Applications of Artificial Intelligence in Molecular Modelling and Drug Design

Leach, Andrew R.

doi:10.1007/978-1-349-12973-7_6

Cited by 323 publications

(443 citation statements)

References 59 publications

Supporting

Mentioning

420

Contrasting

Unclassified

Order By: Relevance

“…For all radical ion species 0.75 < S 2 < 0.78 -indicating acceptably low spin-contamination in all cases. [42][43][44] All unconstrained equilibrium geometries referred to in the following discussion were confirmed by IR calculations; spectra confirming real equilibrium minima by exhibiting no imaginary modes (no negative infrared frequencies observed for any equilibrium geometry). [42][43][44] Most previous determinations of λ h/e values for organic charge transfer materials [23, 30-36, 38, 39, 45] have used the B3LYP density functional [46][47][48] which (over and above specific training set based empirical parameters) differs from M06-2X in that i) it does not conform to the free electron gas limit;…”

Section: Methodsmentioning

confidence: 83%

Torsional angle dependence and switching of inner sphere reorganisation energies for electron and hole transfer processes involving phenyl substituted diketopyrrolopyrroles; a density functional study

2015

View full text Add to dashboard Cite

angle dependence and switching of inner sphere reorganisation energies for electron and hole transfer processes involving phenyl substituted diketopyrrolopyrroles; a density functional study ', Dyes and Pigments, Vol. 113, pp. 609-617, February 2015 AbstractDetermination of inner sphere reorganisation energies is important in the development of organic charge mediating materials and electron transfer reactions. In this study, hole and electron inner sphere reorganisation energies, λ h and λ e respectively, have been computed for the first time for a series of structurally related diketopyrrolopyrrole (DPP) molecular motifs. Inner sphere reorganisation energies for self-exchange electron transfer reactions are calculated as being lower than those associated hole transfer processes in model planar phenyl and thiophenyl substituted DPP systems. It is found that λ e < λ h for all planar ring / DPP core structures examined. The effect on λ h/e of nonplanarity between phenyl substituents and DPP core is explored in detail. The relative ordering of λ h and λ e is dependent upon the torsional angle of phenyl rings and reverses at twist angles of greater than 60⁰ such that λ e > λ h .

show abstract

Section: Methodsmentioning

confidence: 83%

Torsional angle dependence and switching of inner sphere reorganisation energies for electron and hole transfer processes involving phenyl substituted diketopyrrolopyrroles; a density functional study

2015

View full text Add to dashboard Cite

show abstract

“…ref. [15][16][17]. Of course, not all important questions are related to static thermal equilibrium, but even this seemingly simplest of all problems generally requires a massive investment of intelligent computing, and it warns us how much more complicated other tasks (nonequilibrium, kinetics, rare events, etc.)…”

Section: B Principles Of Molecular Modelingmentioning

confidence: 99%

“…Algorithmic developments are an equally important issue, and we refer the reader to recent textbooks in the field, such as the ones by Leach 17 and Frenkel and Smit. 15 …”

Section: Beyond Moleculesmentioning

confidence: 99%

Multiscale modeling of emergent materials: biological and soft matter

Murtola

Bunker

Vattulainen

et al. 2009

Phys. Chem. Chem. Phys.

261

234

View full text Add to dashboard Cite

On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models Moritz Winger, Daniel Trzesniak, Riccardo Baron and Wilfred F. In this review, we focus on four current related issues in multiscale modeling of soft and biological matter. First, we discuss how to use structural information from detailed models (or experiments) to construct coarse-grained ones in a hierarchical and systematic way. This is discussed in the context of the so-called Henderson theorem and the inverse Monte Carlo method of Lyubartsev and Laaksonen. In the second part, we take a different look at coarse graining by analyzing conformations of molecules. This is done by the application of self-organizing maps, i.e., a neural network type approach. Such an approach can be used to guide the selection of the relevant degrees of freedom. Then, we discuss technical issues related to the popular dissipative particle dynamics (DPD) method. Importantly, the potentials derived using the inverse Monte Carlo method can be used together with the DPD thermostat. In the final part we focus on solvent-free modeling which offers a different route to coarse graining by integrating out the degrees of freedom associated with solvent.

show abstract

“…In addition, another common practise is not to specify all interaction parameters explicitly but to use the Lorentz-Berthelot combination rules [34] …”

Section: Opls-aa ("Opls")mentioning

confidence: 99%

Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration, and structural properties

Patra¹,

Karttunen²

2004

J Comput Chem

209

View full text Add to dashboard Cite

In this paper we compare different force fields that are widely used (Gromacs, Charmm-22/xPlor, Charmm-27, Amber-1999, OPLS-AA) in biophysical simulations containing aqueous NaCl. We show that the uncertainties of the microscopic parameters of, in particular, sodium and, to a lesser extent, chloride translate into large differences in the computed radial-distribution functions. This uncertainty reflects the incomplete experimental knowledge of the structural properties of ionic aqueous solutions at finite molarity. We discuss possible implications on the computation of potential of mean force and effective potentials.

show abstract

Applications of Artificial Intelligence in Molecular Modelling and Drug Design

Cited by 323 publications

References 59 publications

Torsional angle dependence and switching of inner sphere reorganisation energies for electron and hole transfer processes involving phenyl substituted diketopyrrolopyrroles; a density functional study

Torsional angle dependence and switching of inner sphere reorganisation energies for electron and hole transfer processes involving phenyl substituted diketopyrrolopyrroles; a density functional study

Multiscale modeling of emergent materials: biological and soft matter

Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration, and structural properties

Contact Info

Product

Resources

About