Organometallic Compounds - Science topic

Hi!

d10-d10 interactions are nifty and do exist. A quick search brings up this review on the topic: https://pubs.rsc.org/en/content/articlelanding/2011/cs/c0cs00102c/unauth

Looks like that and a forward search would be a good place to start to see what's out in the literature.

Good luck!

In the case of limited resources, I'd instead suggest density-functional-based tight-binding semi-empirical calculations, check its availability for metals here:

If it is not available in G09, you may try Orca.

Best, Pablo

Dear Maryam,

The following articles may be of help to you. Of course, the M+2/M+3 ratio is essential but pH is critical since it will determine the solubility of the M(OH)2 or M(OH)3 phases.

1- Robertson J. Geochemical characteristics of aluminum and magnesium secondary mineral phases in uranium mill tailings. Ph.D. University of Saskatchewan. 2017.

see JANA2006/2020 software and the papers published by the authors of the software.

larger the band gap, good will be the NLO activity

Dear Sumit, many thanks for sharing this very interesting technical question which is certainly of broad general interest to many other RG members as well. In fact, this is not a trivial question. It is only 15 year ago that researchers discovered what the origin of the garlic-like smell is which is observed when steel is cut or dissolved in acid. The researchers identified small organophosphines like methylphosphine, CH₃PH₂, and dimethylphosphine, (CH₃)₂PH, as the sources for the metallic / garlic-like odor. For more information about this please have a look atvthe following useful link:

Good luck wth your work and best wishes, Frank Edelmann

Dear Eloi, no guarantee, but I assume that the chemical shifts will not change to a great extent. However, I have no idea if the NMR spectra of the complexes can be measured in water / D₂O mixtures. Surprisingly there are rare publications describing water-stable and (partially) water soluble nickel(II)-sigma-methyl complexes. For example, please have a look at the paper entitled "Nickel(II)-Methyl Complexes with Water-Soluble Ligands L [(salicylaldiminato-K2N,O)NiMe(L)] and Their Catalytic Properties in Disperse Aqueous Systems", S. Mecking et al., Organometallics 2007, 26, 1311-1316. In this paper the authors report the synthesis of Ni-CH₃ complexes stabilized by bulky, water-soluble ligands. The CH₃ resonances in the ¹H NMR spectra were found in the range of –1.00 to –1.50 ppm. The complexes are reported to be stable towards water. Three of the complexes were either insoluble or slightly soluble in water. One of the compounds was even found to be water-soluble. The ¹H NMR spectra were measured in C₆D₆, CD₃OD, and acetone-d₆.

The solvent for dibutyl tin oxide you can use THF or dry ether

Dear Berkay Şahin thank you for asking this interesting and important technical question. In general one can say that organometallic compounds can be characterized by the same methods as organic compounds. It just has to be taken into account that many organometallic compounds are air-sensitive (and, to a lesser extent, moisture-sensitive). Thus you should be equipped to prepare your samples e.g. inside a dry-box. The usual set of analytical and spectroscopic methods to fully characterize organometallic compounds includes elemental analysis, IR and NMR spectroscopy, mass spectrometry and single-crystal X-ray diffraction. In your case the "mass rates of elements" can be best determined by elemental analysis. For more general information please refer to the following instructive presentation:

For elemental analysis of air-sensitive compounds please also have a look at the following useful link:

Dear Eric Täuscher here is another interesting paper by the famous henry Gilman entitled "Color Tests for Some Organolithium Compounds"

Here are three publications that deal with the parent ethyne (acetylene):

Synthesis, Characterization and Biological Studies of Ethynyl Nickelocene. Raza, M. A.; Pervaiz, M.; Rasheed, A.; Mustafa .; Adnan, A. Asian Journal of Chemistry 2016, 28(5), 954–956 DOI: 10.14233/ajchem.2016.19277

Acetylenic Nickel Compounds. Dubeck, Michael (Ethyl Corp.) US Pat. No. 3,097,224, 09 Jul 1963

Tricarbonylcyclopentadienyliron-cyclopentadienylnickel and some new cyclopentadienylnickel-irontricarbonyl–acetylene complexes. Tilney-Bassett, J. F. Journal of the Chemical Society 1963, 4784–4788 DOI: 10.1039/JR9630004784

Dear Donia Said, we're talking about organometallic compounds when direct metal-carbon (M–C) bonds of some sort (sigma- or pi-bonded) are present. In the case of your ligand (phenyl pyridyl ketoxime) most (if not all) metal complexes are NOT organometallic compounds. A typical example is the copper complex in the attached reference. In this case no M–C bond is present. There could, however, be rare cases in which cyclometalation reactions under formation of M–C bonds might occur.

