A Comparative Study for Molecular Dynamics Simulations of Liquid Benzene

Fu, Cen‐Feng; Tian, Shan Xi

doi:10.1021/ct2002122

Cited by 75 publications

(130 citation statements)

References 94 publications

(261 reference statements)

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“…One of the interactions exactly mimics the important stacking that is observed between ring I and GUA 1491 in the RNA A‐site even though the Amber force field does not include a separate term for stacking interactions. It has been previously shown that although the thermodynamic and energetic properties of these interactions were not well reproduced in the classical force fields, the distance and orientation of the rings were in agreement with experiments and quantum calculations 82, 83. We hypothesize that the stacking interactions inside AAC also form with other aminoglycosides, since rings I and II, which are involved in the stacking, are a common structure for the majority of these drugs.…”

Section: Discussionmentioning

confidence: 74%

Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes

2012

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Aminoglycoside antibiotics are used against severe bacterial infections. They bind to the bacterial ribosomal RNA and interfere with the translation process. However, bacteria produce aminoglycoside modifying enzymes (AME) to resist aminoglycoside actions. AMEs form a variable group and yet they specifically recognize and efficiently bind aminoglycosides, which are also diverse in terms of total net charge and the number of pseudo-sugar rings. Here, we present the results of 25 molecular dynamics simulations of three AME representatives and aminoglycoside ribosomal RNA binding site, unliganded and complexed with an aminoglycoside, kanamycin A. A comparison of the aminoglycoside binding sites in these different receptors revealed that the enzymes efficiently mimic the nucleic acid environment of the ribosomal RNA binding cleft. Although internal dynamics of AMEs and their interaction patterns with aminoglycosides differ, the energetical analysis showed that the most favorable sites are virtually the same in the enzymes and RNA. The most copied interactions were of electrostatic nature, but stacking was also replicated in one AME:kanamycin complex. In addition, we found that some water-mediated interactions were very stable in the simulations of the complexes. We show that our simulations reproduce well findings from NMR or X-ray structural studies, as well as results from directed mutagenesis. The outcomes of our analyses provide new insight into aminoglycoside resistance mechanism that is related to the enzymatic modification of these drugs.

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Section: Discussionmentioning

confidence: 74%

Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes

2012

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“…Figure 5 shows that, in the n = 2, 3, and 4 clusters, two nearest neighboring molecules take perpendicular geometries. The population of the perpendicular configuration in the clusters (>75%) is larger than that in the liquid (57%) obtained by the MD simulation of liquid benzene 26 with the OPLS-AA potential. The population of the parallel configuration in the clusters is smaller than the corresponding value of the liquid 24% except for the n = 10 cluster (25%).…”

Section: Structures Of All-atom Opls Clustersmentioning

confidence: 64%

Structural Features of Small Benzene Clusters (C₆H₆)_n (n ≤ 30) As Investigated with the All-Atom OPLS Potential

Takeuchi

2012

J. Phys. Chem. A

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The structures of the simplest aromatic clusters, benzene clusters (C(6)H(6))(n), are not well elucidated. In the present study, benzene clusters (C(6)H(6))(n) (n ≤ 30) were investigated with the all-atom optimized parameters for liquid simulation (OPLS) potential. The global minima and low-lying minima of the benzene clusters were searched with the heuristic method combined with geometrical perturbations. The structural features and growth sequence of the clusters were examined by carrying out local structure analyses and structural similarity evaluation with rotational constants. Because of the anisotropic interaction between the benzene molecules, the local structures consisting of 13 molecules are considerably deviated from regular icosahedron, and the geometries of some of the clusters are inconsistent with the shapes constructed by the interior molecules. The distribution of the angle between the lines normal to two neighboring benzene rings is anisotropic in the clusters, whereas that in the liquid benzene is nearly isotropic. The geometries and energies of the low-lying configurations and the saddle points between them suggest that most of the configurations previously detected in supersonic expansions take different orientations for one to four neighboring molecules.

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“…15b) using the OPLS-AA force-field which has been shown to reproduce the structure of liquid benzene well. 64 Further details of the simulations are given in the ESI † (SI-S5). The plots of g(r,y) show that the OPLS force-field gives a qualitatively similar g(r,y) for pyridine, albeit with a slightly higher shoulder for parallel neighbours.…”

Section: Comparison To Simulationmentioning

confidence: 99%

The structures of liquid pyridine and naphthalene: the effects of heteroatoms and core size on aromatic interactions

Headen

Cullen

Patel

et al. 2018

Phys. Chem. Chem. Phys.

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Total neutron scattering has been used in conjunction with H/D and *N/ 15 N isotopic substitution to determine the detailed liquid-state structures of pyridine and naphthalene. Analysis of the data via an empirical potential-based structure refinement method has allowed us to interrogate the full six-dimensional spatial and orientational correlation surfaces in these systems, and thereby to deduce the fundamental effects of a heteroatom and aromatic core-size on intermolecular p-p interactions. We find that the presence of a nitrogen heteroatom, and concomitant dipole moment, in pyridine induces surprisingly subtle departures from the structural correlations observed in liquid benzene: in both cases the most probable local motif is based on perpendicular (edge-to-face) intermolecular contacts, while parallel-displaced configurations give rise to a clear shoulder in the correlation surface. However, the effect of the heteroatom is revealed through detailed analysis of the intermolecular orientational correlations. This analysis shows a tendency for neighbouring pyridine molecules to direct one meta-and one para-hydrogen towards the neighbouring aromatic p-orbitals in edge-to-face configurations, while head-to-tail alignment of adjacent nitrogen atoms is favoured in faceto-face configurations. In contrast to this, increasing aromatic core size from one to only two rings has a clear and profound effect on the p-p interactions and liquid structure. Our experiments show that naphthalenenaphthalene contacts are dominated by parallel-displaced configurations, akin to those found in graphite. This marks a fundamental difference with the structure of liquid benzene, in which perpendicular geometries are favoured. Furthermore, it is remarkable to note that in the systems studied, the most favoured spatioorientational configurations observed in the liquid state are not predicted from ab initio calculations and/or solid state crystallographic studies. This highlights the need for caution when extrapolating the results of crystallographic and computational studies to aromatic interactions in liquids and disordered systems.

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A Comparative Study for Molecular Dynamics Simulations of Liquid Benzene

Cited by 75 publications

References 94 publications

Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes

Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes

Structural Features of Small Benzene Clusters (C₆H₆)_n (n ≤ 30) As Investigated with the All-Atom OPLS Potential

The structures of liquid pyridine and naphthalene: the effects of heteroatoms and core size on aromatic interactions

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A Comparative Study for Molecular Dynamics Simulations of Liquid Benzene

Cited by 75 publications

References 94 publications

Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes

Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes

Structural Features of Small Benzene Clusters (C6H6)n (n ≤ 30) As Investigated with the All-Atom OPLS Potential

The structures of liquid pyridine and naphthalene: the effects of heteroatoms and core size on aromatic interactions

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Structural Features of Small Benzene Clusters (C₆H₆)_n (n ≤ 30) As Investigated with the All-Atom OPLS Potential