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Hexadecane

Hexadecane is a saturated aliphatic hydrocarbon with the molecular formula C16H34.
It is a colorless, odorless liquid found naturally in crude oil and used as a solvent, lubricant, and fuel additive.
Hexadecane plays a role in various industrial and scientific applications, including chemical synthesis, materials science, and biofuel production.
Researchers can utilize PubCompare.ai to streamline their Hexadecane-related experimentation and identify the most effective and reproducible protocols from literature, pre-prints, and patents.
This innovative AI-powered tool helps optimize Hexadecane research by facilitating side-by-side comparisons of relevant methods, enhancing workflow efficiency and experimental outcomes.

Most cited protocols related to «Hexadecane»

For the lipid tails hexadecane
was chosen as a model compound for computing the charges. It is well-known
that partial atomic charges are conformation dependent52 but previous FFs have been parametrized from optimized
geometries. In order to address this issue, we performed a 10 ns long
MD simulation with pure hexadecane with FF parameters earlier derived
by our group.31 (link) After the simulation, 54
random conformations were extracted and used for computing the charges
which were then averaged over all conformations in order to obtain
a final set. In this way, we obtained Boltzmann-averaged charges over
an ensemble of conformations in a procedure equivalent to the one
used by Sonne et al.30 (link) We hope that by
averaging over an ensemble of conformations the effects of the conformational
dependence of partial charges are minimized. In computation of atomic
charges, a dielectric constant of 2.04 was used to mimic the dielectric
environment of the membrane’s hydrophobic part.
Atomic
charges for the lipid head group were obtained in a similar fashion
where 26 random conformations were chosen from a 20 ns long simulation
of an equilibrated bilayer (DMPC) with the same FF parameters used
in the initial simulation of hexadecane. A large part of the hydrophobic
parts of the lipids were then cut off in order to save CPU time and
the cropped lipids were placed in dielectric continuum with ε
= 78.4 in order to mimic the aqueous environment. Inclusion of solvent
effects results in a FF with implicitly polarized charges optimized
for condensed phase simulations. This has been proven to give reliable
results without any performance loss.53 (link)For each molecular conformation, the charges were computed
using
the restricted electrostatic potential approach54 (RESP) with the DFT method using the B3LYP exchange-correlation
functional55 −58 and the cc-pVTZ basis set.59 The electrostatic
potential was sampled with the Merz–Singh–Kollman scheme60 by single-point calculations and fitted during
the two-stage procedure developed by Cornell et al.61 All solvent effects were modeled by placing the molecule
in a polarizable continuum with different dielectric constant (see
above) with the IEFPCM continuum solvent model.62 ,63 The quantum mechanical calculations were performed with the Gaussian09
software package,64 and the RESP calculations
were performed with the Red software.65 (link) In subsequent molecular dynamics simulations, Coulombic 1–4
interactions were scaled by a factor of 0.8333.
The way the
atomic charges have been calculated and used in MD
simulations makes them compatible with the AMBER03 FF53 (link) and since the charges in all AMBER FFs are derived from
the RESP the lipid FF presented here is compatible with most members
of the AMBER FF family. This is of importance since there is a growing
interest in simulating membrane proteins in their native environment19 (link),66 (link) and also peptide partitioning in biological membranes.67 (link),68 (link) Ongoing work aims to clarify which AMBER biomolecular FFs that work
sufficiently well together with the current parameters. A preliminary
test of the compatibility of the lipid parameters and the AMBER03
FF is presented further down.
Boltzmann averaging over charges
introduces temperature dependency
on the charges and in order to see the impact of temperature, simulations
with different temperatures (298, 303, 310, 318, and 325 K) were performed
with hexadecane using the methodology described above. No explicit
temperature dependence could be found over this range of temperatures,
making the charges reliable and robust with respect to temperature,
at least within the interval tested here (data not shown).
