Using porphyrin-amino acid pairs to model the electrochemistry of heme proteins: experimental and theoretical investigations.

Quasi reversibility in electrochemical cycling between different oxidation states of iron is an often seen characteristic of iron containing heme proteins that bind dioxygen. Surprisingly, the system becomes fully reversible in the bare iron-porphyrin complex: hemin. This leads to the speculation that the polypeptide bulk (globin) around the iron-porphyrin active site in these heme proteins is probably responsible for the electrochemical quasi reversibility. To understand the effect of such polypeptide bulk on iron-porphyrin, we study the interaction of specific amino acids with the hemin center in solution. We choose three representative amino acids-histidine (a well-known iron coordinator in bio-inorganic systems), tryptophan (a well-known fluoroprobe for proteins), and cysteine (a redox-active organic molecule). The interactions of these amino acids with hemin are studied using electrochemistry, spectroscopy, and density functional theory. The results indicate that among these three, the interaction of histidine with the iron center is strongest. Further, histidine maintains the electrochemical reversibility of iron. On the other hand, tryptophan and cysteine interact weakly with the iron center but disturb the electrochemical reversibility by contributing their own redox active processes to the system. Put together, this study attempts to understand the molecular interactions that can control electrochemical reversibility in heme proteins. The results obtained here from the three representative amino acids can be scaled up to build a heme-amino acid interaction database that may predict the electrochemical properties of any protein with a defined polypeptide sequence.

Influence of a Counterion on the Ion Atmosphere of an Anion: A Molecular Dynamics Study of LiX and CsX (X = F(-), Cl(-), I(-)) in Methanol.

We report molecular dynamics (MD) simulations to explore the influence of a counterion on the structure and dynamics of cationic and anionic solvation shells for various ions in methanol at 298 K. We show that the variation in ionic size of either the cation or the anion in an ion pair influences the solvation structure of the other ion as well as the diffusivity in an electrolyte solution of methanol. The extent of ionic association between the cation and its counteranion of different ionic sizes has been investigated by analyzing the radial distribution functions (RDFs) and the orientation of methanol molecules in the first solvation shell (FSS) of ions. It is shown that the methanol in the FSS of the anion as well the cation exhibit quite different radial and orientational structures as compared to methanol which lie in the FSS of either the anion or the cation but not both. We find that the coordination number (CN) of F(-), Cl(-), and I(-) ions decreases with increasing size of the anion which is contrary to the trend reported for the anions in H2O. The mean residence time (MRT) of methanol molecules in the FSS of ions has been calculated using the stable states picture (SSP) approach. It is seen that the ion-counterion interaction has a considerable influence on the MRT of methanol molecules in the FSS of ions. We also discuss the stability order of the ion-counterion using the potentials of mean force (PMFs) for ion pairs with ions of different sizes. The PMF plots reveal that the Li(+)-F(-) pair (small-small) is highly stable and the Li(+)-I(-) pair is least stable (small-large) in electrolyte solutions.

Relation between the diffusivity, viscosity, and ionic radius of LiCl in water, methanol, and ethylene glycol: a molecular dynamics simulation.

A molecular dynamics (MD) investigation of LiCl in water, methanol, and ethylene glycol (EG) at 298 K is reported. Several structural and dynamical properties of the ions as well as the solvent such as self-diffusivity, radial distribution functions, void and neck distributions, velocity autocorrelation functions, and mean residence times of solvent in the first solvation shell have been computed. The results show that the reciprocal relationship between the self-diffusivity of the ions and the viscosity is valid in almost all solvents with the exception of water. From an analysis of radial distribution functions and coordination numbers the nature of hydrogen bonding within the solvent and its influence on the void and neck distribution becomes evident. It is seen that the solvent−solvent interaction is important in EG while solute−solvent interactions dominate in water and methanol. From Voronoi tessellation, it is seen that the voids and necks within methanol are larger as compared to those within water or EG. On the basis of the void and neck distributions obtained from MD simulations and literature experimental data of limiting ion conductivity for various ions of different sizes, we show that there is a relation between the void and neck radius on the one hand and dependence of conductivity on the ionic radius on the other. It is shown that the presence of large diameter voids and necks in methanol is responsible for maximum in limiting ion conductivity (λ0) of TMA+, while in water and EG, the maximum is seen for Rb+. In the case of monovalent anions, maximum in λ0 as a function ionic radius is seen for Br− in water and EG but for the larger ClO4 − ion in methanol. The relation between the void and neck distribution and the variation in λ0 with ionic radius arises via the Levitation effect which is discussed. These studies show the importance of the solvent structure and the associated void structure.

