Posts Tagged ‘chemistry’

Need to make a molecule? Ask this AI for instructions

April 7, 2018

Need to make a molecule? Ask this AI for instructions #DeepLearning to do better #retrosynthesis. Perhaps other things in chemistry could be learned as well!

“The tool, described in Nature on 28 March1, is not the first software to wield artificial intelligence (AI) instead of human skill and intuition. Yet chemists hail the development as a milestone, saying that it could speed up the process of drug discovery and make organic chemistry more efficient.

“What we have seen here is that this kind of artificial intelligence can capture this expert knowledge,” says Pablo Carbonell, who designs synthesis-predicting tools at the University of Manchester, UK, and was not involved in the work. He describes the effort as “a landmark paper”.”

Remembering organic chemistry legend Robert Burns Woodward | April 10, 2017 Issue – Vol. 95 Issue 15 | Chemical & Engineering News

April 28, 2017

Organic chemistry legend…#Woodward Well illustrates cleverness in synthesis, eg porphyrin analogy for chlorophyll

“Woodward’s work was less about inventing reactions, although he did do that on occasion. He didn’t, for example, design a reaction and then apply it over and over again to many natural products, a strategy that became common after Woodward’s death,

Woodward’s synthesis of the once popular antihypertensive drug reserpine, published in 1956, is one that many chemists point to as a highlight in the history of total synthesis of natural products. “It was founded on visionary ideas and published right about the time organic chemists were worrying about how to utilize the principles of conformational analysis in synthesis design,” Sorensen says. Woodward built reserpine’s intricate structure using simple reagents. At the end of the synthesis, he and his group corrected an errant
stereocenter by forcing an intermediate compound into an unfavorable conformation so that it epimerized into the correct stereoisomer. …
Sorensen points to Woodward’s synthesis of chlorophyll, which took four years to complete and was published in 1960, as a prime example of strategic risk taking in organic synthesis. Woodward thought the molecular architecture that defines the chlorins—a structural family that includes chlorophyll—might originate from a highly substituted porphyrin with a crowded periphery because of structural similarities, Sorensen explains.”

Remembering organic chemistry legend Robert Burns Woodward | April 10, 2017 Issue – Vol. 95 Issue 15 | Chemical & Engineering News

Periodic Graphics: The Chemistry Of Barbecue | July 13, 2015 Issue – Vol. 93 Issue 28 | Chemical & Engineering News

July 28, 2016

Periodic Graphics: The #Chemistry Of Barbecue Flavor-forming #Maillard reaction occupies center stage

Throw caution to the wind?

March 15, 2016

Throw caution to the wind? Interesting piece about#Nobelprizes. Negative on the continuation of the #chemistry one

@Chemjobber I agree. Sad to see chemistry so assaulted!

Identification of an iridium-containing compound with a formal oxidation state of IX : Nature : Nature Publishing Group

March 7, 2015

Is this tetrahedral?

Ir-containing compound w/ a formal #oxidation state of IX
Surpassing OsO4, removing d electron gives [IrO4]+ cation

"Removal of the remaining d electron from IrO4 would lead to the iridium tetroxide cation ([IrO4]+)"

relative_abundance.jpg (3038×2414)

December 30, 2014

Periodic Table, scaled to abundance on Earth Illustrates importance of 1st row HT @pickover

Next-Gen Sequencing Is A Numbers Game | August 18, 2014 Issue – Vol. 92 Issue 33 | Chemical & Engineering News

September 1, 2014

NextGen #Sequencing Is A Numbers Game Overview of contenders w/ snippets categorizing #chemistry, eg seq-by-synthesis


So far, Illumina leads the race. In January, the San Diego-based firm

launched its HiSeq X Ten system with a price tag of $10 million.
Consisting of 10 ultra-high-throughput sequencers, each capable of
generating up to 1.8 terabases of data in less than three days

Illumina uses a sequencing-by-synthesis method. After DNA fragments

are amplified on a chip, sequencing occurs by synthesizing a DNA
strand complementary to the target strand by enzymatically attaching
fluorescently labeled nucleotides one at a time. When reactions occur,
the labels are optically imaged to identify what was attached, and the

cycle is repeated.

Thermo Fisher holds second place in the NGS market, with about 16% of
sales. ….ABI launched its first NGS system based on sequencing by
oligonucleotide ligation and detection, known as SOLiD.

Unlike highly accurate but less parallelizable Sanger methods, NGS

systems carry out massive numbers of reactions, or sequence reads, at
one time. Like Illumina’s approach, SOLiD uses sequencing by synthesis
of amplified DNA fragments on either a bead or chip. Instead of
nucleotides, it uses fluorescently labeled probes that are repeatedly

ligated to the growing strand, optically imaged, and cleaved off. How
long these processes can be kept going determines the “read length”
that can be sequenced in a run.

