[note: Figures are in the source article and not highlighted in this summary]
This is a summary of work reported in the Journal of Inorganic Chemistry concerning macrocyclic coordination chemistry in the periodic S group. In the literature concerning these molecules we see that large cyclic chelate-type ligands, termed macrocyclic ligands, are often useful in transition metal chemistry due to their multidentate properties. Their multiple bonding allowing for higher achievable stabilities through the macrocyclic effect. The macrocyclic effect follows the entropy driven principle set forth by the chelate effect, however it is enhanced by the locked cyclic structure of the ligand itself. The area of macrocyclic research Champion1 and associates reports on the use of thioether ligands bonding with s group elements, primarily sodium. A type of bonding typically reserved for crown ethers and a handful of thio-oxa and selena-oxa macrocyclic complexes1.
Since s block complexes containing thioether only coordination bonds are completely unknown1, the group’s goal was to determine possibility of this coordination. Their method focused on a thioether macrocycle in reaction with a sodium cation bonded with the weak [BArF]-1 ([BArF]-1 here, termed “BARF”, corresponds to: [B[3,5-(CF3)2C6H3]4]−) anion in tetrahydrofuran (THF) solution. The BARF anion being so weak provides less competition in response to the macrocycle reacting with the sodium atom.
The group reports the first group 1 thioether only complex, seen as an unexpected cation geometry in [Na([24]aneS8)]+. The BARF anion provides charge balance here. Due to the instability of the metal-ligand bonds, unless supporting ligands were used, isolation of the unexpected cation would be improbable. These group 1 hard cation-soft ligand bonds being one of the reasons behind the lack of previous discoveries concerning these types of complexes. Isolation and crystallography was acquired for a partial sandwich complex of Na-S tridentate coordination and two THF ligands.1 In order to explore the electronic and orbital properties of the complex computational chemistry was used.
At minimal energy state, the complex has S4 Symmetry, and in experimental or solid state occupies a dodecahedral geometry.1 Bond lengths and angles were matched with crystallography data. Further computations were ran to understand the charge distribution across the macrocyclic ligand, which showed that Na+ attracts the lone pairs found on the S atoms. These are then stabilized via resonance across the neighboring C-C and C-H bonds.1 The density functional theory (DFT) calculations showed the S atoms to have a positive charges and the C atoms to have negative charges.1 H atoms exhibit a slight positive charge which is within the norm. Orbital plots were also developed using the optimized, minimum energy, structures HOMO and LUMO calculations, and were visualized in Figure 3. HOMO orbitals show electron transfer into the 3s and 3p of the Na+.
It is proposed that using the above data, further group 1 macrocyclic coordination complexes can be achieved. High bonding complexes would prove most capable at displacing any possible ligand competition, such as that found in THF. In essence higher denticity in soft donors leads to higher stability of group 1 s block acceptor complexes.
Summary: 2/13/2016
Reference
Champion, M., Dyke, J., Levason, W., et al; Sodium Thioether Macrocyclic Chemistry: Remarkable Homoleptic Octathia coordination to Na+, J. Inorganic Chemistry, 2015, 54, 2497-2499.
Below is a 3D rendering of a Human Rhinovirus (C-15) , one of the ~100 rhinovirus types which occur worldwide. These viruses are responsible for what is commonly referred to as the common cold. The symptoms are wide and cover a variety of systems from sore throat, runny nose, and nasal congestion, to sneezing and coughing. These are the most common symptoms, but in some the virus can manifest additional symptoms: muscle aches, fatigue, malaise, headache, muscle weakness, or loss of appetite. This is typically not an issue for most people, but the young, elderly, and immunocompromised individuals should take care and see their physician when needed. The plus is that fever and extreme fatigue are not typically present, being a more common occurrence in Influenza infections. In essence, thank this little guy for all those Pharmaceutical commercials.
The rhinovirus is spread by two modes of transmission. You can become infected if you 1) come in contact with aerosols of respiratory droplets from an infected person or 2) through contact with contaminated surfaces (This includes direct person-to-person contact). To prevent transmission, people should cover their mouth and nose with a tissue when coughing, and wash their hands regularly. It is good practice to use your elbow to cover your mouth when coughing or sneezing, so as to avoid contaminating your hands. The cold season typically starts around September and ends in April!
Influenza
What is interesting about the rhinovirus, and problematic for virologists, is the fact that there are so many types of these viruses. Add that macro variety, on top of continuous genetic mutations within each, and you have a ever changing group of entities. This is why we do not have a “cold” shot vaccine like we do for the flu. The flu,or influenza, has only 3 main types: A, B, and C. Talk about something that’s a lot easier to control.
