Photosynthetic organisms are so widespread around the globe they have adapted to various solar lighting conditions to thrive. The bacteria Blastochloris viridis absorbs light in the near infrared region of the electromagnetic spectrum, in fact, it holds the record for the longest wavelength (~1015 nm) absorbing organism whose Light Harvesting complex 1 (LHC1) has been elucidated. Despite their adaptation to a wide number of light conditions, photosynthetic organism can only make use of so many pigments or chromophores; the LHC1 (Figure 1) in B. viridis in fact is made up of Bacteriochlorophyll-b (BChl-b) molecules, one of the most abundant photosynthetic pigments on Earth, whose main absorption in solution (MeOH) is observed at 795 nm.
So, how can B. viridis use BChl-b molecules to absorb near IR radiation and how does it achieve this remarkable red-shifting effect? The LHC1 structure was solved in 2018 by Qian et al. through Cryo-EM at a 2.9 Å resolution; it is comprised of 17 protein subunits surrounding the so called photosynthetic pigments special pair. Each of these subunits is made up of three α-helix structures surrounding two BChl-b and one dihydroneurosporene (DHN) molecule for a total of 34 of these photosynthetic pigments inside the LHC and 17 DHN molecules interacting between the protein structures and the
main BChl-b pigments.
It was Dr. Jacinto Sandoval and Gustavo “Gus” Mondragón who brought this facts to our attention during their survey of potential candidates for calculating exotic exciton transfer mechanisms in photosynthetic organisms, part of Gustavo’s PhD thesis. To them, it was clear from the start that some sort of cooperative effect between pigments was operating and possibly leading to the red-shifted absorption, therefore a careful dissection of all possible pigments combinations was carried out and their UV-Vis spectra were calculated at the CAMB3LYP/cc-pVDZ on PBE0/6-31G(d) optimized geometries, leading to the systems shown below in figure 2.
System B7 reproduced the red-shifted absorption at 1026 nm, but since the original structure was fitted from the Cryo-EM with a 2.9 Å resolution, “Gus” suggested reaching out to the group of Prof. Andrés Gerardo Cisneros and Dr. Jorge Nochebuena at UT Dallas for carrying out QM/MM calculations; this optimization included the proteins surrounding the pigments in the MM layer and the interacting residues (Hys coordinated to Mg2+ ions in BChl-b) along the chromophores were incorporated into the QM layer, however the thus obtained minima for the B7 system lost the main absorption in the near-IR region, therefore, Dr. Nochebuena suggested running an MD simulation (45 ns) and took a random sampling of ten structures (Figure 3).
All structures in the sampling reproduced the red-shifted absorption (~1000 nm) successfully proving that cooperative and dynamic effects allow B. viridis to perform photosynthesis with low energy radiation (Figure 4). Therefore, close intermolecular interactions along with thermal/dynamical fluctuations allow for a regular pigment such as BChl-b to form near-IR absorbing photosystems for organisms to thrive in low conditions of solar light.
If you want to read further details, this work is now published in the Journal of Chemical Theory and Computation of the American Chemical Society. I’ll talk about this and other ventures in photosynthesis next week at the WATOC conference in Vancouver, swing by to talk CompChem!
Stabilizing Gold in low oxidation states is a longstanding challenge of organometallic chemistry. To do so, a fine tuning of the electron density provided to an Au atom by a ligand via the formation of a σ bond. The group of Professor Rong Shang at the University of Nagasaki has accomplished the stabilization of an aurate complex through the use of a boron, nitrogen-containing heterocyclic carbene; DFT calculations at the wB97XD/(LANL2TZ(f),6-311G(d)) level of theory revealed that this ligand exhibits a high π-withdrawing character of the neutral 4π B,N-heterocyclic carbene (BNC) moiety and a 6π weakly aromatic character with π-donating properties, implying that this is the first cyclic carbene ligand that is able to be tuned between π-withdrawing (Fischer-type)- and π-donating (Schrock-type) kinds.
