Blog Archives

Collaborations in Inorganic Chemistry


I began my path in computational chemistry while I still was an undergraduate student, working on my thesis under professor Cea at unam, synthesizing main group complexes with sulfur containing ligands. Quite a mouthful, I know. Therefore my first calculations dealt with obtaining Bond indexed for bidentate ligands bonded to tin, antimony and even arsenic; yes! I worked with arsenic once! Happily, I keep a tight bond (pun intended) with inorganic chemists and the recent two papers published with the group of Prof. Mónica Moya are proof of that.

In the first paper, cyclic metallaborates were formed with Ga and Al but when a cycle of a given size formed with one it didn’t with the other (fig 1), so I calculated the relative energies of both analogues while compensating for the change in the number of electrons with the following equation:

Fig 1

Imagen1

Under the same conditions 6-membered rings were formed  with Ga but not with Al and 8-membered rings were obtained for Al but not for Ga. Differences in their covalent radii alone couldn’t account for this fact.

ΔE = E(MnBxOy) – nEM + nEM’ – E(M’nBxOy)                     Eq 1

A seamless substitution would imply ΔE = 0 when changing from M to M’

Imagen2.jpg

Hipothetical compounds optimized at the B3LYP/6-31G(d,p) level of theory

The calculated ΔE were: ΔE(3/3′) = -81.38 kcal/mol; ΔE(4/4′) = 40.61 kcal/mol; ΔE(5/5′) = 70.98 kcal/mol

In all, the increased stability and higher covalent character of the Ga-O-Ga unit compared to that of the Al analogue favors the formation of different sized rings.

Additionally, a free energy change analysis was performed to assess the relative stability between compounds. Changes in free energy can be obtained easily from the thermochemistry section in the FREQ calculation from Gaussian.

This paper is published in Inorganic Chemistry under the following citation: Erandi Bernabé-Pablo, Vojtech Jancik, Diego Martínez-Otero, Joaquín Barroso-Flores, and Mónica Moya-Cabrera* “Molecular Group 13 Metallaborates Derived from M−O−M Cleavage Promoted by BH3” Inorg. Chem. 2017, 56, 7890−7899

The second paper deals with heavier atoms and the bonds the formed around Yttrium complexes with triazoles, for which we calculated a more detailed distribution of the electronic density and concluded that the coordination of Cp to Y involves a high component of ionic character.

This paper is published in Ana Cristina García-Álvarez, Erandi Bernabé-Pablo, Joaquín Barroso-Flores, Vojtech Jancik, Diego Martínez-Otero, T. Jesús Morales-Juárez, Mónica Moya-Cabrera* “Multinuclear rare-earth metal complexes supported by chalcogen-based 1,2,3-triazole” Polyhedron 135 (2017) 10-16

We keep working on other projects and I hope we keep on doing so for the foreseeable future because those main group metals have been in my blood all this century. Thanks and a big shoutout to Dr. Monica Moya for keeping me in her highly productive and competitive team of researchers; here is to many more years of joint work.

Advertisements

Comparing the Relative Stability of Non-Equivalent Molecules


How do you compare the stability of two or more compounds which differ in some central atom(s)?

If you simply calculate the energy of both compounds you get a misleading answer since the number of electrons is different from one to the next -in fact, the answer is not so much misleading as it is erroneous. Take compounds 1 and 2 shown in figure 1, for example. Compound 1 was recently synthesized characterized through X-Ray crystallography by my friend Dr. Monica Moya’s group; compound 2 doesn’t exist and we want to know why – or at least know if it is relatively unstable respect to 1.

Figure 1. Compound 1 exists but compound 2 is apparently less stable. Is it?

Figure 1. Compound 1 exists but compound 2 is apparently less stable. Is it?

Although stoichiometry is the same, varying only by the substitution of Ga by Al the number of electrons is quite different. We then made the following assumption: Since the atomic radii of Ga and Al are quite similar (according to the CCDC their respective covalent radii are 122[4] and 121[3] pm), relative stability must rely on the bonding properties rendering 2 harder to obtain, at least through the method used for 1. The total energy for compound 1 was calculated at the M06-2X/6-31G(d,p) level of theory; then both Al atoms were changed by Ga and the total energy was calculated again at the same level. Separately, the energy of isolated Ga and Al atoms were calculated. Compensating the number of electrons was now a simple algebraic problem:

ΔE = E(MnBxOy) – nEM + nEM’ – E(M’nBxOy)

 The absolute energy difference E1 – E2 is staggering due to the excess of 36 electrons in 2. But after this compensation procedure we now have a more reliable result of ΔE value of ca. 81 kcal/mol in favor of compound 1. In strict sense, we performed geometry optimizations at various stages: first on compound 1 to remove the distorsions due to the crystal field and then on the substituted compound 2 to make sure Ga atoms would find a right fit in the molecule but since their covalent radii are similar, no significant changes in the overall geometry were observed confirming the previous assumption.

We now have the value of the energy difference between 1 and 2 and other similar cases, the next step is to find the distal causes of the relative stability which may rely on the bonding properties of the Ga-O bond respect to the Al-O bonds.

What do you think? Is there another method you can share for tackling this problem? Please share your thoughts on the comments section.

Thanks for reading.

%d bloggers like this: