Tacticity effects on conformational structure and hydration of poly-(methacrylic acid) in aqueous solutions-a molecular dynamics simulation study
TL;DR: In this article, the influence of tacticity on chain dimensions, backbone and side-group conformational states and relaxation dynamics, intermolecular hydrogen bonding and its relaxation dynamics was investigated for 30 repeat unit poly(methacrylic acid) (PMA) as a function of the degree-of-neutralisation, f (i.e. charge density) [0, ǫa-PMA>ǫ s-PAMA].
Abstract: The influence of tacticity on chain dimensions, backbone and side-group conformational states and relaxation dynamics, intermolecular hydrogen bonding and its relaxation dynamics was investigated for 30 repeat unit poly(methacrylic acid) (PMA) as a function of the degree-of-neutralisation, f (i.e. charge density) [0 a-PMA > s-PMA. At high charge density, a higher probability of trans state is obtained at meso dyads as compared to racemic dyads and the side group in i-PMA relative to ot...
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TL;DR: In this article, the authors investigated the microscopic conformation behaviors of poly(acrylic acid) (PAA) with different chain sizes, tacticities, and sodium chloride concentrations.
Abstract: Physical properties of polyelectrolytes have been shown to be significantly related to their chain conformations. Atomistic simulation has been used as an effective method for studying polymer chain structures, but few simulations have focused on the effects of chain length and tacticity in the presence of monovalent salts. This paper investigated the microscopic conformation behaviors of poly(acrylic acid) (PAA) with different chain sizes, tacticities, and sodium chloride concentrations. The hydrogen behaviors and corresponding radial distribution functions were obtained. The results showed that the increase of salt concentrations led to the collapse of PAA chains, especially for longer chains. It was found that the effects of salt were mainly attributed to the shielding screening effect by sodium ions rather than the hydrogen bonding effect. Two different structures were formed by isotactic PAA and syndiotactic PAA, respectively, which were due to the deprotonation patterns along the PAA chain.
17 citations
TL;DR: In this article, the most important features of stereoregular polymers, with significant impact on morphology and on a variety of properties such as conformational, thermal, rheological, mechani
Abstract: Tacticity is one of the most important features of stereoregular polymers, with significant impact on morphology and on a variety of properties such as conformational, thermal, rheological, mechani
14 citations
TL;DR: Results suggest that reversible acid–base switching between the arginine protonation states is able to drive the rearrangement of the polyarginine coating around AgNPs, which could be important for a rational design of “intelligent” multifunctional core–shell nanosystems.
Abstract: Polyarginine (poly-Arg) and arginine-rich peptides have been attracting enormous interest in chemical and cell biology as cell-penetrating peptides capable of direct intracellular penetration. Owing to advances in protein engineering, arginine-rich fragments are often incorporated into multifunctional bioorganic/inorganic core–shell nanoparticles, enabling them the novel unique ability to cross cells and deliver biopharmaceutical cargos. Therefore, understanding the molecular details of the adsorption, packing, and release of poly-Arg onto or from metal nanoparticles is one of the current challenges. In this work, we carry out atomistic molecular dynamics simulations to identify the most favorable location, orientation, and conformation of poly-Arg adsorbed onto a silver nanoparticle (AgNP). Herein, we utilize the constant protonation approach to identify the role of protonation of side chain arginine moieties in the adsorption of poly-Arg to AgNP as a function of pH. The strong adsorption of unprotonated poly-Arg30 onto the quasispherical surface of AgNP with an average diameter of 3.9 nm is primarily governed by multiple interactions of side chain guanidinium (Gdm) moieties, which get stacked and align flat onto the surface. The protonation of the arginine side chain enhances the protein–solvent interactions and promotes the weakening of the protein–nanoparticle binding. The formation of multiple H-bonds between the protonated Arg residues and water molecules favors exposing the charged Gdm+ moieties to the solvent. Protonated poly-Arg30 is found to be partially bound to AgNP due to some weak protein–nanoparticle contacts, maintained by binding of the amide oxygen atoms of the peptide bond. These results suggest that reversible acid–base switching between the arginine protonation states is able to drive the rearrangement of the polyarginine coating around AgNPs, which could be important for a rational design of “intelligent” multifunctional core–shell nanosystems.Polyarginine (poly-Arg) and arginine-rich peptides have been attracting enormous interest in chemical and cell biology as cell-penetrating peptides capable of direct intracellular penetration. Owing to advances in protein engineering, arginine-rich fragments are often incorporated into multifunctional bioorganic/inorganic core–shell nanoparticles, enabling them the novel unique ability to cross cells and deliver biopharmaceutical cargos. Therefore, understanding the molecular details of the adsorption, packing, and release of poly-Arg onto or from metal nanoparticles is one of the current challenges. In this work, we carry out atomistic molecular dynamics simulations to identify the most favorable location, orientation, and conformation of poly-Arg adsorbed onto a silver nanoparticle (AgNP). Herein, we utilize the constant protonation approach to identify the role of protonation of side chain arginine moieties in the adsorption of poly-Arg to AgNP as a function of pH. The strong adsorption of unprotonated...
