Organometallics - Science topic

If it's small enough, you should do DFT! Metal-ligand interactions aren't well done with most docking software. Even semi-empirical methods get metals wrong. See for example: Application of Semiempirical Methods to Transition Metal Complexes: Fast Results but Hard-to-Predict Accuracy | Journal of Chemical Theory and Computation (acs.org))

LAC3VP is the de-contracted basis of LANL2DZ developed by Schrodinger Inc. From memory, I recall that it has Hay and Wadt ECP and similar valance functions as in LANL2TZ or LANLO8 basis sets.

There is no need to prioritize that specific basis set unless you use Jaguar.

Organotransition Metal Chemistry: From Bonding to Catalysis by John Hartwig

Hi Kyle Fisch ,

You need to add another line at the end of your input file.

It should be like this:

H C O 0

6-31G(d)

****

Mo 0

LANL2DZ

****

Mo 0

LANL2DZ

(Don't forget to leave a space here after the LANL2DZ line)

In case the calculation still not working, feel free to use this input file. I have redrawn the structure and tried running the calculation. It works. Hope this helps.

What about HPLC-MS coupling? This may answer your question which compound is "in your peak".

Dear Onyeka Stanislaus Okwundu thank you for sharing this very interesting chemical question with the RG community. As a synthetic inorganic chemistry I absolutely not an expert in this area of research. However, I at least found two literature references which at least come close to answering your question in part. Both describe the dehydrogention of cyclohexylamine under formation of aromatic amines. Please have a look at these articles:

and

The second paper is even freely available as public full text. You can find and access other related articles by searching the "Publications" section of RG for the term "dehydrogenative aromatization":

Other articles are found when searching for terms like "acceptorless dehydrogenative aromatization". When searching for literature references, I think you should better avoid the term "uncompromising" as in your original question. This word seems to be rather unusual in this context.

I hope this helps. Good luck with your work and best wishes, Frank Edelmann

In order to record classical CV, your "synthesized deep eutectic solvent" must have a high electric conductivity (low resistance). Commonly, an electrolyte is added to decrease a resistance. If your solution contain an electrochemically active species, you can see it as a CV peak. You can try whatever reference electrode, but you must calibrate it, for example, against ferrocene couple.

I would propose to use a Pt wire and Ferrocene in the solution. Measure the potentials of your system against Fc/Fc+ Some people use Ag/AgNO3/ACN but you have to cover this reference electrode to hide it from light because it is not stable in light. Check often its potential against another reference electrode.

Dear Lucas Almir Cavalcante Minho I think that the recommendations provided by Corentin Lefebvre are already very useful and comprehensive. In addition, I suggest that you also check the "Publications" section of RG for lectures and courses on certain topics of interest. Just search for the term "advanced inorganic chemistry". Then click on "Publications" and select from the list in the upper left corner either "Presentations" or "Books". You will find that many useful lectures, courses and books have been posted as public full texts which can be freely downloaded as pdf file.

See e.g. for presentations: https://www.researchgate.net/search.Search.html?type=publication&query=Advanced%20Inorganic%20chemistry&subfilter[publicationType]=presentation

Good luck with your work!

Dear Shafikul,

many thanks for your kind response and explanation. Unfortunately I have absolutely no idea what "TVEC 50 and 52" are....😳

According to the famous organometallic chemist Albert Cotton, a metal cluster is defined as "a finite group of metal atoms that are held together mainly, or at least to a significant extent, by bonds directly between metal atoms, even though some non-metal atoms may also be intimately associated with the cluster" (see attached presentation). Moreover "molecular clusters are composed of 3 or more metal atomsstabilized by small molecules acting as ligands, and characterized by metal-metal bonds, either localized or delocalized over the metal framework." I know that the term "metal cluster" is often used in a broader sense. Personally I prefer to adhere to the definition in the strict sense. Thus if you have a metal complex wich comprises three metal atoms but only one or two M-M bonds or even no M-M bond, I would better call this a "trinuclear complex" instead of a cluster.

