Effects of -H and -OH Termination on Adhesion of Si-Si Contacts Examined Using Molecular Dynamics and Density Functional Theory.

The contact between nanoscale single-crystal silicon asperities and substrates terminated with -H and -OH functional groups is simulated using reactive molecular dynamics (MD). Consistent with previous MD simulations for self-mated surfaces with -H terminations only, adhesion is found to be low at full adsorbate coverages, be it self-mated coverages of mixtures of -H and -OH groups, or just -OH groups. As the coverage reduces, adhesion increases markedly, by factors of ∼5 and ∼6 for -H-terminated surfaces and -OH-terminated surfaces, respectively, and is due to the formation of covalent Si-Si bonds; for -OH-terminated surfaces, some interfacial Si-O-Si bonds are also formed. Thus, covalent linkages need to be broken upon separation of the tip and substrate. In contrast, replacing -H groups with -OH groups while maintaining complete coverage leads to negligible increases in adhesion. This indicates that increases in adhesion require unsaturated sites. Furthermore, plane-wave density functional theory (DFT) calculations were performed to investigate the energetics of two Si(111) surfaces fully terminated by either -H or -OH groups. Importantly for the adhesion results, both DFT and MD calculations predict the correct trends for the relative bond strengths: Si-O > Si-H > Si-Si. This work supports the contention that prior experimental work observing strong increases in adhesion after sliding Si-Si nanoasperities over each other is due to sliding-induced removal of passivating species on the Si surfaces.

Interfacial Properties of Linear Alkane/Nitrogen Binary Mixtures: Molecular Dynamics Vapor-Liquid Equilibrium Simulations.

Molecular dynamics simulations were used to investigate the vapor-liquid equilibria (VLE) and interfacial properties of binary mixtures of N2 with either ethane, propane, n-decane, or n-dodecane. Alkanes and N2 were modeled by using the TraPPE-UA and Rivera force fields, respectively. The typically used Lorentz-Berthelot combining rules resulted in liquid phases that are too N2-rich compared to experiment. To improve the accuracy of VLE predictions, the hydrocarbon-nitrogen interactions were fine-tuned, and these improved parameters were used to investigate interfacial properties. Scaling the interaction strength between nitrogen and -CH3 and -CH2- groups by factors of 0.95 and 0.85, respectively, relative to the Lorentz-Berthelot value, was found to minimize error in pressure-composition phase diagrams. These scaling parameters gave excellent agreement with experimental phase diagrams for mixtures of N2 with ethane, propane, or n-dodecane over a range of state points. For ethane/N2 and n-decane/N2 mixtures, trends in surface tension as a function of temperature and pressure are correctly reproduced, although the simulated values are slightly too high compared to experimental values. To assess how the accuracy of hydrocarbon-N2 interaction strength impacts interfacial property predictions, we have compared density profiles and surface tension using several different scaling factors. Using the Lorentz-Berthelot combining rules rather than optimized parameters gave the same qualitative trends, although some quantitative results, such as liquid-phase N2 mole fraction, were found to differ by a factor of ∼1.5. Using the optimized interaction parameters, interfacial behavior was examined by calculating density and free energy profiles. Nitrogen molecules preferentially adsorb at the interfacial region between the liquid and vapor phases. This interfacial adsorption becomes less energetically favorable as either the temperature, pressure, or length of the alkane chain increases.

Impact of Molecular Structure on Properties of n-Hexadecane and Alkylbenzene Binary Mixtures.

Because of the complexity of petroleum-based fuels, researchers typically use simplified mixtures, known as surrogates, to study combustion behavior and to attempt to identify how physical properties are related to combustion. The process of determining the surrogate composition to yield a desired set of thermophysical properties can be a complicated and time-consuming task. As a result, the use of computer simulations to narrow the number of possible surrogate compositions is beginning to be explored. Herein, molecular dynamics (MD) simulations are used to model binary mixtures of n-hexadecane with either benzene, toluene, n-ethylbenzene, n-propylbenzene, or n-butylbenzene. Calculated densities are in quantitative agreement with experimental values. With the exception of the mixtures containing benzene, simulated excess molar volumes are also in very good agreement with measured values. Isentropic bulk moduli are in qualitative agreement with experiment, and reproduce interesting trends observed in the experimental data. Specifically, minima in the bulk moduli at intermediate compositions of several of the alkylbenzenes are correctly reproduced. In addition, the structures of the fluids are also examined. For mixtures of n-hexadecane with alkylbenzenes with longer chains, the orientation of the aromatic rings is not substantially impacted by composition. In contrast, increasing n-hexadecane content increases the ratio of parallel to perpendicular arrangements of benzene and toluene molecules. In those mixtures, this change in orientation of the aromatic rings could be responsible for the minima observed in the bulk moduli data. These results show that MD simulations can assist in development of fuel surrogates, both by predicting thermophysical properties and by providing insight into how molecular structure and composition affect those properties.

pH-Responsive Self-Assembly of Polysaccharide through a Rugged Energy Landscape.

