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Chemistry Central Journal themed issue: Current Topics in Chemical Crystallography
Chemistry, Faculty of Natural and Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
Chemistry Central Journal 2014, 8:69 doi:10.1186/s13065-014-0069-9
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Homepage @ University of Southampton
Intermolecular bonding and supramolecular chemistry
One of the first themes which emerged from our increasing interest in intermolecular bonding was a strong focus on hydrogen bonding strengths and patterns and, before very long, about variations in such patterns. This was not new science, with much of the ideas and groundwork having been laid for some time. The early work of Pauling [8], Powell [9] and Wells [10] and others, prompted the realisation that hydrogen bonding was not just a way of holding protein chains together [11], but a force to be recognised in chemical crystallography in general. The informative writings of Hamilton and Ibers [12], Jeffrey [13] and the papers of Etter [14],[15] were fundamental in promoting this subject, which provided most significant contributions to key areas such as the study of polymorphism [16] and, of course, the whole area of organic solid forms. These were the starting points for the conception of supramolecular chemistry [17] and the development of crystal engineering [18]. Advances in this theme have been spectacular, with many reviews, textbooks and Meetings. A flavour for what is currently in vogue is nicely summarised in the program of a recent Gordon Conference on the subject [19].
In a not unrelated way, studies on the synthesis and structural characterisation of metal co-ordination compounds, especially the use of bi- or multi-coordinating ligands led to the equally significant, and popular area of metal-organic frameworks, or MOFs [20]. In many ways, these types of compound have provided remarkable analogues of the structural characteristics and properties of zeolite and related phases, which had already been utilised as scaffolds for separation science and synthesis and catalysis [21]. Ian Williams and co-workers from Hong Kong University of Science and Technology: HKUST will be contributing to this Issue, with a paper on reduced symmetry of sodalite (SOD) MOFs and the concept of conformational isomers for these frameworks.
Integrating computational chemistry and chemical crystallography
Knowing that the electrons in the molecule were responsible for the scattering of X-rays, the 1980’s saw experiments devised and performed to see whether we could determine and model not only the atomic positions and thermal motion characteristics, but the actual distribution of electrons, on the atoms and in the bonds. Initial work in this area, which became described as “Charge Density Studies”, and its development is nicely presented in a review co-authored by Philip Coppens, one of the early proponents of the subject [22], and taken up by many other researchers. The early work was based on data collected at low temperature on serial diffractometers, sometimes with supporting data from neutron scattering experiments. As in all other areas of x-ray scattering, major developments were made as the technology and data processing software for area detectors provided efficient collection of data of excellent quality, and yet another major theme grew. Integrating the experimental methods with new procedures for refining, which provided descriptions of the electron density in bonds, including intermolecular connections again led to a major involvement with computational chemistry methods. A number of recent publications highlight the impressive levels to which this area has developed, including the combined use of X-ray and neutron scattering to measure both charge and spin densities [23]-[25]. It is very pleasing to have an update on application of charge density studies in crystal engineering, from Piero Macchi and Anna Krawczuk, for this issue.
The rapidly increasing knowledge base on the properties and descriptions of interatomic and intermolecular bonding, coupled with the hugely increasing amount of structural data, fuelled another successful Chemical Crystallography/Computational Chemistry integration, in the form of Crystal Structure Prediction. New computational platforms were designed and assembled, which generated large numbers of possible structures and then classified them in terms of computed lattice energies. The remarkable success of this development is nicely charted in the reports of a series of competitive “Blind Tests” [26]-[31], which will continue through 2014/5. A very useful advantage of the computational procedures associated with this topic is the possibility to compute lattice energies for polymorphs in particular, and we have such an example in one of the “home” contributions to this issue, through a collaboration with Frank Leusen and John Kendrick from Bradford. Another contributed paper, from Thomas Gelbrich and Ulrich Griesser from the University of Innsbruck, will highlight the use of a further energy calculation program, PIXEL, written by Angelo Gavezzotti [32],[33], and will describe how the complete set of pairwise intermolecular interactions in a structure, from van der Waals to hydrogen bonds, can be computed, and how these interact in producing the final, overall energy.
Crystallography under extreme conditions and other specialised experiments
Whilst variable, low and high temperature crystallography has become a very general technique, allowing detailed studies of phase transformations, for example, more specialised experiments involving studies under very high pressures have also yielded some very interesting results, particularly in the area, again, of phase transitions. The origins and development of the technique, the use of which is still not as widespread as low temperature crystallography, are nicely summarised by Andrzej Katrusiak [34]. Simon Parsons from Edinburgh and co-workers will be contributing a paper on a new study to this issue.
A second type of specialised technique, which has blossomed with the availability of pulsed synchrotron sources, is that of time-resolved crystallography. Here we irradiate a sample with pulsed radiation of a relevant wavelength and capture the diffraction pattern in synchonisation with the pulsing. Much of the work in this area is devoted to the study of macromolecules, but reports of studies on short-lived species in small molecule systems are increasing significantly. A review, summarising the history and the state-of-the-art in this technique has recently been published [35].