Transport in nanoporous zeolites: relationships between sorbate size, entropy, and diffusivity.

Molecular dynamics simulations have been performed on monatomic sorbates confined within zeolite NaY to obtain the dependence of entropy and self-diffusivity on the sorbate diameter. Previously, molecular dynamics simulations by Santikary and Yashonath [J. Phys. Chem. 98, 6368 (1994)], theoretical analysis by Derouane et al. [J. Catal. 110, 58 (1988)] as well as experiments by Kemball [Adv. Catal. 2, 233 (1950)] found that certain sorbates in certain adsorbents exhibit unusually high self-diffusivity. Experiments showed that the loss of entropy for certain sorbates in specific adsorbents was minimum. Kemball suggested that such sorbates will have high self-diffusivity in these adsorbents. Entropy of the adsorbed phase has been evaluated from the trajectory information by two alternative methods: two-phase and multiparticle expansion. The results show that anomalous maximum in entropy is also seen as a function of the sorbate diameter. Further, the experimental observation of Kemball that minimum loss of entropy is associated with maximum in self-diffusivity is found to be true for the system studied here. A suitably scaled dimensionless self-diffusivity shows an exponential dependence on the excess entropy of the adsorbed phase, analogous to excess entropy scaling rules seen in many bulk and confined fluids. The two trajectory-based estimators for the entropy show good semiquantitative agreement and provide some interesting microscopic insights into entropy changes associated with confinement.

Dependence of diffusivity on density and solute diameter in liquid phase: a molecular dynamics study of Lennard-Jones system.

Investigations into the variation of self-diffusivity with solute radius, density, and degree of disorder of the host medium is explored. The system consists of a binary mixture of a relatively smaller sized solute, whose size is varied and a larger sized solvent interacting via Lennard-Jones potential. Calculations have been performed at three different reduced densities of 0.7, 0.8, and 0.933. These simulations show that diffusivity exhibits a maximum for some intermediate size of the solute when the solute diameter is varied. The maximum is found at the same size of the solute at all densities which is at variance with the prediction of the levitation effect. In order to understand this anomaly, additional simulations were carried out in which the degree of disorder has been varied while keeping the density constant. The results show that the diffusivity maximum gradually disappears with increase in disorder. Disorder has been characterized by means of the minimal spanning tree. Simulations have also been carried out in which the degree of disorder is constant and only the density is altered. The results from these simulations show that the maximum in diffusivity now shifts to larger distances with decrease in density. This is in agreement with the changes in void and neck distribution with density of the host medium. These results are in excellent agreement with the predictions of the levitation effect. They suggest that the effect of disorder is to shift the maximum in diffusivity towards smaller solute radius while that of the decrease in density is to shift it towards larger solute radius. Thus, in real systems where the degree of disorder is lower at higher density and vice versa, the effect due to density and disorder have opposing influences. These are confirmed by the changes seen in the velocity autocorrelation function, self part of the intermediate scattering function and activation energy.

A molecular dynamics study and molecular level explanation of pressure dependence of ionic conductivity of potassium chloride in water.

Experimental ionic conductivity of different alkali ions in water shows markedly different dependences on pressure. Existing theories such as that of Hubbard-Onsager are unable to explain these dependences on pressure of the ionic conductivity for all ions. We report molecular dynamics investigation of potassium chloride solution at low dilution in water at several pressures between 1 bar and 2 kbar. Two different potential models have been employed. One of the models successfully reproduces the experimentally observed trend in ionic conductivity of K(+) ions in water over the 0.001-2 kbar range. We also propose a theoretical explanation, albeit at a qualitative level, to account for the dependence of ionic conductivity on pressure in terms of the previously studied Levitation Effect. It also provides a microscopic picture in terms of the pore network in liquid water.

