Excited state properties of sizable molecules in solution: from structure to reactivity

We review some recent advances in quantum mechanical methods devised specifically for the study of excited electronic state of large size molecules in solution. The adopted theoretical/computational framework is rooted in the density functional theory (DFT) and its time-dependent extension (TD-DFT) for the characterization of ground and excited states, in the polarizable continuum model (PCM) for the treatment of bulk solvent effects, and in time-dependent quantum mechanical methods for chemical dynamics. Selected applications to the simulation of absorption spectra, to the interpretation of time-resolved experiments, and to the computation of dissociative electron transfer rates are presented and discussed.     

Reversible association of telechelic molecules: an application of graph theory

We develop a method for calculating the exact free energy of tree clusters formed from associating telechelic molecules. The method uses the concept of rooted trees from the graph theory to enumerate all topologically distinct trees having a maximum degree of branching; it recursively separates the trees into different classes based on their connectivity, thus enabling the exact summation of the trees weighted by their respective Boltzmann factors. We apply our method to studying the pregel properties in pure telechelic solutions and in mixed telechelic and single-associating-end polymer solutions. We highlight the effect of energetic tendency for branching in the former and the effect of competitive association in the latter.     

Computer simulations of stretching and collapse of polymer molecules in solution

Computer simulations are reported for system of linear polymer molecules, diblock copolymer and dendrimer in dilute solution without and with elongational flow. The effect of fluctuating hydrodynamics interactions (HI) on the coil-stretch transition of linear polymers and dendrimers in elongational flow is studied. The process of coiling of homo- and blockcopolymer from completely extended state is also simulated.     

Theory and simulations of charged polymers: From solution properties to polymeric nanomaterials

Charged polymers are macromolecules with ionizable groups. These polymeric systems demonstrate unique properties that are qualitatively different from their neutral counterparts. In this review I survey the recent progress made in understanding properties of the solutions of charged polymers, swelling of polyelectrolyte gels, conformational transformations of charged dendrimers, complexation between charged macromolecules, adsorption of charged polymers at surfaces and interfaces, and multilayer assembly in ionic systems.     

Multiscale electrostatic embedding simulations for modeling structure and dynamics of molecules in solution: A tutorial review

The main concepts and important technical details of electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) simulations are explained and illustrated with the intent of assisting newcomers in performing and gauging the accuracy of such simulations, focused on smaller molecules in solution. Beginners are advised on how to increase the reliability and accuracy of the simulations through benchmarking. Central considerations on methodologies for QM/MM Molecular Dynamics (MD) simulations are presented, alongside technical fundamentals regarding the construction and manipulation of simulation systems using the python-based Atomic Simulation Environment (ASE). A worked example of QM/MM Born–Oppenheimer MD is included, and a flowchart summarizing the most salient decisions and tasks within the methodology is presented.     

Micellar crystals in solution from molecular dynamics simulations

Polymers with both soluble and insoluble blocks typically self-assemble into micelles, which are aggregates of a finite number of polymers where the soluble blocks shield the insoluble ones from contact with the solvent. Upon increasing concentration, these micelles often form gels that exhibit crystalline order in many systems. In this paper, we present a study of both the dynamics and the equilibrium properties of micellar crystals of triblock polymers using molecular dynamics simulations. Our results show that equilibration of single micelle degrees of freedom and crystal formation occur by polymer transfer between micelles, a process that is described by transition state theory. Near the disordered (or melting) transition, bcc lattices are favored for all triblocks studied. Lattices with fcc ordering are also found but only at lower kinetic temperatures and for triblocks with short hydrophilic blocks. Our results lead to a number of theoretical considerations and suggest a range of implications to experimental systems with a particular emphasis on Pluronic polymers.     

New materials from telechelic polyacetals

Telechelic polyacetals, obtained by cationic ring-opening polymerization of 1,3-dioxolane (DXL) and 1,3-dioxepane (DXP), have been used as building blocks for polymer materials. In the first part of this paper, the synthesis and the properties of networks based on polyDXL α,ω-bis(methacrylates) are discussed. The second part deals with the synthesis and the properties of polyacetal polyurethanes. A thermoplastic polyurethane was prepared with poly(DXL-co-DXP) α,ω-diol as soft segment and the combination butane-1,4-diol and hexamethylene diisocyanate as hard segment. Polyurethane networks were obtained from polyacetal polyols and diphenylmethane diisocyanate (MDI). Some physical properties of these new materials are reported.     

Hydrodynamic and conformational properties of cellulose myristate molecules in solution

Cellulose myristate samples with a degree of substitution of 230–250 have been studied by the methods of molecular hydrodynamics (viscometry, analytical ultracentrifugation (flotation), and isothermal translational diffusion) in chloroform in the range M = (56–652) × 10³. The experimental evidence has been interpreted within the framework of the generalized wormlike Yamakawa-Fuji model with the following parameters: the persistence length a = 115 × 10^?8 cm, the chain diameter d = 45 × 10^?8 cm, and the molecular mass per unit chain length M _L = 270 × 10⁸ cm^?1. It has been inferred that the polymer dissolves in chloroform in the form of dimers.     

