Molecular thermodynamics approach on phase equilibria of dendritic polymer systems

Jang, Jeong Gyu; Park, Ho Bum; Lee, Young Moo

doi:10.1007/bf02697255

Cited by 4 publications

(3 citation statements)

References 33 publications

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“…The initial conformational search algorithm relies on the excluded-volume constraints method to generate configurations for the dendrimer–drug pair in a fast and efficient manner . The excluded-volume constraint method has been applied in a variety of situations to sample the molecular energy landscape of systems that present diverse complexity. , The procedure generates dendrimer–drug conformation pairs, where molecules are located in arrangements until their van der Waals (vdW) surfaces are barely touching, thus, avoiding interpenetrations. The sampling protocol was as follows: (A) Molecule 1 (monomer or a fragment ( g , m ) of dendrimer) and molecule 2 (drug) are located at the geometric center of the pair and placed at the origin of the Cartesian coordinates frame.…”

Section: Theoretical Methodsmentioning

confidence: 99%

“…31 The excluded-volume constraint method has been applied in a variety of situations to sample the molecular energy landscape of systems that present diverse complexity. 29,30 The procedure generates dendrimer−drug conformation pairs, where (D) After translation, the coordinates of these dendrimer(fragment)−drug conformations are sent to a GRID system, where single-point energies are calculated using a PM6-DH+ semiempirical quantum chemistry method, as implemented in MOPAC2009 versioń 11.038 L (LINUX). 33 Steps A through D are repeated until a million different configurations and their corresponding total energies are generated.…”

Section: Theoretical Methodsmentioning

confidence: 99%

“…Here we present an efficient methodology for calculating the interaction energies between pairs of molecules (dendrimer–drug) along an exploratory path. The method offers a protocol based on the Metropolis Monte Carlo algorithm to build large sets of PAMAM–drug conformational pairs with the aim of providing a good conformational sampling of the present interactions. − The process for calculating the energy of each pair is distributed in a specific node of a GRID computing system. Our distribution algorithm is based on a fast and efficient MPI program written using Single-Program Multiple-Data (SPMD) programming style, which helps to drastically reduce the computational cost and runtime of the energy calculations.…”

Section: Introductionmentioning

confidence: 99%

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Study of Interaction Energies between the PAMAM Dendrimer and Nonsteroidal Anti-Inflammatory Drug Using a Distributed Computational Strategy and Experimental Analysis by ESI-MS/MS

et al. 2012

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The structure of a dendrimer exhibits a large number of internal and superficial cavities, which can be exploited, to capture and deliver small organic molecules, enabling their use in drug delivery. Structure-based modeling and quantum mechanical studies can be used to accurately understand the interactions between functionalized dendrimers and molecules of pharmaceutical and industrial interest. In this study, we implemented a Metropolis Monte Carlo algorithm to calculate the interaction energy of dendrimer–drug complexes, which can be used for in silico prediction of dendrimer–drug affinity. Initially, a large-scale sampling of different dendrimer–drug conformations were generated using Euler angles. Then, each conformation was distributed on different nodes of a GRID computational system; where its interaction energy was calculate by semi-empirical quantum mechanical methods. These energy calculations were performed for four different non-steroidal anti-inflammatory drugs, each showing different affinities for PAMAM–G4 dendrimer. The affinities were also characterized experimentally by using Cooks’ kinetic method to calculate PAMAM–drug dissociation constants. The quantitative structure–activity relationship between the interaction energies and dissociation constants showed statistical correlations with r2 > 0.9.

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