Quantum mechanical force fields for condensed phase molecular simulations

Giese, Timothy J.; York, Darrin M.

doi:10.1088/1361-648x/aa7c5c

Cited by 32 publications

(34 citation statements)

References 223 publications

(385 reference statements)

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“…Due to the generally weaker effect of these interactions when compared to electrostatics, this uncoupled formulation is the standard in QM/MM descriptions and only very few attempts to go beyond that have been proposed for water as solvent, 14 and for more complex environments including biological systems. [15][16][17] On the contrary, various methods have been presented so far to include mutual polarization effects. A strategy is to introduce the effect of polarization using "ab initio" FFs which are fully built on first principles and require no fitted parameters.…”

Section: Introductionmentioning

confidence: 99%

Polarizable embedding QM/MM: the future gold standard for complex (bio)systems?

Bondanza

Nottoli

Cupellini

et al. 2020

Phys. Chem. Chem. Phys.

153

187

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Section: Introductionmentioning

confidence: 99%

Polarizable embedding QM/MM: the future gold standard for complex (bio)systems?

Bondanza

Nottoli

Cupellini

et al. 2020

Phys. Chem. Chem. Phys.

153

187

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“…First of all, the computational cost involved necessarily requires new numerical strategies in order to go beyond model systems and extremely short time-scales. In the last years, a large activity has been focused on improving the scaling of the QM calculations, 78,[130][131][132] also by introducing novel semiempirical methods 133 including Density Functional tight binding. 134 However, also the classical models have to be reconsidered in terms of their scaling as, when coupled to fast QM methods, they can become the real bottleneck of the calculation.…”

Section: Discussionmentioning

confidence: 99%

Multiscale modelling of photoinduced processes in composite systems

2019

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| In the last decades, the quantum mechanical modeling has moved from isolated molecules made of few atoms, to large supramolecular aggregates embedded in complex environments. This has been made possible by the important progress achieved by multiscale models based on the integration of QM methods with classical descriptions. One of the first example of this integration is represented by continuum solvation models that starting from the eighties of the last century have been largely and successfully applied to predict properties and processes of solvated molecules. Almost in the same years, another alternative classical description, based on Molecular Mechanics (MM) has been coupled to QM methods to give the hybrid QM/MM approach. Since their first formulations, these QM/classical models have seen an enormous development in terms of accuracy, robustness and generalizability. This progress has allowed their application to systems of increasing complexity and to processes never faced before within a QM framework. An important example of such an achievement is represented by the novel insights reached in the fundamental understanding and the possible exploitation of photoinduced processes in biomolecules, nanomaterials and, more in general, composite systems where different "objects" of molecular, nano and mesoscopic scale are coupled together. In this review, we highlight the potentials and the limitations of such modeling, thereby showing which developments are still needed to definitely make the QM-based multiscale strategy the gold-standard for explaining the outputs of novel advanced spectroscopic techniques and predicting the outcome of light-activated events in composite systems. The multiscale strategiesIn the years, two main strategies to combine QM descriptions of the target and classical models of the environment, have been proposed. Interestingly, their first formulations date back to the same years, namely the end of the seventies of the previous century. [8][9][10] The two strategies refer to continuum and discrete (or atomistic) descriptions of the environment, respectively. In the latter case, the atoms of the environment (or group of atoms in coarser grained versions of the model) are treated through a Molecular Mechanics (MM) force field (FF). [11][12][13][14][15] In the former case, instead, the atomic nature of the environment is lost and a continuum description in terms of macroscopic properties is introduced instead. 16-18 Despite this huge "modellistic" difference, the two formulations present important common elements when reconsidered from the point of view of the QM target. In any case, for simplicity's sake two separate presentations will be given. QM/continuum. If the environment loses its atomic nature, an effective description has to be introduced which is based on some macroscopic properties. This is exactly what is done in continuum models where the target sees the environment as an infinite dielectric medium characterized by a (generally) frequency and position dependent permittivit...

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“…As an example, Huang et al 32 recently introduced a multidimensional B-spline correction map (BMAP) to the sugar puckering in the AM1/ d-PhoT 33 semiempirical Hamiltonian, which was successfully applied to reproduce different RNA transesterification reactions. Similarly, York's group has presented exciting results on RNA systems using quantum mechanical force fields (QMFFs), 34 which scale linearly with system size and are then much faster than fully coupled QM methods.…”

Section: What Have We Learned About Rna Structure From Qm and Qm/mm Mmentioning

confidence: 99%

Modeling, Simulations, and Bioinformatics at the Service of RNA Structure

Dans

Gallego

Balaceanu

et al. 2019

Chem

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Although chemically close to DNA, RNA can adopt a wide range of structures from regular helices to complex globular conformations, showing a complexity similar to that of proteins. The determination of the structure of RNA molecules, crucial for functional understanding, is severely handicapped by their size and flexibility, which makes the systematic use of experimental approaches difficult. Simulation techniques are also suffering from very severe problems related to the accuracy of the methods and their ability to sample a large and complex conformational landscape. Here, we systematically review recent approaches created to reduce the shortcoming of the current generation of simulation methods-from highly accurate models able to deal with small systems to coarse-grained approaches that are less accurate but applicable to dealing with large models. WHAT HAVE WE LEARNED ABOUT RNA STRUCTURE FROM QM AND QM/MM METHODS?Physics teaches us that ab initio quantum mechanics (QM) can represent with high accuracy any biomolecular system, among them RNA. Unfortunately, because of their computational cost, the practical application of ab initio QM formalisms to large systems such as RNA is often impossible. In fact, even simpler QM methods such as those based on density functional theory (DFT) fail to treat systems larger than 10 2 atoms, several orders of magnitude less than the size required to study RNAs in solution. 1 Further simplifications of the basic QM formalism, such as those implicit in semiempirical (SE) methods, can extend the range of applicability of QM theory but at the expense of an expected loss of accuracy. 2 High-level QM and DFT calculations have had a central role in the development and validation of recent RNA force fields (FFs; see below). A recent example is the B97D3/AUG-CC-PVTZ study of the backbone and glycosidic torsions by Aytenfisu et al., 3 who highlighted systematic errors in current RNA FFs that might lead to incorrect molecular dynamics (MD) trajectories. Different conclusions were reached by the group led by Sponer, who again used DFT calculations as a reference, namely that the errors in current RNA FFs are related to imbalanced hydration and not to intrinsic errors in the classical gas phase Hamiltonian. 4 The same group recently studied 46 different backbone conformations of the UpU dinucleotide step (see Figure 1) by using a variety of QM methods from the state-of-the-art CCSD(T) to the latest-generation SE algorithms, 5 providing the community with an invaluable dataset for refinement of RNA FFs. Very recently our group used DFT/MM (density functional theory and molecular mechanics) calculations to fit some dihedrals directly for QM calculations in solution, opening a new approach to using DFT calculations in the refinement of RNA FF (see the next section). 6 The Bigger PictureRNAs are the ultimate frontier of structural biology. They are large and complex molecules that can adopt complex structures displaying a wide variety of functions from carriers of genetic information to regu...

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Quantum mechanical force fields for condensed phase molecular simulations

Cited by 32 publications

References 223 publications

Polarizable embedding QM/MM: the future gold standard for complex (bio)systems?

Polarizable embedding QM/MM: the future gold standard for complex (bio)systems?

Multiscale modelling of photoinduced processes in composite systems

Modeling, Simulations, and Bioinformatics at the Service of RNA Structure

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