperature dependent PL studies. The formation process of nano-flowers is investigated and a qualitative mechanism is proposed.

A molecular dynamics study of cage-to-cage migration in sodium Y zeolite: role of surface-mediated diffusion

The details of cage-to-cage migration have been obtained from an analysis of the molecular dynamics trajectory of a probe adsorbate. It is observed that particles utilize the region within a radius of 2 angstrom from the window center but with diffusion taking place predominantly at 1.6 angstrom from the window center and a potential energy of nearly -12 kJ/mol. A barrier of about 0.5 kJ/mol is observed for surface-mediated diffusion. Surprisingly, for diffusion without surface mediation for a particle going from one cage center to another, there is an attractive well near the window instead of a barrier. At low adsorbate concentrations and room temperature, the predominant mode for cage-to-cage migration is surface-mediated diffusion. The analysis suggests that particles slide along the surface of the inner walls of the alpha-cages during migration from one cage to another.

A possible role for a low molecular weight peptide in regulation of testosterone production by rat Leydig cells

Sodium dodecyl sulphate-polyacrylamide gel electrophoresis of Percoll purified Leydig cell proteins from 20- and 120-day-old rats revealed a significant decrease in a low molecular weight peptide in the adult rats. Administration of human chorionic gonadotropin to immature rats resulted in a decrease in the low molecular weight peptide along with increase in testosterone production. Modulation of the peptide by human chorionic gonadotropin could be confirmed by Western blotting. The presence of a similar peptide could be detected by Western blotting in testes of immature mouse, hamster, guinea pig but not in adrenal, placenta and corpus luteum. Administration of testosterone propionate which is known to inhibit the pituitary luteinizing hormone levels in adult rats resulted in an increase in the low molecular weight peptide, as checked by Western blotting. It is suggested that this peptide may have a role in regulation of acquisition of responsiveness to luteinizing hormone by immature rat Leydig cells.

X-ray and molecular-dynamics studies on Mycobacterium leprae single-stranded DNA-binding protein and comparison with other eubacterial SSB structures

The crystal structures of two forms of Mycobacterium leprae single-stranded DNA-binding protein (SSB) have been determined at 2.05 and 2.8 A resolution. Comparison of these structures with the structures of other eubacterial SSBs indicates considerable variation in their quaternary association, although the DNA-binding domains in all of them exhibit the same OB-fold. This variation has no linear correlation with sequence variation, but could be related to variation in protein stability. Molecular-dynamics simulations have been carried out on tetrameric molecules derived from the two forms and the prototype Escherichia coli SSB and the individual subunits of both proteins. Together, the X-ray studies and molecular-dynamics simulations yield information on the relatively rigid and flexible regions of the molecule and on the effect of oligomerization on flexibility. The simulations provide insight into the changes in subunit structure on oligomerization. They also provide insight into the stability and time evolution of the hydrogen bonds/water bridges that connect the two pairs of monomers in the tetramer.

Crystal and molecular structure of l-valyl-l-lysine hydrochloride

l-Valyl-l-lysine hydrochloride, C11N3O3H23 HCl, rystallizes in the monoclinic space group P2, with a = 5.438(5), b = 14.188(5), c = 9.521(5) Å, β= 95.38(2)° and Z = 2. The crystal structure, solved by direct methods, refined to R = 0.036, using full matrix least-squares method. The peptide exists in a zwitterionic form, with the N atom of the lysine side-chain protonated. The two γ-carbons of the valine side-chain have positional disorder, giving rise to two conformations, χ111= -67.3 and 65.9°, one of which (65.9°) is sterically less favourable and has been found to be less popular amongst residues branching at β-C. The lysine side-chain has the geometry of g− tgt, not seen in crystal structures of the dipeptides reported so far. Interestingly, χ32 (63.6°) of lysine side-chain has a gauche+ conformation unlike in most of the other tructures, where it is trans. The neighbouring peptide molecules are hydrogen bonded in a head-to-tail fashion, a rather uncommon interaction in lysine peptide structures. The structure shows considerable similarity with that of l-Lys-l-Val HO in conformational angles and H-bond interactions [4].

Crystal and molecular structure of sym-homospermidine monohydrate

Sym-homospermidine, [formula; see text] is a naturally occurring rare-polyamine found in relatively large concentration in sandal leaves. As part of our studies on structure and interactions of polyamines, ym-homospermidine was purified from sandal leaves and its structure was determined by single crystal X-ray diffraction technique. The phosphate salt of the molecule crystallized in the triclinic space group P1- with a = 8.246(1)A, b = 8.775(1)A, c = 15.531(2)A, alpha = 74.20(1) degrees, beta = 88.36(1) degrees and gamma = 65.41(1) degrees. The structure was determined by direct methods and refined to a final R factor of 5.4% for 2087 reflections with magnitude of F(obs) greater than 5 sigma [F(obs)]. The amine exists in its most favourable all trans conformation. For each amine molecule three phosphate groups exist in the crystal structure, suggesting that two of the oxygens of each phosphate group are protonated. There is also a single water molecule in the asymmetric unit in contrast to that of spermidine phosphate which has 3 water molecules. These differences probably reflect the hydrogen bonding properties of mono-ionic and di-ionic phosphate groups. The structure is predominantly stabilized by a network of hydrogen bonds.