Publication 2012
Amber Biopharmaceuticals Dimyristoylphosphatidylcholine Electrostatics factor A Head hexadecane Lipid A Lipids Membrane Proteins Peptides Respiratory Rate Solvents Tail Tissue, Membrane
Quantification of isobutyl acetate ester in engineered strains was performed as previously described with some modifications [27 (link)]. Engineered strains were pre-cultured in 5-mL aliquots in MGYH overnight and used to inoculate 10 mL modified MGY-glu medium in 50 mL Corning tubes as described in “Screening of KDC and ADH candidate enzymes” section. The yeast cultures were overlaid with 10 mL hexadecane (Sigma) to reduce evaporation of the acetate esters. The cultures were grown at 30 °C and 250 rpm in an orbital shaking incubator. Samples were taken to determine biomass, extracellular metabolites and production of higher alcohols and acetate esters. The amount of acetate esters dissolved in the hexadecane layer was determined using gas chromatography–mass spectrometry (GC–MS). The GC program was as follows: an initial temperature of 40 °C was maintained for 4 min, followed by ramping to 300 °C at a rate of 45 °C per min, where the temperature was held for 3 min. The injector temperature was held at 250 °C. The injection volume was 5 μL, injected at a 10:1 split ratio. Hydrogen was used as the carrier gas. The MS is a GCMS-QP2010S (Shimadzu). The ion source temperature was 200 °C, and the interface temperature was 250 °C. The solvent cut time was 2 min. The start m/z was 40, and the end m/z was 500. Mass spectra and retention times from samples were compared with authentic standards (Sigma).
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Publication 2018
Acetate Alcohols ARID1A protein, human Enzymes Esters Gas Chromatography-Mass Spectrometry hexadecane Hydrogen isobutyl acetate Mass Spectrometry Retention (Psychology) Solvents Strains Yeasts
For GC–MS analysis a protocol according to Weckwerth et al. was used (Weckwerth et al. 2004 (link)). Deep frozen plant material was ground to a fine powder using a mortar and pestle under constant adding of liquid nitrogen. About 45 mg of each replicate was transferred to pre-cooled reaction tubes. For the extraction process, 1 ml of ice cold extraction mixture (methanol:chloroform:water, 5:2:1, v:v:v) was subsequently added. Additionally, 10 μl of internal 13C6-Sorbitol standard were added into each tube. Tubes were vortexed for several seconds and incubated on ice for 8 min to achieve a good extraction. Hereupon, the samples were centrifuged for 4 min at 14,000×g, separating the soluble compounds from remaining cell structure components. For phase separation, the supernatant was then carried over into a new tube containing 500 μl deionized water and 200 μl chloroform. After 2 min of centrifugation at 14,000×g, the water/methanol phase, containing the polar metabolites, was separated from the subjacent chloroform phase and completely dried out overnight.
Samples were derivatised by dissolving the dried pellet in 20 μl of a 40 mg methoxyamine hydrochloride per 1 ml pyridine solution and incubation on a thermoshaker at 30 °C for 90 min. After adding of 80 μL of N-methyl-N-trimethylsilyltrifluoroacetamid (MSTFA), the mixture was again incubated at 37 °C for 30 min with strong shaking.
A solution of even-numbered alkanes (Decane C10, Dodecane C12, Tetradecane C14, Hexadecane C16, Octadecane C18, Eicosane C20, Docosane C22, Tetracosane C24, Hexacosane C26, Octacosane C28, Triacontane C30, Dotriacontane C32, Tetratriacontane C34, Hexatriacontane C36, Octatriacontane C38, Tetracontane C40) was spiked into the derivatized sample before GC–MS analysis in order to infer the retention time and create the retention index.
