Henrik G. Kjaergaard

Definition of the hydrogen bond (IUPAC Recommendations 2011)

A novel definition for the hydrogen bond is recommended here. It takes into account the theoretical and experimental knowledge acquired over the past century. This definition insists on some evidence. Six criteria are listed that could be used as evidence for the presence of a hydrogen bond.

A large source of low-volatility secondary organic aerosol

Forests emit large quantities of volatile organic compounds (VOCs) to the atmosphere. Their condensable oxidation products can form secondary organic aerosol, a significant and ubiquitous component of atmospheric aerosol, which is known to affect the Earth’s radiation balance by scattering solar radiation and by acting as cloud condensation nuclei. The quantitative assessment of such climate effects remains hampered by a number of factors, including an incomplete understanding of how biogenic VOCs contribute to the formation of atmospheric secondary organic aerosol. The growth of newly formed particles from sizes of less than three nanometres up to the sizes of cloud condensation nuclei (about one hundred nanometres) in many continental ecosystems requires abundant, essentially non-volatile organic vapours, but the sources and compositions of such vapours remain unknown. Here we investigate the oxidation of VOCs, in particular the terpene α-pinene, under atmospherically relevant conditions in chamber experiments. We find that a direct pathway leads from several biogenic VOCs, such as monoterpenes, to the formation of large amounts of extremely low-volatility vapours. These vapours form at significant mass yield in the gas phase and condense irreversibly onto aerosol surfaces to produce secondary organic aerosol, helping to explain the discrepancy between the observed atmospheric burden of secondary organic aerosol and that reported by many model studies. We further demonstrate how these low-volatility vapours can enhance, or even dominate, the formation and growth of aerosol particles over forested regions, providing a missing link between biogenic VOCs and their conversion to aerosol particles. Our findings could help to improve assessments of biosphere–aerosol–climate feedback mechanisms, and the air quality and climate effects of biogenic emissions generally.

Unexpected Epoxide Formation in the Gas-Phase Photooxidation of Isoprene

No NO Isoprene, a five-carbon diene produced by plants, is the most abundant nonmethane hydrocarbon released into the atmosphere and plays an important role in tropospheric chemistry. Isoprene is also thought to affect climate by acting as a source of atmospheric aerosols. Paulot et al. (p. 730; see the Perspective by Kleindienst) now describe how isoprene may lead to the formation of secondary organic aerosols. In laboratory experiments, the photooxidation of isoprene in low-NO conditions, such as those which occur in vegetated regions far from anthropogenic influence, produced high yields of dihydroxy epoxides, a suspected precursor of the aerosols. This discovery could help to explain some of the more puzzling aspects of isoprene chemistry in remote regions. The oxidation of isoprenes in the absence of nitric oxide produces epoxides that can facilitate formation of organic aerosols. Emissions of nonmethane hydrocarbon compounds to the atmosphere from the biosphere exceed those from anthropogenic activity. Isoprene, a five-carbon diene, contributes more than 40% of these emissions. Once emitted to the atmosphere, isoprene is rapidly oxidized by the hydroxyl radical OH. We report here that under pristine conditions isoprene is oxidized primarily to hydroxyhydroperoxides. Further oxidation of these hydroxyhydroperoxides by OH leads efficiently to the formation of dihydroxyepoxides and OH reformation. Global simulations show an enormous flux—nearly 100 teragrams of carbon per year—of these epoxides to the atmosphere. The discovery of these highly soluble epoxides provides a missing link tying the gas-phase degradation of isoprene to the observed formation of organic aerosols.

Defining the hydrogen bond: An account (IUPAC Technical Report)

The term “hydrogen bond” has been used in the literature for nearly a century now. While its importance has been realized by physicists, chemists, biologists, and material scientists, there has been a continual debate about what this term means. This debate has intensified following some important experimental results, especially in the last decade, which questioned the basis of the traditional view on hydrogen bonding. Most important among them are the direct experimental evidence for a partial covalent nature and the observation of a blue-shift in stretching frequency following X–H···Y hydrogen bond formation (XH being the hydrogen bond donor and Y being the hydrogen bond acceptor). Considering the recent experimental and theoretical advances, we have proposed a new definition of the hydrogen bond, which emphasizes the need for evidence. A list of criteria has been provided, and these can be used as evidence for the hydrogen bond formation. This list is followed by some characteristics that are observed in typical hydrogen-bonding environments.

Peroxy radical isomerization in the oxidation of isoprene

We report experimental evidence for the formation of C(5)-hydroperoxyaldehydes (HPALDs) from 1,6-H-shift isomerizations in peroxy radicals formed from the hydroxyl radical (OH) oxidation of 2-methyl-1,3-butadiene (isoprene). At 295 K, the isomerization rate of isoprene peroxy radicals (ISO2•) relative to the rate of reaction of ISO2• + HO2 is k(isom)(295)/(k(ISO2•+HO2)(295)) = (1.2 ± 0.6) x 10(8) mol cm(-3), or k(isom)(295) ≃ 0.002 s(-1). The temperature dependence of this rate was determined through experiments conducted at 295, 310 and 318 K and is well described by k(isom)(T)/(k(ISO2•+HO2)(T)) = 2.0 x 10(21) exp(-9000/T) mol cm(-3). The overall uncertainty in the isomerization rate (relative to k(ISO2•+HO2)) is estimated to be 50%. Peroxy radicals from the oxidation of the fully deuterated isoprene analog isomerize at a rate ∼15 times slower than non-deuterated isoprene. The fraction of isoprene peroxy radicals reacting by 1,6-H-shift isomerization is estimated to be 8-11% globally, with values up to 20% in tropical regions.

