Progressive Hydrophobicity of Fluorobenzenes

Kumar, Anuj; Mahato, Jaladhar; Dixit, Manasvi; Patwari, G. Naresh

doi:10.1021/acs.jpcb.9b08057

Cited by 8 publications

(7 citation statements)

References 47 publications

(66 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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“…However, in the field of computer aided molecular design of small molecules, usually high-level quantum mechanics calculations are performed to assess the strength of stacking interactions of aromatic heterocycles. , Nevertheless, recent work has revealed a direct correlation of vacuum stacking interactions and the solvation free energy of heteroaromatics . Furthermore, the substitutions on a heteroaromatic core substantially influence the electrostatic properties and alter not only the strength and favored stacking geometry but also the solvation properties . Including hydration properties in computational approaches has been a hurdle in structure-based drug design .…”

Section: Introductionmentioning

confidence: 99%

“…19 Furthermore, the substitutions on a heteroaromatic core substantially influence the electrostatic properties and alter not only the strength and favored stacking geometry but also the solvation properties. 20 Including hydration properties in computational approaches has been a hurdle in structurebased drug design. 21 Programs like GIST, 22,23 SZMAP, 24 design.…”

Section: ■ Introductionmentioning

confidence: 99%

STACKED – Solvation Theory of Aromatic Complexes as Key for Estimating Drug Binding

Loeffler

Fernández‐Quintero

Schauperl

et al. 2020

J. Chem. Inf. Model.

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The use of fragments to biophysically characterize a protein binding pocket and determine the strengths of certain interactions is a computationally and experimentally commonly applied approach. Almost all drug like molecules contain at least one aromatic moiety forming stacking interactions in the binding pocket. In computational drug design, the strength of stacking and the resulting optimization of the aromatic core or moiety is usually calculated using high level quantum mechanical approaches. However, as these calculations are performed in a vacuum, solvation properties are neglected. We close this gap by using Grid Inhomogeneous Solvation Theory (GIST) to describe the properties of individual heteroaromatics and complexes and thereby estimate the desolvation penalty. In our study, we investigated the solvation free energies of heteroaromatics frequently occurring in drug design projects in complex with truncated side chains of phenylalanine, tyrosine, and tryptophan. Furthermore, we investigated the properties of drug-fragments crystallized in a fragment-based lead optimization approach investigating PDE-10-A. We do not only find good correlation for the estimated desolvation penalty and the experimental binding free energy, but our calculations also allow us to predict prominent interaction sites. We highlight the importance of including the desolvation penalty of the respective heteroaromatics in stacked complexes to explain the gain or loss in affinity of potential lead compounds.

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“…In our framework, the interactions governing solvent–solvent, solvent–solute, and solute–solute dynamics are considered to be pairwise additive, encompassing both Lennard-Jones and Columbic components. Complete details of methodology and simulation protocols can be found in our previous work. , The PMF are extensively used to determine the stability of the contact pair, solvent-assisted pair, solvent-shared pair, and solvent-separated pair. − ,− The computation of the ion pair’s PMF, denoted as W ( r ), within the solvent milieu is achievable through the approach, which has been discussed extensively in our previous work and defined as − W ( r ) = prefix− ∫ r 0 r ′ normalΔ F ( r ′ ) normald r ′ + 2 k B T ln r r 0 …”

Section: Methods and Computational Detailsmentioning

confidence: 99%

“…The potentials of mean force (PMF) has been extensively utilized to unveil the ion pairing within ILs in aqueous solutions as well as ion pairing in mixed polar mixtures. − Notably, the structural and dynamic attributes of water-alkyl-3-methylimidazolium IL mixtures exhibit dependence on both anion hydrophobicity and cation chain length . Meanwhile, Chen et al have extensively employed molecular force fields to simulate both the crystalline and liquid states of [BMIM]Cl as well as its binary mixtures with ethanol, shedding light on their structural characteristics.…”

Section: Introductionmentioning

confidence: 99%

Ionic Pairing and Selective Solvation of Butylmethylimidazolium Chloride Ion Pairs in DMSO–Water Mixtures: A Comprehensive Examination via Molecular Dynamics Simulations and Potentials of Mean Force Analysis

Dixit,

Hajari,

Meti

et al. 2024

J. Phys. Chem. B

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Ionic liquids (ILs) with dimethyl sulfoxide (DMSO) and water act as a promising solvent medium for the dissolution of cellulose in an efficient manner. To develop a proper solvent system, it is really important to understand the thermodynamics of the molecular solutions consisting of ILs, DMSO, and water. The ion-pairing propensity of the ILs in the presence of DMSO and water plays a crucial role in governing the property of the solvent mixtures. Employing all-atom molecular dynamics simulations, we estimate the potentials of mean force between BMIM + and Cl − ions in DMSO−water mixtures. Analysis reveals a significant increase in the thermodynamic stability of both contact ion pair (CIP) and solvent-assisted ion pair (SAIP) states with a rising DMSO mole fraction. Thermodynamic assessments highlight the entropic stabilization of CIP states and SAIP states in pure water, in DMSO−water mixtures, and in pure DMSO. The structural analysis reveals that in comparison to the DMSO local density, the local water density is relatively very high around ion pairs, more specifically in the solvation shell of a chloride ion. Preferential binding coefficients also consistently indicate exclusion of DMSO from the ion pair in DMSO−water mixtures. To enhance our understanding regarding the solvent molecules kinetics around the ion pairs, the survival probabilities of DMSO and water are computed. The calculations reveal that the water molecules prefer a prolonged stay in the solvation shell of Cl − ions.

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Progressive Hydrophobicity of Fluorobenzenes

Cited by 8 publications

References 47 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

STACKED – Solvation Theory of Aromatic Complexes as Key for Estimating Drug Binding

Ionic Pairing and Selective Solvation of Butylmethylimidazolium Chloride Ion Pairs in DMSO–Water Mixtures: A Comprehensive Examination via Molecular Dynamics Simulations and Potentials of Mean Force Analysis

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