For LC–MS analysis, frozen plant leaf material was ground as for GC–MS sample preparation, followed by addition of 1 ml pre-chilled 80/20 v:v MeOH/H2O extraction solution containing each 1 μg of the internal standards Ampicillin and Chloramphenicol per 50 mg of fresh weight. Samples were hereupon centrifuged at 15,000×g for 15 min and the supernatant was placed into a new tube and completely dried out overnight. The resulting pellet was then dissolved in 100 μl of a 50/50 v:v MeOH/H2O solution and centrifuged again for 15 min at 20,000×g. The remaining supernatant was then filtered through a STAGE tip (Empore/Disk C18, diameter 47 mm) into a vial with a micro insert tip. Before analysis lipid components were removed by adding 500 µl of chloroform, centrifugation and separation of the non-polar-phase to avoid contamination of the ESI ion transfer capillary.
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Publication 2012
Alkanes Ampicillin Capillaries Cellular Structures Centrifugation Chloramphenicol Chloroform Cold Temperature decane DNA Replication docosane dotriacontane eicosane Empore Freezing Gas Chromatography-Mass Spectrometry hexadecane Lipids Methanol methoxyamine methoxyamine hydrochloride n-dodecane Neoplasm Metastasis Nitrogen octacosane octadecane octatriacontane PER1 protein, human Plant Leaves Plants Powder pyridine pyridine hydrochloride Retention (Psychology) Sorbitol Strains tetracosane tetradecane
Single channel recording of OmpG was similar to the previous study.50 (link) Briefly, experiments were performed in an apparatus containing two chambers separated by a 25 μm thick Teflon film. An aperture of approximately 100 μm diameter had been made near the center of the film with an electric spark. The aperture was pretreated with a hexadecane/pentane (10% v/v) solution before each chamber was filled with buffers as indicated specifically. An Ag/AgCl electrode was immersed in each chamber with the cis chamber grounded. 1,2-Diphytanoyl-sn-glycerol-3-phosphocholine (Avanti Polar Lipids, USA) dissolved in pentane (10mg/ml) was deposited on the surface of the buffer in both chambers and monolayers formed after the pentane evaporated. The lipid bilayer was formed by raising the liquid level up and down across the aperture. OmpG proteins (~1 nM, final concentration) were added to the cis chamber and +200mV was applied to facilitate OmpG insertion. After a single OmpG pore inserted, the applied voltage was lowered to 50 mV for recording. OmpG proteins inserted in the planar lipid bilayer bi-directionally with its extracellular loops located at either cis or trans side. After 10 min recording, the orientation of the OmpG pore in the lipid bilayer was determined by analyzing the asymmetrical gating pattern at positive and negative potentials.61 (link) Streptavidin or antibodies were added to the cis or trans chamber depending on the pore orientation and the solution was stirred for 10 s. We define a positive potential as the potential of the chamber where the extracellular loops were exposed to is positive. Current was amplified with an Axopatch 200B integrating patch clamp amplifier (Axon Instruments, Foster City, CA). Signals were filtered with a Bessel filter at 2 kHz (unless otherwise stated) and then acquired by a computer (sampling at 50 μs) after digitization with a Digidata 1320A/D board (Axon Instruments).
Publication 2015
Antibodies Axon Buffers Electricity hexadecane Lanugo Lipid Bilayers Lipids pentane Proteins sn-glycerol-3-phosphocholine Streptavidin Teflon
The main focus of the parametrization
procedure has been on the hydrophobic tails of the lipids, since these
parameters were previously shown to have strong influence on simulated
properties of bilayers, and the partial atomic charges for the whole
lipid. As model compounds for the hydrophobic tails, a range of n-alkanes has been chosen (hexane to hexadecane). The assumption
that the hydrophobic core behaves similar to a bulk alkane liquid
has proven to be valid a number of times.13 (link),22 (link),23 ,31 (link),35 (link),49 If the fitting is done
simultaneously for a series of alkanes, the results are generally
better.49 Furthermore, studies on NMR relaxation
rates have shown that the hydrophobic part of the lipid bilayer behaves
similar to bulk alkane solutions.50 (link)The following potential energy function was chosen for this work which is a standard form for FFs like AMBER,
CHARMM, and GROMOS. As a starting point for our parametrization, we
took parameters of the CHARMM36 (C36) FF.27 (link) Parameters for all covalent bonds and angles as well as LJ and torsional
parameters for the lipid head group were taken from the FF described
by Klauda et al.27 (link) We then derived new
parameters (as described in detail below): partial atomic charges
for the whole lipid and LJ and torsion parameters describing the lipid
tails.
