Parametrization and Molecular Dynamics Simulations of Nitrogen Oxyanions and Oxyacids for Applications in Atmospheric and Biomolecular Sciences

Cordeiro, Rodrigo M.; Yusupov, Maksudbek; Razzokov, Jamoliddin; Bogaerts, Annemie

doi:10.1021/acs.jpcb.9b08172

Cited by 17 publications

(8 citation statements)

References 52 publications

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“…The average coordination number of the nitrite ion in water was calculated. A very recent study by Cordeiro et al 39 presented a systematic development of molecular mechanical models for both nitrate and nitrite ions and their oxyacids and described the solvation and ion-pairing properties through classical simulations. In particular, the model captured experimentally supported properties such as the enrichment of HNO 3 at the water surface and also the surface-induced ion pairing of NaNO 2 .…”

Section: Introduction Aqueous Solutions Of Nitrite (Nomentioning

confidence: 99%

Solvation Shell of the Nitrite Ion in Water: An Ab Initio Molecular Dynamics Study

Yadav

Chandra

2020

J. Phys. Chem. B

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We performed ab initio molecular dynamics simulation of a nitrite ion in water to investigate the structural and dynamical properties of its hydration shell. The nitrite ion is found to exhibit strong asymmetry toward hydrogen bonding due to its two different types of hydrogen bond acceptor sites. This difference is better captured through further partitioning of the hydration shell into its proximal and distal regions. The frequency shifts of the stretch modes of hydration shell water reveal that the nitrogen site forms a stronger hydrogen bond than its oxygen sites with the latter forming hydrogen bonds, which are similar in strength to that between a pair of water molecules. The escape dynamics of water from the hydration shell is found to be rather slow, which seems to classify the nitrite ion as a structure-maker. However, the dynamics of orientational and hydrogen bond relaxation reveal a faster mobility of water molecules in the hydration shell than bulk water in spite of strong ion–water interactions. It is found that the nitrite ion can hold water molecules in its solvation shell and still make them rotate fast in its vicinity through switching of their hydrogen bonds between its nitrogen and oxygen acceptor sites. The dipole moment of the solute in water is also calculated in the present study.

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Section: Introduction Aqueous Solutions Of Nitrite (Nomentioning

confidence: 99%

Solvation Shell of the Nitrite Ion in Water: An Ab Initio Molecular Dynamics Study

Yadav

Chandra

2020

J. Phys. Chem. B

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“…We carried out MD simulations, in order to study the transport capability of the following RONS from vacuum into the water bulk: H 2 O 2 , HO 2 , OH, O 3 , NO, NO 2 , trans -HNO 2 , cis -HNO 2 , HNO 3 , trans-perp -ONOOH, cis-perp -ONOOH (throughout the main text, tp for trans-perp and cp for cis-perp notations are used) and N 2 O 4 . GROMACS program package (GPU version) [ 41 ] was employed to perform MD simulations by introducing GROMOS united atom force field parameters for RONS developed in the literature [ 42 , 43 , 44 , 45 ]. Initially, the cubic box was filled with an SPC water model [ 46 ] by making use of Packmol software [ 47 ].…”

Section: Simulation Setupmentioning

confidence: 99%

“…Moreover, it is quite complex to mimic a real condition in computer simulations due to the large number of particles in model systems. However, the parameters of the current model system are sufficient to study the permeation process of molecules into the liquid content [ 43 ].…”

Section: Simulation Setupmentioning

confidence: 99%

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Mechanistic Insight into Permeation of Plasma-Generated Species from Vacuum into Water Bulk

Razzokov

Fazliev

Kodirov

et al. 2022

IJMS

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Due to their potential benefits, cold atmospheric plasmas (CAPs), as biotechnological tools, have been used for various purposes, especially in medical and agricultural applications. The main effect of CAP is associated with reactive oxygen and nitrogen species (RONS). In order to deliver these RONS to the target, direct or indirect treatment approaches have been employed. The indirect method is put into practice via plasma-activated water (PAW). Despite many studies being available in the field, the permeation mechanisms of RONS into water at the molecular level still remain elusive. Here, we performed molecular dynamics simulations to study the permeation of RONS from vacuum into the water interface and bulk. The calculated free energy profiles unravel the most favourable accumulation positions of RONS. Our results, therefore, provide fundamental insights into PAW and RONS chemistry to increase the efficiency of PAW in biological applications.

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“…The parameters of CER, FFA, and CHO were based on the study of Berger et al [ 39 ] and Höltje et al [ 40 ] The parameters of 5α‐CH were derived from the study reported by Neto and Cordeiro. [ 41 ] The RONS parameters were obtained from the studies reported in References [42–45]. It is noted that HNO 2 has two configurations, that is, trans ‐HONO and cis ‐HONO, and both of them were studied in this study.…”

Section: Computer Simulationsmentioning

confidence: 99%

The penetration of reactive oxygen and nitrogen species across the stratum corneum

Duan

Yusupov

et al. 2020

Plasma Processes & Polymers

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The penetration of reactive oxygen and nitrogen species (RONS) across the stratum corneum (SC) is a necessary and crucial process in many skin-related plasma medical applications. To gain more insights into this penetration behavior, we combined experimental measurements of the permeability of dry and moist SC layers with computer simulations of model lipid membranes. We measured the permeation of relatively stable molecules, which are typically generated by plasma, namely H 2 O 2 , NO 3 − , and NO 2 −. Furthermore, we calculated the permeation free energy profiles of the major plasma-generated RONS and their derivatives (i.e., H 2 O 2 , OH, HO 2 , O 2 , O 3 , NO, NO 2 , N 2 O 4 , HNO 2 , HNO 3 , NO 2 − , and NO 3 −) across native and oxidized SC lipid bilayers, to understand the mechanisms of RONS permeation across the SC. Our results indicate that hydrophobic RONS (i.e., NO, NO 2 , O 2 , O 3 , and N 2 O 4) can translocate more easily across the SC lipid bilayer than hydrophilic RONS (i.e., H 2 O 2 , OH, HO 2 , HNO 2 , and HNO 3) and ions (i.e., NO 2 − and NO 3 −) that experience much higher permeation barriers. The permeability of RONS through the SC skin lipids is enhanced when the skin is moist and the lipids are oxidized. These findings may help to understand the underlying mechanisms of plasma interaction with a biomaterial and to optimize the environmental parameters in practice in plasma medical applications.

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Parametrization and Molecular Dynamics Simulations of Nitrogen Oxyanions and Oxyacids for Applications in Atmospheric and Biomolecular Sciences

Cited by 17 publications

References 52 publications

Solvation Shell of the Nitrite Ion in Water: An Ab Initio Molecular Dynamics Study

Solvation Shell of the Nitrite Ion in Water: An Ab Initio Molecular Dynamics Study

Mechanistic Insight into Permeation of Plasma-Generated Species from Vacuum into Water Bulk

The penetration of reactive oxygen and nitrogen species across the stratum corneum

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