Dynamic properties of metallocenium ion pairs in solution by atomistic simulations

We report a molecular dynamics study of the dynamics and energetic of the [H(2)Si(Cp)(2)ZrMe(+)][MeB(C(6)F(5))(3)(-)], IP1, and [Me(2)Si(Cp)(2)ZrMe(+)][B(C(6)F(5))(4)(-)], IP2, ion pairs in benzene. The metrical parameters obtained for the IP1 ion pair are in excellent agreement with the NMR data reported for the strictly related [Me(2)Si(Cp)(2)ZrMe(+)][MeB(C(6)F(5))(3)(-)] ion pair (J. Am. Chem. Soc. 2004, 126, 1448). This validates the molecular modeling protocol we developed. Simulation of the IP2 ion pair suggests that the counterion oscillates between two geometries characterized by a different coordination pattern of the F atoms to the Zr cation. In one case the B(C(6)F(5))(4)(-) coordinates to the metal with two F atoms of the same aryl ring, whereas in the other case two F atoms of different aryl rings are involved in the coordination. Strong solvent reorganization occurs around IP1 and IP2, as well as around the two isolated cations. In the case of the two ion pairs solvent is never coordinated directly to the metal, whereas in the absence of the counterion one benzene molecule is coordinated to the metal through a cation-pi interaction. Free energy calculations result in ion pair free energies of separation of 36.8 and 23.3 kcal/mol for IP1 and IP2, respectively. Simulations with the Zr-B distance fixed at values > 7 A have been also performed. This mimics the situation occurring after counterion displacement by an inserting monomer molecule during olefin polymerization by the title catalysts.     

Computer simulations of nucleation of nanoparticle superclusters from solution

This paper presents simulation studies of nanoparticle supercluster (NPSC) nucleation from a temperature quenched system. The nanoparticles are represented as 5 nm, spherical gold nanoparticles ligated with alkane thiols. The pair potential accounts for the van der Waals interaction between the metallic cores and ligand-ligand and ligand-solvent interactions. Phenomena well-known for molecular systems are observed including a prenucleation induction period, fluctuating prenucleation clusters that predominately add monomers one at a time, a critical nucleus size, and growth of NPSCs from solution in the presence of an equilibrium supernatant, all consistent with classical nucleation theory. However, only the largest prenucleating clusters are dense, and the cluster size can occasionally range greater than the critical size in the prenucleation regime until a cluster with low enough energy occurs, then nucleation ensues. Late in the nucleation process, the clusters display a crystalline structure that is a random mix of face-centered cubic (fcc) and hexagonal close-packed (hcp) lattices and indistinguishable from a randomized icosahedra structure.     

On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: aqueous glycerol

The rotational isomeric states (RIS) of glycerol at infinite dilution have been characterized in the aqueous phase via a 1 micros conventional molecular dynamics (MD) simulation, a 40 ns enhanced sampling replica exchange molecular dynamics (REMD) simulation, and a reevaluation of the experimental NMR data. The MD and REMD simulations employed the GLYCAM06/AMBER force field with explicit treatment of solvation. The shorter time scale of the REMD sampling method gave rise to RIS and theoretical scalar 3J(HH) coupling constants that were comparable to those from the much longer traditional MD simulation. The 3J(HH) coupling constants computed from the MD methods were in excellent agreement with those observed experimentally. Despite the agreement between the computed and the experimental J-values, there were variations between the rotamer populations computed directly from the MD data and those derived from the experimental NMR data. The experimentally derived populations were determined utilizing limiting J-values from an analysis of NMR data from substituted ethane molecules and may not be completely appropriate for application in more complex molecules, such as glycerol. Here, new limiting J-values have been derived via a combined MD and quantum mechanical approach and were used to decompose the experimental 3J(HH) coupling constants into population distributions for the glycerol RIS.     

Hydrodynamic and conformational properties of cellulose valerate molecules in dilute solution

Using the methods of molecular hydrodynamics, structural-conformational studies have been performed for a number of cellulose valerate and acetovalerate samples in the molecular-mass range M = (58.1–464.3) × 10³ and with a mean degree of substitution of 182.4 with respect to valeric acid isomers. The conformations of valerate-substituted cellulose molecules are characterized by an increased local packing density of monomer units. The molecular conformations are quantitatively described in terms of the helix formed by the succession of vectors connecting glycoside oxygens of a chain. The molecular-hydrodynamic and conformational characteristics of cellulose valerate are compared with the corresponding characteristics of cellulose myristate.     

Biomolecular simulations of membranes: physical properties from different force fields

Phospholipid force fields are of ample importance for the simulation of artificial bilayers, membranes, and also for the simulation of integral membrane proteins. Here, we compare the two most applied atomic force fields for phospholipids, the all-atom CHARMM27 and the united atom Berger force field, with a newly developed all-atom generalized AMBER force field (GAFF) for dioleoylphosphatidylcholine molecules. Only the latter displays the experimentally observed difference in the order of the C2 atom between the two acyl chains. The interfacial water dynamics is smoothly increased between the lipid carbonyl region and the bulk water phase for all force fields; however, the water order and with it the electrostatic potential across the bilayer showed distinct differences between the force fields. Both Berger and GAFF underestimate the lipid self-diffusion. GAFF offers a consistent force field for the atomic scale simulation of biomembranes.     

