RESUMEN

COordinated Responsive Arrays of Surface-Linked polymer islands (CORALS) allow for the creation of molecular surfaces with novel and switchable properties. Critical components of CORALs are the uniformly distributed islands of densely grafted polymer chains (nanoislands) separated by regions of bare surface. The grafting footprint and separation distances of nanoislands are comparable to that of the constituent polymer chains themselves. Herein, we characterize the structural features of the nanoislands and semiflexible polymers within to better understand this critical constituent of CORALs. We observe different characteristics of grafted semiflexible polymers depending on the polymer island's size and distance from the center of the island. Specifically, the characteristics of the chains at the island periphery are similar to isolated tethered polymer chains (full flexible chains), while chains in the center of the island experience the neighbor effect such as chains in the classic polymer brush. Chains close to the edge of the islands exhibit unique structural features between these two regimes. These results can be used in the rational design of CORALs with specific interfacial characteristics and predictable responses to external stimuli. It is hoped that this the discussion of the different morphologies of the polymers as a function of distance from the edge of the polymer will find applications in a wide variety of systems.

RESUMEN

We present a computational study of the effect of chemical modifications of the meta and para substituents in the coordinating pendant arm of a modified 1,4,7,10-tetraazacyclododecane-N, N', N″, N‴-tetraamide (DOTAM) ligand on the Chemical Exchange Saturation Transfer (CEST) signal. Magnetic Resonance Imaging (MRI) is currently one of the most widely used techniques available. MRI has led to a new class of pharmaceuticals termed "imagining" or "contrast" agents. These agents usually work by incorporating lanthanide metals such as Gadolinium (Gd) and Europium (Eu). This allows the contrast agents to take advantage of the paramagnetic properties of the metals, which in turn enhances the signal detectable by MRI. The effect of simple electron-withdrawing (e.g., nitro) and electron-donating (e.g., methyl) substituents chemically attached to a modified chelate arm (pendant arm) is quantified by charge transfer interactions in the coordinated water-chelate system computed from quantum mechanics. This study attempts to reveal the origin of the substituent effect on the CEST signal and the electronic structure of the complex. We find that the extent of Charge Transfer (CT) depends on orbital orientations and overlaps. However, CT interactions occur simultaneously from all arms, which causes a dilution effect with respect to the pendant arm.

RESUMEN

Polyphosphazenes, because of their unique properties, have generated many opportunities to explore a variety of applications. These applications include areas such as biomedical research (e.g. drug delivery) and material science (e.g. fire-resistant polymers). Phosphazenes potentially have more variations then benzene analogues because of different substitution patterns. Here we present A computational study of the chemical modifications to a group of cyclic phosphazenes mainly hexachlorophosphazene (PNCl2)3. This study focuses on the relative energies of reactivity of hexachlorophosphazene to understand their geometry and the complexes they likely form. We compare diols, amino alcohols, and diamines with a carbon linker of 1-7 atoms. These heteroatom chains are attached to a single phosphorus atom or adjoining phosphorus atoms to form ring structures of geminal, vicinal (cis), and vicinal (trans) moieties. We find that the reactivities of "heteroatom caps" are predicted to be O,O (diol) > N,O (amino alcohol) > N,N (diamine). These results can be used to predict energetics and thus the stability of new compounds for biomedical and industrial applications.

RESUMEN

Using molecular dynamics simulations, we studied the structure, interhelix interactions, and dynamics of transmembrane proteins. Specifically, we investigated homooligomeric helical bundle systems consisting of synthetic α-helices with either the sequence Ac-(LSLLLSL)3-NH2 (LS2) or Ac-(LSSLLSL)3-NH2 (LS3). The LS2 and LS3 helical peptides are designed to have amphipathic characteristics that form ion channels in membrane. We simulated bundles containing one to six peptides that were embedded in palmitoyl-oleoyl-phosphatidylcholine (POPC) lipid bilayer and placed between two lamellae of water. We aim to provide a fundamental understanding of how amphipathic helical peptides interact with each other and their dynamical behaviors in different homooligomeric states. To understand structural properties, we examined the helix lengths, tilt angles of individual helices and the entire bundle, interhelix distances, interhelix cross-angles, helix hydrophobic-to-hydrophilic vector projections, and the average number of interhelix hydrophilic (serine-serine) contacts lining the pore of the transmembrane channel. To analyze dynamical properties, we calculated the rotational autocorrelation function of each helix and the cross-correlation of the rotational velocity between adjacent helices. The observed structural and dynamical characteristics show that higher order bundles containing four to six peptides are composed of multiple lower order bundles of one to three peptides. For example, the LS2 channel was found to be stable in a tetrameric bundle composed of a "dimer of dimers." In addition, we observed that there is a minimum of two strong hydrophilic contacts between a pair of adjacent helices in the dimer to tetramer systems and only one strong hydrophilic interhelix contact in helix pairs of the pentamer and hexamer systems. We believe these results are general and can be applied to more complex ion channels, providing insight into ion channel stability and assembly.

