We have performed density functional theory (DFT) calculations of iron−porphyrin (FeP) and its complexes with O2, CO, NO, imidazole (Im). Our fully optimized structures agree well the available experimental data for synthetic heme models. Comparison crystallographic proteins highlights interesting features carbon monoxymyoglobin. The diatomic molecule induces a 0.3−0.4 Å displacement Fe atom out porphyrin nitrogen (Np) plane doming overall ring. energy iron−diatomic bond increases in order...

We show that new aspects of the physics microclusters can be investigated accurately with ab initio molecular dynamics. present results on a number properties ${\mathrm{Si}}_{N}$ aggregates ($N$ up to 10) at both zero and finite temperatures. The dynamical simulated annealing for ground state point complex growth sequence. Simulations temperatures existence two regimes, solidlike liquidlike, substantially different electronic structural properties.

The properties of the three-dimensional uniform electron gas in Fermi liquid regime are analyzed using variational Monte Carlo (VMC) and fixed-node diffusion methods. Our study extends those Ceperley [Phys. Rev. B 18, 3126 (1978)] Alder Lett. 45, 566 (1980)] to larger system sizes with improved statistics and, more importantly, partial spin polarization. density range 0.8\ensuremath{\le}${\mathit{r}}_{\mathit{s}}$\ensuremath{\le}10, which is most relevant for functional computations, studied...

The stability of different phases the three-dimensional non-relativistic electron gas is analyzed using stochastic methods. With decreasing density, we observe a {\it continuous} transition from paramagnetic to ferromagnetic fluid, with an intermediate range ($25\pm 5 \leq r_s\leq 35 \pm 5$) for partially} spin-polarized liquid. freezing into Wigner crystal occurs at $r_s=65 10$. We discuss relative magnetic structures in solid phase, as well possibility disordered phases.

Room temperature ionic liquids (RTILs) and biomolecules are both paradigmatic classes of organic molecules, each consisting a prodigious number distinct chemical species, organized into large families homologous compounds. Their combination is set to open new avenues for discoveries applications in biochemistry, biomedicine pharmacology, food science, nanotechnology. We provide survey past current investigations the physics properties systems made RTILs biomolecules, focusing on most...

Binary mixtures of additive (d 12 = 1 + d 2)/2) and non-additive ≠ hard spheres have been studied with new integral equations. Accurate Monte Carlo results for some cases generated tables radial distribution functions are explicitly given. Comparison structural thermodynamic demonstrates that an approximate equation recently proposed by Martynov Sarkisov one-component significantly improves on the Percus-Yevick approximation also in mixture case, without introducing free parameters. A simple...

Neutron reflectometry (NR) measurements were carried out to probe the structure and stability of two model biomembranes consisting 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) phospholipid bilayers hydrated by water solutions prototypical room-temperature ionic liquids (RTILs), namely, 1-butyl-3-methyl-imidazolium chloride ([bmim][Cl]) choline ([Chol][Cl]) at concentrations 0.1 M 0.5 M, respectively. The raw data analyzed...

This study deals with a novel molecular simulation technique, named adiabatic bias dynamics (MD), which provides simple and reasonably inexpensive route to generate MD trajectories joining points in conformational space separated by activation barriers. Because of the judicious way biasing potential is updated during runs, technique allows some additional effort computation free energy change experienced trajectory. The method has been applied nontrivial problem: unfolding an atomistic model...

Molecular dynamics simulations based on an empirical force field have been carried out to investigate the properties of a zwitter-ionic phospholipid (POPC) bilayer in contact with water solution [bmim][Cl], [bmim][PF(6)] and [bmim][Tf(2)N] at concentration c = 0.5 M. The results reveal important specific interactions cations anions bilayer. [bmim](+) cation, particular, shows clear tendency be incorporated tail-first into [Cl](-) remains solution, [PF(6)](-) forms thin layer lipid surface,...

Empirical evidence and conceptual elaboration reveal rationalize the remarkable affinity of organic ionic liquids for biomembranes. Cations so-called room-temperature (RTILs), in particular, are readily absorbed into lipid fraction biomembranes, causing a variety observable biological effects, including generic cytotoxicity, broad antibacterial potential, anticancer activity. Chemical physics analysis model systems made phospholipid bilayers, RTIL ions, water confirm partially explain this...

Molecular dynamics simulations in the NPT ensemble have been carried out to investigate effect of two room temperature ionic liquids (RTILs), on stacks phospholipid bilayers water. We consider RTIL compounds consisting chloride ([bmim][Cl]) and hexafluorophosphate ([bmim][PF6]) salts 1-buthyl-3-methylimidazolium ([bmim]+) cation, while bilayer is made 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). Our investigations focus structural dynamical properties water molecules that could...

