Average energy relaxation and rearrangement of solute-solvent radial distribution function in solvation dynamics: A connection between spectroscopic results and RISM theory

2001 ◽  
Vol 90 (1-3) ◽  
pp. 251-260 ◽  
Author(s):  
Katsura Nishiyama ◽  
Fumio Hirata ◽  
Tadashi Okada
2020 ◽  
Author(s):  
Bruna Nery Martins ◽  
Allane C. C. Rodrigues ◽  
Arsênio P. V. Neto ◽  
Ademir J. Camargo ◽  
Heibbe C. B. de Oliveira

Norepinephrine, synthesized from tyrosine, is a neurotransmitter of sympathetic post-ganglion neurons. Norepinephrine regulates many critical functions which include attention, memory, learning and cardiovascular functions. This neurotransmitter has several pharmacological uses, such as adrenergic stimulants, widely used in the treatment of hypertension, cardiac surgery and in myocardial infarction. It is extremely important to study the interaction between drugs and water molecules, for a better understanding of absorption, transport and biological action. Within this context, the Car-Parrinello Molecular Dynamics, by treating the solvent explicitly, becomes ideal for the study of solvated media. In this sense, the objective of this work is to analyze the effects of aqueous solvation on the geometric and electronic parameters of norepinephrine using the Molecular Dynamics of Car-Parrinelo. The solvation dynamics was performed using the CPMD program package (version 4.1). The Radial Distribution Function of the hydrogen and oxygen atoms of the water molecules in the first solvation shell were performed for the O1, O2, O3, N7, H4, H5, H6, H8 and H9 atoms of the norepinephrine. The Radial Distribution Function analyzes indicate that most sites have a well-defined peak (N7, O1, O3, H4, H5 and H6). For the O2, H8 e H9 atoms, there are no well-defined peaks, suggesting that these sites do not interact with the atoms of the water molecules, or even the possibility of intra-molecular interactions. These criteria were considered for the next stages of this work, which are already being carried out, and they are analyzes of possible interactions of hydrogen with these sites.


The differential cross-section and the average energy loss of 45°K neutrons for scattering by liquid helium have been measured at angles of scatter near 0 and 180° and for liquid temperatures from 1∙6 to 5∙2°K. From these data the second moments of the radial distribution function and the zero-angle cross-sections have been calculated. The latter are close to those given by the theory of density fluctuations in a liquid. The energy transfers cannot be explained in the absence of a liquid model. The backward scattering can be explained as either a free atom process or one in which phonons are excited. Data on the scattering of 45°K neutrons by the saturated helium vapour at 4∙2°K are given and it is concluded that the moments of the radial distribution function are larger for the gas than the liquid.


Author(s):  
Jurica Novak ◽  
Maria A. Grishina ◽  
Vladimir A. Potemkin

: In this letter the newly introduced approach based on the radial distribution function (RDF) weighted by the number of va-lence shell electrons is applied for a series of HIV-1 protease enzyme and its complexes with inhibitors to evaluate the influ-ence of hydrogen atoms on the performance of the model. The multiple linear regression method was used for the selection of the relevant descriptors. Two groups of residues having dominant contribution to the RDF descriptor are identified as relevant for the inhibition. In the first group are residues like Arg8, Asp25, Thr26, Gly27 and Asp29, which establish direct interaction with the inhibitor, while the second group consists of the amino acids at the interface of the two homodimer sub-units or with the solvent. The crucial motif pointed out by our approach as the most important for inhibition of the enzyme’s activity and present in all inhibitors is hydroxyl group that establish hydrogen bond with Asp25 side chain. Additionally, the comparison to the model without hydrogen showed that both models are of similar quality, but the downside of the current model is the need for the determination of residues’ protonation states.


2008 ◽  
Vol 47-50 ◽  
pp. 375-378 ◽  
Author(s):  
Zheng Han Hong ◽  
Shun Fa Hwang ◽  
Te Hua Fang

The mixing situation of Co atoms implanting onto Cu(001) substrate is investigated with regard to incident energy and substrate temperature by molecular dynamics. The results indicate that higher substrate temperature and/or incident energy will result in higher intermixing between the incident atoms and the substrate atoms. Furthermore, the value of the first peak of the radial distribution function (RDF) becomes lower and wider for the Co-Cu system as the substrate temperature and/or incident energy are increased.


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