Design and fabrication of an indigenous molecular beam ultraviolet photoelectron spectrometer

An ultraviolet photoelectron spectrometer for the study of van der Waals molecules has been designed and fabricated indigenously. The spectrometer consists of an HeI discharge lamp, a molecular beam sample inlet system, an electrostatic lens, a 180-degrees hemispherical electrostatic analyser and a channeltron detector. Performance of the spectrometer is illustrated with an example.

Detection and molecular epidemiology of tick-borne encephalitis virus infections

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Structural Studies of Analgesics and Their Interactions. V.* The Crystal and Molecular Structure of Metamizol Monohydrate

Metamizol, Na[Ct3H16N3045], C13H16N304S-Na +, a sulphonyl derivative of amidopyrine, is perhaps the most widely used non-narcotic analgetic and antiinflammatory pyrazolone derivative. The monohydrate of the compound crystallizes in the monoclinic space group P2Jc with eight molecules in a unit cell of dimensions a = 9.143 (3), b = 49.50 (2), c = 7.314 (2)/k and fl = 90.9 (1) °. The structure was solved by direct methods and refined to an R value of 0.080 for 4466 observed reflections. The two crystallographically independent molecules in the structure have similar dimensions. The elongated molecules are hydrophobic at one end and hydrophilic at the other with the middle portion partly hydrophobic and partly hydrophilic. The pyrazolone group in the structure has dimensions similar to those found in uncomplexed antipyrine and amidopyrine. The crystal structure can be described as consisting of double layers of metamizol molecules stacked perpendicular to the b axis. The adjacent double layers are separated by a layer of Naions and water molecules.

Molecular hydrodynamic theory of non‐Markovian collective orientational relaxation in dense dipolar liquids

A microscopic study of the non‐Markovian (or memory) effects on the collective orientational relaxation in a dense dipolar liquid is carried out by using an extended hydrodynamic approach which provides a reliable description of the dynamical processes occuring at the molecular length scales. Detailed calculations of the wave‐vector dependent orientational correlation functions are presented. The memory effects are found to play an important role; the non‐Markovian results differ considerably from that of the Markovian theory. In particular, a slow long‐time decay of the longitudinal orientational correlation function is observed for dense liquids which becomes weaker in the presence of a sizeable translational contribution to the collective orientational relaxation. This slow decay can be attributed to the intermolecular correlations at the molecular length scales. The longitudinal component of the orientational correlation function becomes oscillatory in the underdamped limit of momenta relaxations and the frequency dependence of the friction reduce the frictional resistance on the collective excitations (commonly known as dipolarons) to make them long lived. The theory predicts that these dipolarons can, therefore, be important in chemical relaxation processes, in contradiction to the claims of some earlier theoretical studies.

Molecular theory of dielectric relaxation in a dense binary dipolar liquid

A molecular theory of dielectric relaxation in a dense binary dipolar liquid is presented. The theory takes into account the effects of intra- and interspecies intermolecular interactions. It is shown that the relaxation is, in general, nonexponential. In certain limits, we recover the biexponential form traditionally used to analyze the experimental data of dielectric relaxation in a binary mixture. However, the relaxation times are widely different from the prediction of the noninteracting rotational diffusion model of Debye for a binary system. Detailed numerical evaluation of the frequency-dependent dielectric function epsilon-(omega) is carried out by using the known analytic solution of the mean spherical approximation (MSA) model for the two-particle direct correlation function for a polar mixture. A microscopic expression for both wave vector (k) and frequency (omega) dependent dielectric function, epsilon-(k,omega), of a binary mixture is also presented. The theoretical predictions on epsilon-(omega) (= epsilon-(k = 0, omega)) have been compared with the available experimental results. In particular, the present theory offers a molecular explanation of the phenomenon of fusing of the two relaxation channels of the neat liquids, observed by Schallamach many years ago.

