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Molecular dynamics (MD) simulations are used to investigate $^1$H nuclear magnetic resonance (NMR) relaxation and diffusion of bulk $n$-C$_5$H$_{12}$ to $n$-C$_{17}$H$_{36}$ hydrocarbons and bulk water. The MD simulations of the $^1$H NMR relaxation times $T_{1,2}$ in the fast motion regime where $T_1 = T_2$ agree with measured (de-oxygenated) $T_2$ data at ambient conditions, without any adjustable parameters in the interpretation of the simulation data. Likewise, the translational diffusion $D_T$ coefficients calculated using simulation configurations are well-correlated with measured diffusion data at ambient conditions. The agreement between the predicted and experimentally measured NMR relaxation times and diffusion coefficient also validate the forcefields used in the simulation. The molecular simulations naturally separate intramolecular from intermolecular dipole-dipole interactions helping bring new insight into the two NMR relaxation mechanisms as a function of molecular chain-length (i.e. carbon number). Comparison of the MD simulation results of the two relaxation mechanisms with traditional hard-sphere models used in interpreting NMR data reveals important limitations in the latter. With increasing chain length, there is substantial deviation in the molecular size inferred on the basis of the radius of gyration from simulation and the fitted hard-sphere radii required to rationalize the relaxation times. This deviation is characteristic of the local nature of the NMR measurement, one that is well-captured by molecular simulations., Comment: Revision: References 27 and 28 were updated. Formatting of last name in acknowledgement was corrected; Expressions for Larmor frequency in terms of magnetic field was included. Caption for figure 7 was corrected (table I should read table II)

In this paper we develop a thermodynamic perturbation theory for two site associating fluids which exhibit bond cooperativity. We include both steric hindrance and ring formation such that the equation of state is bond angle dependent. Here the bond angle is the angle separating the centers of the two association sites. As a test, new Monte Carlo simulations are performed, and the theory is found to accurately predict the internal energy as well as the distribution of associated clusters as a function of bond angle and bond cooperativity., Comment: To appear in The Journal of Chemical Physics

In this work we extend Wertheim's thermodynamic perturbation theory (TPT) to binary mixtures (species A and species B) of patchy colloids where each species has a single patch which can bond a maximum of twice (divalent). Colloids are treated as hard spheres with a directional conical asssociation site. We restrict the system such that only patches between unlike species share attractions; meaning there are AB attractions but no AA or BB attractions. The theory is derived in Wertheim's two density formalism for one site associating fluids. Since the patches are doubly bondable, associated chains, of all chain lengths, as well as 4-mer rings consisting of two species A and two species B colloids are accounted for. With the restriction of only AB attractions, triatomic rings of doubly bonded colloids, which dominate the corresponding pure component case, cannot form. The theory is shown to be in good agreement with Monte Carlo simulaion data for the structure and thermodynamics of these patchy colloid mixtures as a function of temperature, density, patch size and composition. It is shown that 4-mer rings dominate at low temperatures, inhibiting the polymerization of the mixture into long chains. Mixtures of this type have been recently synthesized by researchers. This work provides the first theory capable of accurately modelling these mixtures.

We develop a classical density functional theory (DFT) for two site associating fluids in spatially uniform external fields which exhibit orientational inhomogeneities. The Helmholtz free energy functional is obtain using Wertheim's thermodynamic perturbation theory and the orientational distribution function is obtained using DFT in the canonical ensemble. It is shown that an orienting field significantly enhances association by ordering the molecules thereby reducing the entropic penalty of association. It is also shown that association enhances orientational order for fixed field strength., Comment: Fixed a typo in equation (2)

In this paper we extend our previous theory [B. D. Marshall and W.G. Chapman, J. Chem. Phys. 139, 104904 (2013)] for mixtures of single patch colloids (p colloids) and colloids with spherically symmetric attractions (s colloids) to the case that the p colloids can have multiple patches. The theory is then applied to the case of a binary mixture of bi-functional p colloids which have an A and B type patch and s colloids which are not attracted to other s colloids and are attracted to only patch A on the p colloids. This mixture reversibly self assembles into both colloidal star molecules, where the s colloid is the articulation segment and the p colloids form the arms, and free chains composed of only p colloids. It is shown that temperature, density, composition and relative attractive strengths can all be varied to manipulate the number of arms per colloidal star molecule, average arm length and the fraction of chains (free chains + arms) which are star arms.

We develop a resummed thermodynamic perturbation theory for bond cooperativity in associating fluids by extension of Wertheim's multi - density formalism. We specifically consider the case of an associating hard sphere with two association sites and both pairwise and triplet contributions to the energy. To test the theory we perform new monte carlo simulations. Theory and simulation are found to be in excellent agreement.

A monte carlo density functional theory is developed for chain molecules which both intra and intermolecularly associate. The approach can be applied over a range of chain lengths. The theory is validated for the case of an associating 4-mer fluid in a planar hard slit pore. Once validated the new theory is used to study the effect of chain length and temperature on the competition between intra and intermolecular association near a hard wall. We show that this competition enhances intramolecular association near wall contact and inverts the chain length dependence of the fraction bonded intermolecularly in the inhomogeneous region.

Using the framework of Wertheim's thermodynamic perturbation theory we develop the first density functional theory which accounts for intramolecular association in chain molecules. To test the theory new Monte Carlo simulations are performed at a fluid solid interface for a 4 segment chain which can both intra and intermolecularly associate. The theory and simulation results are found to be in excellent agreement. It is shown that the inclusion of intramolecular association can have profound effects on interfacial properties such as interfacial tension and the partition coefficient.

We develop the first comprehensive approach to model associating fluids with small bond angles using Wertheim's perturbation theory. We show theoretically and through monte carlo simulations that as bond angle is varied various modes of association become dominant. The new theory is shown to be in excellent agreement with monte carlo simulation for the prediction of the internal energy, pressure and fractions in rings, chains, double bonded over the full range of bond angles.

We develop a new theory for associating fluids with multiple association sites. The theory accounts for small bond angle effects such as steric hindrance, ring formation and double bonding. The theory is validated against monte carlo simulations for the case of a fluid of patchy colloid particles with three patches and is found to be very accurate. Once validated, the theory is applied to study the phase diagram of a fluid composed of three patch colloids. It is found that bond angle has a significant effect on the phase diagram and the very existence of a liquid - vapor transition.

In this work we develop the first theory to model self assembling mixtures of single patch colloids and colloids with spherically symmetric attractions. In the development of the theory we restrict the interactions such that there are short ranged attractions between patchy and spherically symmetric colloids, but patchy colloids do not attract patchy colloids and spherically symmetric colloids do not attract spherically symmetric colloids. This results in the temperature, density and composition dependent reversible self assembly of the mixture into colloidal star molecules. This type of mixture has been recently synthesized by grafting of complimentary single stranded DNA [Feng et al., Advanced Materials 25 (20), 2779-2783 (2013)] As a quantitative test of the theory, we perform new monte carlo simulations to study the self assembly of these mixtures; theory and simulation are found to be in excellent agreement., Comment: Added comma between author names