Research Overview

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McMahon Group Research Overview

The McMahon group combines synthetic organic chemistry with spectroscopy and computational techniques to study reactive intermediates and unusual organic molecules.  Our molecules of interest lie at the intersection of astrochemistry, combustion, carbon condensation, organic materials, and mechanistic organic chemistry.  The common link between these diverse subjects is the study of relatively unstable organic species such as radicals, carbenes, and highly-unsaturated carbon molecules.  By necessity, the study of these species relies on our ability as synthetic organic chemists to synthesize the molecule of interest or a suitable precursor.  To characterize such species, we employ a variety of methods, including traditional spectroscopies of organic chemistry as well as matrix-isolation IR, UV/VIS, and EPR due to the high reactivity of our molecules of interest.  We have recently expanded our spectroscopic techniques to include rotational spectroscopy, specifically in the millimeter-wave region.  In order to interpret our spectroscopic results and to understand the theoretical aspects of our research, we utilize ab initio and DFT methods to predict which isomerizations and reactions are likely for these species.  Additionally, our spectoscopic detections are dependent upon our ability to predict, with a high degree of accuracy, the expected IR absorptions of our precursors and reactive species.  With all of these tools available, we seek to understand the nature and behavior of these species to provide insight to ourselves and the broader scientific community.

Carbon Chains InvestigatedOne long-standing avenue of research in the McMahon group is the structure and spectroscopy of highly-unsaturated carbon chains.  These molecules and their chemical reactivity are expected to play a large role in the makeup of the interstellar medium and could be involved in the explanation of the diffuse interstellar bands (DIBS).  We have investigated the smallest odd-numbered carbon chains of HC3H - HC7H which must contain either a diradical or carbene, making them highly reactive species.  Several past and current investigations explore the spectroscopy and photochemistry of the parent species shown to the right and their substituted derivatives.  Most recently, we have reported on the synthesis and characterisation of a few HC5H  derivatives and all of the carbon-13 isotopomers of HC3H.

Investigated CarbenesIn addition to the study of linear, unsaturated carbon molecules, our group has investigated the spectroscopy, electronic structure, and reactivity of numerous other carbenes.  Some of these investigations also have large implications for solving the DIBS puzzle such as cyanocarbene and propadienylidene, shown to the left.  Additionally, the invesitgations of phenyl, napthyl, and o-tolyl carbenes have produced several publications that describe their photochemical and thermal reactivites.  Often these carbenes are generated by the synthesis of an appropriate diazo-containing precursor which can be photolyzed to produce a carbene.  An interesting investigation reported the photochemical interconversion of 2- and 3-naphthylcarbenes via a carbene insertion into the aromatic ring.  More recently, similar investigations have resulted in some surprising differences in the chemistry of furanyl, thienyl, and benzothienyl carbenes relative to the naphthylcarbene.

A mainstay of the McMahon group is its collaborative nature, both between group members and with other research groups. These produce investigations into a diverse set of topics within organic chemistry, physical chemistry, theoretical chemistry, and astronomy.  Recent examples include our project with Claude Woods and John Stanton working with rotational scpectroscopy and the attempted isolation and characterization of diazirinone and carbonyl diazide.  A fruitful collaboration with Scott Reid and Fleming Crim has recently begun to investigate the isomerization of halons and other similar halogenated species via a combination of matrix-isolation IR spectroscopy, ultra-fast IR spectroscopy, and computational chemistry.   Recently, a collaboration with Henning Hopf investigated the astrochemically relevant dimerization and trimerization of cyanoacetylene.  Our long-standing collaboration with Mark Ediger, spanning a couple of graduate student careers, has resulted in numerous publications about the nature of stable organic glasses.  These collaborations continue to play a central role in the research carried out by members of the McMahon group.