Levitation effect: role of symmetry and dependence of diffusivity on the bond length of homonuclear and heteronuclear diatomic species.

Molecular dynamics investigation of model diatomic species confined to the α-cages of zeolite NaY is reported. The dependence of self-diffusivity on the bond length of the diatomic species has been investigated. Three different sets of runs have been carried out. In the first set, the two atoms of the diatomic molecule interact with the zeolite atoms with equal strength (example, O(2), the symmetric case). In the second and third sets which correspond to asymmetric cases, the two atoms of the diatomic molecule interact with unequal strengths (example, CO). The result for the symmetric case exhibits a well-defined maximum in self-diffusivity for an intermediate bond length. In contrast to this, the intermediate asymmetry leads to a less pronounced maximum. For the large asymmetric case, the maximum is completely absent. These findings are analyzed by computing a number of related properties. These results provide a direct confirmation at the microscopic level of the suggestion by Derouane that the supermobility observed experimentally by Kemball has its origin in the mutual cancellation of forces. The maximum in diffusivity from molecular dynamics is seen at the value predicted by the levitation effect. Further, these findings suggest a role for symmetry in the existence of a diffusivity maximum as a function of diameter of the diffusant often referred to as the levitation effect. The nature of the required symmetry for the existence of anomalous diffusivity is interaction symmetry which is different from that normally encountered in crystallography.

Ions in water: role of attractive interactions in size dependent diffusivity maximum.

A molecular dynamics study of model ions in water is reported. The van der Waals diameter of both the cations and anions is varied. We have carried out two sets of simulations--with and without dispersion interaction--between the ion and water. Self-diffusivity of the ions exhibits an anomalous maximum as a function of the van der Waals diameter for both these sets. This existence of a maximum in self-diffusivity when there is no dispersion interaction between the ion and the water is attributed to the attractive term from electrostatic interactions. Detailed analysis of this effect shows that the solvent shell is more strongly defined in the presence of dispersion interactions. A smaller ion exhibits biexponential decay while a single exponential decay is seen for the ion with maximum diffusivity in the self-part of the intermediate scattering function. The solvent structure around the ion appears to determine much of the dynamics of the ion. Interesting trends are seen in the activation energies and these can be understood in terms of the levitation effect.

Levitation effect in zeolites: Quasielastic neutron scattering and molecular dynamics study of pentane isomers in zeolite NaY.

We report the quasielastic neutron scattering (QENS) and molecular dynamics (MD) investigations into diffusion of pentane isomers in zeolite NaY. The molecular cross section perpendicular to the long molecular axis varies for the three isomers while the mass and the isomer-zeolite interaction remains essentially unchanged. Both QENS and MD results show that the branched isomers neopentane and isopentane have higher self-diffusivities as compared with n-pentane at 300 K in NaY zeolite. This result provides direct experimental evidence for the existence of nonmonotonic, anomalous dependence of self-diffusivity on molecular diameter known as the levitation effect. The energetic barrier at the bottleneck derived from MD simulations exists for n-pentane which lies in the linear regime while no such barrier is seen for neopentane which is located clearly in the anomalous regime. Activation energy is in the order E(a)(n-pentane)>E(a)(isopentane)>E(a)(neopentane) consistent with the predictions of the levitation effect. In the liquid phase, it is seen that D(n-pentane)>D(isopentane)>D(neopentane) and E(a)(n-pentane)

Correlation between conductivity or diffusivity and activation energy in amorphous solids.