Hi Zhenbo Mo, quite often FLP's are not organometallic compounds, e.g. when they are based on main-group elements such as boron of silicon. However, they can be organometallic compounds e.g. when they contain a ferrocene moiety. Generally we talk about organometallic compounds when at least one M-C bond is present.

Thank you Professor Frank T. Edelmann for the reference.

This Article can help you

As with many questions here, a little more detail would help potential answers to be more useful. Is the compound soluble in methanol or insoluble and just holding onto methanol tightly. Since you don't want to use a rotovap, I am guessing it is soluble. As Ross says above, you can find a solvent to precipitate your compound and then you can filter. Is your compound neutral or ionic? If ionic, you could use a suitable counterion to precipitate it.

Dear Marcel, not only the gas phase...calculations using solvent models are also single point calculations. So, the contribution from other possible conformers are not considered. Moreover, all the solvent models are implicit. To mimic the real system you actually need to do quantum molecular dynamics with explicit solvents and a finite temperature.

Hi

The computational study of organometallic complexes is not especially straightforward, and depending on what properties you want to calculate the level of theory you should use might be different. For this reason, it is typical to perform benchmarking studies of different DFT functionals to see which functional is more suitable for your system.

Nevertheless, there is an excellent review by Schoenebeck and co-workers discussing common DFT functionals for organometallic complexes (Chem. Rev., 2015, 115 (17), pp 9532–9586). Probably you will find useful starting points there.

In regard to the basis sets to be employed, the choice depends on the size of your system and the computational power you have available. As pointed above, metals are typically treated with pseudopotentials (e.g. SDD).

I hope you find this useful.

Best wishes,

Martí

You may find an answer here:

Dear Athar

What kind of error you are getting. Or you may send me the input file.

Magnesium ethoxide, once formed then it will not give any color (as you mentioned), even keeping the same in open atomosphere.If you can eleoberate the reaction then more chemistry can be thought upon.

If you are trying to prepare by reacting of magnesium metal with ethanol in the presence of some initiator like iodine then the reaction will start and will complete at higher temperature and if the moisture content is at higher side in the used ethanol then reaction will take more time for completion and if the moisture is very high then reaction will not proceed further and can not be completed even at higher temperature.

Maybe SCF=XQC is the best to save time because it use expensive QC option only when your system is not converged by default method.

There is no simple rule in tuning the emission of Pt(II) complexes. Every ligand system is different. What one should consider is whether that (electron-rich) group is placed on a moiety acting as HOMO or LUMO. Usually F is added to the phenyl ring of a cyclometalating ligand to increase the emission energy of the metal complex. But the following paper shows that addition of F to a phenyl ring can lead to red shift. The degree to which the emission is affected also depends on the substitution pattern.

Apart from this, usually we take it for granted that extending the conjugation of a ligand will lead to redshift in emission. But there are also exceptions:

It is kind of hairy, the original definition of organometallic requires that the metal make a bond with a carbon in an organic compound; however, organometallic is also used often when referring to complexes where only N, O, S, or P are chelating atoms but are part of an organic compound (containing carbon). Metal-organic frameworks are typically bigger and usually have a cavity / porosity.

Thanks Dr. Bojidarka B. Ivanova. I know Chromatography is method for separation. It does not provide structural information about fragment ions. My main interest is in the Mass Spectroscopy. The compound in question is pure but I don't have access to only MS, thanks.

