Two new papers on the development of chemosensors for different applications were recently published and we had the opportunity to participate in both with the calculation of electronic interactions.
A chemosensor requires to have a measurable response and calculating either that response from first principles based on the electronic structure, or calculating another physicochemical property related to the response are useful strategies in their molecular design. Additionally, electronic structure calculations helps us unveil the molecular mechanisms underlying their response and efficiency, as well as providing a starting point for their continuous improvement.
In the first paper, CdTe Quantum Dots (QD’s) are used to visualize in real time cell-membrane damages through a Gd Schiff base sensitizer (GdQDs). This probe interacts preferentially with a specific sequence motif of NHE-RF2 scaffold protein which is exposed during cell damage. This interactions yields intensely fluorescent droplets which can be visualized in real time with standard instrumentation. Calculations at the level of theory M06-2X/LANL2DZ plus an external double zeta quality basis set on Gd, were employed to characterize the electronic structure of the Gd³⁺ complex, the Quantum Dot and their mutual interactions. The first challenge was to come up with the right multiplicity for Gd³⁺ (an f⁷ ion) for which we had no experimental evidence of their magnetic properties. From searching the literature and talking to my good friend, inorganic chemist Dr. Vojtech Jancik it was more or less clear the multiplicity had to be an octuplet (all seven electrons unpaired).
As can be seen in figure 1a the Gd-N interactions are mostly electrostatic in nature, a fact that is also reflected in the Wiberg bond indexes calculated as 0.16, 0.17 and 0.21 (a single bond would yield a WBI value closer to 1.0).
PM6 optimizations were employed in optimizing the GdQD as a whole (figure 1f) and the MM-UFF to characterize their union to a peptide sequence (figure 2) from which we observed somewhat unsurprisingly that Gd³⁺interacts preferently with the electron rich residues.
This research was published in ACS Applied Materials and Interfaces. Thanks to Prof. Vojtech Adam from the Mendel University in Brno, Czech Republic for inviting me to collaborate with their interdisciplinary team.
The second sensor I want to write about today is a more closer to home collaboration with Dr. Alejandro Dorazco who developed a fluorescent porphyrin system that becomes chiefly quenched in the presence of Iodide but not with any other halide. This allows for a fast detection of iodide anions, related to some gland diseases, in aqueous samples such as urine. This probe was also granted a patent which technically lists yours-truly as an inventor, cool!
The calculated interaction energy was huge between I⁻ and the porphyrine, which supports the idea of a ionic interaction through which charge transfer interactions quenches the fluorescence of the probe. Figure 3 above shows how the HOMO largely resides on the iodide whereas the LUMO is located on the pi electron system of the porphyrine.
This research was published in Sensors and Actuators B – Chemical.
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:
ΔE = E(MnBxOy) – nEM + nEM’ – E(M’nBxOy) Eq 1
A seamless substitution would imply ΔE = 0 when changing from M to M’
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.
A new paper is coming out! These are always good news for someone whose productivity is evaluated by the number of his/her publications, and in my case the pleasure is double. It turns out that despite the fact a scientist is continuously working, there isn’t always the possibility of having results put “out there”. Back in Mexico we have the “National Researchers System” in which the National Council for Science and Technology encourages us to keep on working by providing economical stimuli and evaluating our productivity by, yes, the number of papers published each year. For three years I worked for a private research center in which fundamental science was tackled as far as it was economically possible and cost effective. Practically all of the work carried out there was confidential since the company it belonged to is leader in its market, not only in Mexico but in Latin America and southern USA! At this facility some papers were published from time to time (most of them came from research in molecular modeling) but not without struggle against the administrators. We can thank for most of the struggle (and the papers!) to Dr. Armando Gama-Goicochea, a great physicist as well as a great friend of mine.
Anyway, the bottom line here is that I’m excited about having a new paper coming out again, even if I’m nowhere close to being first author. This three year paper fastening seems to be over and let us hope it’s only the first of various now that I’m holding a postdoc position here in Romania.
In this paper we tackled the bonding properties of some Aluminum complexes with three chalcogeno triazoles. The electrostatic potential mapped onto a density surface of one of those compounds is currently shown in the header of this blog, btw. We concluded that the bonding in such compounds is mainly covalent as opposed to the more conventional electrostatic notion prevailing for such hard atoms. In order to get this information we resorted to Natural Bonding Analysis calculations with the RHF method and somewhat large basis sets in order to get a full description of the electronic density.
I very much like these systems in which several bonding possibilities occur. The fact that nature is chosing one out of many has always a reason which can be assessed by our models and may serve us to learn how to modify it’s behaviour.
Coordination Diversity of Aluminum Centers Molded by Triazole Based Chalcogen Ligands
Jocelyn Alcántara-García, Vojtech Jancik, Joaquín Barroso, Sandra Hidalgo-Bonilla, Raymundo Cea-Olivares, Rubén A. Toscano and Mónica Moya-Cabrera