Dear Gourab Mukherjee many thanks for posting this very interesting technical question on RG. I assume that solubility problems are the main reason why the synthesis of iridium porphyrin complexes usually starts with organometallic iridium complexes and not with the chlorides. Iridium trichloride exists in two forms. The anhydrous IrCl₃ is insoluble in water and common organic solvents. Then there is the trihydrate, IrCl₃(H₂O)₃. This compound is well soluble only in water, but not in organic solvents. Thus both trichlorides are more or less unsuitable for the synthesis of iridium porphyrin complexes which is normally done in high-boiling organic solvents. Basically the same is true for ruthenium trichloride. In contrast, compounds like Ru₃(CO)₁₂ and [Ir(COD)Cl]₂ are well soluble in a variety of organic solvents. Particularly the iridium complex [Ir(COD)Cl]₂ is every easily accessible in high yields from IrCl₃(H₂O)₃ and COD (= 1,5-cyclooctadiene). You can regard [Ir(COD)Cl]₂ as a soluble form or iridium(I) chloride which is otherwise not accessible. Ru₃(CO)₁₂ is more difficult to make and should perhaps better be obtained from commercial sources, although it is very expensive. Both complexes can be used to synthesize porphyrin complexes of the mono- and trivalent metals. For a typical literature reference please have a look at the following article:

Good luck with your research and best wishes, Frank Edelmann

Dear J. Narayanan, this is clearly a question of great current interest and importance. I believe it is entirely up to you; there is no genuine consensus on the literature in my opinion. Some people use an abbreviation that highlights their university or place of origin (UiO, MIL, STAM, UMCM, SNU, DUT), while others merely use the formula unit (Fe2dobdc, Zn2bdc2dabco or [Fe2dobdc]n, [Zn2bdc2dabco]n). If the formula isn't too hard, I like to use the formula unit so that everyone knows what it is. However, how you name your MOF after publication is entirely up to you; as long as it makes sense, no referee should object.

I hope this gives you some useful initial information. Good luck with your research and best wishes!

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

Dear Nasir Ali thank you very much for your interesting technical question. Please go through the following Open Access article which might help you in your analysis:

The same software was employed in the following relevant studies:

and

Unfortunately the program is not free, but you can test a free 7 days trial:

You can use HRMS for organometallic characterization, if elemental analysis has not done.

Dear Srividya Swaminathan thank you again for your interesting question. If you would provide a few more details what you additional ligand Z is, I could do a SciFinder search and look for the reactivity and hydrolysis of the particular ruthenium complex. Is you starting ruthenium(II) complex a known or a new compound? It would also be interesting to know why you are carrying out this hydrolysis study. If you want to isolate the hydrolysis product, which is presumably a cationic species, you could try to isolated it by precipitation with a large anion such as tetraphenylborate,

Dear Tuna

Usually we asgin oxidation state for stable compounds not for radicals. However, if we have a radical cation such as O2+, O2 molecule which lost one electron, still we can say that the oxidation state of each O atom is +1/2.

It is always preferable to crystallize using different solvents with different and lesser temperatures, and the process must be repeated several times, sometimes using a mixture of solvents, and we follow up the results and improvements, sometimes we need column chromatography.

This article can probably help you regarding Organogold

@ Hanieh Moradi I misread your post, but I am glad it helps :)

My understanding of fluxes is that in general they acted more as a solvent and simply physically removed the oxide layer, then provided an anaerobic/reducing layer to protect the metal briefly.

The actual mode of action is surely very complex and different for different fluxes and metals.

But at least some do not vaporise the oxide layer and simply move it out of the area being soldered.

I suspect you have been given a very oversimplified mode of action and the reality is much more empirical (if it works, use it as a flux).

Interpretation of this UV-Visible spectra . First find out wave length of maximum absorption.It looks above 380 nm this means that compd. absorbs in the near UV region. Usually conjugated compds. show absorption above 240 nm. As absorption is above 38o nm which indicates that it is congugated compd. conaining double bonds.

TGA shoud be suitable. If you check under air you need to ramp the temp in a constant rate (usually 5 degrees/min is ok) to high temprature (let's say ~500C) and measure isotherm for ~30 minutes . While the organic part will evaporate or will be burnt, the inorganic part will remain as metal/metal-oxide. I must say this can be tricky because at high temperature the metal can undergo oxidation to metal oxides and then you will see some weight gain, so some optimizations should be done.

P.S. Don't tell you boss that I suggested to you to skip the sulfur values... 😂

Here an update:

We recently published experimental values for a variety of dye molecules with pyridine and bipyridine groups:

Here, the Ru dyes with more pyridine rings tended to have lower areal densities, compared to Re dyes with fewer pyridine rings. Probably, the diameter of the Ru dyes on the surface was larger due to the different anchoring with multiple bipyridine groups.

To obtain thin CdS layers of 50-70 nm, I used thiourea. The SILAR reaction was carried out at room temperature.

Dear Richard, in theory you can use sieves 3A for removing water from hydrates, since water bonds to the sieves stronger than in many hydrates, however there are a lot of variables there...if you want to try maybe dissolve it in ether and add stabilizer and sieves 3A. But i strongly recommend to do what Anthony suggested.

Hi Dhungana

You should select all electron basis set for the Si, O, C, and H such as 6-311++g(d,p). Beside, effective core potential is good choice for transition metal for example LANL2DZ or LANL2TZ and so on.

You always select suitable basis set fro following site:

best regards

You can check the attached paper. In this paper they have docked various organometallic ligands using different docking software's like

Autodock, Gold and Glide.

Shubhangi, you should use some solvent that solubilize your product. If you do not use, you are going to lose your product. After filtering your reaction it is just necessary to evaporate the solvent to obtain your product. Depending on what you are working with it should be necessary to purify it.

Dear Rick,

If we have a "slow - fast - slow" behavior, then for a single chemical reaction I associate with autocatalysis - which does not mean that each autocatalytic process has to ran like this. Of course in nature and not only there are a number of processes and phenomena of such and more complicated course.

Regards,

PS. Now we are discussing something different than in the question.

LANL2DZ for the metals and something like 6-31G(d,p) for the rest is the somewhat traditional method.

Alternatively, you can use Def2TZVP or Def2TZVPP for all elements.

Radiative rate constant is calculated from quantum yield and lifetime. Getting to know the radiative rate constant simply from lifetime won't be easy.

You need to make a little change in your input structure right at the region where the oscillation occurs during the optimization procedure. It may be a dihedral angle or torsion strain.

Good luck

New review.

LANL2DZ is a double zeta basis set, i.e. it doesn't include any polarization functions, but it does have relativistic effects through the use of pseudopotentials. The 6-31G basis is non-relativistic, and very small as well.

You don't need to mix basis sets to get good results. E.g. the Karlsruhe def2 basis sets are available for all the periodic table, contain relativistic effects and the split valence sets are quite affordable, so instead of using lanl2dz + 6-31g* you can just use def2-sv(p).

From the snapshot it looks that water is attached to the complex. what is the distance of Re-OH2?

You can specify basis sets not only for each atom of any kind (like every Oxygen atom) but also for each atom in your input separately: see http://gaussian.com/gen/ . Something like, e.g.

1 0

6-31G*

2 0

6-311G**

will put the 6-31G* ont he first atom in input, while 6-311G** on the second one.

Hi. Here is an example of an input using multiple basis set:

#N B3LYP/gen pseudo=read OPT

name of the complex

1 1

C O H 0 6-311+G(2d,p) **** Re 0 sdd **** blank line Re0 sdd blank line

Obviously the blank line means you leave the line empty.

I don't know why but the gaussian input of these type must have two blank lines at the end.

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:

If we look at the Schrödinger equation we cannot find any temperature term in it. Then results from all ab initio methods which in some approximate way solve the electronic part of Schrödinger equation are in 0 K.