Common Techniques

Matrix Isolation Photochemistry & Spectroscopy

To study highly reactive molecules, such as carbenes, nitrenes, and highly-strained rings, a technique known as matrix isolation is used. A precursor or the reactive intermediate is generated in the gas phase and then frozen in an inert gas (N2, Ar, Ne, Xe) at 10 to 25 K on a spectroscopic window. The matrix-isolated compounds can then be studied using IR, UV-vis, or EPR spectroscopy. Often, irradiation of the precursor using a Hg lamp, Xe lamp, or laser yields a reactive species, whose identity is confirmed by comparison to ab initio or DFT calculated spectra. The matrix can then be further irradiated with different wavelengths of light to study the photochemical properties and reactivity of these species.

A depiction of HC7H isolated in an inert matrix.

Matrix Isolation Window

As potential molecules present in the interstellar me  dium and as theoretical precurors and intermediates, we have been studying several substituted cylobutadienes.  Recently, we have synthesized an appropriate pyrone precursor to cyanocylcobutadiene and depositied it into an argon matrix at 25 K.  Upon irradiation at λ ≥ 299 nm, the 2-Oxo-2H-pyran-5-carbonitrile (red) is converted to a bicyclic, dewar-benzene-like, lactone (blue).  Upon further irradiation, the lactone undergoes a retro [2+2] cycloaddition to yield cyanocyclobutadiene by extrusion of carbon dioxide.

Pyrone Irradiation

In this case, a positive identification of both the original pyrone and its bycyclic lactone can be seen by subtraction IR spectroscopy and its comparison to  computed B3LYP/6-31G(d) infrared spectra.  In a subtraction spectrum, peaks with negative absorbance (identified by red dots) were consumed in the reaction and peaks with positive absorbance (identified by blue dots) were produced by the reaction.

Experimental infrared subtraction spectrum for the conversion of a cyano-pyrone to its bicyclic-lactone.

Subtraction IR


Experimental Mechanistic & Kinetic Studies

We are highly interested in the mechanistic aspects of organic chemistry and have recently published a featured article in Journal of Organic Chemistry regarding the reported production of diazirinone as a reactive species.  Unfortunately, our attempts to identify this species by matrix isolation IR spectroscopy and rotational spectroscopy forced us to conclude that it is not generated in detectable quantity, but that 3-chloro-3-(p-nitrophenoxy)diazirine reacts with fluoride to produce CO and N2 almost instantaneously.  Subsequent to our publication, another group successfully generated diazirinone from carbonyldiazide, CON6 by pyrolysis.

Experimentally observed green pathway showing the direct production of CO and N2 and not the production of diazirinone.

Shaffer et al. 2010


Additionally, we are currently investigating the mechanism and kinetics of the Bergman Cyclization and the role that this reaction may have in carbon condensation which leads to the formation of fullerenes and nanotubes.  The thermal reaction of tetraethynylethylene in the presence of a hydrogen trapping agent will produce 1,2-diethynylbenzene, which undergoes subsequent cyclization to naphthalene as shown below.

Bergman Kinetic Study


Organic Synthesis


In order for us to carry out all of the chemical studies that are of interest, we must be able to synthesize some fairly unstable precursors.  Frequently, we are interstested in producing a diazo-substituted precursor which upon irradiation will likely generate our desired reactive species, (carbenes, diradicals, etc).  A common route used in our group is to produce an aldehye which can be converted to a tosylhydrazone.  Following deprotonation to produce a sodium or lithium salt and subsequent heating, these hydrazones readily yield our desired diazo compounds.

During our attempted characherizations of the highly unsaturated MeC7H, a rearrangement product was clearly present in both argon and nitrogen matrices.  Ab initio and DFT computational predictions suggested that the lowest-energy, open-chain, isomer on the C8H4 potential energy surface was oct-7-ene-1,3,5-triyne making it a likely candidate for the rearrangement product.  In order to conclusively confirm this assignement, oct-1-ene-3,5,7-triyne was synthesized, in the manner shown below, to use as an authentic standard for one of our matrix isolation photochemistry experiments.

Synthesis of oct-7-ene-1,3,5-triyne

Another synthetic project involved the generation of a 2,3,6,7-tetrabromonaphthalene to use as an authentic standard in the mass spectrometry and 1H NMR mechanistic studies of the Bergman Cyclization of a tetrabromo-substituted tetraethynylethylene.



