<i>n</i>-Octanol

Shallard-Brown, Howard A.; Watkin, David J.; Cowley, Andrew R.

doi:10.1107/s1600536804032775

Cited by 16 publications

(24 citation statements)

References 6 publications

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“…In the latter, the long-axes orientations of the molecules can then form a zigzag pattern, as obtained in Figure 6, for 1-octanol and 1-nonanol, or a parallel arrangement. Experimentally 1-octanol 38 at 150 K and 1-pentanol 37 at 183 K exhibit a much stronger zigzag pattern than that displayed in Figure 6. Besides the difference in the temperatures, a plausible reason for the discrepancy is that the cubic shape of the simulation box suppresses larger tilting between the layers.…”

Section: Results and Discussionmentioning

confidence: 76%

Refinement of the OPLSAA Force-Field for Liquid Alcohols

Zangi

2018

ACS Omega

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We employ the popular all-atom optimized potential for liquid simulations, OPLSAA, force-field to model 17 different alcohols in the liquid state. Using the standard simulation protocol for few hundred nanosecond time periods, we find that 1-octanol, 1-nonanol, and 1-decanol undergo spontaneous transition to a crystalline state at temperatures which are 35–55 K higher than the experimental melting temperatures. Nevertheless, the crystal structures obtained from the simulations are very similar to those determined by X-ray powder diffraction data for several n -alcohols. Although some degree of deviations from the experimental freezing points are to be expected, for 1-nonanol and 1-decanol, the elevation of the freezing temperature warrants special attention because at room temperature, these alcohols are liquids; however, if simulated by the OPLSAA force-field, they will crystallize. This behavior is likely a consequence of exaggerated attractive interactions between the alkane chains of the alcohols. To circumvent this problem, we combined the OPLSAA model with the L-OPLS force-field. We adopted the L-OPLS parameters to model the hydrocarbon tail of the alcohols, whereas the hydroxyl head group remained as in the original OPLSAA force-field. The resulting alcohols stayed in the liquid state at temperatures above their experimental melting points, thus, resolving the enhanced freezing observed with the OPLSAA force-field. In fact, the mixed-model alcohols did not exhibit any spontaneous freezing even at temperatures much lower than the experimental values. However, a series of simulations in which these mixed-OPLSAA alcohols started from a coexistence configuration of the liquid and solid phases resulted in freezing transitions at temperatures 14–25 K lower than the experimental values, confirming the validity of the proposed model. For all of the other alcohols, the mixed model yields results very similar to the OPLSAA force-field and is in good agreement with the experimental data. Thus, for simulating alcohols in the liquid phase, the mixed-OPLSAA model is necessary for large (7 carbons and above) hydrocarbon chains.

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Section: Results and Discussionmentioning

confidence: 76%

Refinement of the OPLSAA Force-Field for Liquid Alcohols

Zangi

2018

ACS Omega

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“…The alkyl chain of the benzimidazole moiety is unfolded. The octan-1-ol solvent molecule also has an unfolded chain, as is observed in the crystal structure of octan-1-ol (Shallard-Brown et al, 2005). Other octan-1-ol solvates and inclusion compounds in which octan-1-ol is a guest exhibit bent or S-shaped octanol struc- Normalized emission spectra of (3) in ethanol.…”

Section: Synthesis and Spectroscopymentioning

confidence: 78%

Synthesis and characterization of a novel long-alkyl-chain ester-substituted benzimidazole gelator and its octan-1-ol solvate

et al. 2017

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The synthesis of a novel benzimidazole derivative with a long-chain-ester substituent, namely methyl 8-[4-(1H-benzimidazol-2-yl)phenoxy]octanoate, (3), is reported. Ester (3) shows evidence of aggregation in solution and weak gelation ability with toluene. The octan-1-ol solvate, methyl 8-[4-(1H-benzimidazol-2-yl)phenoxy]octanoate octan-1-ol monosolvate, CHNO·CHO, (4), exhibits a four-molecule hydrogen-bonded motif in the solid state, with N-H...O hydrogen bonds between benzimidazole molecules and O-H...N hydrogen bonds between the octan-1-ol solvent molecules and the benzimidazole unit. The alkyl chains of the ester and the octan-1-ol molecules are in unfolded conformations. The phenylene ring is canted by 10.27 (6)° from the plane of the benzimidazole ring system. H...C contacts make up 20.7% of the Hirshfeld surface coverage. Weak C-H...π interactions involving the benzimidazole alkyl chain and three aromatic rings are observed.

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“…The X-ray 6 and 1 H NMR data 7 point to nearly spheric arrangements of the hydroxyls. Molecular dynamics simulations 8 result in linear networked chains of H-bonded hydroxyls, which look like remnants of those seen by X-ray crystallography 9 at 150K. Spectroscopic data indicate that water in saturated 1-octanol does not disturb the H-bonding of 1-octanol molecules present in neat 1-octanol and forms pockets maintaining a similar structure as bulk water in the proximity of hydroxyls.…”

Section: Introductionmentioning

confidence: 82%

Structural Determinants of Drug Partitioning in n-Hexadecane/Water System

Natesan

Wang

Lukáčová

et al. 2013

J. Chem. Inf. Model.

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Surrogate phases have been widely used as correlates for modeling transport and partitioning of drugs in biological systems, taking advantage of chemical similarity between the surrogate and the phospholipid bilayer as the elementary unit of biological phases, which is responsible for most of transport and partitioning. Solvation in strata of the phospholipid bilayer is an important drug characteristics because it affects the rates of absorption and distribution, as well as the interactions with the membrane proteins having the binding sites located inside the bilayer. The bilayer core can be emulated by n-hexadecane (C16), and the headgroup stratum is often considered a hydrophilic phase because of the high water content. Therefore, we tested the hypothesis that the C16/water partition coefficients (P) can predict the bilayer locations of drugs and other small molecules better than other surrogate systems. Altogether 514 PC16/W values for nonionizable (458) and completely ionized (56) compounds were collected from the literature or measured, when necessary. With the intent to create a fragment-based prediction system, the PC16/W values were factorized into the fragment solvation parameters (f) and correction factors based on the ClogP fragmentation scheme. A script for the PC16/W prediction using the ClogP output is provided. To further expand the prediction system and reveal solvation differences, the fC16/W values were correlated with their more widely available counterparts for the 1-octanol/water system (O/W) using solvatochromic parameters. The analysis for 50 compounds with known bilayer location shows that the available and predicted PC16/W and PO/W values alone or the PC16/O values representing their ratio do not satisfactorily predict the preference for drug accumulation in bilayer strata. These observations indicate that the headgroups stratum, albeit well hydrated, does not have solvation characteristics similar to water and is also poorly described by the O/W partition characteristics.

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n-Octanol

Abstract: The structure of n‐octanol, C8H17OH, at 150 K consists of infinite hydrogen‐bonded chains forming a ribbon parallel to the b axis.

Cited by 16 publications

References 6 publications

Refinement of the OPLSAA Force-Field for Liquid Alcohols

Refinement of the OPLSAA Force-Field for Liquid Alcohols

Synthesis and characterization of a novel long-alkyl-chain ester-substituted benzimidazole gelator and its octan-1-ol solvate

Structural Determinants of Drug Partitioning in n-Hexadecane/Water System

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