We started our parametrization by computing partial atomic
charges
for typical configurations of alkanes and averaging over these configurations.
Because of the known difficulties of reproducing the vdW dispersion
interaction by ab initio methods, experimental heats of vaporization
and densities were used during the fitting of the LJ parameters. First,
the new charges were used with the original parameters from C36 (LJ
and torsional) and the LJ parameters were then altered until satisfactory
agreement between simulations and experiments was obtained. After
this, the torsional potentials were fitted from ab initio computations
for the model compound. After one round in the parametrization scheme,
it was necessary to refit the LJ parameters again and the torsional
potentials until self-consistency was obtained. The Lorentz–Berthelot
combination rules were used for the vdW interactions.51 The introduction of scaling factors for the 1–4
interactions with the CHARMM FFs for lipids together with a new set
of charges have earlier been proven to be successful.31 (link) Below, we present more detailed descriptions of each parametrization
step.
Publication 2012
Alkanes Amber Dietary Fiber Head hexadecane Lipid A Lipid Bilayers Lipids n-hexane Tail

Most recents protocols related to «Hexadecane»

Before the batch reactions, RuM3/CeO2 and
M3/CeO2 (M = Fe, Co, Ni) catalysts were reduced
in a tube furnace by a 50 vol % H2/Ar flow at elevated
temperatures for 60 min with a ramp rate of 10 °C/min, with
the reduction temperature being determined via H2-TPR profiles,
similar to those described for CO chemisorption experiments. There
was no prereduction process for Ru/CeO2 since Ru could
be fully reduced below the reaction temperature (250 °C). Afterward,
the reduced sample was cooled down in Ar to room temperature and passivated
by 1 vol % O2/Ar for 15 min before being transferred to
the batch reactor, a 4598 Parr micro stirred reactor. For each measurement,
10–200 mg of the reduced catalyst was loaded into a small beaker
and mixed with 1 g of reactant (LDPE with Mw ∼ 4000 Da or n-hexadecane) before being
added to a 100 mL stainless steel autoclave. The reactor was tightly
sealed and purged with H2 (18 bar) six times prior to being
filled to the target H2 pressure (5 or 18 bar). The reactor
was heated to reaction temperature (200 or 250 °C) in 40 min,
maintained at the reaction temperature for a specific time (30–600
min) under agitation, and then cooled down to room temperature before
collecting gases, liquids, and solid residues for product analysis.
Publication 2024
In a 300-mL two-necked round-bottomed flask
equipped with
a magnetic stirring bar, a rubber septum and an argon balloon, hexadecane-1,16-diol
(16.7 g, 64.8 mmol) in pyridine (130 mL), and TsCl (32.1 g, 168 mmol)
were added, respectively.16 (link) After stirring
for 12 h at 0 °C, ice water (100 mL) was added to quench the
reaction and filtered with the Büchner funnel washing with
ice water (50 mL) and cooled hexane (50 mL) to give a crude product,
which was recrystallized from toluene to give the titled compound 2f (25.1 g, 68%).
Publication 2024
5-Benzyl-1,5,8,12-tetraazabicyclo[10.2.2]hexadecane (1.10 g, 3.47 mmol) was dissolved in degassed anhydrous MeOH (25 mL). An anhydrous methanolic (10 mL) solution of nickel(ii) nitrate hexahydrate (1.11 g, 3.82 mmol) was added dropwise and the mixture was refluxed under argon for 12 h. Solvent was removed in vacuo and the macrocycle complex was purified via size exclusion chromatography (Sephadex LH20) in MeOH to yield bright orange crystals (1.51 g, 87%). Elemental analysis: calculated (%) for [C19H32N4Ni](NO3)2·0.1H2O·0.1MeOH: C, 45.50; H, 6.52; N, 16.67. Found (%): C, 45.51; H, 6.77; N, 16.65. MS (ESI): m/z = 436.19 ([[C19H32N4Ni](NO3)]+). HRMS (ESI): calculated for [C19H32N4Ni]2+, 187.0985; found 187.0981.