The first lower-cost, nonoptical system appeared in 2010 after Life

Technologies—now part of Thermo Fisher and formed from the 2008 merger
of ABI and Invitrogen—acquired Ion Torrent for $725 million. Its
systems use sequencing by synthesis, but with unlabeled nucleotides on
a semiconductor chip. The chip electrically senses the release of

hydrogen ions when bases attach. The full sequence is read by
sequentially adding bases and tracking reactions across millions of

Pacific Biosciences’ single-molecule real-time sequencing is a
sequencing-by-synthesis approach that doesn’t use an amplified set of
DNA fragments and doesn’t require stopping and starting the reaction

to add reagents and image results. Reactions on individual DNA
molecules are tracked in real time across 150,000 nanoscale wells
where isolated polymerases read the DNA and incorporate fluorescently
tagged nucleotides. Because detection occurs only at the bottom of the

wells, the background noise from the other reactions is reduced.

Stability of the sequencing process depends in large part on the
polymerase. Pacific Biosciences has modified a simple bacteriophage
enzyme, slowing it down so that it incorporates about three bases per

second and its detector can keep up.


Most interest has been in the U.K.’s Oxford Nanopore Technologies as
it moves closer to launching a new sequencing device. Its MinION uses

protein nanopores held in a polymer membrane to sequence
single-stranded DNA in real time. Individual bases are identified
through changes in electrical current as a linear, single-stranded DNA
molecule moves through a nanopore.


Master of Missing Elements » American Scientist

August 23, 2014

Master of Missing #Elements, Moseley Xray spectra show charge not mass orders periodic table, fixing K-Ar reversal

Lethal Chemistry at Harvard –

March 17, 2014

Lethal #Chemistry at Harvard. Disaster before the last bond in synthesis. An #oldie but still relevant to #phd life.

Many letters – eg

Little Interactions Mean a Lot » American Scientist

March 1, 2014

Little Interactions Mean a Lot. Nice overview of small energies determining structure, eg ~5kcal/mol hbond #chem 1/2

Little Interactions Mean a Lot. C18H38 alkane is a great example: 2 gauche turns allow a kink & favorable folding-over VDW interactions 2/2


What is big from one perspective is small from another, and energy can be measured in a variety of ways. By “big energies,” I mean those equal or greater than about 1 electron volt per molecule, which is equal to 23.1 kilocalories per mole, or 96.5 kilojoules per mole. A photon of yellow light has an energy of about 2.1 electron volts.

In theoretical chemistry, I was looking for molecules that in one bonding arrangement could be at least 1 electron volt per molecule more stable than in an alternative configuration, or that would require an activation energy (the barrier to a reaction taking place) that is at least 1 electron volt lower than a competing reaction, thus proceeding much more expeditiously. I knew that the strength of the hydrogen bonds that hold together the base pairs of the DNA in my body are, per pair of atoms involved, at least an order of magnitude smaller than 1 electron volt. So are the “dispersion” forces (more on these in a moment) that make the molecules around me–be they acetaminophen or ethanol–solids and liquids rather than gases. …

In addition to the hydrogen bonding mentioned earlier, there are other small forces, like multipole interactions that convert an asymmetry of the way electrons are distributed in a molecule into forces between them. And dispersion forces, which are responsible for molecules and atoms condensing and eventually freezing.


Prototypical hydrogen bonding, the noncovalent bond associated with wet hair and brushes, occurs when the hydrogen of a polar
oxygen-hydrogen (O-H) or nitrogen-hydrogen (N-H) bond comes near an electron source, typically the lone pair of electrons of a nearby oxygen or nitrogen atom. …
Despite such disagreement on origins, there is no disagreement at all on the magnitude of the energy involved, generally less than 5 kilocalories per mole. Small again, but there are oh-so-many of them.

Small energies play out in other interesting ways in some of the simplest organic molecules: the unbranched long-chain hydrocarbons, such as the liquid to waxy “normal” alkanes, which are written chemically as CH3(CH2)nCH3. The molecules in gasoline belong to this family with n = 6 or so; increasing n from six leads to diesel fuel, jet fuel, oil, and lubricants…..At each interior point in the hydrocarbon chain, for every four carbons, a choice is available between an extended conformation, which chemists refer to as all-anti, and two mirror-image curled-up forms, known as gauche conformations. …
The energy difference between the two conformations is truly minuscule. The gauche geometry is merely about one kilocalorie per mole in energy above the global minimum of the anti form; ….

That kinking costs energy, but only a wee amount–each gauche turn has an associated penalty of about 1 kilocalorie per mole. What is accomplished by the kink ….
the second part of the chain is brought near the first. In that conformation, or actually in a family of conformations looking roughly like that, there is a new source of stabilization that is unavailable in the extended, all-anti geometry: attractive dispersion forces between the two parts of the chain.

Small as they individually are, dispersion interactions add up. For an isolated molecule, for some n in CH3(CH2)n CH3 for example, the energy lowering (stabilization) in dispersion interaction will win out over the increase in energy (destabilization) in kinking, the latter accomplished by two or more gauche conformations along the chain.

To my knowledge, Jonathan Goodman first wrote down this idea in 1999. Theory in his and others’ hands confirmed the notion: For
CH3(CH2)nCH3, the crossover from extended to kinked (and eventually curled in a more complex way) comes at around n = 16, or 18 carbon atoms. Remarkably, the experimental proof for this hypothesis has recently come forward, in work by N. O. B. Lüttschwager and