Thanks Dr. Fatma Ulusal. But I dont have access to only MS. I only have access to GC-MS and LC-MS..........................

 chloroform is the best solvent

If I correctly understood the theme, Cu was not leached from solution but mainly from HKUST-1 net. This happens even without organic molecules interacting with Cu2+ ion, but merely with the presence of water media. If there are unstructured Cu2+ in the pores of the net, hence they should be displaced to the solvent phase through water/ethanol washings. But if you use adduct or chelating agents the scavenging of the metallic center from the net is driven through adduct, chelate or macrocyclic effect depending on the employed substance that interacts, with Cu in this case. Its own dissolution or coordinating assisted dissolution happens due to the fact that the HKUST-1 crystallites are surface open/labile materials containing -COOH, -COO- and -COOCu sides or functionalities directed to the interaction with the solvent. Therefore having these terminals, these components should displace to the media since Cu is efficiently solvated with water molecules. In this way the displacement of both Cu ions and trimesate or trimesic acid towards water is observed by UV-vis, therefore the loss of material is attained. Having less and larger crystals should diminish the dissolution rate, but if you have more and smaller crystals, the dissolution rate should be higher. I hope to be sufficiently clear in this explanation. If you need further details in order to understand the issue please contact me and looking forward to help in the analysis of your experiments. Best regards. Hiram

Thank Hyun-Sue! Do you have any idea about the etching rate of each metal?

Do you actually mean PhPH₂ ?  If so, it oxidizes very quickly and should not be exposed to air.  If you mean Ph₃P, or triphenylphosphine, brief exposure is fine.

You can by choosen strong  ligand more than ammine

The band gap will be affected if the substituent position is able to interact with the HOMO or LUMO. Since this is a pi-system, and you are substituting in the plane of the molecule (orthogonal to the pi-system), the likely mode of interaction will be through hyperconjugation.

DFT calculations or old school HMO calculations should elucidate the positions of electron density within the HOMO and LUMO

Hi, I think Pedro got the right answer and you have paramagnetic species in your sample. The other option would be convection in the sample that can also affect topshim. Try "topshim convcomp". This compensates for convection. If this still does not help it is most likely the paramagnetism.

I have not gone through the cited references, may be they have given better answers to your question. However i will answer your question around the logic that creatinine (2-Amino-1-methyl-5H-imidazol-4-one)  in its stable tautomeric form has an amine group attached to 5 membered ring which is an excellent ligand to most transition metals especially copper(II) and cobalt(III). so a copper(II) fragment can selectively bind to the creatinine with a significant thermochemistry. Some literature references for copper complexes of creatinine are as under:

DOI: 10.1016/S0277-5387(00)83797-3

In fact the Quantification of creatinine in biological samples is also based on the pseudoenzyme activity of copper–creatinine complex see the ref.http://dx.doi.org/10.1016/j.saa.2012.02.104

The Fluorescent creatinine assay is a method of detecting creatinine in body fluids using an indicator which produces a fluorescent response when oxidized in the presence of a copperII/creatinine complex. A preferred indicator is 4-(1-methylhydrazino)-7-nitro benzooxadiazole (MNBDH) see ref.(US 6872573 B2)

Fundamentals of Urine and Body Fluid Analysis

Nancy A. Brunzel - 2013.

In summary a copper(II) based fragment either from the above cited references or a newly designed one can do the job one such designed complex in described in the reference DOI: 10.1016/j.saa.2015.10.028 .

Good luck

OK, thank you very much for your answer :)

I also recommend PTC, but I don't necessarily agree that you could not use DMF or DMSO.  If your ligand forms a stronger complex, than it would compete with DMSO to give you a desired product.   It may even be the case that your metal plus ligand is less soluble and thus will precipitate from solution.

Further, if you find a solvent system in which your ligand is even just a little soluble, the equilibrium could be driven and your complex will be formed even if the ligand doesn't completely go into solution.