A π-withdrawing character on part of the ligand is important to allow the electron-rich gold center back donate some of its excess electron density, this way preventing its oxidation. A modification of Bertrand’s cyclic (alkyl)(amino)carbene (CAAC) has allowed Shang and co-workers to perform the two electrons Au(I) reduction to form the aurate shown in figure 1 (CCDC 2109027). This work also reports on the modular synthesis of the BNC-1 ligand and the mechanism was calculated once again by Leonardo “Leo” Lugo.
The ability of the BNC-1 ligand to accept gold’s back donation is reflected on the HOMO/LUMO gap as shown in Figure 2; while BNC-1 has a gap of 7.14 eV, the classic NHC carbene has a gap of 11.28 eV, furthermore, in the case of NHC the accepting orbital is not LUMO but LUMO+1. Additionally, the NBO delocalization energies show that the back donation from Au 5d orbital to the C-N antibonding π* orbital is about half that expected for a Fischer type carbene, suggesting an intermediate character between π accepting and π donating carbene. On the other hand, the largest interaction corresponds to the carbanion density donated to Au vacant p orbital (ca. 45 kcal/mol). All these observations reveal the successful tuning of the electron density on BNC-1.
This study is available in Dalton Transactions. As usual, I’m honored to be a part of this international collaboration, and I’m deeply thankful to the amazing Prof. José Oscar Carlos Jiménez-Halla for inviting me to be a part of it.
Yoshitaka Kimura, Leonardo I. Lugo-Fuentes, Souta Saito, J. Oscar C. Jimenez-Halla, Joaquín Barroso-Flores, Yohsuke Yamamoto, Masaaki Nakamoto and Rong Shang* “A boron, nitrogen-containing heterocyclic carbene (BNC) as a redox active ligand: synthesis and characterization of a lithium BNC-aurate complex”, Dalton Trans., 2022,51, 7899-7906 https://doi.org/10.1039/D2DT01083F
The format of a research paper hasn’t changed much throughout history, despite the enormous changes in platforms available for their consumption and the near extinction of the library issue. Convenient electronic files such as PDFs still resemble printed-and-bound-in-issues papers in their layout instead of exploiting the seemingly endless capabilities of the electronic format.
For instance, why do we still need to have page numbers? a DOI is a full, traceable and unique identification for each work and there are so many nowadays that publishers have to pour them out as e-first, ASAPs, and just accepted before having them assigned page numbers, a process which is still a concern for some researchers (and even for some of the organizations funding them or evaluating their performance). Numbers for Issues, Volumes and Pages are library indexes needed to sort and retrieve information from physical journals but in the e-realm where one can browse all issues online, perform a search and download the results these indexes are hardly of any use, only the year is helpful in establishing a chronological order to the development of ideas. This brings me to the next issue (no pun intended): If bound-issues are no longer a thing then neither should be covers. Being selected for a cover is a huge honor, it means the editorial staff think your work stands out from the published works in the same period; but nowadays is an honor that comes to a price, sometimes a high price. With the existence of covers, back-covers, inner-covers and inner-back-covers and whatnot at USD$1,500 a piece, the honor gets a bit diluted. Advertisers know this and now they place their ads as banners, pop-ups and other online digital formats instead of -to some extent- paying for placing ads in the pages of the journals.
I recently posted a quick informal poll on Twitter about the scientific reading habits of chemists and I confirmed what I expected: only one in five still prefers to mostly read papers on actual paper*, the rest rely on an electronic version such as HTML full text or the most popular PDF on a suitable reader.
— Joaquin Barroso (@joaquinbarroso) June 3, 2019
What came as a surprise for me was that in the follow up poll, Reference Manager programs such as Mendeley, Zotero, EndNote or ReadCube are only preferred by 15% while 80% prefer the PDF reader (I’m guessing Acrobat Reader might be the most popular.) A minority seems to prefer the HTML full text version, which I think is the richest but hardly customizable for note taking, sharing, or, uhm hoarding.
A follow up on the previous poll. Dear #ChemTweeps, if you mostly read papers in electronic format what is your preferred platform?