Asunto(s)

RESUMEN

Theoretical approximations to the sum frequency vibrational spectroscopy (SFVS) of the carbon tetrachloride/water interface are constructed using the quantum-corrected time correlation functions (TCF) to aid in interpretation of experimental data and to predict novel vibrational modes. Instantaneous normal mode (INM) methods are used to characterize the observed modes leading to the TCF signal, thus providing molecular resolution of the vibrational lineshapes. Detailed comparisons of the theoretical signals are made with those obtained experimentally and show excellent agreement for the spectral peaks in the O-H stretching region of water. An intermolecular mode, unique to the interface, at 848 cm(-1) is also identifiable, similar to the one seen for the water/vapor interface. INM analysis reveals the resonance is due to a wagging mode (hindered rotation) that was previously identified (Perry et al 2005 J. Chem. Phys. 123 144705) as localized on a single water molecule with both hydrogens displaced normal to the interface-generally it is found that the symmetry breaking at the interface leads to hindered translations and rotations at hydrophilic/hydrophobic interfaces that assume finite vibrational frequencies due to anchoring at the aqueous interface. Additionally, examination of the real and imaginary parts of the theoretical SFVS spectra reveal the spectroscopic species attributed the resonances and possible subspecies in the O-H region; these results are consistent with extant experimental data and associated analysis.

Asunto(s)

RESUMEN

We present the results of coarse grained molecular dynamics simulation using a charge free model that is able to capture different regions of the morphological phase diagram of charged diblock copolymers. Specifically, we were able to reproduce many phases of the poly(acrylic acid)-(1,4)-polybutadiene (PAA-PBA) diblock copolymer, Ca(2+) and water systems as a function of pH and calcium concentration with short-range LJ type potentials. The morphologies observed range from bilayers to cylinders to spherical micelles. Such polyanionic/cationic amphiphiles in water typically present multiple challenges for molecular simulations, particularly due to the many charge interactions that are long ranged and computationally costly. Further, it is precisely these interactions that are thought to modulate large amphiphile assemblies of interest such as lipid rafts. However, our model is able to reproduce different morphologies due to pH and with or without the addition of Ca(2+) as well as the lateral phase segregation and the domain registration observed in neutral and charged diblock copolymer mixtures. The results suggest that the overall effect of charges is a local structural rearrangement that renormalizes the steric repulsion between the headgroups. This simple model, which is devoid of charges, is able to reproduce the complex phase diagram and can be used to investigate collective phenomena in these charged systems such as domain formation and registration or colocalization of lipid rafts across bilayer leaflets.

Asunto(s)

RESUMEN

The free energy surfaces (FESs) of alanine dipeptide are studied to illustrate a new strategy to assess the performance of classical molecular mechanics force field on the full range of the (ϕ-ψ) conformational space. The FES is obtained from metadynamics simulations with five commonly used force fields and from ab initio density functional theory calculations in both gas phase and aqueous solution. The FESs obtained at the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d,p) level of theory are validated by comparison with previously reported MP2 and LMP2 results as well as with experimentally obtained probability distribution between the C5-ß (or ß-PPII) and αR states. A quantitative assessment is made for each force field in three conformational basins, LeRI (C5-ß-C7eq), LeRII (ß2-αR), and LeRIII(αL-C7ax-αD) as well as three transition-state regions linking the above conformational basins. The performance of each force field is evaluated in terms of the average free energy of each region in comparison with that of the ab initio results. We quantify how well a force field FES matches the ab initio FES through the calculation of the standard deviation of a free energy difference map between the two FESs. The results indicate that the performance varies largely from region to region or from force field to force field. Although not one force field is able to outperform all others in all conformational areas, the OPLSAA/L force field gives the best performance overall, followed by OPLSAA and AMBER03. For the three top performers, the average free energies differ from the corresponding ab initio values from within the error range (<0.4 kcal/mol) to ∼1.5 kcal/mol for the low-energy regions and up to ∼2.0 kcal/mol for the transition-state regions. The strategy presented and the results obtained here should be useful for improving the parametrization of force fields targeting both accuracy in the energies of conformers and the transition-state barriers.