There exist many investigations of ionic transport in a variety of glasses. These studies exhibit strong correlation between ionic conductivity and activation energy: Typically, it is found that higher conductivity is associated with lower activation energies and vice versa. Although there are explanations for this at a phenomenological level, there is no consistent physical picture to explain the correlation between conductivity and activation energy. We have carried out molecular dynamics simulation as a function of the size of the impurity atom or diffusant (both neutral and charged) in a host amorphous matrix. We find that there is a maximum in self-diffusivity as a function of the size of the impurity atom suggesting that there is an appropriate size for which the diffusivity is maximum. The activation energy is found to be the lowest for this size of the impurity. A similar maximum has been previously found in other condensed phases, such as confined fluids and dense liquids, and has its origin in the levitation effect. The implications of this result for understanding ionic conductivity in glasses are discussed. Our results suggest that there is a relation between microscopic structure of the amorphous solid, diffusivity or conductivity, and activation energy. The nature of this relationship is discussed in terms of the levitation parameter showing that diffusivity is maximum when the size of the neck or doorway radius is comparable with the size of the diffusant. Our computational results here are in excellent agreement with independent experimental results of Nascimento et al. [Braz. J. Phys. 35, 626 (2005)] that structural features of the glass are important in determining the ionic conductivity.

Diffusion in nanoporous phases: size dependence and levitation effect.

Self-diffusivity, D, of diffusants in widely differing mediums such as liquids (e.g., solution), porous solids (e.g., guests in zeolites), or ions in polar solvents exhibit strong size dependence. We discuss the nature of the size dependence observed in these systems. Altogether, different theoretical approaches have been proposed to understand the nature of size dependence of D not only across these widely differing systems but even in just one medium or class of systems such as, for example, ions in polar solvents. But molecular dynamics investigations in the past decade have shown that the size dependence of self-diffusion in guest-porous solids could have origins in the mutual cancellation of forces that occurs when the size of the diffusant is comparable to the size of the void. The effect leading to the maximum in D is known as the levitation effect (LE). Such a cancellation is a consequence of symmetry. This effect exists in all porous solids irrespective of the geometrical and topological details of the pore network provided by the solid. Recent studies show that the levitation effect and size-dependent diffusivity maximum exists for uncharged solutes in solvents. One of the consequences of this is the breakdown in the Stokes-Einstein relationship over a certain range of solute-solvent size ratio. Experimental measurements of ionic conductivity over the past hundred years have found the existence of a size-dependent diffusivity maximum leading to violation of the Walden's rule for ions in polar solvents. Molecular dynamics simulations and experimental data suggest that even this maximum has its origin in LE. Simulation studies of impurity atom diffusion in close-packed solids as well as ions in superionic and other solids suggest the existence of a size-dependent diffusivity maximum in these materials as well. The levitation effect is a universal effect leading to a maximum in diffusivity of a diffusant in a variety of condensed matter phases. The only condition for its existence appears to be the presence of van der Waals or electrostatic interactions.

Breakdown of the Stokes-Einstein relationship: role of interactions in the size dependence of self-diffusivity.

Einstein and others derived the reciprocal dependence of the self-diffusivity D on the solute radius r(u) for large solutes based on kinetic theory. We examine here (a) the range of r(u) over which Stokes-Einstein (SE) dependence is valid and (b) the precise dependence for small solutes outside of the SE regime. We show through molecular dynamics simulations that there are two distinct regimes for smaller solutes: (i) the interaction or Levitation effect (LE) regime for solutes of intermediate size and (ii) the D proportional, variant 1/r(u)(2) for still smaller solutes. We show that as the solute-solvent size ratio decreases, the breakdown in the Stokes-Einstein relationship leading to the LE regime has its origin in dispersion interaction between the solute and the solvent. These results explain reports of enhanced solute diffusion in solvents existing in the literature seen for small solutes for which no explanation exists.

Existence of a size-dependent diffusivity maximum for uncharged solutes in water and its implications.

