: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

We demonstrate how an iterative method for potential inversion from distribution functions developed for simple liquid systems can be generalized to polymer systems. It uses the differences in the potentials of mean force between the distribution functions generated from a guessed potential and the true distribution functions to improve the effective potential successively. The optimization algorithm is very powerful: convergence is reached for every trial function in few iterations. As an extensive test case we coarse-grained an atomistic all-atom model of polyisoprene (PI) using a 13:1 reduction of the degrees of freedom. This procedure was performed for PI solutions as well as for a PI melt. Comparisons of the obtained force fields are drawn. They prove that it is not possible to use a single force field for different concentration regimes. © 2003 Wiley Periodicals, Inc. J Comput Chem 13: 1624–1636, 2003

Deriving effective mesoscale potentials from atomistic simulations.

Polymers can be theoretically and computationally described by models pertaining to different length scales and corresponding time scales. These models have traditionally been used independently of each other. Recently, considerable progress has been made in systematically linking models of different scales. This Review focuses on the generation of lattice and off-lattice coarse-grained polymer models, whose "monomers" correspond to roughly a chemical repeat unit, from chemically detailed atomistic simulations of the same polymers. Computational methods are described as well as applications to polymers in the melt and in solution. The success of multiscale simulations in solving real-world polymer problems that could not be solved in any other way suggests that they will have an important role to play in the future.

Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back.

By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.

Perspective: Coarse-grained models for biomolecular systems.

This article presents a topical review of coarse grain simulation techniques. First, we motivate these techniques with illustrative examples from biology and materials science. Next, approaches in the literature for increasing the efficiency of atomistic simulations are mentioned. Considerations related to a specific coarse grain modelling approach are discussed at length, and the consequences arising from the loss of detail are given. Finally, a large number of results are presented to give the reader a feeling for the types of problem which can be addressed.

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Coarse grain models and the computer simulation of soft materials

The COMPASS II force field has been developed by extending the coverage of the COMPASS force field (J Phys Chem B 102(38):7338–7364, 1998) to polymer and drug-like molecules found in popular databases. Using a fragmentation method to systematically construct small molecules that exhibit key functional groups found in these databases, parameters applicable to database compounds were efficiently obtained. Based on the same parameterization paradigm as used in the development of the COMPASS force field, new parameters were derived by a combination of fits to quantum mechanical data for valence parameters and experimental liquid and crystal data for nonbond parameters. To preserve the quality of the original COMPASS parameters, a quality assurance suite was used and updated to ensure that additional atom-types and parameters do not interfere with the existing ones. Validation against molecular properties, liquid and crystal densities, and enthalpies, demonstrates that the quality of COMPASS is preserved and the same quality of prediction is achieved for the additional coverage.

COMPASS II: extended coverage for polymer and drug-like molecule databases.

We survey the use of the Monte Carlo method within the Materials Studio application, which integrates a large number of modules for molecular simulation. Several of these modules work by generating...

Monte Carlo methods in Materials Studio

In this study we explore a systematic procedure to coarsen a microscopic model towards a mesoscopic model. The procedure is applied to a system of chains of ten beads, representing a low molecular weight polymer melt. Our method consists of defining coarse-grained sites in the microscopic system, and calculating their spatial distribution on the pair level. The effective interaction between the coarse-grained sites is then obtained by bringing the pair interaction in consistence with the pair density. We investigate both a dynamic and a stochastic method for this step. The so obtained mesoscopic interaction is used in a molecular dynamics simulation to investigate the pressure of the coarse-grained system. We found that the pair interaction that reproduces the pair density predicts a pressure that is significantly lower than the microscopic value, even if we take the state-dependency of the coarse-grained interactions into account. We therefore conclude that coarse-grained models lack thermodynamic consistency.

A structure-based coarse-grained model for polymer melts

In this study we present the coarse-graining of one polymer chain in a melt to a single dimer. By using the projector operator formalism we derive the equation of motions for the dimer. The different forces that occur in this equation of motion are calculated from molecular dynamics simulations of the microscopic model, using constraint forces to fix the dimer configuration. The mean constraint force serves as the conserved part of the interaction, whereas the time correlation of the constraint force fluctuation leads to the nonconserved interactions: the dissipative and fluctuating forces. Using the configurational dependent coarse-grained interactions we have performed stochastic dynamics simulations of the dimer. Dimer properties of the microscopic and the coarse-grained model are shown to be in reasonable agreement. We also discuss the application of the framework to coarse-graining polymer melts into more detail, i.e., beyond the dimer.

Coarse-grained dynamics of one chain in a polymer melt

The irreversible polymerization of a monomer liquid has been studied by molecular-dynamics simulation in two and three dimensions. The growth process is studied under good solvent conditions in the dilute regime and up to semidilute and concentrated regimes. In the dilute regime we observe a reaction limitation due to trapping of the growing centers, which is more pronounced in the lower dimension. At higher concentrations the presence of other chains decreases the monomer mobility and reaction rate. Conformational properties are studied by scaling analysis of end-to-end and gyration radii. A crossover from swollen conformations towards screened conformations is observed as growth proceeds.

Reinier L. C. Akkermans

Papers

COMPASS II: extended coverage for polymer and drug-like molecule databases.

Monte Carlo methods in Materials Studio

A structure-based coarse-grained model for polymer melts

Coarse-grained dynamics of one chain in a polymer melt

Molecular dynamics of polymer growth