— Joaquin Barroso (@joaquinbarroso) June 10, 2019
I’m a Mendeley user because I like the integration between users, its portability between platforms and the synchronization features but if I were to move to another reference manager software it would be ReadCube. I like taking notes, highlighting text, and adding summaries and ideas onto the file but above all I like the fact that I can conduct searches in the myriad of PDF files I’ve acumulated over the years. During my PhD studies I had piles of (physical) paper and folders with PDF files that sometimes were easier to print than to sort and organize (I even had a spreadsheet with the literature read-a nightmarish project in itself!)
So, here is my wish list for what I want e-papers in the 21st century to do. Some features are somewhat available in some journals and some can be achieved within the PDF itself others would require a new format or a new platform to be carried out. Please comment what other features would you like to have in papers.
- Say goodbye to the two columns format. I’m zooming to a single column anyway.
- Pop-up charts/plots/schemes/figures. Let me take a look at any graphical object by hovering (or 3D touching in iOS, whatever) on the “see Figure X” legend instead of having to move back and forth to check it, specially when the legend is “see figure SX” and I have to go to the Supporting Information file/section.
- Pop-up References. Currently some PDFs let you jump to the References section when you click on one but you can’t jump back but scroll and find the point where you left.
- Interactive objects. Structures, whether from X-ray diffraction experiments or calculations could be deposited as raw coordinates files for people to play with and most importantly to download** and work with. This would increase the hosting journals need to devote to each work so I’m not holding my breath.
- Audio output. This one should be trickier, but far most helpful. I commute long hours so having papers being read out loud would be a huge time-saver, but it has to be smart. Currently I make Siri read papers by opening them in the Mendeley app, then “select all“, “voice“, but when it hits a formula, or a set of equations the flow is lost (instead of reading water as ‘H-Two-O‘, it reads ‘H-subscript Two-O‘; try having the formula of a perovskite be read)
- A compiler that outputs the ‘traditional version‘ for printing. Sure, why not.
I realize this post may come out as shallow in view of the Plan-S or FAIR initiatives, sorry for that but comfort is not incompatible with accessibility.
What other features do you think research papers should have by now?
* It is true that our attention -and more importantly- our retention of information is not the same when we read on paper than on a screen. Recently there was an interview on this matter on Science Friday.
** I absolutely hate having a Supporting Information section with long PDF lists of coordinates to copy-paste and fix into a new input file. OpenBabel, people!
Calculating the pKa value for a Brønsted acid is very hard, like really hard. A full thermodynamic cycle (fig. 1) needs to be calculated along with the high-accuracy solvation free energy for each of the species under consideration, not to mention the use of expensive methods which will be reviewed here in another post in two weeks time.
Finding descriptors that help us circumvent the need for such sophisticated calculations can help great deal in estimating the pKa value of any given acid. We’ve been interested in the reactivity of σ-hole bearing groups in the past and just like Halogen, Tetrel, Pnicogen and Chalcogen bonds, Hydrogen bonds are highly directional and their strength depends on the polarization of the O-H bond. Therefore, we suggested the use of the maximum surface electrostatic potential (VS,max) on the acid hydrogen atom of carboxylic acids as a descriptor for the strength of their interaction with water, the first step in the deprotonation process.
We selected six basis sets; five density functionals; the MP2 method for a total of thirty-six levels of theory to optimize and calculate VS,max on thirty carboxylic acids for a grand total of 1,080 wavefunctions, which were later passed onto MultiWFN (all calculations were taken with PCM = water). Correlation with the experimental pKa values showed a great correlation across the levels of theory (R2 > 0.9), except for B3LYP. Still, the best correlations were obtained with LC-wPBE/cc-pVDZ and wB97XD/cc-pVDZ. From this latter level of theory the linear correlation yielded the following equation:
pKa = -0.2185(VS,max) + 16.1879
Differences in pKa turned out to be less than 0.5 units, which is remarkable for such a straightforward method; bear in mind that calculation of full thermodynamic cycles above chemical accuracy (1.0 kcal/mol) yields pKa differences above 1.0 units.
