PCCP Blog

Hydrogen is the only element in the periodic table that is not truly part of a group, although it is often nominally assigned to group 1. All chemists are familiar with the concept of the hydrogen bond, but how many think of the halogen bond in the same light? How many are even aware of the halogen bond as a special entity, less still that the two interactions are to all intents and purposes the same thing?

In his recent paper, Grabowski uses theoretical techniques to show that both interactions are ruled by the same electrostatic mechanism. He also provides an excellent summary and comparison of the information currently known about the two interactions that indicates a clear progression in some bonding properties from hydrogen through to the heavy halogens.

He describes how the atomic volume of the halogen decreases as the positive charge on it increases, and that this effect is magnified by shortening the internuclear distance. This information accompanies the observation that the strength of the Lewis acid-base interaction increases with the increasing atomic number of the halogen involved, although with some exceptions, hydrogen bonds are generally stronger still.

This discovery clearly has important implications for our understanding of non-covalent molecular interactions, and our understanding of how best to classify hydrogen based on its bonding properties.

by Victoria Wilton

Read this HOT PCCP article today:

Hydrogen and halogen bonds are ruled by the same mechanisms
Sławomir J. Grabowski
DOI: 10.1039/C3CP50537E

The fact that modern life relies heavily on fossil fuels is a environmental and a political problem, which will become your problem come when our supplies of fossil fuels run out. Solutions that deal with our need for domestic and industrial energy demands are—more or less—readily available. Our main problem is how to find transportable energy materials to fuel our cars, planes and ships, when no oil-based fuels are available. In the group of Tejs Vegge they have focused on ammonia as a possible mobile energy material.

The main issue in generating next-generation fuels is to remove the energy cost associated with transforming electricity into chemical energy. The solution is catalysts. The manufacture of ammonia, through the Haber–Bosch process, is enabling planet Earth to sustain the 7 billion humans that inhabit it today. If the process were stopped a couple of billion humans would die. Research has made the process of making ammonia very efficient, and has revolutionized our understanding of heterogeneous catalysis. Even so, the Haber–Bosch process is a high-energy process, consuming approximately 2 % of our total energy production.

The paper titled ‘DFT based study of transition metal nano-clusters for electrochemical NH₃ production’ is focusing on finding a process where electricity can be used to generate ammonia in an electrochemical cell. That is, how to make ammonia efficiently in a small scale, low temperature process on site at/in wind turbines and solar power plants. Using computational chemistry several catalysts are screened.

by Dr Thomas Just Sørensen

If you want to learn more see the paper, which was published in PCCP:

DFT based study of transition metal nano-clusters for electrochemical NH₃ production
J. G. Howalt, T. Bligaard, J. Rossmeisl and T. Vegge
Phys. Chem. Chem. Phys., 2013, 15, 7785-7795
DOI: 10.1039/C3CP44641G

The complex electronic structure of the lanthanides and actinides is largely a mystery. The f-shell is not readily explained in our theoretical treatment of atoms and molecules, and coupled with the difficulty of obtaining readily interpreted experimental data. The result is that we are still struggling to understand the elements at the bottom of the periodic table. Xu and co-workers conduct a good and meticulous computational study of lanthanide trifluorides, and do significantly increase our understanding of the rare earth elements, albeit in simple molecules in the gas phase. My problem is that I work in aqueous solution, where lanthanide ions have not just three ligands—as the molecules investigated in this paper have—they have eight, nine or ten.

The bonding orbitals in the lanthanide series can, in theory, be 4f, 5d, and 6s orbitals. Traditionally, the contracted f-shell orbitals have been viewed as shielded, and the interaction between lanthanide ions and ions of the opposite charge has to be regarded as purely ionic in nature. This work shows that our current computational models include a significant covalent contribution in the bonding of fluoride to trivalent lanthanide ions.

I look forward to the paper where lanthanide ions with a full coordination sphere are treated, although I fear it will be a long wait. Luckily, the papers reporting the progress towards a full computational treatment of lanthanide in solution are also worth reading, even for experimentalists like me.

On structure and bonding of lanthanoid trifluorides LnF₃ (Ln = La to Lu)
Wei Xu, Wen-Xin Ji, Yi-Xiang Qiu, W. H. Eugen Schwarz and Shu-Guang Wang
Phys. Chem. Chem. Phys., 2013, 15, 7839-7847
DOI: 10.1039/C3CP50717C

by Dr Thomas Just Sørensen

The products of thermally exfoliating graphite oxide to make graphene are much more complex than previously thought, new research shows. The volatile compounds formed vary with reaction conditions, and may influence the graphene’s structure.

The most common way to prepare graphene is by thermally reducing – or ‘exfoliating’ – graphite oxide. But the graphene produced often contains defects and lacks the perfect honeycomb structure. One explanation is that these defects may be the result of organic by-products forming and escaping as gases during the reaction.

Interested to know more? Read the full article by Emma Stoye in Chemistry World here…

Complex organic molecules are released during thermal reduction of graphite oxides
Zdeněk Sofer, Petr Šimek and Martin Pumera
Phys. Chem. Chem. Phys., 2013, Advance Article
DOI: 10.1039/C3CP51189H

The products of making graphene by thermally exfoliating graphite oxide are much more complex than previously thought, new research shows.

The most common way to prepare graphene is by thermally reducing – or ‘exfoliating’ – graphite oxide. But the graphene produced in the process often contains defects and lacks the perfect ‘honeycomb’ structure. One explanation is that these defects may be the result of organic by-products forming and escaping as gases during the reaction.

