Vitaliy Kapko

Flexibility of ideal zeolite frameworks

We explore the flexibility windows of the 194 presently-known zeolite frameworks. The flexibility window represents a range of densities within which an ideal zeolite framework is stress-free. Here, we consider the ideal zeolite to be an assembly of rigid corner-sharing perfect tetrahedra. The corner linkages between tetrahedra are hard-sphere oxygen atoms, which are presumed to act as freely-rotating, force-free, spherical joints. All other inter-tetrahedral forces, such as coulomb interactions, are ignored. Thus, the flexibility window represents the null-space of the kinematic matrix that governs the allowable internal motions of the ideal zeolite framework. We show that almost all of the known aluminosilicate or aluminophosphate zeolites exhibit a flexibility window. Consequently, the presence of flexibility in a hypothetical framework topology promises to be a valuable indicator of synthetic feasibility. We describe computational methods for exploring the flexibility window, and discuss some of the exceptions to this flexibility rule.

Energetics and kinetics of primary charge separation in bacterial photosynthesis.

We report the results of molecular dynamics (MD) simulations and formal modeling of the free-energy surfaces and reaction rates of primary charge separation in the reaction center of Rhodobacter sphaeroides. Two simulation protocols were used to produce MD trajectories. Standard force-field potentials were employed in the first protocol. In the second protocol, the special pair was made polarizable to reproduce a high polarizability of its photoexcited state observed by Stark spectroscopy. The charge distribution between covalent and charge-transfer states of the special pair was dynamically adjusted during the simulation run. We found from both protocols that the breadth of electrostatic fluctuations of the protein/water environment far exceeds previous estimates, resulting in about 1.6 eV reorganization energy of electron transfer in the first protocol and 2.5 eV in the second protocol. Most of these electrostatic fluctuations become dynamically frozen on the time scale of primary charge separation, resulting in much smaller solvation contributions to the activation barrier. While water dominates solvation thermodynamics on long observation times, protein emerges as the major thermal bath coupled to electron transfer on the picosecond time of the reaction. Marcus parabolas were obtained for the free-energy surfaces of electron transfer by using the first protocol, while a highly asymmetric surface was obtained in the second protocol. A nonergodic formulation of the diffusion-reaction electron-transfer kinetics has allowed us to reproduce the experimental results for both the temperature dependence of the rate and the nonexponential decay of the population of the photoexcited special pair.

On the collapse of locally isostatic networks

We examine the flexibility of periodic planar networks built from rigid corner-connected equilateral triangles. Such systems are locally isostatic, since for each triangle the total number of degrees of freedom equals the total number of constraints. These nets are two-dimensional analogues of zeolite frameworks, which are periodic assemblies of corner-sharing tetrahedra. If the corner connections are permitted to rotate, as if pin-jointed, there is always at least one collapse mechanism in two dimensions (and at least three mechanisms in three dimensions). We present a number of examples of such collapse modes for different topologies of triangular net. We show that the number of collapse mechanisms grows with the size of unit cell. The collapsible mechanisms that preserve higher symmetry of the network tend to exhibit the widest range of densities without sterical overlap.

Density of mechanisms within the flexibility window of zeolites.

By treating idealized zeolite frameworks as periodic mechanical trusses, we show that the number of flexible folding mechanisms in zeolite frameworks is strongly peaked at the minimum density end of their flexibility window. 25 of the 197 known zeolite frameworks exhibit an extensive flexibility, where the number of unique mechanisms increases linearly with the volume when long wavelength mechanisms are included. Extensively flexible frameworks therefore have a maximum in configurational entropy, as large crystals, at their lowest density. Most real zeolites do not exhibit extensive flexibility, suggesting that surface and edge mechanisms are important, likely during the nucleation and growth stage. The prevalence of flexibility in real zeolites suggests that, in addition to low framework energy, it is an important criterion when searching large databases of hypothetical zeolites for potentially useful realizable structures.

Flexibility mechanisms in ideal zeolite frameworks

Zeolites are microporous crystalline aluminosilicate materials whose atomic structures can be usefully modelled in purely mechanical terms as stress-free periodic trusses constructed from rigid corner-connected SiO4 and AlO4 tetrahedra. When modelled this way, all of the known synthesized zeolite frameworks exhibit a range of densities, known as the flexibility window, over which they satisfy the framework mechanical constraints. Within the flexibility window internal stresses are accommodated by force-free coordinated rotations of the tetrahedra about their apices (oxygen atoms). We use rigidity theory to explore the folding mechanisms within the flexibility window, and derive an expression for the configurational entropic density throughout the flexibility window. By comparison with the structures of pure silica zeolite materials, we conclude that configurational entropy associated with the flexibility modes is not a dominant thermodynamic term in most bulk zeolite crystals. Nevertheless, the presence of a flexibility window in an idealized hypothetical tetrahedral framework may be thermodynamically important at the nucleation stage of zeolite formation, suggesting that flexibility is a strong indicator that the topology is realizable as a zeolite. Only a small fraction of the vast number of hypothetical zeolites that are known exhibit flexibility. The absence of a flexibility window may explain why so few hypothetical frameworks are realized in nature.