Self-assembling polysaccharides can form complex networks with structures and properties highly dependent on the sequence of triggering cues. Controlling the emergence of such networks provides an opportunity to create soft matter with unique features; however, it requires a detailed understanding of the subtle balance between the attractive and repulsive forces that drives the stimuli-induced self-assembly. Here we employ all-atom molecular dynamics simulations on the order of 100 ns to study the mechanisms of the pH-responsive gelation of the weakly basic aminopolysaccharide chitosan. We find that low pH induces a sharp transition from gel to soluble state, analogous to pH-dependent folding of proteins, while at neutral and high pH self-assembly occurs via a rugged energy landscape, reminiscent of RNA folding. A surprising role of salt is to lubricate the conformational search for the thermodynamically stable states. Although our simulations represent the early events in the self-assembly process of chitosan, which may take seconds or minutes to complete, the atomically detailed insights are consistent with recent experimental observations and provide a basis for understanding how environmental conditions modulate the structure and mechanical properties of the self-assembled polysaccharide systems. The ability to control structure and properties via modification of process conditions will aid in the technological efforts to create complex soft matter with applications ranging from bioelectronics to regenerative medicine.

Recent development and application of constant pH molecular dynamics.

Solution pH is a critical environmental factor for chemical and biological processes. Over the last decade, significant efforts have been made in the development of constant pH molecular dynamics (pHMD) techniques for gaining detailed insights into pH-coupled dynamical phenomena. In this article we review the advancement of this field in the past five years, placing a special emphasis on the development of the all-atom continuous pHMD technique. We discuss various applications, including the prediction of pKa shifts for proteins, nucleic acids and surfactant assemblies, elucidation of pH-dependent population shifts, protein-protein and protein-RNA binding, as well as the mechanisms of pH-dependent self-assembly and phase transitions of surfactants and peptides. We also discuss future directions for the further improvement of the pHMD techniques.

Predicting proton titration in cationic micelle and bilayer environments.

Knowledge of the protonation behavior of pH-sensitive molecules in micelles and bilayers has significant implications in consumer product development and biomedical applications. However, the calculation of pKa's in such environments proves challenging using traditional structure-based calculations. Here we apply all-atom constant pH molecular dynamics with explicit ions and titratable water to calculate the pKa of a fatty acid molecule in a micelle of dodecyl trimethylammonium chloride and liquid as well as gel-phase bilayers of diethyl ester dimethylammonium chloride. Interestingly, the pKa of the fatty acid in the gel bilayer is 5.4, 0.4 units lower than that in the analogous liquid bilayer or micelle, despite the fact that the protonated carboxylic group is significantly more desolvated in the gel bilayer. This work illustrates the capability of all-atom constant pH molecular dynamics in capturing the delicate balance in the free energies of desolvation and Coulombic interactions. It also shows the importance of the explicit treatment of ions in sampling the protonation states. The ability to model dynamics of pH-responsive substrates in a bilayer environment is useful for improving fabric care products as well as our understanding of the side effects of anti-inflammatory drugs.

Self-assembly and bilayer-micelle transition of fatty acids studied by replica-exchange constant pH molecular dynamics.

Recent interest in the development of surfactant-based nanodelivery systems targeting tumor sites has sparked our curiosity in understanding the detailed mechanism of the self-assembly and phase transitions of pH-sensitive surfactants. Toward this goal, we applied a state-of-the-art simulation technique, continuous constant pH molecular dynamics (CpHMD) with the hybrid-solvent scheme and pH-based replica-exchange protocol, to study the de novo self-assembly of 30 and 40 lauric acids, a simple model titratable surfactant. We observed the formation of a gel-state bilayer at low and intermediate pH and a spherical micelle at high pH, with the phase transition starting at 20-30% ionization and being completed at 50%. The degree of cooperativity for the transition increases from the 30-mer to the 40-mer. The calculated apparent or bulk pKa value is 7.0 for the 30-mer and 7.5 for the 40-mer. Congruent with experiment, these data demonstrate that CpHMD is capable of accurately modeling large conformational transitions of surfactant systems while allowing the simultaneous proton titration of constituent molecules. We suggest that CpHMD simulations may become a useful tool in aiding in the design and development of pH-sensitive nanocarriers for a variety of biomedical and technological applications.

Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids.

Detailed knowledge of the self-assembly and phase behavior of pH-sensitive surfactants has implications in areas such as targeted drug delivery. Here we present a study of the formation of micelle and bilayer from lauric acids using a state-of-the-art simulation technique, continuous constant pH molecular dynamics (CpHMD) with conformational sampling in explicit solvent and the pH-based replica-exchange protocol. We find that at high pH conditions a spherical micelle is formed, while at low pH conditions a bilayer is formed with a considerable degree of interdigitation. The mid-point of the phase transition is in good agreement with experiment. Preliminary investigation also reveals that the effect of counterions and salt screening shifts the transition mid-point and does not change the structure of the surfactant assembly. Based on these data we suggest that CpHMD simulations may be applied to computational design of surfactant-based nano devices in the future.

Diarylcyclopentendione metabolite obtained from a Preussia typharum isolate procured using an unconventional cultivation approach.