Are Bond Critical Points Really Critical for Hydrogen Bonding

Atoms in Molecules (AIM) theory is routinely used to assess hydrogen bond formation; however its stringent criteria controversially exclude some systems that otherwise appear to exhibit weak hydrogen bonds. We show that a regional analysis of the reduced density gradient, as provided by the recently introduced Non-Covalent Interactions (NCI) index, transcends AIM theory to deliver a chemically intuitive description of hydrogen bonding for a series of 1,n-alkanediols. This regional definition of interactions overcomes the known caveat of only analyzing electron density critical points. In other words, the NCI approach is a simple and elegant generalization of the bond critical point approach, which raises the title question. Namely, is it the presence of an electron density bond critical point that defines a hydrogen bond or the general topology in the region surrounding it?

Design aspects of bright red emissive silver nanoclusters/DNA probes for microRNA detection.

The influence of the nucleic acid secondary structure on the fast (1 h) formation of bright red emissive silver nanoclusters (AgNCs) in a DNA sequence (DNA-12nt-RED-160), designed for the detection of a microRNA sequence (RNA-miR160), was investigated. The findings show that especially the propensity for mismatch self-dimer formation of the DNA probes can be a good indicator for the creation and stabilization of red emissive AgNCs. Also, the role of the thermal stability of the secondary DNA structures (mismatch self-dimer and hairpin monomers) and the observed AgNC red emission intensity were investigated. These findings can form the basis for a rationale to design new red emissive AgNC-based probes. As an example, a bright red emissive AgNC-based DNA probe was designed for RNA-miR172 detection. The latter opens the possibility to create a variety of AgNC-based DNA probes for the specific detection of plant and animal miRNAs.

Calculation of Vibrational Transition Frequencies and Intensities in Water Dimer: Comparison of Different Vibrational Approaches

We have calculated frequencies and intensities of fundamental and overtone vibrational transitions in water and water dimer with use of different vibrational methods. We have compared results obtained with correlation-corrected vibrational self-consistent-field theory and vibrational second-order perturbation theory both using normal modes and finally with a harmonically coupled anharmonic oscillator local mode model including OH-stretching and HOH-bending local modes. The coupled cluster with singles, doubles, and perturbative triples ab initio method with augmented correlation-consistent triple-zeta Dunning and atomic natural orbital basis sets has been used to obtain the necessary potential energy and dipole moment surfaces. We identify the strengths and weaknesses of these different vibrational approaches and compare our results to the available experimental results.

Calculation of OH-stretching band intensities of the water dimer and trimer

We have calculated fundamental and overtone OH-stretching vibrational band intensities of the water dimer and trimer. The intensities were determined with a simple harmonically coupled anharmonic oscillator (HCAO) local mode model and ab initio dipole moment functions. The dipole moment functions were calculated at the self-consistent-field Hartree–Fock and quadratic configuration interaction including single and double excitations levels of theory with the 6–31G(d), 6–311+G(d,p), and 6–311++G(2d,2p) basis sets. The overtone spectra of the dimer and trimer have not been observed and a method of obtaining local mode parameters from scaled ab initio calculations has been suggested. We find that the falloff in absolute intensity with increasing overtone of the dimer and trimer is similar to the falloff observed for the monomer. Our calculations show that the total overtone intensity of the dimer and trimer, although distributed differently, is close to two and three times the total intensity of the monomer f...

The Formation of Highly Oxidized Multifunctional Products in the Ozonolysis of Cyclohexene

The prompt formation of highly oxidized organic compounds in the ozonolysis of cyclohexene (C6H10) was investigated by means of laboratory experiments together with quantum chemical calculations. The experiments were performed in borosilicate glass flow tube reactors coupled to a chemical ionization atmospheric pressure interface time-of-flight mass spectrometer with a nitrate ion (NO3(-))-based ionization scheme. Quantum chemical calculations were performed at the CCSD(T)-F12a/VDZ-F12//ωB97XD/aug-cc-pVTZ level, with kinetic modeling using multiconformer transition state theory, including Eckart tunneling corrections. The complementary investigation methods gave a consistent picture of a formation mechanism advancing by peroxy radical (RO2) isomerization through intramolecular hydrogen shift reactions, followed by sequential O2 addition steps, that is, RO2 autoxidation, on a time scale of seconds. Dimerization of the peroxy radicals by recombination and cross-combination reactions is in competition with the formation of highly oxidized monomer species and is observed to lead to peroxides, potentially diacyl peroxides. The molar yield of these highly oxidized products (having O/C > 1 in monomers and O/C > 0.55 in dimers) from cyclohexene ozonolysis was determined as (4.5 ± 3.8)%. Fully deuterated cyclohexene and cis-6-nonenal ozonolysis, as well as the influence of water addition to the system (either H2O or D2O), were also investigated in order to strengthen the arguments on the proposed mechanism. Deuterated cyclohexene ozonolysis resulted in a less oxidized product distribution with a lower yield of highly oxygenated products and cis-6-nonenal ozonolysis generated the same monomer product distribution, consistent with the proposed mechanism and in agreement with quantum chemical modeling.