Supramolecular Packing Drives Morphological Transitions of Charged Surfactant Micelles.

The shape and size of self-assembled structures upon local organization of their molecular building blocks are hard to predict in the presence of long-range interactions. Combining small-angle X-ray/neutron scattering data, theoretical modelling, and computer simulations, sodium dodecyl sulfate (SDS), over a broad range of concentrations and ionic strengths, was investigated. Computer simulations indicate that micellar shape changes are associated with different binding of the counterions. By employing a toy model based on point charges on a surface, and comparing it to experiments and simulations, it is demonstrated that the observed morphological changes are caused by symmetry breaking of the irreducible building blocks, with the formation of transient surfactant dimers mediated by the counterions that promote the stabilization of cylindrical instead of spherical micelles. The present model is of general applicability and can be extended to all systems controlled by the presence of mobile charges.

Temperature dependent mechanical unfolding of calixarene nanocapsules studied by molecular dynamics simulations.

Using atomistic molecular dynamics simulations, we study the temperature dependence of the mechanical unfolding of a model supramolecular complex, a dimer of interlocked calixarene capsules. This system shows reversible transitions between two conformations that are stabilized by different networks of hydrogen bonds. We study the forced dissociation and formation of these networks as a function of temperature and find a strong impact of the nonequilibrium conditions imposed by pulling the system mechanically. The kinetics of the transition between the two conformations is ideally suited to investigate the range of validity of the stochastic models employed in the analysis of force dependent kinetic rates obtained from experimental or simulation data. These models usually assume activated dynamics for the relevant transitions, and therefore, the analytical expressions for the kinetic rates are of an Arrhenius form. A study of the temperature- and force-dependent kinetics by simulation allows an analysis of the transition rates without any model assumption. We find that the temperature dependence of the rates is well described by an Arrhenius law for each value of the force. This enables us to determine the activation free energy and the bare kinetic rate as a function of force independent of each other. In accord with the common model assumptions, we find that the activation free energy decreases with increasing force. The force dependence of the bare rates is compatible with the results of model calculations in the low force regime, and deviations are observed at high forces.

Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding.

We present a dynamic coarse-graining technique that allows one to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSMs), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling, we additionally perform steered molecular dynamics simulations and find excellent agreement between the results of the fully atomistic and the dynamically coarse-grained simulations. Our technique allows the determination of the rates of mechanical unfolding in a dynamical range from approximately 10-8/ns to 1/ns thus reaching experimentally accessible time regimes without abandoning atomistic resolution.

Force probe simulations using a hybrid scheme with virtual sites.

Hybrid simulations, in which a part of the system is treated with atomistic resolution and the remainder is represented on a coarse-grained level, allow for fast sampling while using the accuracy of atomistic force fields. We apply a hybrid scheme to study the mechanical unfolding and refolding of a molecular complex using force probe molecular dynamics (FPMD) simulations. The degrees of freedom of the solvent molecules are treated in a coarse-grained manner while atomistic resolution is retained for the solute. The coupling between the solvent and the solute is provided using virtual sites. We test two different common coarse-graining procedures, the iterative Boltzmann inversion method and the force matching procedure, and find that both methodologies give similar results. The results of the FPMD simulations are compared to all-atom simulations of the same system and we find that differences between these simulations and the ones using the hybrid scheme are in a similar range as the differences obtained when using different atomistic force fields. Thus, a hybrid scheme yields qualitatively correct results in the strong non-equilibrium situation the system is experiencing in FPMD simulations.

Mechanical and Structural Tuning of Reversible Hydrogen Bonding in Interlocked Calixarene Nanocapsules.

We present force probe molecular dynamics simulations of dimers of interlocked calixarene nanocapsules and study the impact of structural details and solvent properties on the mechanical unfolding pathways. The system consists of two calixarene "cups" that form a catenane structure via interlocked aliphatic loops of tunable length. The dimer shows reversible rebinding, and the kinetics of the system can be understood in terms of a two-state model for shorter loops (≤14 CH2 units) and a three-state model for longer loops (≥15 CH2 units). The various conformational states of the dimer are stabilized by networks of hydrogen bonds, the mechanical susceptibility of which can be altered by changing the polarity and proticity of the solvent. The variation of the loop length and the solvent properties in combination with changes in the pulling protocol allows to tune the reversibility of the conformational transitions.

Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in an Aqueous Environment.

We develop and test specific coarse-grained models for charged amphiphilic systems such as palmitoyloleoylphosphatidylglycerol (POPG) lipid bilayer and sodium dodecyl sulfate (SDS) surfactant in an aqueous environment, to verify the ability of the hybrid particle-field method to provide a realistic description of polyelectrolytes. According to the hybrid approach, the intramolecular interactions are treated by a standard molecular Hamiltonian, and the nonelectrostatic intermolecular forces are described by density fields. Electrostatics is introduced as an additional external field obtained by a modified particle-mesh Ewald procedure, as recently proposed [Zhu et al. Phys. Chem. Chem. Phys. 2016 , 18 , 9799 ]. Our results show that, upon proper calibration of key parameters, electrostatic forces can be correctly reproduced. Molecular dynamics simulations indicate that the methodology is robust with respect to the choice of the relative dielectric constant, yielding the same correct qualitative behavior for a broad range of values. In particular, our methodology reproduces well the organization of the POPG bilayer, as well as the SDS concentration-dependent change in the morphology of the micelles from spherical to microtubular aggregates. The inclusion of explicit electrostatics with good accuracy and low computational cost paves the way for a significant extension of the hybrid particle-field method to biological systems, where the polyelectrolyte component plays a fundamental role for both structural and dynamical molecular properties.

Evaluation of organ weights for rodent and non-rodent toxicity studies: a review of regulatory guidelines and a survey of current practices.

The Society of Toxicologic Pathology convened a working group to evaluate current practices regarding organ weights in toxicology studies. A survey was distributed to pharmaceutical, veterinary, chemical, food/nutritional and consumer product companies in Europe, North America, and Japan. Responses were compiled to identify organs routinely weighed for various study types in rodent and non-rodent species, compare methods of organ weighing, provide perspectives on the value of organ weights and identify the scientist(s) responsible for organ weight data interpretation. Data were evaluated as a whole as well as by industry type and geographic location. Regulatory guidance documents describing organ weighing practices are generally available, however, they differ somewhat dependent on industry type and regulatory agency. While questionnaire respondents unanimously stated that organ weights were a good screening tool to identify treatment-related effects, opinions varied as to which organ weights are most valuable. The liver, kidneys, and testes were commonly weighed and most often considered useful by most respondents. Other organs that break were commonly weighed included brain, adrenal glands, ovaries, thyroid glands, uterus, heart, and spleen. Lungs, lymph nodes, and other sex organs were weighed infrequently in routine studies, but were often weighed in specialized studies such as inhalation, immunotoxicity, and reproduction studies. Organ-to-body weight ratios were commonly calculated and were considered more useful when body weights were affected. Organ to brain weight ratios were calculated by most North American companies, but rarely according to respondents representing veterinary product or European companies. Statistical analyses were generally performed by most respondents. Pathologists performed interpretation of organ weight data for the majority of the industries.

Society of Toxicologic Pathology position paper: organ weight recommendations for toxicology studies.

The evaluation of organ weights in toxicology studies is an integral component in the assessment of pharmaceuticals, chemicals, and medical devices. The Society of Toxicologic Pathology (STP) has created recommendations for weighing organs in GLP general toxicology studies lasting from 7 days to 1 year. The STP recommends that liver, heart, kidneys, brain, testes, and adrenal glands be weighed in all multidose general toxicology studies. Thyroid gland and pituitary gland weights are recommended for all species except mice. Spleen and thymus should be weighed in rodent studies and may be weighed in non-rodent studies. Weighing of reproductive organs is most valuable in sexually mature animals. Variability in age, sexual maturity, and stage of cycle in non-rodents and reproductive senescence in female rodents may complicate or limit interpretation of reproductive organ weights. The STP recommends that testes of all species be weighed in multidose general toxicology studies. Epididymides and prostate should be weighed in rat studies and may be weighed on a case-by-case basis in non-rodent and mouse studies. Weighing of other organs including female reproductive organs should be considered on a case-by-case basis. Organ weights are not recommended for any carcinogenicity studies including the alternative mouse bioassays. Regardless of the study type or organs evaluated, organ weight changes must be evaluated within the context of the compound class, mechanism of action, and the entire data set for that study.