Influenza Type A and B are the main ones responsible for the annual influenza epidemics. These epidemics can seriously affect all populations and occur globally. The highest risk of complications occur among children younger than 2 years, and adults older than 65 years. Pregnant women and people of any age with certain medical conditions (such as chronic heart, lung, kidney, liver, blood or metabolic diseases (i.e. diabetes), or weakened immune systems) are also at a high risk for infection. These viruses cause up to ~17-30% of the population to exhibit those sniffling, aching, coughing, and fever symptoms, statistically shown as an estimated attack rate of 5%–10% in adults and 20%–30% in children. As far as Type C, it also causes flu; however, type C flu symptoms are much less severe and occur much less frequently which is why this type is not tested for in clinical laboratories (at least not in any I have worked in as due to its lack of severity this would constitute a waste of resources) or vaccinated for.
Influenza ranks in the top 10 causes of death in the U.S., and causes more death then chronic liver disease, cirrhosis, and septicemia. The CDC links it to between 3,000-4,000 deaths and 200,000 hospitalizations each year. The World Health Organization (WHO) reports annual worldwide mortality rates between 250 000 to 500 000, with 3 to 5 million estimated cases. The seasonal flu vaccine was created to try to avert these epidemics.
CDC Weekly fluview report, accessed 03/29/2016
CDC mortality report, 2013. Deaths = 3,697
Each influenza type has different characteristics. Type A flu, or the influenza A viruses, are capable of infecting animals as well as humans, though infection in humans is more common. Wild birds commonly act as hosts for this flu type. Type B flu viruses are only found in humans and may cause a less severe reaction than type A flu virus. Occasionally, type B flu can still harmful. Influenza type B viruses are not classified by sub-type and do not cause pandemics.
Below are two videos which explore the influenza virus in more detail; one an NPR video illustrating the flu virus infecting a human cell, and the second walking through the anatomy of the virus itself.
How many viruses are there?
Estimating the diversity of life is a persistent challenge in the field of biology. At such a micro scale scientists are unable to differentiate viruses, or even bacteria, based on morphology alone. They must rely on novel methods, and advances in technology, to view and categorize them appropriately. Microbiologists have even indicated, using phylogeny based gene sequencing, that multiple species would thrive in environments once thought impossible. This negates some important variables, but the indication holds much potential for bacterial and viral discovery.
With that said, how many different viruses are there? To get an exact value is hard, but Dr. Stephen Morse of Columbia University School of Health suggested that there were about one million viruses of vertebrates. This estimate was arrived at by assuming ~20 different viruses for each of the 50,000+ vertebrates on Earth. This was before pathogen discovery experts Ian Lipkin and Joe DeRisi, out of Weill Medical College at Cornell, released the results of a new study, suggesting that at least 320,000 different viruses infect mammals (58 viruses for each species). The authors state that this is likely to be an underestimate as only 9 viral families were targeted by the study and the polymerase chain reaction (PCR) approach used could only detects viruses similar to those that we already know. Using these new numbers though we can perhaps have an idea of Earth’s potential virus diversity. First let us establish that there are 5,416 different mammal species in the world, and a total of 66,178 vertebrate species according to the International Union for Conservation of Nature (IUCN). Since mammals only make up around 8% of total vertebrates we can see that using Lipkins estimates for vertebrate species alone allows for a large zoonotic pool. If we assume the quoted figure of 320,000 viruses for 5,400 species, in a pool of 66,000 species, the total estimated virus load would obviously far exceed Dr. Morse calculation at 1.73 billion. Even with other variables considered it is still quite plausible to have one million species with that large of a number.
According to the Catalogue of Life and the World Register of Marine Species there are 1.2 million species officially registered as being present and accounted for on planet Earth. These hold there place in the taxonomic classification system started 253 years ago by Carl Linnaeus. This is a large number, but every scientist knows we are far from discovering every species out there. I mean researchers report more than 15,000 new species annually. A good example of this is seen in a new calculation published in PLoS Biology by the Census of Marine Life scientists. It is based on a statistical study of the taxonomic classification system currently known and derives its data extrapolating from patterns in its branches. These patterns are found in the higher levels of taxonomic divisions, like order and phylum, and the number of species within each. The numerical value calculated for the potential eukaryotic species was at the 8.74 million mark, give or take 1.3 million. A huge difference which really sums up the potential underlying biodiversity surrounding us.You may see, in looking at some of this data, that biodiversity looks like it increases the smaller something gets. That’s what I saw, and accordingly, in 1988 at the University of Oxford an evolutionary biologist named Robert May observed this as well. His work focused on the calculation of the diversity of smaller animals and concerned land animals, but the correlation between diversity and size is one I hypothesize will hold going forward.