Temperature appears in methods like statistical thermodynamics which treats the collective behavior of molecules. The frequency calculations in Gaussian are based on the statistical thermodynamics but the program needs first to solve Schrödinger equation to obtain the energy term to calculate the partition function. As Thomas responded, temperature is applicable just in frequency calculations.

you can read .... it will help you 

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..........................

by phase extraction( adding a miscible solvent like acetone) or by adding a salt i think 

I'm not an expert for SQUID magnetometry, but I'm not sure if this is possible with liquids, at least I have only used solids for SQUID. As antiferromagnetic coupling should require very low temperatures, you will have a frozen solution at this point. This would not really be a solution anymore, so you could as well do measurements in solid state. Furthermore, if you have a large quantity of diamagnetic frozen solvent and dilute paramagnetic analytes, this will probably not be very helpful in SQUID measurements, depite the sensitivity. Preparing the samples in an inert gas glovebox should not be a problem.

However, if you are interested in the magnetic properties in (still liquid) solution, I can recommend using an NMR based approach which was proposed by Evans. This is fairly standard and will work with any NMR spectrometer. You can find some information in the linked publications.

Remember that Mercury is a visualiser that is useful for looking at the arrangement of molecules, but it has only very basic functionality for looking at the interactions between molecules: Mercury bases this mostly on finding atom pairs that are closer than some cutoff distance, such as the sum of van der Waals radii. It is important to realise that interactions do not switch off at this distance. Most of the interactions between molecules are much longer-ranged than this - dispersion and particularly electrostatic interactions are still significant well beyond van der Waals radii. If you want to assess the interactions that are holding the crystal structure together, you need to perform some calculations using force fields or an electronic structure method.

 Ionic liquid can be synthesized  in two steps     quaternization followed by reaction with inorganic salt containing desired anion  

(R)3N +RCl  ---NaBF4 -----(R)3NBF4

Dear Tuqeer Nasir

I believe that these attached materials can answer your question

Best regards

how about PLANTS1.2 ?

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

Hi...,

small amount of water can form milky color solution with ethanol therefore  You need to dry (purify) your ethanol and TTIP from water as much as possible avoid any water vapors before and during  making solution,and do not pass saturation limits.

We generally say that the reaction is driven by the redox potential of the corresponding metals. The reactions could be considered as Nucleophilic Substitution

Dear Prof. Carlos

Thank you for your response and advice.

Regards

You can by choosen strong  ligand more than ammine

Thioamides are better ligands and more likely to cleave than amides. The Ru could activate the thioamide to nucleophilic attack by solvent or adventitious water if you in a non-aqueous solution. 

Thank you very much for the links, Vit.

Best Regards,

Yannick 

You're reducing the Cu, what about starting from 4-formyl benzoic acid? if you make the reaction ie 4-amino aniline, you'll have the schiff bases which can be easily reduced to the amine group, those are very stable with copper in different solutions. Be sure to protect the acid group at the beginning. 

More reduced states open the door for closer distances between the metal atoms. Higher order bonds require the metals to be in very low oxidation states so they can get very close to each other. Moreover, lower oxidation states result in larger orbitals which allows them to have a much better overlap.

Additionally, we can use very bulky ligands to protect such bonds. 

The change of colour from light to dark is due to the removal of the axial ligand (ethanol, DMF or water) from the copper acetate lantern, then the dark to light colour change is due to atmospheric water binding onto this coordination site. I find it's a good way to visually identify whether the activated samples have been exposed to air.

At 110 degrees Celcius, HKUST-1 should not have degraded, but it is worth checking by PXRD anyway. I have never done this desolvation when the sample wasn't under vacuum, so I'm not sure whether the air interacts with HKUST-1 at these comparatively low temperatures.

Some ideas:

1. Look for a 6-coordinated Mn complex in the CCDC database. Ideally with similar bonding pattern (4 O and 2 N), although 6 O or 6 N should also do. Get the 3d structure(s) and build your system based on the crystal one. Preoptimize in PM6/PM7 (perhaps start with the Mn-O and Mn-N bond distances frozen at a reasonable value) and check if the results are OK. If so, run DFT.

2. Do the same but start with a simple, ideally octahedral Mn complex (like Mn(H2O)6). Build your system based on this by replacing all atoms except for the 6 ligating O atoms. Don't worry if the bond lengths / angles are not perfect, PM6/PM7 will take care of it in preoptimization.