Previous calculations of the structures isomers phosphorus clusters up to P11 (density functional with simulated annealing, local spin density approximation exchange-correlation energy) have been extended arsenic clusters. The Asn are characterized by an almost uniform expansion (∼ 9%) corresponding Pn isomers. All cluster also studied using a nonlocal, gradient corrected (Becke–Perdew) energy functional. While unchanged, there significant improvements in cohesive energies all We present...

Ab initio pseudopotentials for the IIA and IIB elements have been generated in framework of density-functional theory, including gradient corrections to local-density approximation (LDA). Their accuracy transferability tested by extensive atomic computations. We applied these evaluation bonding properties homonuclear dimers. Our molecular computations, not restricted light elements, allow a wide assessment importance finite systems. For all dimers considered here, LDA error bond energies is...

We present an ab initio molecular dynamics study of the ground state, finite temperature, dynamical and electronic properties Na20 Na10K10 microclusters. For lowest-energy structure has several bulklike features. The vibrational spectrum at 200 K is compared to that liquid. From our results we derive a rationale for so far unexplained dependence mass on nozzle temperature compositional abundance mixed clusters. implications calculations validity shell model are discussed in detail.

We study the martensitic phase transformation in ${\mathrm{Ni}}_{\mathit{x}}$${\mathrm{Al}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$ composition range 0.60x0.66 with quasiharmonic approximation and molecular dynamics. These alloys present a high-temperature bcc (austenite) transforming at low temperature into compact 3M structure (martensite). In our computation potential energy of system is approximated by an embedded-atom calibrated to reproduce selected properties pure elements fcc Ni-Al...

Mixtures of room temperature ionic liquids (IL) with neutral organic molecules provide a valuable testing ground to investigate the interplay and molecular-dipolar state in dense Coulomb systems at near ambient conditions. In present study, viscosity eta conductivity sigma 1-n-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6])/naphthalene mixtures T = 80 degrees C have been measured 10 stoichiometries spanning composition range from pure naphthalene [bmim][PF6]. The grows nearly...

The combination of amino acids in their deprotonated and thus anionic form with a choline cation gives origin to new potentially important class organic ionic compounds. A series such neutral ion pairs has been investigated by first principle methods. results reveal intriguing structural motives as well regular patterns the charge distribution predict number vibrational optical properties that could guide experimental investigation these replacement its phosphocholine analogue causes...

We briefly review experimental and computational studies of room temperature ionic liquids (RTILs) interacting with important classes biomolecules, including phospholipids, peptides proteins, nucleic acids carbohydrates. Most these have been driven by the interest for RTILs applications as solvents. Thus, available data cover primarily thermodynamic properties such reciprocal solubility bio-molecules, well phase boundaries. Less extensive are also on transport diffusion viscosity homogeneous...

Polysaccharides play a crucial role in virtually all living systems. They also represent the biocompatible and fully sustainable component of variety nanoparticles, which are increasing interest biomedicine, food processing, cosmetics, structural reinforcement polymeric materials. The computational modeling complex polysaccharide phases will assist understanding properties behavior these In this paper, structural, bonding, mechanical 10 wt % cellulose–callose hydrogels (β-glucans coexisting...

Density functional calculations have been performed for ring isomers of sulfur with up to 18 atoms, and chains ten atoms. There are many both types, the predict existence new forms. Larger rings very flexible, numerous local energy minima. Apart from a small, but consistent overestimate in bond lengths, results reproduce experimental structures where known. Calculations also on surfaces S8 rings, interaction between pair such reaction one triplet diradical chain. The potential energies,...

We investigate the stability and structural properties of dense hydrogen-helium mixtures under planetary interior conditions (Jupiter Saturn). The excess free energy mixing $\ensuremath{\Delta}G(x)$ is determined as a function helium atomic fraction $x$ by ab initio molecular dynamics simulations in pressure range $4\ensuremath{\le}P\ensuremath{\le}24\mathrm{Mbar}$ at temperatures $T\ensuremath{\le}3000\mathrm{K}$. Energy, volume, entropic contributions are evaluated. Demixing...

Minimum-energy structures of O2, CO, and NO iron–porphyrin (FeP) complexes, computed with the Car–Parrinello molecular dynamics, agree well available experimental data for synthetic heme models. The diatomic molecule induces a 0.3–0.4 Å displacement Fe atom out porphyrin nitrogen (Np) plane doming overall ring. energy iron–diatomic bond increases in order Fe(SINGLE BOND)O2 (9 kcal/mol) < BOND)CO (26 BOND)NO (35 kcal/mol). presence an imidazole axial ligand strength bonds (15 35 kcal/mol,...