We then took this equation for a test with 10 different carboxylic acids and the prediction had a correlation of 98% (fig. 2)
I think this method can really catch on for a quick way to predict the pKa values of any carboxylic acid imaginable. We’re now working on the model extension to other groups (i.e. Bronsted bases) and putting together a black-box workflow so as to make it even more accessible and straightforward to use.
We’ve recently published this work in the journal Molecules, an open access publication. Thanks to Prof. Steve Scheiner for inviting us to participate in the special issue devoted to tetrel bonding. Thanks to Guillermo Caballero for the inception of this project and to Dr. Jacinto Sandoval for taking the time from his research in photosynthesis to work on this pet project of ours and of course the rest of the students (Gustavo Mondragón, Marco Diaz, Raúl Torres) whose hard work produced this work.
Photosynthesis, the basis of life on Earth, is based on the capacity a living organism has of capturing solar energy and transform it into chemical energy through the synthesis of macromolecules like carbohydrates. Despite the fact that most of the molecular processes present in most photosynthetic organisms (plants, algae and even some bacteria) are well described, the mechanism of energy transference from the light harvesting molecules to the reaction centers are not entirely known. Therefore, in our lab we have set ourselves to study the possibility of some excitonic transference mechanisms between pigments (chlorophyll and its corresponding derivatives). It is widely known that the photophysical properties of chlorophylls and their derivatives stem from the electronic structure of the porphyrin and it is modulated by the presence of Mg but its not this ion the one that undergoes the main electronic transitions; also, we know that Mg almost never lies in the same plane as the porphyrin macrocycle because it bears a fifth coordination whether to another pigment or to a protein that keeps it in place (Figure 1).
During our calculations of the electronic structure of the pigments (Bacteriochlorophyll-a, BChl-a) present in the Fenna-Matthews-Olson complex of sulfur dependent bacteria we found that the Mg²⁺ ion at the center of one of these pigments could in fact create an intermolecular interaction with the C=C double bond in the phytol fragment which lied beneath the porphyrin ring.
This would be the first time that a dihapto coordination is suggested to occur in any chlorophyll and that on itself is interesting enough but we took it further and calculated the photophysical implications of having this fifth intramolecular dihapto coordination as opposed to a protein or none for that matter. Figure 3 shows that the calculated UV-Vis spectra (calculated with Time Dependent DFT at the CAM-B3LYP functional and the cc-pVDZ, 6-31G(d,p) and 6-31+G(d,p) basis sets). A red shift is observed for the planar configuration, respect to the five coordinated species (regardless of whether it is to histidine or to the C=C double bond in the phytyl moiety).
Before calculating the UV-Vis spectra, we had to unambiguously define the presence of this observed interaction. To that end we calculated to a first approximation the C-Mg Wiberg bond indexes at the CAM-B3LYP/cc-pVDZ level of theory. Both values were C(1)-Mg 0.022 and C(2)-Mg 0.032, which are indicative of weak interactions; but to take it even further we performed a non-covalent interactions analysis (NCI) under the Atoms in Molecules formalism, calculated at the M062X density which yielded the presence of the expected critical points for the η²Mg-(C=C) interaction. As a control calculation we performed the same calculation for Magnoscene just to unambiguously assign these kind of interactions (Fig 4, bottom).
This research is now available at the International Journal of Quantum Chemistry. A big shoutout and kudos to Gustavo “Gus” Mondragón for his work in this project during his masters; many more things come to him and our group in this and other research ventures.
I’ve lately reviewed a ton of papers whose titles begin with some version of “Computational studies of…“, “Theoretical studies of…” or even more subtly just subtitled “A theoretical/computational study” and even when I gotta confess this is probably something I’ve done once or twice myself, it got me thinking about the place and role of computational chemistry within chemistry itself.
As opposed to physicists, chemists are pressed to defend a utilitarian view of their work and possibly because of that view some computational chemists sometimes lose sight of their real contribution to a study, which is far from just performing a routine electronic structure calculation. I personally don’t like it when an experimental colleague comes asking for ‘some calculations’ without a clear question to be answered by them; Computational Chemistry is not an auxiliary science but a branch of physical chemistry in its own right, one that provides all the insight experiments -chemical or physical- sometimes cannot.