Hi,

You will find a detailed answer to your question in the attached file. A description of the theoretical approach for calculating the fractions of basic structural units is given in Sectons 5.3 and 5.4. It is based on information on the Gibbs free energies of formation of crystalline compounds existing in a given system together with information about their structure. Figure 5.6 shows the results of calculation of the content of basic structural units present in sodium borate glasses. You can use it for an approximate estimation of the possible content of triangles with one non-bridging oxygen atom in your glass if you consider the total content of  Na2O, ZnO and TiO2 as that equal to the content of Na2O because, being an acidic oxide, B2O3 tends to mainly interact with more alkaline oxide, Na2O. Due to this, the contribution from ZnO and TiO2 is hardly very large. To perform rigorouse calculations, you should follow a procedure descriped in Section 5.3 and use Eq.(5.12) for determining the fraction of triangles with one NBO. Good luck.    

Mr./Miss/Mrs Tidjani,

Methionine, in particular, and methyonyl-containing peptides, in a more general context, exhibit a competitive coordination ability to large scale metal ions, involving N, O and S - centers. We have series of works on metal complexes (mainly transition metal ions) with methyonyl-containing peptides (eg. [Ref. 1], attachment), where the bonding is via S-center.

In this context, if you do not have the ability to isolate single crystal, allowing you X-ray diffraction structural study, you should obligatory conduct NMR (attachment) and tandem MS/MS mass spectrometric experiments in order to determine the coordination of (CH3)S. In the NMR, it is a very characteristic and intensive signal of CH3S- protons, which is significantly affected by coordination of S(CH3) group. The same is valid for MS/MS signals of fragment species containing M-S bonded complexes at low m/z values.

Not exactly. one reason of poor adhesion can be the oxide layer formation on the platinum surface.

Yes, but we would need more info to help with specifics. Solvent selection can play a role, and you can also add additives that react with products, thus shifting the equilibrium via Le Chatlier's principle. 

Hi - I guess you are learning to work with nickel- the answer of course is that it's quite easy. If you need any advice for coordination chemistry; the tricks the professions use then just ask, best wishes, Ian.

Dear all respected teachers (Rafik Karaman, Bojidarka B. Ivanova, and Saeideh Hosseini),

Thank you very much for your reply and cooperation. I had used L-pyroglutamic acid because of the similarity in chemical structure to aglycon and it is commercially available. However, to synthesize aglycon is highly important to get accuracy. I got many information from this discussion especially Prof. Bojidarka B. Ivanova. Thank you all for the help!

Lanl2dz is best as a basis set. One should also add ECP for the same.

If you haven't yet searched in SciFinder Scholar or another database, I would strongly suggest that you start there.  A good librarian should be able to assist you in starting that search/facilitating that search.

You can use nanomaterials and proteins (NFkb- factor expression)

Refer this link:onlinelibrary.wiley.com/doi/10.1002/ppap.200931111/pdf

Refer this link:onlinelibrary.wiley.com/doi/10.1002/masy.200750441/pdf

Refer this link:www.igb.fraunhofer.de › ... › Plasma processes

Refer this link:www.kps.or.kr/jkps/downloadPdf.asp?articleuid=%7BC8A15F53.

Some organometallics can react with N₂ so argon is preferable inert gas; Li metal surface also reacts with N₂ . Noted 1% seems to be too large amount for dissolved nitrogen

First, please don't call a compound of Hg and S "organometallic" This term is confined to compounds with a direct metal-carbon bond. Naturally a Hg-S compound cannot be "organometallic".

Second, Hg and S can form HgS which has two forms. The red form, known as cinnabar, has a polymeric zigzac chain structure: ... -Hg-S-Hg-S-Hg-S-... with covalent Hg-S bonds with a 236 pm Hg-S bond length. The black form which is metastable, exhibits the sphalerite (zinc blende) structure. The interactions between Hg and S are a bit more ionic in this case. Since the most stable form of HgS is red, the black form is unstable and Hg2S does not exist,  I don't believe that you produce mercury sulfide by this procedure.

Furthermore, the black material you are producing is presumably not even a pure compound, but a mixture of things (Michael is probably very right in this point). Therefore, you cannot seriously discuss "the bond structure". You should first try to determine the different species which occur in this mixture.

