Molecular dynamics simulation studies of the conformation and lateral mobility of a charged adsorbate biomolecule: Implications for estimating the critical value of the radius of a pore in porous media

Effect of Nanopore Geometry in the Conformation and Vibrational Dynamics of a Highly Confined Molecular Glass

The effect of nanoporous confinement on the glass transition temperature (T_g) strongly depends on the type of porous media. Here, we study the molecular origins of this effect in a molecular glass, N,N'-bis(3-methylphenyl)-N,N'-diphenylbenzidine (TPD), highly confined in concave and convex geometries. When confined in controlled pore glass (CPG) with convex pores, TPD's vibrational spectra remained unchanged and two T_g's were observed, consistent with previous studies. In contrast, when confined in silica nanoparticle packings with concave pores, the vibrational peaks were shifted due to more planar conformations and T_g increased, as the pore size was decreased. The strong T_g increases in concave pores indicate significantly slower relaxation dynamics compared to CPG. Given TPD's weak interaction with silica, these effects are entropic in nature and are due to conformational changes at molecular level. The results highlight the role of intramolecular degrees of freedom in the glass transition, which have not been extensively explored.

Application of molecular dynamics simulation to improve the theoretical prediction for collisional cross section of aromatic compounds with long alkyl chains in crude oils

RATIONALE

Molecular dynamics (MD) simulations with finite temperature were performed to improve the theoretical prediction of collisional cross section (CCS) values, especially for aromatic compounds containing long alkyl chains.

METHODS

In this study, the CCS values of 11 aromatic compounds with long alkyl chains were calculated by MD simulations while considering internal energy at 300, 500, and 700 K, and the results were compared with experimentally determined values.

RESULTS

The CCS values calculated at higher energies showed better agreement with the experimental values. Polycyclic aromatic hydrocarbons (PAHs) such as pentacene and benz[b]anthracene were also investigated, and better agreement between the theoretical and experimental results was observed when higher temperature (or higher internal energy) was considered.

CONCLUSIONS

The data presented in this study show that the internal degrees of freedom of ions must be considered to accurately predict the CCS values of aromatic compounds with a flexible structure measured by ion mobility mass spectrometry.

Ion exchange chromatography of antibody fragments

Effects of pH and conductivity on the ion exchange chromatographic purification of an antigen-binding antibody fragment (Fab) of pI 8.0 were investigated. Normal sulfopropyl (SP) group modified agarose particles (SP Sepharosetrade mark Fast Flow) and dextran modified particles (SP Sepharose XL) were studied. Chromatographic measurements including adsorption isotherms and dynamic breakthrough binding capacities, were complemented with laser scanning confocal microscopy. As expected static equilibrium and dynamic binding capacities were generally reduced by increasing mobile phase conductivity (1-25 mS/cm). However at pH 4 on SP Sepharose XL, Fab dynamic binding capacity increased from 130 to 160 (mg/mL media) as mobile phase conductivity changed from 1 to 5 mS/cm. Decreasing protein net charge by increasing pH from 4 to 5 at 1.3 mS/cm caused dynamic binding capacity to increase from 130 to 180 mg/mL. Confocal scanning laser microscopy studies indicate such increases were due to faster intra-particle mass transport and hence greater utilization of the media's available binding capacity. Such results are in agreement with recent studies related to ion exchange of whole antibody molecules under similar conditions.

The effect of the pore structure and zeta potential of porous polymer monoliths on separation performance in ion-exchange mode