RESUMEN

Recently, we reported new coarse grain (CG) force fields for lipids and phenyl/fullerene based molecules. Here, we developed the cross parameters necessary to unite those force fields and then applied the model to investigate the nature of benzene and C(60) interactions with lipid bilayers. The interaction parameters between the phenyl and lipid CG sites are based on experimental and all atom (AA) molecular dynamics (MD) data. The resulting force field was tested on benzene rich lipid bilayers and shown to reproduce general behavior expected from experiments. The parameters were then applied to C(60) interactions with lipid bilayers. Overall, the results showed excellent agreement with AA MD and experimental observations. In the C(60) lipid systems, the fullerenes were shown to aggregate even at the lowest concentrations investigated.

Asunto(s)

RESUMEN

Understanding mesoscopic phenomena in terms of the fundamental motions of atoms and electrons poses a severe challenge for molecular simulation. This challenge is being met by multiscale modeling techniques that aim to bridge between the microscopic and mesoscopic time and length scales. In such techniques different levels of theory are combined to describe a system at a number of scales or resolutions. Here we review recent advancements in adaptive hybrid simulations, in which the different levels are used in separate spatial domains and matter can diffuse from one region to another with an accompanying resolution change. We discuss what it means to simulate such a system, and how to enact the resolution changes. We show how to construct efficient adaptive hybrid quantum mechanics/molecular mechanics (QM/MM) and atomistic/coarse grain (AA/CG) molecular dynamics methods that use an intermediate healing region to smoothly couple the regions together. This coupling is formulated to use only the native forces inherent to each region. The total energy is conserved through the use of auxiliary bookkeeping terms. Error control, and the choice of time step and healing region width, is obtained by careful analysis of the energy flow between the different representations. We emphasize the CG → AA reverse mapping problem and show how this problem is resolved through the use of rigid atomistic fragments located within each CG particle whose orientation is preconditioned for a possible resolution change through a rotational dynamics scheme. These advancements are shown to enable the adaptive hybrid multiscale molecular dynamics simulation of macromolecular soft matter systems.

RESUMEN

The conformations of model transmembrane peptides are studied to understand the structural and dynamical aspects of tetrameric bundles using a series of coarse grain (CG) molecular dynamics (MD) simulations since membrane proteins play a crucial role in cell function. In this work, two different amphipathic models have been constructed using similar hydrophobic/hydrophilic characteristics with two structurally distinct morphologies to evaluate the effect of roughness and hydrophilic topology on the structure of tetrameric bundles, one class that forms an ion-channel and one class that does not. Free energy calculations of typical amphipathic peptide topologies show that using a relatively smooth surface morphology allows for a stable conformation of the tetramer bundle in a diamond formation. However, the model with side chains attached to the core in order to roughen the surface has a stable square tetramer bundle which is consistent with experimental data and all-atom (AA) MD simulations. Comparisons of the CG simulations with AA MD simulations are in reasonable agreement with the formation of tetrameric homo-oligomers, partitioning within the lipid bilayer and tilt angle with respect to the bilayer normal. We concluded that a square or diamond shape tetrameric homo-oligomers could be stabilized by rational design of the peptide morphology and topology of the surface, thus allowing us to tune the permeability of the bundle or channel.

Asunto(s)

RESUMEN

A coarse-grained intermolecular potential has been parametrized for phenyl-based molecules. The parametrization was accomplished by fitting to experimental thermodynamic data. Specifically, the intermolecular potentials, which were based on Lennard-Jones functional forms, were parametrized and validated using experimental surface tension, density, and partitioning data. This approach has been used herein to develop parameters for coarse-grained interaction sites that are applicable to a variety of phenyl-based molecules, including analogues of the amino acid side chains of phenylalanine and tyrosine. Comparison of the resulting coarse-grain model to atomistic simulations shows a high level of structural and thermodynamic agreement between the two models, despite the fact that no atomistic simulation data was used in the parametrization of the coarse-grain intermolecular potentials.

