Specific quantum mechanical/molecular mechanical capping-potentials for biomolecular functional groups

Ihrig, Arvid Conrad; Schiffmann, Christoph; Sebastiani, Daniel

doi:10.1063/1.3664300

Cited by 19 publications

(22 citation statements)

References 52 publications

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“…There exist a variety of approaches to describe that frontier bond, for example capping potentials [22,26], generalized hybrid orbitals [16] or localized self-consisted field [3,33,40], but the simplest, yet very accurate [2] and therefore also highly popular [27,36] method is hydrogen capping [39].…”

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confidence: 99%

Optimizing link atom parameters for DNA QM/MM simulations

et al. 2016

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utilize popular force fields like AMBER [9], CHARMM [8], OPLS [23] or GROMOS [35] is the ability to describe effects stemming from the intra-or intermolecular shifts of electron density for any desired chemical system. Due to this, phenomena such as charge transfers, the cleavage or formation of covalent bonds and polarization effects can be studied in-depth. Additionally, the influence of different spin states, Jahn Teller distortion and even electronic excitations can be investigated without having to resort to specifically tailored force fields.One of the major challenges for that kind of investigation is a proper description of the interface between the QM and the MM region, especially if covalent bonds are reaching through the boundary between the two regions [27]. There exist a variety of approaches to describe that frontier bond, for example capping potentials [22,26], generalized hybrid orbitals [16] or localized self-consisted field [3,33,40], but the simplest, yet very accurate [2] and therefore also highly popular [27,36] method is hydrogen capping [39].A big question regarding hydrogen-capping approaches is the proper placement of the inserted atom, so that its influence on the behavior of the surrounding atoms is minimized as much as possible. In a previous work [18], this was discussed in detail for amino acids, with the recommendation to use separate parameters for each type of sidechain to considerably improve the description of the link bond. In this work, the focus lies on the QM/MM separation of DNA nucleosides, with the C-N bond between the deoxyribose and the nucleobase acting as the link bond. Abstract This work optimizes the link bond description of the quantum mechanical/molecular mechanical separation of deoxynucleosides. The nucleosides are separated at the C-N bond between the nucleobase and the deoxyribose, with the former acting as the quantum mechanically described species. By using a flexible link atom-ansatz plus a harmonic potential to correct the energy deviation from a full quantum mechanical description, the potential energy well of the bond's stretching motion is mimicked with very high accuracy.

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confidence: 99%

Optimizing link atom parameters for DNA QM/MM simulations

et al. 2016

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“…Since Hellmann and Gombás' development of the first pseudopotentials in the 1930s, pseudopotential methods have been employed in a variety of theoretical chemistry problems. In recent years, pseudopotentials have been used to provide enhancements or corrections to other methods, with examples including their use as link atoms in QM/MM calculations, or the efforts to use them alongside DFT calculations in correcting for DFT errors in the effect of van der Waals forces . Their primary use, however, has always been that of increasing computational efficiency as compared with all‐electron solutions for the same systems.…”

Section: Introductionmentioning

confidence: 99%

Atomic pseudopotentials for reproducing π‐orbital electron behavior in sp² carbon atoms

Punter

Nava

Carissan

2019

Int J of Quantum Chemistry

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“…In such situations stochastic global optimizers like Genetic Algorithms (GA), 11 simulated annealing (SA) 12 can be very useful. GA, [13][14][15][16][17][18][19][20] swarm intelligence techniques, 21,22 minima hoping, 19,20,23,24 basin hoping, [25][26][27] have been successful and popular among the cluster physics community. The standard serial GA is population based.…”

Section: Introductionmentioning

confidence: 99%

Single string based global optimizer for geometry optimization in strongly coupled finite clusters: An adaptive mutation-driven strategy

Sarkar

Bhattacharyya

2013

The Journal of Chemical Physics

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We propose and implement a simple adaptive heuristic to optimize the geometries of clusters of point charges or ions with the ability to find the global minimum energy configurations. The approach uses random mutations of a single string encoding the geometry and accepts moves that decrease the energy. Mutation probability and mutation intensity are allowed to evolve adaptively on the basis of continuous evaluation of past explorations. The resulting algorithm has been called Completely Adaptive Random Mutation Hill Climbing method. We have implemented this method to search through the complex potential energy landscapes of parabolically confined 3D classical Coulomb clusters of hundreds or thousands of charges--usually found in high frequency discharge plasmas. The energy per particle (EN∕N) and its first and second differences, structural features, distribution of the oscillation frequencies of normal modes, etc., are analyzed as functions of confinement strength and the number of charges in the system. Certain magic numbers are identified. In order to test the feasibility of the algorithm in cluster geometry optimization on more complex energy landscapes, we have applied the algorithm for optimizing the geometries of MgO clusters, described by Coulomb-Born-Mayer potential and finding global minimum of some Lennard-Jones clusters. The convergence behavior of the algorithm compares favorably with those of other existing global optimizers.

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Specific quantum mechanical/molecular mechanical capping-potentials for biomolecular functional groups

Cited by 19 publications

References 52 publications

Optimizing link atom parameters for DNA QM/MM simulations

Optimizing link atom parameters for DNA QM/MM simulations

Atomic pseudopotentials for reproducing π‐orbital electron behavior in sp² carbon atoms

Single string based global optimizer for geometry optimization in strongly coupled finite clusters: An adaptive mutation-driven strategy

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Specific quantum mechanical/molecular mechanical capping-potentials for biomolecular functional groups

Cited by 19 publications

References 52 publications

Optimizing link atom parameters for DNA QM/MM simulations

Optimizing link atom parameters for DNA QM/MM simulations

Atomic pseudopotentials for reproducing π‐orbital electron behavior in sp2 carbon atoms

Single string based global optimizer for geometry optimization in strongly coupled finite clusters: An adaptive mutation-driven strategy

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Product

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Atomic pseudopotentials for reproducing π‐orbital electron behavior in sp² carbon atoms