Personally, I would guess that the material contains largely elemental Hg in finely divided particles. Most of real mercury compounds such as kalomel Hg2Cl2, HgCl2, HgS (there is no Hg2S or HgS2), HgO are NOT black, many of them are colourless, yellow or red. Hg in elemental form is black.

Hi James!

Yes, they are different. However, I know that it can be done as I think I have synthesised the complex but as a powder and not as a good crystal. That was done.with another similar method.

Hello Ching,

With bulky ligands such as Bn, Np, CH2SiMe3 you are likely to generate "alkylidenes" through alpha-H abstraction. TiMe3 versions are likely to survive (in the absence of other chelating ligands / donor ligands) simply because they lack steric crowding that otherwise facilitates alpha-H elimination.

Here are two accounts you can read and benefit from.

Dear Maolong,

Please see follow papers:

1. Masoud Mirzaei , V. Lippolis , Hossein Eshtiagh Hosseini , milad mahjoobizadeh , Decaaquabis(μ3-4-hydroxypyridine-2,6-dicarboxylato)bis(4-hydroxypyridine-2,6-dicarboxylato)tetramanganese(II) 3.34-hydrate: a new three-dimensional open metal-organic framework based on a tetranuclear MnII complex of chelidamic acid and undecameric stitching water clusters , Acta Crystallographica Section C: Structural Chemistry , Volume ( 68 ) , 2011-12, Pages 7-11.

2. Masoud Mirzaei Shahrabi , H. Aghabozorg , Hossein Eshtiagh Hosseini , A Brief Review on Structural Concepts of Novel Supramolecular Proton Transfer Compounds and Their Metal Complexes Part(II) , Journal of the Iranian Chemical Society , Volume ( 8 ) , 2011-4, Pages 580-607.

For further papers on di-carboxylic acid transition metal complexes go to this link:

I do not know which kind of QSAR you want to develop, but one approach for NHCs and their transition metal complexes is working with Tolman's Parameter and with steric considerations (Buried Volume). See the attached paper. Although in German, it might provide helpful literature references for you.

Regarding the "unnecessary H" I agree with you complaints. It is a frequently used but nevertheless incorrect way of drawing NHC complexes in the way you did it, for this graphic represents an "alkyl" rather than a "carbene" complex.

The solid state also reliable to compare by taking equal quantity of samples (better all with more sample ) and same instrumental parameters like the energy of the laser. But quantum yield is a better measure of energy transfer efficiency.

Hi Ramin,

The main problem is that one can hardly suggest you a solvent for a compound, having no idea about its structure.

As far as I remember you were going to synthesize a metal complex of tetraphenylporphyrin (TPP), although you didn't specify what is the metal ion.

If this is the case, then the problem with the solubility of the product and by-product could be expected from the very beginning.

In fact, you may not find a "good" solvent for this compound. Try benzonitrile under heating. But the best solution is to use a porphyrin with higher solubility, then TPP, e.g. the one containg alkyl groups in the aryl.

By the way it is not clear, why you think the crystalline material is a by-product. It could be a portion of your product, which crystallizes from the reaction mixture.

Dear Mostafa,

Please, find attached three papers that deal directly with the determination of platinum content in plasma and urine.

All the best,

Niko

Hi Rajbinder, 

So your compound precipitates in methanol, which is convenient for collecting your product, but not so convenient for running reactions, am I understanding correctly? One resource that I really like using when I'm in a problem like this is this polarity chart. You've probably already seen this, so I apologize if I'm just stating the obvious to you. <http://www.pallavchemicals.com/images/Tech_Center/Solvent%20Miscibility%20Chart.png> Since you're dealing with a peptide, I would assume you would have to deal with solvents that can dissolve amides. It's unfortunate that DMF didn't work, that's the first solvent I would have recommended. Would it be safe to heat your compound in DMF to induce solubility? Or is your metal conjugate too unstable to withstand that kind of energy? In other words, does it need to be kept at a low temperature? When nothing seems to work, and it's safe to do so, heating helps. And in fact, a lot of the reactions I am running depend on the temperature of my solvent. It is convenient, because your starting material will precipitate out when you cool down again, making work up a little easier. A little more information about your reaction conditions would help me answer more helpfully. 