Asunto(s)

RESUMEN

The interaction of fullerenes with biological systems and the environment is a topic of current interest. Coarse-grained molecular dynamics (CGMD) simulations are well-suited to investigate some of the factors involved because they provide access to time and length scales that are not accessible using fully atomistic simulation methods. In the case of buckyballs (C(60)) and single-walled carbon nanotubes (SWNTs), it is necessary to parametrize a CG force field that accurately captures the balance between fullerene-fullerene and fullerene-solvent interactions. Herein, we derive CG force field parameters for C(60) and SWNTs by using the optimized benzene parameters from part I [DeVane, R.; Chiu, C.-c.; Nielsen, S. O.; Shinoda, W.; Moore, P. B.; Klein, M. L. J. Phys. Chem. B 2010, doi: 10.1021/jp9117369]. Solubility, transfer free energy, and dimerization free-energy data for C(60) and SWNTs obtained using the proposed models show excellent agreement with experimental and fully atomistic MD data. In particular, cluster analysis of C(60) aggregation in a hydrocarbon melt corroborates the force field parameters. The aggregation behavior of the present CG force field differs considerably from that of models currently in widespread use. The combined results provide a strong basis for applying this model for further large-scale MD studies involving C(60) and SWNTs.

Asunto(s)

RESUMEN

The physical properties of a liquid in contact with a solid are largely determined by the solid-liquid surface tension. This is especially true for nanoscale systems with high surface area to volume ratios. While experimental techniques can only measure surface tension indirectly for nanoscale systems, computer simulations offer the possibility of a direct evaluation of solid-liquid surface tension although reliable methods are still under development. Here we show that using a mean field approach yields great physical insight into the calculation of surface tension and into the precise relationship between surface tension and excess solvation free energy per unit surface area for nanoscale interfaces. Previous simulation studies of nanoscale interfaces measure either excess solvation free energy or surface tension, but these two quantities are only equal for macroscopic interfaces. We model the solid as a continuum of uniform density in analogy to Hamaker's treatment of colloidal particles. As a result, the Hamiltonian of the system is imbued with parametric dependence on the size of the solid object through the integration limits for the solid-liquid interaction energy. Since the solid-liquid surface area is a function of the size of the solid, and the surface tension is the derivative of the system free energy with respect to this surface area, we obtain a simple expression for the surface tension of an interface of arbitrary shape. We illustrate our method by modeling a thin nanoribbon and a solid spherical nanoparticle. Although the calculation of solid-liquid surface tension is a demanding task, the method presented herein offers new insight into the problem, and may prove useful in opening new avenues of investigation.

RESUMEN

Until now, adaptive atomistic-coarse-grain (A/CG) molecular dynamics simulations have had very limited applicability because the on-the-fly CG → A transformation is problematic for all but those molecules whose CG representation consists of a single particle. Here, we solve this problem by combining a transitional healing region with a rotational dynamics of rigid atomistic fragments in the CG region. Error control is obtained by analysis of the A ↔ CG energy flow. We illustrate the method with adaptive multiscale simulations of liquid hexane and of a dilute polymer solution in a theta solvent.

Asunto(s)

RESUMEN

Inorganic nanoparticles (NPs) display unique size-dependent properties and have applications in many different areas such as medicine and the semiconductor industry. In order to take advantage of these properties, the organization of the NPs must be controlled, either to promote crystallization or to prevent agglomeration. This control is typically acheived by using covalently bound amphiphilic ligands. While the properties of the NPs themselves have been well-characterized, much less is known about the organic ligand coating. Here, we present a theoretical and computer simulation approach to compute the surface area occupied per ligand molecule as a function of the NP radius and of the ligand hydrophilic to lipophilic balance. We employ a self-consistent method which takes into account the full free energy of the NP/ligand/solvent system, which for this study is composed of hydrophobic NPs, alkyl poly(oxyethylene) ligands, and water. We find an order of magnitude higher ligand coverage on NPs compared to flat surfaces, in agreement with some experimental reports. Our approach is fundamentally different from existing computational methods in the literature and builds a foundation for studies of the organization of colloidal NPs in solvents or at interfaces.