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Publication 2024
In a 300-mL two-necked round-bottomed flask
equipped with a magnetic stirring bar, a rubber septum and an argon
balloon, NaH (60% dispersion in mineral oil, 5.28 g, 132 mmol), and
THF (28 mL) were added, respectively. The reaction mixture was cooled
to 0 °C and 18-crown-6 (7.01 g, 26.6 mmol) in THF (7.0 mL) and
ethyl 2-hydroxypropanoate (14 mL, 120 mmol) in THF (35 mL) were added
to this reaction mixture. The mixture was stirred for 1 h at 0 °C
then hexadecane-1,16-diyl bis(4-methylbenzenesulfonate) 2f (23.9 g, 42.1 mmol) within THF (44 mL) was added to the reaction
mixture. The reaction mixture was warmed to reflux and stirred for
13.5 h. The pH was adjusted to 7 with 5 M H2SO4 solution to quench the reaction. The whole mixture was extracted
with diethyl ether (5 × 10 mL). The combined organic phases were
washed with brine (20 mL), dried (with Na2SO4), and concentrated in vacuo to give a crude product. The crude product
was purified by flash column chromatography on silica gel (n-hexane/ethyl acetate = 10:1) to give the title compound 3f (7.79 g, 40%). Yellow oil; 1H NMR (500 MHz,
CDCl3) δ 4.27–4.15 (m, 4H), 3.93 (q, J = 6.8 Hz, 2H), 3.55 (dt, J = 6.7, 9.0
Hz, 2H), 3.36 (dt, J = 6.7, 9.0 Hz, 2H), 1.63–1.56
(m, 4H), 1.39 (d, J = 6.8 Hz, 6H), 1.33–1.24
(m, 30H); 13C{1H} NMR (126 MHz, CDCl3) δ 173.6, 75.0, 70.4, 60.7, 29.7, 29.6, 29.6, 29.5, 29.4,
26.0, 18.7, 14.2; IR (neat) 2983, 2925, 2854, 1750, 1460, 1371, 1268,
1194, 1142, 755 cm–1; HRMS (EI) m/z: [M-C3H5O2]+ calcd for C23H45O4 385.3318,
found 385.3307.
Publication 2024
In a 50-mL two-necked round-bottomed
flask equipped
with a magnetic stirring bar, a rubber septum and an argon balloon,
diester 3f (5.26 g, 11.5 mmol), 1,4-dioxane (20 mL),
and NaOH aq (3M, 23 mL) were added, respectively. The reaction mixture
was warmed to reflux and stirred for 12 h. The pH was adjusted to
1 with 2 M H2SO4 solution to quench the reaction.
The whole mixture was extracted with diethyl ether (5 × 10 mL).
The combined organic phases were washed with H2O (20 mL),
dried (with Na2SO4), and concentrated in vacuo
to give a crude product. In a 1000-mL one-necked round-bottomed flask
equipped with a magnetic stirring bar, a rubber septum and an argon
balloon, crude product, EtOH (35 mL), and MeSNa aq (15 wt %, 10 mL)
were added, respectively. The reaction mixture was warmed to 40 °C
and stirred for 44 h. After the reaction, reaction mixture was concentrated
in vacuo, and the pH was adjusted to 1 with 2 M H2SO4 solution. The whole mixture was extracted with diethyl ether
(5 × 10 mL). The combined organic phases were washed with H2O (20 mL), dried (with Na2SO4), and
concentrated in vacuo to give a crude product. The crude product was
recrystallized by ethyl acetate to give the title compound 4f (4.31 g, 93%). White powder; mp 80–82 °C; 1H NMR (500 MHz, CDCl3) δ 4.00 (q, J = 6.7 Hz, 2H), 3.58–3.49 (m, 4H), 1.65–1.58 (m, 4H),
1.46 (d, J = 6.7 Hz, 6H), 1.39–1.25 (m, 24H); 13C{1H} NMR (126 MHz, CDCl3) δ
176.4, 74.6, 74.5, 70.6, 29.6, 29.4, 29.4, 29.2, 25.9, 17.9; IR (neat)
3678, 2917, 2849, 1705, 1471, 1245, 1158, 1126, 1076, 1019, 914, 739
cm–1; HRMS (EI) m/z: [M-CHO2]+ calcd for C21H41O4 357.3005, found 357.3006.
