Thermodynamics of site-specific small molecular ion interactions with DNA duplex: a molecular dynamics study

Ghosh, Soumadwip; Dixit, Manasvi; Chakrabarti, Ramananda

doi:10.1080/08927022.2015.1085123

Cited by 7 publications

(8 citation statements)

References 64 publications

(78 reference statements)

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“…Although the encountering of end groups can be observed with a certain fraction, it is not sufficient to determine if the encountered end groups form a stable physical junction or cluster. To assess the stability of clusters, potentials of mean force (PMFs) are commonly employed. ,,− Hence, we performed calculations of the PMFs between the terminal groups employing the following equation W ( r ) = prefix− k normalB T log ( g false( r false) ) where k B denotes the Boltzmann constant in kJ mol –1 /K, T represents the system’s temperature, and g ( r ) corresponds to the RDF between the terminal groups. Figure illustrates the PMFs between the two terminal groups, displayed as a function of the distance.…”

Section: Resultsmentioning

confidence: 99%

Role of Terminal Groups of cis-1,4-Polyisoprene Chains in the Formation of Physical Junction Points in Natural Rubber

Dixit

Taniguchi

2023

Biomacromolecules

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The terminal structures of cis-1,4-polyisoprene (PI) chains play a vital role in the excellent comprehensive performance of Hevea natural rubber (NR) with properties such as high toughness, tear-resistance, and wet skid resistance. The cis-1,4polyisoprene chain constituting NR exhibits a distinct composition of terminal groups comprising two distinct types, namely, the ω and α terminal groups. The structures of the ω terminal [dimethyl allyl (DMA)-(trans-1,4-isoprene) 2 ] and six kinds of α end groups of the polymer chain of NR have been explored by utilizing a newly developed 2D NMR method. In the present work, we examine different kinds of PI melt systems, and we choose various combinations of terminal groups: Hydrogen, one DMA unit with two trans isoprene units as ω end groups and ester-terminated isopentene (α1), hydroxy-terminated isopentene (α2), ester-terminated isobutane (α3), hydroxy-terminated isobutane (α4), esterterminated 1,4-cis-isoprene (α5), and hydroxy-terminated 1,4-cis-isoprene (α6), i.e., H PI H (PI 0 )−pure PI (Hydrogen terminal), ω PI α1 (PI I ), ω PI α2 (PI II ), ω PI α3 (PI III ), ω PI α4 (PI IV ), ω PI α5 (PI V ), and ω PI α6 (PI VI ). We evaluated dynamic and static properties of PI chains such as the end-to-end vector autocorrelation function (C(t)), its average relaxation time (τ), end-to-end distance (R ee ), and radius of gyration (R g ). We also estimated the diffusion coefficients of polyisoprene chains and pair correlation functions [radial distribution functions (RDFs)], potentials of mean force (PMFs) in between end residues, and survival probability (P(τ)) of end groups around the end group by analyzing the equilibrated trajectories of full-atom MD simulations. As per the examination of C(t), rotational relaxation time τ, and RDFs, we discovered that the existence of a strong hydrogen bond in α2−α2, α4−α4, and α6−α6 residues makes the dynamics of hydroxy-terminated polyisoprene chains in ω PI α2,α4,α6 melt systems slower. From the analyses of RDFs and PMFs (W(r)), the association between [α2]−[α2], [α4]−[α4], and [α6]−[α6] terminals in ω PI α2,α4,α6 melt systems is significantly stronger than in [ISO]−[ISO] [Hydrogen terminated 1,4-cis-isoprene:(ISO)] in H PI H and ω−ω, [α1]−[α1], [α3]−[α3], and [α5]− [α5] in ω PI α1,α3,α5 systems. We quantified the fraction of cluster formation of terminal groups of a given size in the seven PI melt systems by employing the criteria of PMFs. It is revealed that no stable cluster exists in the H PI H , ω PI α1 , ω PI α3 , and ω PI α5 melt systems. Conversely, in the ω PI α2 , ω PI α4 , and ω PI α6 systems, we perceived stable clusters of [(α2) p ] [(α4) p ] and [(α6) p ] end groups where p (2 ≤ x ≤ 6). These stable clusters validate the presence of physical junction points in between hydroxy-terminated polyisoprene chains through their α2, α4, and α6 terminals. These physical junction points might be crucial for superior properties of NR such as high toughness, crack growth resistance, and strain-induced crystallization.

