Spectroscopic identification of fragment ions of DNA/RNA building blocks: the case of pyrimidine

Physical Chemistry Chemical Physics : PCCP
Kuntal Chatterjee, Otto Dopfer

Abstract

Pyrimidine (Pym, 1,3-diazine, 1,3-diazabenzene) is an important N-heterocyclic building block of nucleobases. Understanding the structures of its fragment and precursor ions provides insight into its prebiotic and abiotic synthetic route. The long-standing controversial debate about the structures of the primary fragment ions of the Pym+ cation (C4H4N2+, m/z 80) resulting from loss of HCN, C3H3N+ (m/z 53), is closed herein with the aid of a combined approach utilizing infrared photodissociation (IRPD) spectroscopy in the CH and NH stretch ranges (νCH/NH) and density functional theory (DFT) calculations. IRPD spectra of cold Ar/N2-tagged fragment ions reveal that the C3H3N+ population is dominated by cis-/trans-HCCHNCH+ ions (∼90%) along with a minor contribution of the most stable H2CCCNH+ and cis-/trans-HCCHCNH+ isomers (∼10%). We also spectroscopically confirm that the secondary fragment resulting from further loss of HCN, C2H2+ (m/z 26), is the acetylene cation (HCCH+). The spectroscopic characterization of the identified C3H3N+ isomers and their hydrogen-bonded dimers with Ar and N2 provides insight into the acidity of their CH and NH groups. Finally, the vibrational properties of Pym+ in the 3 μm range are probed by IRPD o...Continue Reading

References

Sep 1, 1977·Bio Systems·A W Schwartz, G J Chittenden
Oct 20, 1965·Journal of the American Chemical Society·J M RiceM Barber
Apr 14, 1999·Proceedings of the National Academy of Sciences of the United States of America·R Shapiro
Jan 1, 1984·Advances in Space Research : the Official Journal of the Committee on Space Research (COSPAR)·B BasileJ Oró
Jan 10, 2002·International Journal of Radiation Biology·H Abdoul-Carime, L Sanche
Oct 9, 2002·Angewandte Chemie·Nicola Solcà, Otto Dopfer
Oct 31, 2002·Journal of the American Chemical Society·Hyuk KangSeong Keun Kim
Apr 15, 2004·Chemical Reviews·Carlos E Crespo-HernándezBern Kohler
Dec 25, 2004·Proceedings of the National Academy of Sciences of the United States of America·Ali Abo-RiziqMattanjah S de Vries
Jul 9, 1971·Nature·C E FolsomeC Ponnamperuma
Jun 16, 2006·The Journal of Chemical Physics·Séverine Boyé-PéronneJacques Liévin
Feb 13, 2007·Annual Review of Physical Chemistry·Mattanjah S de Vries, Pavel Hobza
Dec 4, 1964·Science·R Hayatsu
Nov 15, 2007·Angewandte Chemie·Horia-Sorin AndreiOtto Dopfer
Feb 22, 2008·Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy·Abdelmonem RawashdehDeeb Marji
Oct 29, 2008·Journal of Synchrotron Radiation·Feng WangElena Ivanova
Aug 28, 2009·The Journal of Chemical Physics·Partha P BeraHenry F Schaefer
Sep 26, 2009·The Journal of Chemical Physics·Rachael A RelphMark A Johnson
Aug 27, 2010·Cold Spring Harbor Perspectives in Biology·Michael P Robertson, Gerald F Joyce
Dec 1, 2010·Angewandte Chemie·Alexander PatzerOtto Dopfer
Aug 13, 2011·Proceedings of the National Academy of Sciences of the United States of America·Michael P CallahanJason P Dworkin
Sep 29, 2011·The Journal of Physical Chemistry. a·Otto DopferNicola Solcà
Apr 26, 2016·Physical Chemistry Chemical Physics : PCCP·Gustavo A PinoChristophe Jouvet
Jan 13, 2018·Science·Christine Joblin, José Cernicharo
Nov 27, 2018·Angewandte Chemie·Kuntal ChatterjeeOtto Dopfer
Aug 8, 2019·The Journal of Physical Chemistry. a·Kuntal Chatterjee, Otto Dopfer
Sep 29, 2019·Nature Communications·Yasuhiro ObaAkira Kouchi
Nov 8, 2019·Physical Chemistry Chemical Physics : PCCP·Kuntal Chatterjee, Otto Dopfer

❮ Previous
Next ❯

Methods Mentioned

BETA
electron diffraction

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.