Computational Chemistry

We use computational chemistry on a continual basis in close partnership with our experimental work.  Due to the nature of reactive species and the methods required to isolate and characterize them, our ability to estimate their spectral properties is critically important.  We are  particularly interested in an effective way to predict the infrared absorption frequencies of our species of interest, precursors, and any potential rearrangement or trapping products.  We utilize a departmental computer cluster to use programs such as Gaussian 09, CFOUR, and Polyrate with both ab initio and DFT methods for our geometry optimizations and frequency calculations.

The advantage of using matrix isolation for our chemistry is that we can trap very reactive molecules at low temperatures so that thermal reactions become essentially impossible, increasing the importance of tunneling pathways.   In one study, a [1,4]-hydrogen shift was observed in a matrix isolated sample of o-tolylmethylene to produce o-xylylene at 4.6 K!  To address this issue, we have begun using the POLYRATE and GAUSSRATE program packages to investigate the contributions of tunneling to this process.  Using GAUSSIAN09 to find the minimum energy pathway of the reaction, POLYRATE can then find the rate constants for the reaction, including tunneling probabilities.  Improving our understanding and ability to predict the relevance of tunneling proceses will allow us to better predict the observed decompositions and rearrangements in future matrix isolation experiments.

[1,4]-hydrogen shift of o-tolylmethylene to o-xylylene

While computational chemistry is a powerful tool when intertwined with experimental results, our group also performs purely theoretical studies that may lay the ground work for follow up work.  For example, there has been much attention given to the understanding of fullerene formation, a spin-off of the experimental mechanistic Bergman Cyclization studies completed previously.  Furthermore, fullerenes are interesting to our group due to the C60 and C70 detections in the ISM.  Currently, we are exploring the stability and properties of ethynl-substituted cyclbutadienes, their Bergman Cyclizations to produce p-benzynes, and alternate mechanisms for carbon condensation by a variety of ab initio and DFT methods.  This provides more insight into the proposed ring coalescence and annealing model of fullerene formation, which involve the Bergman Cyclization of similar polyalkynl-substituted intermediates.         

Possible mechanism for fulleren formation



Rotational Spectroscopy

In the past, our group has been involved in several collaborations involving the laboratory rotational spectroscopy of molecules of astrochemical interest such as phenyl radicalo-benzynecorannulenemaleonitrile, and (z)-pent-2-en-4-ynenitrile.  Additionally, we have collaborated in radioastronomical searches for these molecules with the National Radio Astonomy Observatory (NRAO) Green Bank Telescope.  Recently, we have begun a collaboration with R. Claude Woods to continue this work to search for small carbon molecules that are reactive intermediates or may be of astronomical importance.

The millimeter-wave absorption spectrometer being used in this research project has been used previously for the investigation of numerous small inorganic molecules and ions.  The apparatus consists of a three-meter Pyrex discharge chamber with cylindrical electrodes at each end.  The discharge operates at mTorr pressures and at temperatures as low as 77 K, which allows for the generation of highly reactive species.  Traditionally, the microwave signal has been generated by a Gunn-diode microwave source, which is then further amplified and multiplied to reach the desired frequencies.  The signal is focused onto a liquid-helium-cooled indium antimonide detector and read by a lock-in amplifier.

Recent modifications include an upgrade of the computer control system to a PC running LabVIEW, the addition of an electronically-controled gate valve and maglev turbopump, a new microwave source and photomultiplier chain, a room-temperature detector, the addition of an internal glass tube with a series of outlets for our reactive gas designed to distribute our parent molecules evenly throughout the chamber, and the introduction of a chiller to provide fine-tuned control of the experimental temperature.  These improvements will allow for a more uniform discharge, greater control of conditions and increased detectability.

Millimeter-wave spectrum of a sample containing carbonyldiazide, CO(N3)2 

Millimeter-wave Spectrum of Carbonyl Diazide

Schematic of the Millimeter-wave spectrometer

Millimeter-wave Spectrometer  

Neon Gas Discharge in our Millimeter-Wave Spectrometer

Neon Glow


Last updated January 30, 2019.