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Section: Resultsmentioning

confidence: 99%

Role of Terminal Groups of cis-1,4-Polyisoprene Chains in the Formation of Physical Junction Points in Natural Rubber

Dixit

Taniguchi

2023

Biomacromolecules

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Section: Resultsmentioning

confidence: 99%

“…Moreover, in order to comprehensively analyze the micro information on the deposition sites, the binding conformation and the binding energy of different molecules in clusters deposited on different molecules in the sedimentary layer, 47−49 and the potential of mean force (PMF) was calculated from the micro-nano scale. 50,51 The PMF was defined as the average free energy between the particles in reaction coordinate. 52 When the PMF was negative, it indicated that the intermolecular binding reaction could spontaneously be carried out, and the binding state was stable.…”

Section: The Micro Mechanism Of Selective Deposition For Waxy Crude O...mentioning

confidence: 99%

Molecular Dynamics Simulation of Waxy Crude Oil Multiphase System Depositing and Sticking on Pipeline Inner Walls and the Micro Influence Mechanism of Surface Physical–Chemical Characteristics

et al. 2021

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For ensuring the safe and stable operation of waxy crude oil pipeline transportation, in this research, the molecular dynamics model was established to characterize the deposition and wall sticking behavior of waxy crude oil multiphase system pipeline transportation. The equal density interpolation fitting method was proposed to determine the wall contact angle of simulation results. Through verification, the error between the simulation results and the experimental results measured by Dos Santos et al. (2006) was less than 5%, which showed that the established model was accurate and reliable. Using the established model, the deposition and wall sticking behavior of waxy crude oil nucleated clusters was simulated. It was found that the nucleated clusters would first adhere to the wall surface to form the solidified oil layer. Then, the wax and asphaltene molecules would diffuse to the deposit layer, and the oil molecules in the solidified oil layer reverse diffused to the direction of the oil flow. With the adhering and spreading degree of clusters on the wall surface increasing, the deposit layer gradually aged, and the gelled deposit layer with a higher density and hardness would form. On this basis, the micro influence mechanism of the surface free energy was studied. It was found that the higher the surface free energy, the more hydrophilic the pipeline wall was, and the higher the adhesion degree would be. Moreover, based on the ABF sampling and the potential of mean force calculations, the selective deposition process of waxy crude oil deposited on the sedimentary layer was studied. The micro information on the deposition sites, the binding conformation, and the binding energy of different molecules in clusters deposited on different molecules in sedimentary layer were analyzed. The investigations in this study could provide theoretical support for paraffin removal and control, which could ensure the safe and stable operation of the waxy crude oil production system.

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“…First, the lifetime of a hydrogen bond is calculated from the rate constants of hydrogen bond breaking and re-forming, and its distribution is converted into an autocorrelation function. Second, the autocorrelation function is fitted exponentially and then integrated to obtain the hydrogen bond relaxation time 41 . The calculated kinetic and thermodynamic parameters are shown in Table 2.…”

Section: Resultsmentioning

confidence: 99%

In Silico Characterization of the Binding Modes of Surfactants with Bovine Serum Albumin

Nnyigide

Lee

Hyun

2019

Sci Rep

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The binding interactions of the surfactants: anionic sodium dodecyl sulphate (SDS), cationic cetyltrimethylammonium bromide (CTAB), non-ionic octyl glucoside (OG), and zwitterionic 3-[Hexadecyl(dimethyl)ammonio]-1-propanesulfonate (HPS), with bovine serum albumin (BSA) were investigated by computer simulation. The results disclosed that the surfactants bound stably between hydrophobic subdomain IIA and IIIA where tryptophan-213 residue, an important intrinsic fluorophore in BSA is housed. The interactions of the surfactants with the BSA were electrostatic and hydrophobic interactions. The head-groups of SDS, HPS and OG formed hydrogen bonds with the BSA, while that of CTAB was shielded from intermolecular hydrogen-bonding due to intervening methyl groups. Subsequently, molecular dynamics (MD) simulation of the protein-surfactant complexes revealed that hydrogen bonds formed by OG were stronger than those of SDS and HPS. However, the decomposed force-field energies showed that OG had the least interaction energy with the BSA. In addition to MD simulation, it was found by density functional theory (DFT) that the differences in the coulomb interaction energies can be attributed to charge distribution in the surfactants. Overall, free energies calculated by linear interaction energy (LIE) proved that the binding of each surfactant was dominated by differences between van der Waals interactions in bound and free states.

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Thermodynamics of site-specific small molecular ion interactions with DNA duplex: a molecular dynamics study

Cited by 7 publications

References 64 publications

Role of Terminal Groups of cis-1,4-Polyisoprene Chains in the Formation of Physical Junction Points in Natural Rubber

Role of Terminal Groups of cis-1,4-Polyisoprene Chains in the Formation of Physical Junction Points in Natural Rubber

Molecular Dynamics Simulation of Waxy Crude Oil Multiphase System Depositing and Sticking on Pipeline Inner Walls and the Micro Influence Mechanism of Surface Physical–Chemical Characteristics

In Silico Characterization of the Binding Modes of Surfactants with Bovine Serum Albumin

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