Reactivity Of Pph3 Toward Ruiiruiiicl(O2car)4 - Syntheses, Molecular-Structures, And Spectroscopic And Electrochemical Properties Of Ruiiruiii(Oh2)Cl(Mecn)(O2car)4(Pph3)2 And Ruii2(Oh2)(Mecn)2(O2car)4(Pph3)2

By the reaction of Ru2Cl(O2CAr)4 (1) and PPh3 in MeCN-H2O the diruthenium(II,III) and diruthenium(II) compounds of the type Ru2(OH2)Cl(MeCN)(O2CAr)4(PPh3)2 (2) and Ru2(OH2)(MeCN)2(O2CAr)4(PPh3)2 (3) were prepared and characterized by analytical, spectral, and electrochemical data (Ar is an aryl group, C6H4-p-X; X = H, OMe, Me, Cl, NO2). The molecular structure of Ru2(OH2)Cl(MeCN)(O2CC6H4-p-OMe)4(PPh3)2 was determined by X-ray crystallography. Crystal data are as follows: triclinic, P1BAR, a = 13.538 (5) angstrom, b = 15.650 (4) angstrom, c = 18.287 (7) angstrom, alpha = 101.39 (3)-degrees, beta = 105.99 (4)-degrees, gamma = 97.94 (3)-degrees, V = 3574 angstrom 3, Z = 2. The molecule is asymmetric, and the two ruthenium centers are clearly distinguishable. The Ru(III)-Ru(II), Ru(III)-(mu-OH2), and Ru(II)-(mu-OH2) distances and the Ru-(mu-OH2)-Ru angle in [{Ru(III)Cl(eta-1-O2CC6H4-p-OMe)(PPh3)}(mu-OH2)(mu-O2CC6H4-p-OMe)2{Ru(II)(MeCN)(eta-1-O2CC6H4-p-OMe)(PPh3)}] are 3.604 (1), 2.127 (8), and 2.141 (10) angstrom and 115.2 (5)-degrees, respectively. The compounds are paramagnetic and exhibit axial EPR spectra in the polycrystalline form. An intervalence transfer (IT) transition is observed in the range 900-960 nm in chloroform in these class II type trapped mixed-valence species 2. Compound 2 displays metal-centered one-electron reduction and oxidation processes near -0.4 and +0.6 V (vs SCE), respectively in CH2Cl2-TBAP. Compound 2 is unstable in solution phase and disproportionates to (mu-aquo)diruthenium(II) and (mu-oxo)diruthenium(III) complexes. The mechanistic aspects of the core conversion are discussed. The molecular structure of a diruthenium(II) compound, Ru2(OH2)(MeCN)2(O2CC6H4-p-NO2)4(PPh3)2.1.5CH2Cl2, was obtained by X-ray crystallography. The compound crystallizes in the space group P2(1)/c with a = 23.472 (6) angstrom, b = 14.303 (3) angstrom, c = 23.256 (7) angstrom, beta = 101.69 (2)-degrees, V = 7645 angstrom 3, and Z = 4. The Ru(II)-Ru(II) and two Ru(II)-(mu-OH2) distances and the Ru(II)-(mu-OH2)-Ru(II) angle in [{(PPh3)-(MeCN)(eta-1-O2CC6H4-p-NO2)Ru}2(mu-OH2)(mu-O2CC6H4-p-NO2)2] are 3.712 (1), 2.173 (9), and 2.162 (9) angstrom and 117.8 (4)-degrees, respectively. In both diruthenium(II,III) and diruthenium(II) compounds, each metal center has three facial ligands of varying pi-acidity and the aquo bridges are strongly hydrogen bonded with the eta-1-carboxylato facial ligands. The diruthenium(II) compounds are diamagnetic and exhibit characteristic H-1 NMR spectra in CDCl3. These compounds display two metal-centered one-electron oxidations near +0.3 and +1.0 V (vs SCE) in CH2Cl2-TBAP. The overall reaction between 1 and PPh3 in MeCN-H2O through the intermediacy of 2 is of the disproportionation type. The significant role of facial as well as bridging ligands in stabilizing the core structures is observed from electrochemical studies.

Structure of valinomycin by molecular dynamics studies

Valinomycin is an important ionophore which exhibits a high conformational flexibility. The study of various conformations adopted by this molecule together with the study of flexibility in a given conformation can throw light on the ion transport by the ionophore across the membrane. Molecular dynamics (MD) studies are ideal to characterize the flexibility in different parts of the molecule and can also give an idea of various conformations adopted by the molecule at a given temperature. Hence MD studies at 100K have been carried out on the minimized crystal structure of the molecule to scan the possible conformations in the neighbourhood of the well known 'bracelet' like structure of uncomplexed Valinomycin, Properties, like the flexibility, average values, r.m.s. fluctuations of the various intramolecular hydrogen bonds are discussed. Energy minimization has been carried out on selected MD simulated points to analyze the characteristics of the unique conformation adopted by this molecule at this temperature.