Hope this helps.

Good luck!

Diana 

As Bartosz mentioned, 0.74kcal/mol may not be very typical of a large system.  

However, it may depend on the nature of the problem.  If the energy difference is from two structures that are extremely similar, then it could be reliable, because it is essentially a very low dimensional problem with all the other variables remaining the same in the process.  However, if the two structures are significantly different, then that result cannot be taken too seriously.   The basis set is quite small.  DFT also may fail catastrophically for some systems without much reason when it works just fine for others;  this is just a inherent problem of the semi-empirical nature of functional fitting, and there isn't much you can do about it.  M06 is more stable than M11 and M12, but I have been shown results of M06 giving embarrassing numbers for set of test problems before. On top of that, non-relativisitc effects, harmonic oscillation, non adiabatic effects and core correlation/polarization effects can each cause errors larger than 1kcal/mol in a large system.   

In fact, when the system is large, you have many sources of errors that can potentially accumulate or cancel out.  You will therefore expect a much larger variance in the error if you try out many large systems using any method, compared to small systems. Unfortunately most publications utilize lucky error cancellation to the full extent, by tinkering with the setup that give you the closest answer compared to experiment.  For example, result would actually see an increase in error if a larger basis set is used.  The 0.74 kcal/mol error likely came from cancellation of many different error in the calculation that are much larger.   In fact, I have known of experimental groups that misidentified their species in a study, only to find a large number of computational follow ups that claims to reproduce almost exactly the vibrational spectrum they've measured, when in fact it isn't even that molecule!!

In general a good calculation should choose the method/functional/treatment/basis set without using the knowledge of the actually experimental results.  Functionals and basis sets should be chosen to best suit the problem, not just to reproduce that number.  If someone gives a stellar result reproducing an experimental number without justifying or carefully benchmarking his method, then you should take that result with a grain of salt.

I would not recommend work with borane gasses at high temperatures, unless the method (and the apparatus/equipment !) have been very extensively and carefully tested.

Make the Pt(DMSO)2Cl2 complex first, its easy to make just put PtCl2 into DMSO and you get the complex out as long needles almost immediately. You can collect them via filtration. Then react this complex with your ligand.  The ligated DMSO will be replaced first.

It is only a feeling but I think this compound is probably tetrahedral. This feeling comes from an attempt when we tried to determine the X-ray structure of an analogous Pd(0) compound, Pd(BDPP)2 (BDPP = chiral 2,4-bis-(diphenylphosphino)pentane). A square planar structure was out of question, while with the tetrahedral we came very close to the solution. Probably, we did not play long enough with the chelate conformation then.

As a d9 system Cu(II) exhibits Jahn-Teller-distortion in various coordination modes. Actually, the observed SP is a distorted octahedron with two axial ligand indefinitely wide departed.

Depending on the ligand field stabilazation energy (LFSE) a distinct coordination geometry is prefered in a complex. If LFSEs of two different coordination geometries are similar switching between these geometries may occur.

Energy schemes according to ligand field theory may also be helpful for understanding.   

Well it depends what you want, how do you want to tune the band gap?

Hi Farah, 

There are a number of good methods for TBT.  The problem is you are directly injecting salts into the LC/MS.  The build-up of non-volatile salts on the electrospray interface will reduce your signal.  I would highly recommend either Liq/Liq extraction or SPE to remove the salts.  I understand your aversion to incorporating additional sample prep steps in your method, but sometimes the matrix requires it. The following U.S. EPA method has some good tips...

Organotins have an affinity for bonding to glass. Soak all glassware in HCl solution (pH <2) for 24 hrs.  I would also look into silanizing the glassware.

Go isocratic 80% MeOH, 14% Water, 6% Acetic, 0.1% tropolone

Clean your electrospray interface - then try prepping your standard calibration in methanol 1% acetic, run a curve, hows it look now?

I would also investigate extracting TBT out of the water using C18 tips. These are attached to a pipette and the sample is drawn into the tip several times to extract.  Rinse with DI water to remove salts, then extract with acidified methanol.  Shoot into LC/MS.  (simple!!)