Publication 2024

Top products related to «Hexadecane»

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Hexadecane is a saturated hydrocarbon compound with the chemical formula C16H34. It is a colorless, odorless liquid at room temperature. Hexadecane is commonly used as a reference material and solvent in various laboratory applications.
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N-hexadecane is a chemical compound that is a straight-chain alkane with the molecular formula C16H34. It is a colorless, odorless liquid that is insoluble in water and miscible with organic solvents. N-hexadecane is commonly used as a solvent and as a reference material in analytical chemistry.
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N-hexadecane is a straight-chain alkane with the chemical formula C₁₆H₃₄. It is a colorless, odorless liquid at room temperature and atmospheric pressure. N-hexadecane is commonly used as a reference standard and solvent in various analytical and research applications.
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Chloroform is a colorless, volatile liquid with a characteristic sweet odor. It is a commonly used solvent in a variety of laboratory applications, including extraction, purification, and sample preparation processes. Chloroform has a high density and is immiscible with water, making it a useful solvent for a range of organic compounds.
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Tetradecane is a saturated aliphatic hydrocarbon with the chemical formula C14H30. It is a colorless, odorless liquid that is commonly used as a reference material and solvent in various laboratory applications.
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Sodium hydroxide is a chemical compound with the formula NaOH. It is a white, odorless, crystalline solid that is highly soluble in water and is a strong base. It is commonly used in various laboratory applications as a reagent.
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Potassium chloride (KCl) is an inorganic compound that is commonly used as a laboratory reagent. It is a colorless, crystalline solid with a high melting point. KCl is a popular electrolyte and is used in various laboratory applications.
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NaCl is a chemical compound commonly known as sodium chloride. It is a white, crystalline solid that is widely used in various industries, including pharmaceutical and laboratory settings. NaCl's core function is to serve as a basic, inorganic salt that can be used for a variety of applications in the lab environment.
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Decane is a straight-chain alkane hydrocarbon with the chemical formula C10H22. It is a colorless, odorless liquid that is insoluble in water. Decane is commonly used as a solvent and in the synthesis of other organic compounds.

More about "Hexadecane"

Hexadecane, also known as n-hexadecane or cetane, is a saturated aliphatic hydrocarbon with the molecular formula C16H34.
It is a colorless, odorless liquid found naturally in crude oil and has a wide range of industrial and scientific applications.
Hexadecane is commonly used as a solvent, lubricant, and fuel additive due to its favorable properties, such as high boiling point, low viscosity, and excellent thermal stability.
In the chemical industry, it is employed in various synthesis reactions, material science applications, and biofuel production.
Researchers can streamline their Hexadecane-related experimentation and identify the most effective and reproducible protocols by utilizing innovative AI-powered tools like PubCompare.ai.
This tool facilitates side-by-side comparisons of relevant methods from literature, pre-prints, and patents, enhancing workflow efficiency and experimental outcomes.
Closely related compounds, such as N-hexadecane, Tetradecane, and Decane, share similar chemical structures and properties, making them useful in similar applications.
Additionally, common lab reagents like Chloroform, Sodium hydroxide, Sodium dodecyl sulfate, KCl, and NaCl may be employed in Hexadecane-related studies.
By leveraging the insights gained from the MeSH term description and the Metadescription, researchers can optimize their Hexadecane research and explore the full potential of this versatile aliphatic hydrocarbon.