Be aware, though, that for such complicated systems there are many possibilities for their structures, and simple DFT optimziation of 1 of them does not really make a good proof of the structure. You'll need some experimental validation of your results to make it publishable.

Hello Enrique,

Thanks a lot for your reply! Actually, I have tried to perform optimization with both M06-HF and the pure functional M06-L. However, the obtained result is invariant. Therefore, the error must be due to another factor

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

Kamel Landolsi, for Co(II) and Cu(II) NMR spectroscopy is not suitable since they are paramagnetic species (7 and 9 d-electrons). 

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

A few things to note: firstly, HCl is not soluble in toluene, and therefore to say "the HCl content remains as 3-4%" does not sound correct.  In fact, toluene is used as a solvent precisely for this reason (as opposed to THF / Et2O /dioxane, which dissolve HCl; commercial solutions of HCl in these solvents are available ).

2. How do you know you see "3-4% HCl?" NMR? Give some info here.

3. You are working with pyridines; it is very likely whatever you see as "HCl" is the pyridinium salt. Heating and vac distillation probably won't help your cause. You will need to use an external base to deprotonate.

I am not sure I would say they are generally pyrophoric.  Ferrocene is certainly not and there are many, many complexes described that are not pyrophoric.  Now, with respect to many compounds such as lithium, sodium, magnesium , aluminum alkyls the polarization of the bonds make reactions with oxygen ver facile and the liberation of heat and the presence of oxygen  is sufficient to combust the organic fragment.  There are a number of organometallic texts out there that you should look up and consult.

Michael's explanation seems plausible.  However, the aqueous borate system is extremely complicated, and it's impossible for us to know what you might have isolated.  See the diagrams in the attached patent.  I'm sure even more is known today.

thanks for  your answers!

The attached links and papers provided by Saeideh Hosseini is valuable.

A common anion replacement strategy in Ru chemistry is to use an ammonium salt. As mentioned by Ian it's usual to do this exchange with the chloride salt but it may work with triflate. You always need an excess. As regards solubility common solvents in ruthenium chemistry include DMSO, MeCN and water. You'll have to do a solubility screening to find out what works for your complex. I should mention that the use of silver(I) in Ru(II) chemistry can be a problem as it may oxidize you complex. If want to be sure that the exchange has occurred Tl(I) would be better, although it is toxic. 

I personally have not carried out NBO analysis and therefore won't be able to give you much information. However I hope the web link from a previous R^G discussion could be of help.

Now as for the choice of a software to visualize orbitals, I personally use Gabedit (web link attached). It works well, and gives you the extent of orbital participation in each bonding situation with appropriate coefficients. I believe Gaussview can also help you get the same info.

On how to visualize using Gaussview and other similar useful information can be gleaned from "The Hunt Research Group"s web link (attached). It is thorough and walks one through the basics of setting up calculations, visualizing orbitals, and understanding results.

Lastly, you must be able to more or less guess at the d-orbitals involved in bonding even as you look at any structure.  Any inorganic chemistry text (for e.g., by Meissler and Tarr) teaches how to employ Group theory to determine SALCs and the corresponding MO.

One word of caution: Depending on the symmetry of your complex, you will see heavy mixing of orbitals, and orbital images in this regard can be confusing.  So having the necessary background (through knowing what the SALCs are and what MO's to expect) will help in your interpretation. To that end, the book titled "Orbital interactions in Chemistry" is priceless.

Best wishes.

Dear Saba,

I'm not sure what you want, but everything I have is in the .cell file in my earlier post. The file is plain text, so you can just read the lattice vectors (in Cartesians) and fractional positions straight from it (they're the first 2 blocks after the header).

If you want to visualise the structure, you can import the .cell file into jmol directly; in case you haven't come across it before, jmol is a free 3D visualiser, which can be downloaded from http://www.jmol.org.

All the best,

Phil

It can be employed as thickeners agent, sealants, controlled release of drugs,  etc.