A Guide to QM/MM Methodology and Applications

Zhang, Rui; Lev, Bogdan; Cuervo, Javier; Noskov, Sergei Y.; Salahub, Dennis R.

doi:10.1016/s0065-3276(10)59010-5

Cited by 29 publications

(33 citation statements)

References 268 publications

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“…The simplest way would be to randomly break chains, cap the ends with carboxylate groups, and then evaluate how this influences water distribution within the polymer. More complex approaches would be to use either a bond-breaking molecular mechanics (MM) potential, or to conduct combined quantum mechanics and molecular mechanics (QM/MM) simulations, 53 with the QM part focusing on the areas of the polymer where water is predicted by the TIGER2 simulations to be clustered. This could then involve iterative simulations of QM/MM followed by further simulations using TIGER2/TIGER3 to re-equilibrate the water within the polymer after the hydrolysis steps.…”

Section: Resultsmentioning

confidence: 99%

Structure of Hydrated Poly(d,l-lactic acid) Studied with X-ray Diffraction and Molecular Simulation Methods

Murthy

Latour

2012

Macromolecules

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The effect of hydration on the molecular structure of amorphous poly (D, L-lactic acid) (PDLLA) with 50:50 L-to-D ratio has been studied by combining experiments with molecular simulations. X-ray diffraction measurements revealed significant changes upon hydration in the structure functions of the copolymer. Large changes in the structure functions at ~ 10 days of incubation coincided with the large increase in the water uptake from ~1 to ~40% and the formation of voids in the film. Computer modeling based on the recently developed TIGER2/TIGER3 mixed sampling scheme was used to interpret these changes by efficiently equilibrating both dry and hydrated models of PDLLA. Realistic models of bulk amorphous PDLLA structure were generated as demonstrated by close agreement between the calculated and the experimental structure functions. These molecular simulations were used to identify the interactions between water and the polymer at the atomic level including the change of positional order between atoms in the polymer due to hydration. Changes in the partial O-O structure functions, about 95% of which were due to water-polymer interactions, were apparent in the radial distribution functions. These changes, and somewhat smaller changes in the C-C and C-O partial structure functions, clearly demonstrated the ability of the model to capture the hydrogen bonding interactions between water and the polymer, with the probability of water forming hydrogen bonds with the carbonyl oxygen of the ester group being about four times higher than with its ether oxygen.

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Section: Resultsmentioning

confidence: 99%

Structure of Hydrated Poly(d,l-lactic acid) Studied with X-ray Diffraction and Molecular Simulation Methods

Murthy

Latour

2012

Macromolecules

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“…To address the first item, three approaches have been widely used to treat the electrostatic interactions between QM and MM parts: (i) electrostatic, (ii) mechanical, and (iii) polarizable embedding. The electrostatic embedding approach enables the polarization of the QM part since the charge distribution of the MM part is incorporated in the QM calculation . Contrary to the electrostatic embedding approach, in mechanical embedding, the QM atoms are represented as point charges, bond dipoles, or higher multipoles.…”

Section: Models and Methodologiesmentioning

confidence: 99%

Multiscale modeling of enzymes: QM‐cluster, QM/MM, and QM/MM/MD: A tutorial review

Ahmadi

Herrera

Chehelamirani

et al. 2018

Int J of Quantum Chemistry

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135

149

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“…The FEP/MD simulations were carried out via the PERT module of the program CHARMM (Brooks et al, 2009) using Langevin dynamics. The computations with the Drude polarizable force field were carried out using the same procedure with the ion parameters of Yu et al (2010c).bDFT FEP calculations were performed at the PBE/DZVP level of theory (Perdew et al, 1996) using the CHARMM/DeMon2k interface (Lev et al, 2010; Zhang et al, 2010). The DFT relative free energy difference for the ions in bulk was calculated using 16 water molecules restrained within a spherical volume around the ion, mimicking the bulk density.…”

Section: Force Field Induced Polarization and Quantum Mechanics (Qm)mentioning

confidence: 99%

Ion selectivity in channels and transporters

Roux

Bernèche

Egwolf

et al. 2011

Journal of General Physiology

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145

147

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A multitude of biological processes requires the participation of specific cations, such as H + , Na + , K + , Ca 2+ , and Mg 2+ . Many of these processes can take place only when proteins have the ability to discriminate between different ions with a very high fidelity. How this is possible is a fundamental question that has fascinated scientists for a long time. At the most fundamental level, it is anticipated that ion selectivity must result from a delicate balance of strong interactions. Yet, identifying and quantifying the key microscopic factors is difficult, as many of these cannot be directly measured by experiments. Theory and computations can contribute by providing a virtual route to complement the missing information. Because ion selectivity is often dominated by thermodynamic factors, detailed molecular dynamics (MD) free energy simulations become important tools. This was vividly illustrated early on with studies of ion solvation (Straatsma and Berendsen, 1988;Åqvist, 1990) and ion-selective systems (Lybrand et al., 1986;Grootenhuis and Kollman, 1989;Åqvist, 1992). These pioneering studies inspired our own efforts.In this Perspective, we aim to present our understanding of ion selectivity as it has evolved over approximately 15 years from studies based on various specific structures: gramicidin A channels (e.g.

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A Guide to QM/MM Methodology and Applications

Cited by 29 publications

References 268 publications

Structure of Hydrated Poly(d,l-lactic acid) Studied with X-ray Diffraction and Molecular Simulation Methods

Structure of Hydrated Poly(d,l-lactic acid) Studied with X-ray Diffraction and Molecular Simulation Methods

Multiscale modeling of enzymes: QM‐cluster, QM/MM, and QM/MM/MD: A tutorial review

Ion selectivity in channels and transporters

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