Recent studies suggest that there exists a size-dependent diffusivity maximum in binary mixtures interacting via Lennard-Jones potential when the size of one of the two components is varied (Ghorai, P. K.; Yashonath, S. J. Phys. Chem., 2005, 109, 5824). We discuss in the present paper the importance of the existence of a size-dependent maximum for an uncharged solute in liquid or amorphous solid water and its relation to the ionic conductivity maximum in water. We report molecular dynamics investigations into the size dependence of the self-diffusivity, D, of the uncharged solutes in water at low temperatures (30 K) with immobile as well as mobile water. We find that a maximum in self-diffusivity exists as a function of the size of solute diffusing within water at low temperatures but not at high temperatures. This is due to the relatively weak interactions between the solute and the water compared to the kinetic energy at room temperature. Previously, we have shown that a similar maximum exists for guests sorbed in zeolites and is known as the levitation effect (LE). Thus, it appears that the existence of a size-dependent maximum is universal and extends from zeolites to simple liquids to solvents of polyatomic species. We examine the implications of this for the size-dependent maximum in ionic conductivity in polar solvents known for over a hundred years. These results support the view that the size-dependent maximum seen for ions in water has its origin in the LE (see Ghorai, P. Kr.; Yashonath, S.; Lynden-Bell, R. M. J. Phys. Chem. 2005, 109, 8120).

Evidence in support of levitation effect as the reason for size dependence of ionic conductivity in water: a molecular dynamics simulation.

We report extensive molecular dynamics simulations of (i) model ions in water at high concentrations as a function of the size and charge of the ion as well as (ii) realistic simulation of Cl- and Br- ions at low concentrations in water at room temperature. We also analyze existing experimental data in light of the results obtained here. The halide ion simulations have been carried out using the interaction potentials of Koneshan et al. (J. Phys. Chem. B 1998, 102, 4193). We compute structural and dynamical properties of ions in water and explore their variation with size and charge of the ion. We find that ions of certain intermediate sizes exhibit a maximum in self-diffusivity in agreement with previous experimental measurements and computer simulations. We analyze molecular dynamics trajectories in light of the previous understanding of the levitation effect (LE) and the recent suggestion that ionic conductivity has its origin in LE (J. Phys. Chem. B 2005, 109, 8120). We report the distribution of void and neck radii that exist amidst water. Our analysis suggests that the ion with maximum self-diffusivity is characterized by a lower activation energy and a single-exponential decay of F(s)(k,t). The behavior of these and other related quantities of the ion with maximum self-diffusivity are characteristic of the anomalous regime of the LE. The simulation results of Br- and Cl- ions in water also yield results in agreement with the predictions of LE. A plot of experimental conductivity data in the literature for alkali ions in water by Kay and Evans (J. Phys. Chem. 1966, 70, 2325) also yields a lower activation energy for the ion with maximum conductivity in excellent agreement with the LE. To the best of our knowledge, none of the existing theories predict a lower activation energy for the ion with maximum conductivity.

Separation of mixtures at nano length scales: blow torch and levitation effect.

A new conceptual basis for the separation of multicomponent molecular mixtures is proposed. A separation method where different components of the mixtures are driven in opposite directions is realized by a judicious combination of two effects, viz., levitation and blow torch effects. Monte Carlo simulations of two Lennard-Jones binary mixtures with different-sized components are shown to be separated well if at least one of the components lies in the anomalous regime and the others lie in the linear regime. A separation factor of 10(8) is obtained on nano length scales as compared to 10(3), obtainable through conventional methods of separation on macrolength scales.

Diffusion maximum as a function of size in dense liquids.

We study the diffusion of small guest particles of different sizes in a host fluid at liquid densities using molecular dynamics simulations. We observe an enhancement of the diffusivity of guest particles for a size related to the structure of the void space of the host fluid, analogous to the "levitation effect" observed for guest diffusion in porous solids. Friction and activation energy are found to be minimum for the guest size with maximum self-diffusivity. Wavelength dependent self-diffusivity indicates a monotonic and oscillatory dependence on wave number k for anomalous and linear regimes, respectively. These are associated with single and bi-exponential decay of the incoherent intermediate scattering function.

Levitation effect: size-dependent maximum in rotational diffusion in confined systems.