So, let us use the low ball number of viruses for an individual species, as was used by Dr. Morse, and apply it across the low ball number of eukaryotic species we currently know exist. If there are 20 different viruses for each species and there are 1.2 million eukaryotic species they could infect (this is still leaving out viruses which infect bacteria) then that means there is at least 24 million viruses just floating around.If we extend this analysis using the 58 viruses per species model, that number jumps to 69.9 million. Considering that there are 1031 virus particles in the oceans (mostly bacteriophage species) the true number is likely to be substantially higher.
Having a zoonotic pool this large, a growing lack of biodiversity in larger animals, and a considerably smaller globe due to ease of travel creates a melting pot of opportunity for viral species. Genetic mutation is a viruses favorite pastime. They are all just waiting for their chance to mutate, infect us, and eat our brains! This is why the field of pathogen discovery has grown so much in the last decade. It truly is a Virus World.
Herpes Simplex Virus-1 A-Capsid
Resources & References:
Articles & Sites
Influenza – CDC’s Influenza database of flu facts as well as additional flu related resources. There are links to the current fluview reports concerning current epidemiological data as well.
Holly A. Basta, Jean-Yves Sgro, Ann C. Palmenberg, Modeling of the human rhinovirus C capsid suggests a novel topography with insights on receptor preference and immunogenicity, Virology Volume 448, 5 January 2014, Pages 176-184.
BioVisions at Harvard – The BioVisions Department is a collaboration between video & graphic design students and the students in the Bio/Chemistry Departments. The videos they make are highly accurate and a great teaching aid!
The RCSB PDB Molecule of the Month by David S. Goodsell featured many virus capids and viral molecules over the years. 2009 featured Tobacco Mosaic Virus.
It was recently confirmed by the International Union of Pure and Applied Chemistry (Iupac) that four new elements have been successfully synthesized. Their atomic numbers are 113, 115, 117, and 118. With these four new elements we finally fill out the 7th row of the Periodic table.
If you have been living under a rock or you just need to brush up on your chemistry and periodic table trivia then watch this great video bySocratica.
Three groups were credited with creating these elements, hailing from Japan, Russia, and the US, they spent many years gathering enough evidence to convince IUPAC and the International Union of Pure and Applied Physics (IUPAC’s sister union for physics, IUPAP) experts that they had indeed succeeded in their synthesis.
This is difficult because all four of the new elements are very unstable superheavy metals and they decay extremely fast. To create the elements heavy metals were bombarded with ion beams. The detection of the new elements can typically only be measured by means of reading the nuclides and radiation which are put out upon their inevitable decay, which takes delicate instruments and a lot of repeated experiments to ensure their findings are correct. The groups would need a lot of evidence ro support each claim.
Element 113– ununtrium (temporary name)
This was the first element to be discovered in Easten Asia and was created by Kosuke Morita’s group. These scientists worked at the RIKEN Nishina Center for Accelerator-based Science in Japan. They first claimed to have created the element in 2004, but needed more evidence to support their claim as their were still uncertainties which needed to be accounted for.
This element was developed by shooting a beam of zinc-70 at a heavy metal target of bismuth-209. By 2012 they had enough evidence to support their findings.
The next two elements:
Elements 115 – ununpentium (temporary name)
and
Elements 117 – ununseptium (temporary name)
were created by a collaboration between three institutions.
The Lawrence Livermore National Library – US
The Joint Institute for Nuclear Research – Russia
The Oak Ridge National Laboratory – US
and lastly,
Element 118 – ununoctium (temporary name)
which was also created by the Lawrence Livermore-Joint Institute for Nuclear Research collaboration in published work from 2006.
Now that IUPAC and IUPAP have determined that the discoveries are indeed a reality, and the new elements are officially being added to the periodic table, the institutions responsible for finding them will be awarded the honors of naming them.
Pretty much what this all means is that now all those posters, mugs, t-shirts, and tapestries are ALL WRONG! and you need to go buy new ones.
Sadly, it will be a bit longer before the textbooks can all be updated, as the names and symbols will need to be approved by the inorganic chemistry division of IUPAC, who will also submit them for public review. There are an assortment of rules which govern what you can name an element, and these will need to be abide by. The Royal Chemistry Society has a nice list of them here.
They predict it to take between four to six months at the present moment to name the four new elements.
Now, with that behind us, we have to look forward to the next set of elements. Evidently, researchers expect there to be a stable area as we get further on into the superheavy metals beyond atomic number 118. It looks as if time will tell…
nurvus lab repository 