Most often, in bioseparations involving charged macromolecules, the chromatographic systems have low Reynolds and high Peclet numbers. For such systems, an expression is developed and presented in this work for evaluating the throughput in polymeric monoliths where ion-exchange adsorption occurs, as a function of (i) the pressure drop along the length of the monolith, (ii) the functional form and width of the throughpore-size distribution of the monolith, and (iii) the magnitude of the zeta potential on the surface of the throughpores of the monolith. Gaussian and log-normal throughpore-size distributions whose mean throughpore-size and standard deviation values are based on experimentally measured throughpore-size distribution data by mercury porosimetry employed on polymeric monoliths are used in this work, and their effect on the throughput relative to that obtained from a polymeric monolith having a uniform throughpore-size distribution is studied for different values of the ratio of the standard deviation to the mean throughpore-size. The results indicate that relatively modest increases in the throughput, when compared with the throughput that could be achieved in a polymeric monolith having a uniform throughpore-size distribution, could be obtained in polymeric monoliths having disperse throughpore-size distributions, and the magnitude of the increase becomes larger when the disperse distribution is skewed to larger throughpore sizes. Furthermore, the results of this work indicate that, under certain conditions, relatively modest increases in the throughput of a charged analyte could also be achieved by altering the value of the zeta potential on the surface of the throughpores of the monolith. Due to the difficulties inherent in controlling the functional form and width of the throughpore-size distribution during the synthesis of polymeric monoliths, it would appear to be more practical to increase the value of the throughput of a charged analyte by altering the value of the zeta potential through prudent selection of the ion-exchange surface functional groups and fine-tuned with the pH of the mobile phase. Thus, for ion-exchange chromatography systems, the zeta potential could be considered an important parameter for column designers and operators to manipulate, since its alteration could increase the through-put of a charged analyte in polymeric monoliths or in columns packed with charged particles.

An exclusion mechanism in ion exchange chromatography

Protein dynamic binding capacities on ion exchange resins are typically expected to decrease with increasing conductivity and decreasing protein charge. There are, however, conditions where capacity increases with increasing conductivity and decreasing protein charge. Capacity measurements on two different commercial ion exchange resins with three different monoclonal antibodies at various pH and conductivities exhibited two domains. In the first domain, the capacity unexpectedly increased with increasing conductivity and decreasing protein charge. The second domain exhibited traditional behavior. A mechanism to explain the first domain is postulated; proteins initially bind to the outer pore regions and electrostatically hinder subsequent protein transport. Such a mechanism is supported by protein capacity and confocal microscopy studies whose results suggest how knowledge of the two types of IEX behavior can be leveraged in optimizing resins and processes.

Construction by Molecular Dynamics Modeling and Simulations of the Porous Structures Formed by Dextran Polymer Chains Attached on the Surface of the Pores of a Base Matrix: Characterization of Porous Structures

Significant increases in the separation of bioactive molecules by using ion-exchange chromatography are realized by utilizing porous adsorbent particles in which the affinity group/ligand is linked to the base matrix of the porous particle via a polymeric extender. To study and understand the behavior of such systems, the M3B model is modified and used in molecular dynamics (MD) simulation studies to construct porous dextran layers on the surface of a base matrix, where the dextran polymer chains and the surface are covered by water. Two different porous polymer layers having 25 and 40 monomers per main polymer chain of dextran, respectively, are constructed, and their three-dimensional (3D) porous structures are characterized with respect to porosity, pore size distribution, and number of conducting pathways along the direction of net transport. It is found that the more desirable practical implications with respect to structural properties exhibited by the porous polymer layer having 40 monomers per main polymer chain, are mainly due to the higher flexibility of the polymer chains of this system, especially in the upper region of the porous structure. The characterization and analysis of the porous structures have suggested a useful definition for the physical meaning and implications of the pore connectivity of a real porous medium that is significantly different than the artificial physical meaning associated with the pore connectivity parameter employed in pore network models and whose physical limitations are discussed; furthermore, the methodology developed for the characterization of the three-dimensional structures of real porous media could be used to analyze the experimental data obtained from high-resolution noninvasive three-dimensional methods like high-resolution optical microscopy. The MD modeling and simulations methodology presented here could be used, considering that the type and size of affinity group/ligand as well as the size of the biomolecule to be adsorbed onto the affinity group/ligand are known, to construct different porous dextran layers by varying the length of the polymeric chain of dextran, the number of attachment points to the base matrix, the degree of side branching, and the number of main polymeric chains immobilized per unit surface area of base matrix. After the characterization of the porous structures of the different porous dextran layers is performed, then only a few promising structures would be selected for studying the immobilization of adsorption sites on the pore surfaces and the subsequent adsorption of the bioactive molecules onto the immobilized affinity groups/ligands.