I’m no authority on authoring research papers but I encourage my students to think about the titles of their manuscripts in terms of what the manuscript most heavily relies on; whether it’s the phenomenon, the methodology or the object of the study, that should be further stressed on the title. Papers titled “Computational studies of…” usually are followed by ‘the object of study’ possibly overlooking the phenomenon observed throughout such studies. It is therefore a disservice to the science contained within the manuscript, just like experimental papers gain little from titles such as “Synthesis and Characterization of…“. It all comes down to finding a suitable narrative for our work, something that I constantly remind my students. It’s not about losing rigor or finding a way to oversell our results but instead to actually drive a point home. What did you do why and how. Anna Clemens, a professional scientific writer has a fantastic post on her blog about it and does it far better than I ever could. Also, when ranting on Twitter, the book Houston, we have a narrative was recommended to me, I will surely put it my to-read list.
While I’m on the topic of narratives in science, I’m sure Dr. Stuart Cantrill from Nature Chemistry wouldn’t mind if I share with you his deconstruction of an abstract. Let’s play a game and give this abstract a title in the comments section based on the information vested in it.
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.
As if I didn’t have enough things to do I’m launching a new blog inspired by the #365papers hashtag on Twitter and the naturalproductman.wordpress.com blog. In it I’ll hopefully list, write a femto-review of all the papers I read. This new effort is even more daunting than the actual reading of the huge digital pile of papers I have in my Mendeley To-Be-Read folder, the fattest of them all. The papers therein wont be a comprehensive review of Comp.Chem. must-read papers but rather papers relevant to our lab’s research or curiosity.
Maybe I’ll include some papers brought to my attention by the group and they could do the review. The whole endeavor might flop in a few weeks but I want to give it a shot; we’ll see how it mutates and if it survives or not. So far I haven’t managed to review all papers read but maybe this post will prompt to do so if only to save some face. The domain of the new blog is compchemdigest.wordpress.com but I think it should have included the word MY at the beginning so as to convey the idea that it is only my own biased reading list. Anyway, if you’re interested share it and subscribe, those post will not be publicized.
Ever since I read the highly praised article by Floyd Romesberg in Nature back in 2013 I got really interested in synthetic biology. In said article, an unnatural base pair (UBP) was not only inserted into a DNA double strand in vivo but the organism was even able to reproduce the UBPs present in subsequent generations.
Inserting new unnatural base pairs in DNA works a lot like editing a computer’s code. Inserting a couple UBPs in vitro is like inserting a comment; it wont make a difference but its still there. If the DNA sequence containing the UBPs can be amplified by molecular biology techniques such as PCR it means that a polymerase enzyme is able to recognize it and place it in site, this is equivalent to inserting a ‘hello world’ section into a working code; it will compile but it’s pretty much useless. Inserting these UBPs in vivo means that the organism is able to thrive despite the large deformation in a short section of its genetic code, but having it replicated by the chemical machinery of the nucleus is an amazing feat that only a few molecules could allow.
The ultimate goal of synthetic biology would be to find a UBP which codes effectively and purposefully during translation of DNA.This last feat would be equivalent to inserting a working subroutine in a program with a specific purpose. But not only could the use of UBPs serve for the purposes of expanding the genetic code from a quaternary (base four) to a senary (base six) system: the field of DNA origami could also benefit from having an expansion in the chemical and structural possibilities of the famous double helix; marking and editing a sequence would also become easier by having distinctive sections with nucleotides other than A, T, C and G.
It is precisely in the concept of double helix that our research takes place since the available biochemical machinery for translation and replication can only work on a double helix, else, the repair mechanisms get activated or the DNA will just stop serving its purpose (i.e. the code wont compile).
My good friend, Dr. Rodrigo Galindo and I have worked on the simulation of Romesberg’s UBPs in order to understand the underlying structural, dynamical and electronic causes that made them so successful and to possibly design more efficient UBPs based on a set of general principles. A first paper has been accepted for publication in Phys.Chem.Chem.Phys. and we’re very excited for it; more on that in a future post.