Or try liq/liq - acidify sample, extract with hexane, exchange to MeOh, shoot into LC/MS.  Use a 40 mL VOA vial, add 20 mL sample, acidify, add 5 mL hexane.  Shake like crazy for 2 minutes, remove top portion, dry down, and exchange to MeOH/1%acetic. final volume 1 mL - this would give you 20X concentration factor.

good luck!

email if you have questions  philbrook.peter@epa.gov 

I've made it in a drybox in one step from Ni(COD)2, PPh3 and PhCl.  It was yellow all of the times I made it (maybe 3 or 4 times).  That is one way to avoid isolating Ni(PPh3)4.

The napthyl analog is air- and water stable.  It can be made from NiCl2/PPh3/reducing agent/NapCl.  I haven't made it myself, but one of my former coworkers did.  It can also be purchased from Aldrich.

 Olga Novikova,

Thank you so much 

Now i will have more clarity over the basis sets.

Dear Ewa, be careful. Commercial palladium acetate from different sources sometimes behaves differently. A palladiium(II) ion solvated only by dmf as ligands e.g. [Pd(dmf)4]2+  is not known and very probably does not exist. The situation is complicated. See the paper "Non-trivial behavior of palladium(II) acetate" by Cotton et al, Dalton Trans. 2005, 1989-92. In case that you are only interested in the question whether palladium acetate in dmf forms ionic complexes you coould measure the conductivity of the solution. There is a very good review by Geary, Coord. Chem. Rev. 7 (1971) 81-122. There you will find typical conductivity values for 1:1, 1:2, and other types of electrolytes in dmf (and other solvents). dmf has to be perfectly dry, palladium acetate seems to react with traces of water.

The previous answers are correct, but if you want a complete understanding, please read:

WATER AND PROTON EXCHANGE PROCESSES ON METAL IONS

LOTHAR HELM, GAE¨ LLE M. NICOLLE and ANDRE´ E. MERBACH

ADVANCES IN INORGANIC CHEMISTRY

2005 Elsevier Inc.

VOLUME 57 ISSN 0898-8838 / DOI 10.1016/S0898-8838(05)57007-7

This is often a sign of catalysis of the reaction by heterogeneous metal particles.

Best would be to synthesize such molecules using diffusion method which involves layering of reagent over the substrate or vice versa through the walls of the tube very slowly and leaving it undisturbed for few hours to days until you get crystalline material which may not dissolve readily but one can generate a very dilution solution of the same in a solvent such as dmso-D6 for NMR recording, if it is not paramagnetic.

We have crystallized hundreds of such highly insoluble molecules using this method and obtained single crystal X-ray data and solved the structures.

as an alternative: use soxhlet extraction method to get a saturated solution or

try to sublime it if it is stable. Many organometallic compounds can also be sublimed to get X-ray quality crystals. We succeeded on several occasions.

For trace metals try to pass the flue gas through high volume sampler, this way metal particulates will be collected on filter. Note down the volume of the air sucked, weight of the filter paper and then cut and perform acid digestion on the filter paper. Run it on AAS/ICP. For PAH collect the flue gas in some air sampler or simply in a car tyre tube and then run the sample directly on GC-MS through molecular seive to remove particulates. For organometallics, well this one is a long shot and hectic procedure. First make ascertain which metals are present, perform TOC to find out organic content and make a list of possible organometallics from literature, investigate them separately with the help of IR first to determine peaks. This will give you an idea of the functional groups and possible OMs like carbonyls etc. Then go for NMR and Mass spectrometry.

Thanks James for your useful input. I share with you the view of some weak binding with the metal ion, the solvent polarity would have a decisive influence to the stability of the coordinated system and the metal ion size for the number of possible coordinates. Experimental data eventually could show that.

I have used both SS ampoules and other more "researchy" arrangements on ALD and CVD tools for a couple decades. I have used the Sure-pac and other septa-sealed containers to handle air sensitive precursors quite often. However, we only trust them to protect from air when they are maintained above atmospheric pressure. There will be some rate of leak around a canula if you pull vacuum on the bottle. You should also consider safety, especially for a pyrophoric precursor. And do check with Aldrich for the pressure rating of the bottle. You might also consider a glove bag or other inexpensive purging arrangement around container.

Many Thanks, Daniel. I tried the FOX following your suggestions. There are still several questions confusing me and thus I am asking for you help again. As shown in the enclosed figure, I create the molecular (Z matrix) from the cif file of Rubrene, but it seems completely different (right figure) when I import the molecular into the new crystal based on the indexed results. At the step, should I set the occupancy of the molecular as 0.5 (Dynamic occupancy correction is chosen at the beginning)? And What is a typical vale for the C-C anti_bump?

Thanks again.

Linear C-12, C-14, C-16, C-18 hydrocarbon chains are ubiquitous in nature, being found in fats and oils. The compounds can be processed in large quantity, and are commercially available.

Fatty acids with longer chains (very long chain fatty acids) are less abundant in biology. They are not used to store energy (and are less readily metabolized), but seem to be components in brain and retinal tissue.

See:

Poulos, Alf. "Very long chain fatty acids in higher animals—a review." Lipids 30.1 (1995): 1-14.

Thanks very much , I appreciate you help

Dear colleagues, please do not be fooled - magnesium oxide does not react with any of these activators - either with iodine nor with methyl iodide nor with dibromoethane.

Activators react with magnesium in those places where the magnesium oxide film has a small thickness or defective, so the mechanical action improves activation. As a result, these places form cavities filled with a magnesium halide (or Grignard reagent by MeMgI-activation), which leaches by solvent in subsequent steps.

Especially, it can be seen in the preparation of magnesium alcoholates.

In complicated cases, such as the preparation of the Grignard reagent from pentafluoro-chlorobenzene, dibromoethane activation is needed addition in stoichiometric amounts - to refresh magnesium surface because blocking by products of side reactions. Of course, this amount is much larger than the amount of magnesium oxide on the metal surface.

In some cases, such as a Grignard reagent obtaining from CF₃(CF₂CF₂)_nCH₂CH₂-I, presence of homologues with n>= 4 as impurities block reaction completely.

Although I haven't done a Yamamoto myself, and it's with Ni, I can tell you from our experience with Stille cross-couplings, that a Nitrogen adjacent to the Br (in ortho) is a big problem. We have an example for this in J. Linshoeft, A.C.J. Heinrich, S.A.W. Segler, P.J. Gates and A. Staubitz, Org. Lett. 2012 , 14, 5644-5647. See entries 4 and 5. I attach it for you. We speculated that the N complexes the catalyst, but of course, there is no direct proof. However, we see this problem with many N containing aromatic heterocycles: They can be very stubborn in cross-coupling reactions!

Which solvent used to crystallization... My idea is whatever the solvent you can take small amount of solute than the solvent that is main thing..

I agree with Renjith Bhaskaran, it all depends n the size of the data and the accuracy you will need for the results. Assuming you need a high accuracy because you want to compare your data to experimental spectra, you also need to make sure that you structure optimization uses really tight convergence thresholds (like 10^-9 for the energy and 10^-6 for the gradient). This is especially important if you have to use DFT, e.g. because your molecule is too big for MP or CC methods. In that case my experience shows, that hybrid functionals are a good choice, but you should at least go to triple zeta basis sets. Additionally, it makes sense, to go to bigger grids like m5 or comparable.

I think this article will help you, namely, Wei Chen, Huicui Yang, Rong Wang, Ru Cheng, Fenghua Meng, Wenxiang Wei, Zhiyuan Zhong., “Versatile Synthesis of Functional Biodegradable Polymers by Combining Ring-Opening Polymerization and Postpolymerization Modification via Michael-Type Addition Reaction” Macromolecules2010,43, 201–207. You can also look at attachement file.

Add a few drops of 1,4-dioxane. It shifts the schlenk equilibrium to give Bn2Mg and MgCl2 which are very insoluble and then after removing all solvents under reduced pressure, your product can be extracted with aromatic or hydrocarbon solvent, depending on solubility.