Size and Structure of Empty and Filled Nanocontainer Based on Peptide Dendrimer with Histidine Spacers at Different pH

Novel peptide dendrimer with Lys-2His repeating units was recently synthesized, studied by NMR (Molecules, 2019, 24, 2481) and tested as a nanocontainer for siRNA delivery (Int. J. Mol. Sci., 2020, 21, 3138). Histidine amino acid residues were inserted in the spacers of this dendrimer. Increase of their charge with a pH decrease turns a surface-charged dendrimer into a volume-charged one and should change all properties. In this paper, the molecular dynamics simulation method was applied to compare the properties of the dendrimer in water with explicit counterions at two different pHs (at normal pH with neutral histidines and at low pH with fully protonated histidines) in a wide interval of temperatures. We obtained that the dendrimer at low pH has essentially larger size and size fluctuations. The electrostatic properties of the dendrimers are different but they are in good agreement with the theoretical soft sphere model and practically do not depend on temperature. We have shown that the effect of pairing of side imidazole groups is much stronger in the dendrimer with neutral histidines than in the dendrimer with protonated histidines. We also demonstrated that the capacity of a nanocontainer based on this dendrimer with protonated histidines is significantly larger than that of a nanocontainer with neutral histidines.

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Separation of Diffusive Jump Motion and Trapped Motion of Atoms in a Glass Forming Process Via Molecular Dynamics Simulation

MRS Proceedings ◽

10.1557/proc-455-285 ◽

1996 ◽

Vol 455 ◽

Author(s):

J. Matsui ◽

M. Fujisaki ◽

T. Odagaki

Keyword(s):

Molecular Dynamics ◽

Md Simulation ◽

Peak Frequency ◽

Dynamics Simulation ◽

Forming Process ◽

Soft Sphere ◽

Glass Forming ◽

Two Peaks ◽

Dynamical Order ◽

Good Agreement

ABSTRACTWe have carried out the molecular dynamics (MD) simulation for a binary soft-sphere system and calculated the self part of the generalized susceptibility χs(q, ω) at various temperatures. At higher temperatures in liquid state, only one peak appears in the imaginary part of Xa, which tends to split into two peaks, the so-called α- and β- peaks, as the temperature is reduced. The temperature dependence of the peak frequency is well described by the Vogel-Fulcher law for the α- peak, and the peak frequency does not change much for the α- peak. We have also measured the trajectory volume of a tagged atom V(t), which is related to the dynamical order parameter, the “generalized capacity”, in structural glass transitions recently proposed by J. F. Douglas. These results show the transition temperature which is in good agreement with that determined by the trapping diffusion model.

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Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

ASME/JSME 2011 8th Thermal Engineering Joint Conference ◽

10.1115/ajtec2011-44457 ◽

2011 ◽

Author(s):

Toshihiro Kaneko ◽

Kenji Yasuoka ◽

Ayori Mitsutake ◽

Xiao Cheng Zeng

Keyword(s):

Molecular Dynamics ◽

Heat Capacity ◽

Transition Temperature ◽

Peak Position ◽

Temperature Curve ◽

Dynamics Simulation ◽

Lennard Jones ◽

Dynamics Simulations ◽

First Time ◽

Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

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The Structure and Crystallizing Process of NiAu Alloy: A Molecular Dynamics Simulation Method

Journal of Composites Science ◽

10.3390/jcs5010018 ◽

2021 ◽

Vol 5 (1) ◽

pp. 18

Author(s):

Dung Nguyen Trong ◽

Van Cao Long ◽

Ştefan Ţălu

Keyword(s):

Heating Rate ◽

Atomic Number ◽

Crystallization Process ◽

Amorphous State ◽

Simulation Method ◽

Dynamics Simulation ◽

Glass Temperature ◽

Structural Units ◽

The Common ◽

Moving Process

This paper studies the influence of factors such as heating rate, atomic number, temperature, and annealing time on the structure and the crystallization process of NiAu alloy. Increasing the heating rate leads to the moving process from the crystalline state to the amorphous state; increasing the temperature (T) also leads to a changing process into the liquid state; when the atomic number (N), and t increase, it leads to an increased crystalline process. As a result, the dependence between size (l) and atomic number (N), the total energy of the system (Etot) with N as l~N−1/3, and −Etot always creates a linear function of N, glass temperature (Tg) of the NiAu alloy, which is Tg = 600 K. During the study, the number of the structural units was determined by the Common Neighborhood Analysis (CNA) method, radial distribution function (RDF), size (l), and Etot. The result shows that the influencing factors to the structure of NiAu alloy are considerable.