An uncommon 2,5-diarylcyclopentenone compound, preussidone (1), and a new biphenyl compound, 1',5-dimethoxy-3,5'-dimethyl-2,3'-oxybiphenyl-1,2'-diol (4), together with two known biphenyl compounds, 5-methoxy-3,5'-dimethyl-2,3'-oxybiphenyl-1,1',2'-triol (2) and cyperin (3), were obtained from a Preussia typharum isolate that was procured using a panel of unconventional media formulations. The structures of the new compounds were established by NMR and mass spectrometry, while the absolute configuration of 1 was assigned by quantum chemical ECD and VCD calculations. The antimicrobial and DPPH radical scavenging activities of 1-4 were tested. Compounds 2 and 4 exhibited DPPH radical scavenging activities that were comparable to the positive control ascorbic acid.

Nitric oxide coupling mediated by iron porphyrins: the N-N bond formation step is facilitated by electrons and a proton.

The coupling of two NO molecules catalyzed by iron porphyrins is of biological importance. We use density functional theory calculations to examine the factors that control the fundamental N-N bond formation step mediated by a single iron porphyrin. The presence of an axial Im ligand, extra electrons, and most importantly a proton, enhance the N-N bond formation step in our model.

Simulating pH titration of a single surfactant in ionic and nonionic surfactant micelles.

Calculation of surfactant pK(a)'s in micelles is a challenging task using traditional electrostatic methods due to the lack of structural data and information regarding the effective dielectric constant. Here we test the implicit- and hybrid-solvent-based continuous constant pH molecular dynamics (CpHMD) methods for predicting the pK(a) shift of a lauric acid solubilized in three micelles: dodecyl sulfate (DS), dodecyltrimethylammonium (DTA), and dodecyltriethylene glycol ether (DE3). Both types of simulations are able to reproduce the observed positive pK(a) shifts for the anionic DS and nonionic DE3 micelles. However, for the cationic DTA micelle, the implicit-solvent simulation fails to predict the direction of the pK(a) shift, while the hybrid-solvent simulation, where conformational sampling is conducted in explicit solvent, is consistent with experiment, although the specific-ion effects remain to be accurately determined. Comparison between the implicit- and hybrid-solvent data shows that the latter gives a more realistic description of the conformational environment of the titrating probe. Surprisingly, in the DTA micelle, surfactants are only slightly attracted to the laurate ion, which diminishes the magnitude of the electrostatic stabilization, resulting in a positive pK(a) shift that cannot be explained by chemical intuition or other theoretical models. Our data underscores the importance of microscopic models and ionization-coupled conformational dynamics in quantitative prediction of the pK(a) shifts in micelles.

Stabilization of aqueous carbon nanotube dispersions using surfactants: insights from molecular dynamics simulations.

Techniques for separating bundles of carbon nanotubes into homogeneous dispersion are still under development, although a few methods have been successful at the laboratory scale. Understanding the effective interactions between carbon nanotubes in the presence of dispersing agents will provide the necessary information to develop better methods and also to refine the existing ones. We present here results from all-atom molecular dynamics simulations for aqueous flavin mononucleotide (FMN), which has been found experimentally to efficiently separate single-walled carbon nanotubes (SWNTs) based on diameter and chirality. We report results for the aggregate morphology of FMN on SWNTs of different diameters, as well as the potential of mean force between (6,6) SWNTs in the presence of aqueous FMN. The results are compared to the potential of mean force between SWNTs in aqueous sodium dodecyl sulfate (SDS). Our detailed analysis is used to explain the role of FMN, water, and sodium ions in providing a strong repulsive barrier between approaching SWNTs.

Platinum nanoparticles on carbonaceous materials: the effect of support geometry on nanoparticle mobility, morphology, and melting.

Molecular dynamics simulations have been used to investigate the morphology and mobility of platinum nanoparticles of various sizes supported by carbon materials. The embedded-atom method was used to model Pt-Pt interactions, and the Lennard-Jones potential was used to model the Pt-C interactions. The C atoms in the supports were held fixed during the simulations. The supports considered were a single graphite sheet and three bundles of carbon nanotubes. Three sizes of Pt nanoparticles were considered: 130 atoms, 249 atoms, and 498 atoms (Pt(130), Pt(249), and Pt(498) respectively). It was found that for all three sizes, diffusion coefficients were approximately one order of magnitude higher for graphite-supported nanoparticles than for carbon nanotube-supported nanoparticles. In addition, increasing the size of the nanoparticle decreased its diffusion coefficient, with Pt(130) having the highest and Pt(498) the lowest diffusion coefficients. More interestingly, we found that for the Pt nanoparticles of all three sizes the diffusion coefficient increases as temperature increases, reaches a maximum at the melting temperature of the nanoparticle, and then decreases. The melting temperature was found to be strongly dependent on the particle size, but only slightly dependent on the features of the supports. While the size of the nanoparticle was seen to affect the particles' mobility, it did not significantly affect their structure. The nanoparticles supported by graphite have density profiles that indicate a highly ordered, fcc-like structure, while the particles supported by carbon nanotubes have a more disordered structure. An order parameter confirms that the nanoparticles' structure depends on the support morphology.