Molecular dynamics of a model guest tetrahedral molecule AX(4) with differing bond lengths l(AX) for A-X bonds have been carried out in a sphere with different surface roughness. The rotational-diffusion coefficient D(R) shows a maximum for a particular value of l(AX). We show that this corresponds to the distance at which the interaction of the guest with the atoms of the host is most favorable. Although, the intensity of the maximum decreases with increase in the roughness of the confining surface, it is seen that the maximum exists even for a reasonably high degree of roughness. The observed maximum arises from the minimum in the torque on the tetrahedral molecule from its interaction with the confining medium due to mutual cancellation of forces. Activation energy for rotation is seen to be also a minimum for the bond length for which D(R) is a maximum. These results suggest that there is a maximum in the rotational-diffusion coefficient when the rotating molecule is confined to a sphere of comparable size similar to the maximum in translational diffusion coefficient seen in porous solids (the levitation effect) [Yashonath and Santikary J. Phys. Chem. 98, 6368 (1994)]. On increase in the roughness of the sphere surface, the value of l(AX) at which the maximum in D(R) is seen decreases.

Pressure induced orientational ordering in p-terphenyl.

Three different interaction potentials existing in the literature along with a model proposed here have been used to model p-terphenyl under standard conditions. Of these, the model that predicts the room-temperature crystal structure well has been used to understand the behavior of p-terphenyl under pressure. Lattice parameters show good agreement with the X-ray diffraction values reported by Puschnig et al. (Puschnig, P.; Heimel, G.; Weinmeier, K.; Resel, R.; Ambrosch-Draxl, C. High Pressure Res. 2002, 22, 105). The nonplanar structure of p-terphenyl transforms to a planar structure with gradual disappearance of disorder associated with ring flipping. We show that the transformation is accompanied by a change in the potential energy profile from W-shaped to a U-shaped form, which is associated with complete planarization between 1.0 and 1.5 GPa. Our results reported here are in excellent agreement with X-ray diffraction results which also suggest the existence of a similar transition as a function of pressure in polyphenyls such as biphenyl and p-hexaphenyl. Interestingly, the amplitude of the torsional motion is largest at an intermediate pressure of 1.0 GPa. This is attributed to the rather flat potential energy landscape which occurs during the transition from W- to U-shaped potential.

Pressure-induced ordering in adamantane: a Monte Carlo simulation study.

Isothermal-isobaric ensemble Monte Carlo simulation of adamantane has been carried out with a variable shape simulation cell. The low-temperature crystalline phase and the room-temperature plastic crystalline phases have been studied employing the modified Williams potential. We show that at room temperature, the plastic crystalline phase transforms to the crystalline phase on increase in pressure. Further, we show that this is the same phase as the low-temperature ordered tetragonal phase of adamantane. The high-pressure ordered phase appears to be characterized by a slightly larger shift of the first peak toward a lower value of r in C-C, C-H, and H-H radial distribution functions as compared to the low-temperature tetragonal phase. The coexistence curve between the crystalline and plastic crystalline phase has been obtained approximately up to a pressure of 4 GPa.

Levitation effect: Distinguishing anomalous from linear regime of guests sorbed in zeolites through the decay of intermediate scattering function and wavevector dependence of self-diffusivity.

Previous work investigating the dependence of self-diffusivity, D, on the size of the guest diffusing within the porous solid such as zeolite has reported the existence of an anomalous maximum in the diffusion coefficient (J. Phys. Chem. 1994, 98, 6368). Two distinct regimes of dependence of D on sigma(gg), diameter of the guest were reported. D proportional to 1/sigma(gg)2, often referred to as linear regime (LR), is found when sigma(gg) is smaller than sigma(v), the diameter of the void. A maximum in D has been observed when sigma(gg) is comparable to sigma(v) and this regime is referred to as anomalous regime (AR). Here we report the intermediate scattering function for a particle from LR and AR in zeolite faujasite. A particle from LR exhibits a biexponential decay while a particle from AR exhibits a single-exponential decay at small k. Variation with k of the full width at half-maximum of the self-part of the dynamic structure factor is nonmonotonic for a particle in the linear regime. In contrast, this variation is monotonic for a particle in the anomalous regime. These results can be understood in terms of the existence of energetic barrier at the bottleneck, the 12-ring window, in the path of diffusion. They provide additional signatures for the linear regime and anomalous regimes and therefore for levitation effect (LE).