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Femtosecond photoelectron spectroscopy of the I2− anion: A semiclassical molecular dynamics simulation method

The Journal of Chemical Physics ◽

10.1063/1.478263 ◽

1999 ◽

Vol 110 (8) ◽

pp. 3736-3747 ◽

Cited By ~ 63

Author(s):

Victor S. Batista ◽

Martin T. Zanni ◽

B. Jefferys Greenblatt ◽

Daniel M. Neumark ◽

William H. Miller

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Photoelectron Spectroscopy ◽

Simulation Method ◽

Dynamics Simulation

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PAMAM dendrimer: a pH-controlled nanosponge

Canadian Journal of Chemistry ◽

10.1139/cjc-2017-0244 ◽

2017 ◽

Vol 95 (9) ◽

pp. 991-998 ◽

Cited By ~ 6

Author(s):

Prabal K. Maiti

Keyword(s):

Accessible Surface Area ◽

Pamam Dendrimer ◽

Low Ph ◽

Dynamics Simulation ◽

Solvent Accessible Surface Area ◽

Water Molecules ◽

Accessible Volume ◽

Accessible Surface ◽

Solvent Accessible Surface ◽

Ph Controlled

Using fully atomistic molecular dynamics simulation that are several hundred nanoseconds long, we demonstrate the pH-controlled sponge action of PAMAM dendrimer. We show how at varying pH levels, the PAMAM dendrimer acts as a wet sponge; at neutral or low pH levels, the dendrimer expands noticeably and the interior of the dendrimer opens up to host several hundreds to thousands of water molecules depending on the generation number. Increasing the pH (i.e., going from low pH to high pH) leads to the collapse of the dendrimer size, thereby expelling the inner water, which mimics the ‘sponge’ action. As the dendrimer size swells up at a neutral pH or low pH due to the electrostatic repulsion between the primary and tertiary amines that are protonated at this pH, there is dramatic increase in the available solvent accessible surface area (SASA), as well as solvent accessible volume (SAV).

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Self-diffusion of lignite/water under different temperatures and pressure: A molecular dynamics study

Modern Physics Letters B ◽

10.1142/s021798491550253x ◽

2016 ◽

Vol 30 (01) ◽

pp. 1550253 ◽

Cited By ~ 2

Author(s):

Xinjian Liu ◽

Yu Jin ◽

Congliang Huang ◽

Jingfeng He ◽

Zhonghao Rao ◽

...

Keyword(s):

Molecular Dynamics ◽

Water System ◽

Simulation Method ◽

The Self ◽

Dynamics Simulation ◽

Low Rank ◽

Self Diffusion ◽

Change Mechanism ◽

Different Temperatures ◽

Temperature And Pressure

Temperature and pressure have direct and remarkable implications for drying and dewatering effect of low rank coals such as lignite. To understand the microenergy change mechanism of lignite, the molecular dynamics simulation method was performed to study the self-diffusion of lignite/water under different temperatures and pressure. The results showed that high temperature and high pressure can promote the diffusion of lignite/water system, which facilitates the drying and dewatering of lignite. The volume and density of lignite/water system will increase and decrease with temperature increasing, respectively. Though the pressure within simulation range can make lignite density increase, the increasing pressure showed a weak impact on variation of density.

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THE "FOLDING" BEHAVIORS OF HOMOPOLYMERS WITH ONE END FIXED

International Journal of Modern Physics B ◽

10.1142/s0217979204025294 ◽

2004 ◽

Vol 18 (15) ◽

pp. 2123-2139 ◽

Cited By ~ 4

Author(s):

BIN XUE ◽

JUN WANG ◽

WEI WANG

Keyword(s):

Molecular Dynamics ◽

Chain Length ◽

Conformational Changes ◽

Canonical Ensemble ◽

Interaction Strength ◽

Simulation Method ◽

Dynamics Simulation ◽

Radius Of Gyration ◽

Native Conformation ◽

Collapse Temperature

We study the "folding" behaviors of homopolymers with one end fixed. By using canonical ensemble molecular dynamics simulation method, we observe the conformational changes during folding processes. Long chains collapse to the helical nuclei, then regroup to helix from the free-end to form the compact conformations through the middle stages of helix-like coil and helix-like cone, while short chains do not apparently have the above mentioned middle stages. Through simulated annealing, the native conformation of homopolymer chain in our model is found to be helix. We show the relations between specific heat C v (T) and radius of gyration R g (T) as functions of temperature, chain length and the interaction strength, respectively. We find that these two quantities match well and can be combined to interpret the "folding" process of the homopolymer. It is found that the collapse temperature Tθ and the native-like folding temperature T f do not change with the chain length in our model, however the interaction strength affects the values of Tθ and T f .

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