Hydrodynamic and dynamo-optical properties and conformation of cyanoethyl cellulose molecules in solution

Translational diffusion, velocity sedimentation and viscosity in acetone as well as flow birefringence (FB) and viscosity in cyclohexanone have been investigated for cyanoethyl cellulose (CEC) with degree of substitution 2.6 in the range of M = (24.5?317) × 10³. The dependences of [ν], S_o and D_o on M were obtained. The value of the hydrodynamic constant is $\text{A}{}_0\text{= 3.27 × 10}{}^{\mathrm{?10}}\text{erg deg}{}^{\mathrm{?1}}\text{mol}{}^{\mathrm{<mtext>?</mtext><mtext>1</mtext><mtext>3</mtext>}}$. According to hydrodynamic data, the equilibrium rigidity of CEC molecules is characterized by the length of the Kuhn segment $\text{A = 240 ? 350}\text{A}\text{?}$ and the coefficient of hindrance to intramolecular motion σ = 4.5-5.4. The hydrodynamic diameter of the chain is 8–14 Å. According to the FB data, the value of A is 260 Å. This value is in agreement with hydrodynamic data. The high value of optical anisotropy of the monomer unit, a_| - a_⊥ = 17.8 × 10^?25 cm³, is in agreement with the structure and anisotropy of the substituting groups, and the investigation of orientation angles of FB leads to the conclusion that, apart from high equilibrium rigidity, CEC in solution is characterized by considerable kinetic chain flexibility. The data for CEC are compared with the characteristics of other cellulose esters and ethers.     

Electrooptical properties of mesogenic chain molecules in solution and in nematic state

Electrooptical characteristics of mesogenic chain molecules in solution and in mesophase can be described in terms of intra- and intermolecular orientational orders. The value and sign of electric birefringence δn in a solution of kinetically rigid chain molecules are determined by the combination of two factors: intramolecular orientational order which depends on the dipolar and anisotropic architecture of the molecule and intermolecular orientational order caused by the action of the external electric field E. The value and sign of the dielectric anisotropy δε of the polymer nematic phase are also determined by the combination of intra- and intermolecular orders. However, in this case the latter is not maintained by the external field but by the nematic potential of the mesophase. Therefore, comparative investigations of electrooptical properties of polymers in solutions and in nematic melts make it possible to obtain information about the intra- and intermolecular orientational orders of the molecules under investigation in these two states. These investigations were carried out using the method of electric birefringence in solutions and the method of orientational deformations of nematic textures in an electric field. The objects being investigated were nematogenic dimers and trimers. Experimental data obtained for these compounds showed the presence of intramolecular order in their molecules, which is manifested in the odd-even oscillations of the value and sign of Kerr constant K≈δn/E² in solution and δε in the nematic phase when the number of C-C bonds in the methylene spacers of these molecules is varied. This effect is particularly dramatic in the mesophase where it is enhanced by intermolecular nematic potential.     

Well-defined liquid crystal gels from telechelic polymers

Well-defined liquid crystal networks with controlled molecular weight between cross-links and cross-link functionality were prepared by "click" cross-linking of telechelic polymers produced by ring-opening metathesis polymerization (ROMP). The networks readily swell in a small molecule liquid crystal, 5CB, to form LC gels with high swelling ratios. These gels exhibit fast, reversible, and low-threshold optic switching under applied electric fields when they are unconstrained between electrodes. For a given electric field, the LC gels prepared from shorter telechelic polymers showed a reduced degree of switching than their counterparts made from longer polymer strands. The reported approach provides control over important parameters for LC networks, such as the length of the network strands between cross-links, cross-linker functionality, and mesogen density. Therefore, it allows a detailed study of relationships between molecular structure and macroscopic properties of these scientifically and technologically interesting networks.     

Polymerizability,copolymerizability, and properties of cyanoacrylate‐telechelic polyisobutylenes I: three‐arm star cyanoacrylate‐telechelic polyisobutylene

This series of papers concern new materials for possible biological applications created by combining the chemistry of highly reactive cyanoacrylates (CAs) with polyisobutylene (PIB) rubbers. First, a new strategy for the synthesis of CA–telechelic PIBs is described. Subsequently, the strategy is employed for the synthesis of low viscosity (syringible) CA–telechelic three‐arm star PIB [Ø(PIB–CA)₃]. The intermediates of the synthesis route are characterized by ¹H NMR spectroscopy. Injecting liquid Ø(PIB–CA)₃ into living tissue (fresh chicken egg) produces a bolus of crosslinked PIB rubber. The spectacular oxidative resistance of this rubber is documented by its resistance to concentrated HNO₃. A structural model of the crosslinked rubber obtained upon contacting Ø(PIB–CA)₃ with proteinaceous tissue is proposed. Copyright © 2007 John Wiley & Sons, Ltd.