Asunto(s)

RESUMEN

The physical properties of nanoscale materials often vary with their size, unlike the corresponding bulk material properties, which can only be changed by modifying the material composition. In particular, it is believed that hydration phenomena are length scale dependent. The manifestation of hydrophobicity over multiple length scales plays a crucial role in self-assembly processes such as protein folding and colloidal stability. In the case of particles composed of a bulk hydrophobic material, it is well known that the free energy of hydration monotonically increases with particle size. However, the size-dependent free energy of hydration for particles composed of a bulk hydrophilic material has not been studied. Here we show that the free energy of hydration is not a monotonic function of particle size, but rather, changes sign from positive to negative as the particle size increases. In other words, the particle is hydrophobic at small size and hydrophilic at large size. This behavior arises from a purely geometrical effect caused by the curvature of the particle-water interface. We explore the consequences of this phenomenon on colloidal stability and find that it dictates the shape of colloidal aggregates.

RESUMEN

The large quantity of protein sequences being generated from genomic data has greatly outpaced the throughput of experimental protein structure determining methods and consequently brought urgency to the need for accurate protein structure prediction tools. Reduced resolution, or coarse grained (CG) models, have become a mainstay in computational protein structure prediction perfoming among the best tools available. The quest for high quality generalized CG models presents an extremely challenging yet popular endeavor. To this point, a CG based interaction potential is presented here for the naturally occurring amino acids. In the present approach, three to four heavy atoms and associated hydrogens are condensed into a single CG site. The parameterization of the site-site interaction potential relies on experimental data thus providing a novel approach that is neither based on all-atom (AA) simulations nor experimental protein structural data. Specifically, intermolecular potentials, which are based on Lennard-Jones (LJ) style functional forms, are parameterized using thermodynamic data including surface tension and density. Using this approach, an amino acid potential dataset has been developed for use in modeling peptides and proteins. The potential is evaluated here by comparing the solvent accessible surface area (SASA) to AA representations and ranking of protein decoy data sets provided by Decoys 'R' Us. The model is shown to perform very well compared to other existing prediction models for these properties.

RESUMEN

Multiscale computer simulation algorithms are required to describe complex molecular systems with events occurring over a range of time and length scales. True multiscale simulations must solve the interface, or hand-shaking, problem of coupling together different levels of description in different spatial regions of the system. If the spatial regions of different resolution move over time, or if material is allowed to flow over the inter-region boundaries, a mechanism must be introduced into the multiscale algorithm to allow material to dynamically change its representation. While such a mechanism is highly desirable in many instances, it is fraught with technical difficulties. Here, we present a molecular dynamics simulation algorithm which is multiscale in both time and space. We supplement the potential and kinetic energy expressions with auxiliary terms in order to recover the total energy as a conserved quantity, even when the total number of degrees of freedom changes during the simulation. This is crucial for a proper assessment of the quality of adaptive hybrid algorithms, and in particular, it allows us to tune the hierarchy of RESPA levels to optimize the integration scheme.

RESUMEN

Structurally isomeric octanol interfacial systems, water/vapor, 3-octanol/vapor, n-octanol/vapor, 3-octanol/water, and n-octanol/water are investigated at 298 K using molecular dynamics simulation techniques. The present study is intended to investigate strongly associated liquid/liquid interfaces and probe the atomistic structure of these interfaces. The octanol and water molecules were initially placed randomly into a box and were equilibrated using constant pressure techniques to minimize bias within the initial conditions as well as to fully sample the structural conformations of the interface. An interface formed via phase separation during equilibration and resulted in a slab geometry with a molecularly sharp interface. However, some water molecules remained within the octanol phase with a mole fraction of 0.12 after equilibration. The resulting "wet" octanol interfaces were analyzed using density profiles and orientational order parameters. Our results support the hypothesis of an ordered interface only 1 or 2 molecular layers deep before bulk properties are reached for both the 3-octanol and water systems. However, in contrast to most other interfacial systems studied by molecular dynamics simulations, the n-octanol interface extends for several molecular layers. The octanol hydroxyl groups form a hydrogen-bonding network with water which orders the surface molecules toward a preferred direction and produces a hydrophilic/hydrophobic layering. The ordered n-octanol produces an oscillating low-high density of oxygen atoms out of phase with a high-low density of carbon atoms, consistent with an oscillating dielectric. In contrast, the isomeric 3-octanol has only a single carbon-rich layer directly proximal to the interface, which is a result of the different molecular topology. Both 3-octanol and n-octanol roughen the water interface with respect to the water/vapor interface. The "wet" octanol phases, in the octanol/water systems reach bulk properties in a shorter distance than the "dry" octanol/vapor interfaces.

Asunto(s)