Hydrogen bonding and induced dipole moments in water: Predictions from the Gaussian charge polarizable model and Car-Parrinello molecular dynamics

2006 ◽  
Vol 125 (14) ◽  
pp. 144519 ◽  
Author(s):  
Peter J. Dyer ◽  
Peter T. Cummings
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Dipole Moments ◽  
Induced Dipole

scholarly journals Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes

2019 ◽  
Vol 48 (2) ◽  
pp. 561-575 ◽  
Author(s):  
Justin A Lemkul
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dipole Moments ◽  
Sequence Motifs ◽  
Telomeric Dna ◽  
Rna Sequences ◽  
Dna And Rna ◽  
Induced Dipole ◽  
Dynamics Simulations

Abstract DNA and RNA sequences rich in guanine can fold into noncanonical structures called G-quadruplexes (GQs), which exhibit a common stem structure of Hoogsteen hydrogen-bonded guanine tetrads and diverse loop structures. GQ sequence motifs are overrepresented in promoters, origins of replication, telomeres, and untranslated regions in mRNA, suggesting roles in modulating gene expression and preserving genomic integrity. Given these roles and unique aspects of different structures, GQs are attractive targets for drug design, but greater insight into GQ folding pathways and the interactions stabilizing them is required. Here, we performed molecular dynamics simulations to study two bimolecular GQs, a telomeric DNA GQ and the analogous telomeric repeat-containing RNA (TERRA) GQ. We applied the Drude polarizable force field, which we show outperforms the additive CHARMM36 force field in both ion retention and maintenance of the GQ folds. The polarizable simulations reveal that the GQs bind bulk K+ ions differently, and that the TERRA GQ accumulates more K+ ions, suggesting different ion interactions stabilize these structures. Nucleobase dipole moments vary as a function of position and also contribute to ion binding. Finally, we show that the TERRA GQ is more sensitive than the telomeric DNA GQ to water-mediated modulation of ion-induced dipole-dipole interactions.

The chemistry of aliphatic unconjugated nitramines. II. Intramolecular properties and crystal packing

1969 ◽  
Vol 22 (12) ◽  
pp. 2505 ◽  
Author(s):  
J Stals
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Packing ◽  
Dipole Moments ◽  
Molecular Crystals ◽  
Bond Orders ◽  
Bond Energies ◽  
Electric Dipole Moments ◽  
Charge Distributions ◽  
Hydrogen Bonding Interactions ◽  
Vb Structures

The VESCF(BJ)-MO electric dipole moments, molecular ionization potentials, electronic bond energies, charge distributions, and bond orders for nitramide, N-methylnitramine, and s- and as-N,N- dimethylnitramines are reported. The packing of nitramide, RDX, and HNX in their molecular crystals is rationalized in terms of electrostatic and hydrogen-bonding interactions. Simple VB structures do not readily predict their calculated MO charge distributions and bond orders.

Intensity of the Pressure-Induced Fundamental Infrared Band of Gaseous Chlorine

1973 ◽  
Vol 51 (6) ◽  
pp. 696-697 ◽  
Author(s):  
P. T. T. Wong ◽  
E. Whalley
Keyword(s):  
Dipole Moments ◽  
Good Evidence ◽  
Transition Moment ◽  
Infrared Band ◽  
Fundamental Band ◽  
Induced Dipole ◽  
Integrated Intensity ◽  
Type Interaction

The integrated intensity of the pressure-induced fundamental band of gaseous chlorine measured by Winkel, Hunt, and Clouter is about 5 times that calculated assuming that the transition moment arises from the oscillation of quadrupole-induced dipole moments. This provides good evidence that valence-type interaction between gaseous chlorine molecules occurs.

scholarly journals Positively and Negatively Hydrated Counterions in Molecular Dynamics Simulations of DNA Double Helix

2020 ◽  
Vol 65 (6) ◽  
pp. 510
Author(s):  
S. Perepelytsya
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Double Helix ◽  
Dipole Moments ◽  
Hydration Shell ◽  
Minor Groove ◽  
Water Molecules ◽  
Negative Hydration ◽  
Dynamics Simulations ◽  
Dna Double Helix

The DNA double helix is a polyanionic macromolecule that is neutralized in water solutions by metal ions (counterions). The property of counterions to stabilize the water network (positive hydration) or to make it friable (negative hydration) is important in terms of the physical mechanisms of stabilization of the DNA double helix. In the present research, the effects of positive hydration of Na+ counterions and negative hydration of K+ and Cs+ counterions incorporated into the hydration shell of the DNA double helix have been studied using molecular dynamics simulations. The results have shown that the dynamics of the hydration shell of counterions depends on the region of the double helix: minor groove, major groove, and outside the macromolecule. The longest average residence time has been observed for water molecules contacting with the counterions localized in the minor groove of the double helix (about 50 ps for Na+ and lower than 10 ps for K+ and Cs+). The estimated potentials of the mean force for the hydration shells of counterions show that the water molecules are constrained too strongly, and the effect of negative hydration for K+ and Cs+ counterions has not been observed in the simulations. The analysis has shown that the effects of counterion hydration can be described more accurately with water models having lower dipole moments.

scholarly journals Studies of Hydrogen Bonding. Part XXXVI. Dipole Moments of Pyridines, Quinolines and Acridine, and of their Hydrogen-Bonded Complexes with Phenol.

1993 ◽  
Vol 47 ◽  
pp. 985-989 ◽  
Author(s):  
Thor Gramstad ◽  
Arne Haaland ◽  
Kjell-Gunnar Martinsen ◽  
Jürgen Vogt ◽  
Ingmar Grenthe ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Dipole Moments ◽  
Bonded Complexes ◽  
Hydrogen Bonded
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