10 citations
TL;DR: In this paper, structural and dynamic properties of aqueous solution of atactic poly(acrylic) acid in dilute, semi-dilute and concentrated regimes were studied by fully atomistic molecular dynamics simulati...
Abstract: Structural and dynamic properties of aqueous solution of atactic poly(acrylic) acid (PAA) in dilute, semi-dilute and concentrated regimes were studied by fully atomistic molecular dynamics simulati...
9 citations
Cites background or methods or result from "Tacticity effects on conformational..."
...An additional tacticity sequence was not simulated in this study for each system, on the basis of our previous reports in the literature for 30-mer atactic PMA and PAA [24, 57], that an additional tacticity sequence does not improve the statistical accuracy of the properties....
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...The stereochemical sequence of PAA [24] chain chosen for the study is: M-M-M-M-R-R-M-R-R-R-R-M-M-R-R-R-M-M-R-R-MR-R-R-M-R-M-R-R....
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...In our previous studies reported in the literature [16, 24, 57] for polycarboxylate type anionic polyelectrolyte such as PMA and PAA containing 30-mer single chains, multiple initial conformations for each tactcity sequence were simulated in very dilute concentration regime (single chain system) and no appreciable difference in results were found....
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...of such polymers [24,28,50,57] and multi-chain solutions [16,25,51] of polycarboxylate type of polyelectrolytes in...
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TL;DR: The detailed atomistic molecular dynamics simulations studies of multiple chain anionic polyelectrolyte poly(methacrylic acid) PMA was carried out to investigate the effect of monovalent salt ie NaCl on the transport properties such as self-diffusion coefficient of PMA, salt-ions and water molecules in dilute aqueous solutions as mentioned in this paper.
7 citations
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TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
Abstract: In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD A method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling The method is easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints The influence of coupling time constants on dynamical variables is evaluated A leap‐frog algorithm is presented for the general case involving constraints with coupling to both a constant temperature and a constant pressure bath
25,256 citations
TL;DR: An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms.
Abstract: An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms. Timings and accuracies are presented for three large crystalline ionic systems.
24,332 citations
TL;DR: It is demonstrated that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N), which is comparable to that of a simple truncation method of 10 A or less.
Abstract: The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less
17,897 citations
TL;DR: A new implementation of the molecular simulation toolkit GROMACS is presented which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines.
Abstract: Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions Not only does this combination of a
14,032 citations
TL;DR: In this article, an analytical algorithm called SETTLE for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented, which is based on the Cartesian coordinate system and can be used in place of SHAKE and RATTLE.
Abstract: An analytical algorithm, called SETTLE, for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented. This method is still based on the Cartesian coordinate system and can be used in place of SHAKE and RATTLE. We implemented this algorithm in the SPASMS package of molecular mechanics and dynamics. Several series of molecular dynamics simulations were carried out to examine the performance of the new algorithm in comparison with the original RATTLE method. It was found that SETTLE is of higher accuracy and is faster than RATTLE with reasonable tolerances by three to nine times on a scalar machine. Furthermore, the performance improvement ranged from factors of 26 to 98 on a vector machine since the method presented is not iterative. © 1992 by John Wiley & Sons, Inc.
6,109 citations