Scientists from Singapore and the Czech Republic allowed exfoliation to take place in an autoclave at 500 degrees for two hours then analysed the gases produced using gas chromatography–mass spectrometry (GC-MS). They detected many other volatiles in addition to H₂O, CO and CO₂, including polycyclic aromatic molecules, and those containing sulphur and nitrogen heteroatoms that are present as contaminants in the graphite oxide.

Moreover, the nature of the volatiles released varies hugely depending on pressure (2 bar versus 100 bar) and the gaseous atmosphere in which the exfoliation was carried out (hydrogen versus inert argon). The method by which the graphite oxide itself was prepared also had an effect – the Hummers method yielded the highest number of volatiles.

Understanding these by-products is crucial as they can affect the structure of the resultant graphene which influences its future use. The team suggest that measuring the volatiles produced during exfoliation could help determine the nature of defects.

Read this HOT PCCP article in full today:

Complex organic molecules are released during thermal reduction of graphite oxides
Z Sofer, P Šimek and M Pumera
DOI: 10.1039/C3CP51189H

The development of new experimental methods to probe surface functionality is crucial to the understanding of functional materials. For the typically low concentrations of surface functional groups, traditional nuclear magnetic resonance (NMR) spectroscopy lacks the sensitivity to provide chemical information quickly.

In dynamic nuclear polarisation surface enhanced NMR spectroscopy (DNP SENS), a porous or particulate sample is wetted with a radical solution. The large polarisation of the radicals’ unpaired electrons is then transferred to surrounding nuclear spins, with a typical signal enhancement of between 10 and 100. This can decrease experimental time dramatically, whilst probing specifically the surface functionality.

In their recent communication in PCCP, the research groups of Professor Lyndon Emsley and Professor Christophe Copéret collaborated to characterise the organic part of a periodic mesoporous organosilicate (PMO). Structural changes following functionalisation with an organoiridium compound were studied using DNP SENS. Remarkably, ¹⁵N (0.37% natural abundance) DNP SENS spectra revealed the appearance of a new chemical environment following functionalisation, corresponding to nitrogen atoms (in the PMO) bonded to Iridium (III). This key piece of evidence allowed the authors to elucidate a layered structure in which only the surface layers were available for functionalisation.

Whilst the ¹⁵N spectra would have taken weeks to acquire using conventional NMR methods, DNP SENS experiments took only a matter of hours, highlighting the power of this fascinating method.

Full details can be found in the PCCP communication:

Molecular-level characterization of the structure and the surface chemistry of periodic mesoporous organosilicates using DNP-surface enhanced NMR spectroscopy
Wolfram R. Grüning, Aaron J. Rossini, Alexandre Zagdoun, David Gajan, Anne Lesage, Lyndon Emsley and Christophe Copéret
DOI: 10.1039/C3CP00026E

By Alexander Forse

More than 50 % of our bodies are water. Plain and simple, we are more water than anything else. Following that statement it must be said that none of the water in our body is simply water. Excluding the content of your bladder, none of the water in your body is water as you have come to know it from your glass, rain, your local river and the oceans. Your body water surrounds cell membranes, microtubule, proteins, sugars, bones; all the smaller and larger biomolecules that make up our bodies. Not to mention the specific concentrations of salts and inorganic molecules that are required to run our bodies. We are beginning to understand the structure of water itself, and when water solvates simple ions. The work of Takis and co-workers increases the stakes and opens our mind to the specific solvations of small protein fragments.

The research from the groups of Troganis and Melissas at the University of Ioannina is focused on simple dipeptides, and exploits molecular dynamic simulations, density functional theory based calculations and advanced nuclear magnetic resonance spectroscopy. This combination allows them to probe the solvation of the small peptide experimentally, and rationalize the findings by the theoretical approach. Specifically the distances between selected carbon atoms in the peptide structure and water molecules can be measured. The challenge in this approach is the continuous and rapid exchange of the water molecules.

To me, the most readily accessible data is the plots showing the probability of finding water oxygen and hydrogen atoms at a specific distance to selected groups in the peptide structure. Here, extracted from MD simulations. When experimental data can yield similar results, we will be able to start directly investigating how more than half of our bodies are made up.

The excellent work on the solvation of dipeptides is published in the PCCP paper titled:

Probing micro-solvation in “numbers”: the case of neutral dipeptides in water
Panteleimon G. Takis, Konstantinos D. Papavasileiou, Loukas D. Peristeras, Vasilios S. Melissas and Anastassios N. Troganis
Phys. Chem. Chem. Phys., 2013, 15, 7354-7362
DOI: 10.1039/C3CP44606A

by Thomas Just Sørensen

Sometimes you just have to sit back, read, and enjoy the ride. This is exactly the case with the work of Kirsten Harth and Ralf Stannarius from the Institute of Experimental Physics at the Otto von Guericke University Magdeburg. The have investigated the interface tension between soapy water and a smectic liquid crystal.

Apparently, thin films of smectic—and only smectic—liquid crystals readily form in water, where they can form bubbles. In an ingenious experimental set-up Harth and Stannarius can measure the surface tension by letting a single air bubble put the smectic film bubble under tension. Amazing as it sounds, it is a viable procedure and the interface tension can be accurately determined.

The generic appeal of this study makes it one of the more enjoyable reads I have had in a while. The images were just so interesting that my curiosity forced me to download and read the paper.

If you are equally enticed, the paper is published in PCCP:

Measurement of the interface tension of smectic membranes in water
Kirsten Harth and Ralf Stannarius
Phys. Chem. Chem. Phys., 2013, 15, 7204-7209
DOI: 10.1039/C3CP44055A

by Thomas Just Sørensen