Crystallographic computing, data bases and descriptors
Here we come to the crux of how we are really driving Chemical Crystallography, how we are storing our results and how we are using them. The first component of our toolkit are, of course the software tools used to drive the diffractometers, process the captured X-rays, solve and refine the structures and then display and interpret the results. I have experienced this development from the very beginning! My first structure was determined using eye-measured film intensities and calculation of 2D electron density maps using Beevers-Lipson strips! Fortunately this “good for the experience” procedure was then superseded by use of an electron density synthesis program, written by Owen Mills from the University of Manchester, and a least squares refinement program written by John Rollett at the University of Oxford. Diagrams were prepared using rulers, compasses and Indian ink. In contrast to this, the software we now have, for calculations and graphics, is state-of-the art, and we have all been very fortunate to have some superbly skilled crystallographic software experts to provide us with such facilities [36]. However, the problems we are now tackling continue to present new demands, so the development of the software continues apace. Richard Cooper, Amber Thomson and Pascal Parois have kindly agreed to contribute a paper to this Issue, describing strategies for handling bigger and bigger structures, and the way in which these are being implemented in the Oxford CRYSTALS package.
As a result of these highly successful developments, we are, of course living with a continuing data explosion. It goes without saying that this data can be really valuable, if we learn how to use it well, and we must have a way of preserving it, not just for posterity, but for persistent use and re-use. Of course, we are very fortunate to have groups of experts in crystallography and data base protocols, who are taking great care of this task also. The resulting databases cover all fields, and are all listed in the IUCr website [37]. The entries in the CSD currently total well over 700,000, and in all databases, well over one million. We visit the databases according to our areas of interest and activity, firstly, perhaps to check that a proposed structure determination is not a duplication (although this is not necessarily a bad thing), and then to use any significant important information which we find as accompanying data when we write up the results of our study. Many publications use sets of data to present comparative studies. The value of this data is truly immense, but it would be even more valuable if the data from all the structures, which we know lie in filing cabinets or on local computer archives, can be made available for database capture. I see from interrogation of the Cambridge Structural Database (CSD) that more of us are now submitting single structure data as “Private Communications”, and this is truly helping to increase content and thus value. I believe that with just a small amount of collective effort, we can add structures which may not be written up in Journal form as Private Communications, and aim for a CSD total breaking the 1 M mark within 3 or 4 years. Let us try!
In many cases, we can mine data from a database to study multi-structure relationships, make valuable comparisons and learn more about general or specific trends. For this purpose, we have to recognise the real situation this presents us with – “here are more than one million answers: what are the questions”? By this, I mean that we must prepare our database searching questions in a most careful way. For example, a simple statistical probe, requiring an answer equivalent to “yes” or “no” may tell us very little. Accordingly, we must develop our expertise in generating descriptors with which we can encode our questions so that the answers are suitably partitioned. For instance, suppose we wish to study the tendencies of an organic compound containing a particular functional group to crystallise as a hydrate. A search which gives the simple answer x% yes, (100-x%) no, has very little use. We would need to encode into our question other factors – what other functional groups are present, and, for example, what positional relationship they have to the target group?
Careful definition of descriptors is also vital in database mining to explore such questions as - “is my molecule/structure similar to any other” or “how similar is my molecule/structure to another”. This has been a critical component in the structural systematics studies which have been the focus of research in my laboratory for several years [38], which has involved development of the XPac concept and software [39]. As a second “home” contribution, my co-workers David Hughes, Thomas Gelbrich, Terence Threlfall and I will be contributing a paper in which we propose some new thoughts on the way in which one can describe, and thus compare, hydrogen-bonded networks. We hope this will be of interest to many readers.
The electronic version of this article is the complete one and can be found online at: http://journal.chemistrycentral.com/content/8/1/69
image source: The Young Crystallographers Group
Green chemistry and the biorefinery concept
* Corresponding author: Rafal Bogel-Lukasik rafal.lukasik@lneg.pt
Laboratório Nacional de Energia e Geologia, Unidade de Bioenergia, 1649-038, Lisboa, Portugal
[more about author]
Sustainable Chemical Processes 2013, 1:18 doi:10.1186/2043-7129-1-18
Excerpt
"Among the several definitions of biorefinery, the most widely used and recently accomplished by International Energy Agency (IEA) Bioenergy Task 42 is “Biorefining is the sustainable processing of biomass into a spectrum of marketable products and energy”. The biorefinery is an industrial facility (or network of facilities) that cover an extensive range of combined technologies aiming to full sustainable transformation of biomass into their building blocks with the concomitant production of biofuels, energy, chemicals and materials, preferably of added-value [4]. The biorefinery concept embraces a whole crop approach of biomass conversion pathways leading to a whole portfolio of valuable products, drawing direct similarities to today’s fossil oil refineries, in which multiple fuels, basic chemicals, intermediate products and sophisticated products are produced from petroleum [5,6]. To accomplish these needs science developed many less energy-requiring and less waste-generation technologies. However, still need of a new investment requirements and a perceived high risk of adoption of new technologies are slowing down the implementation of new processes. The solution of this problem is the development of more sustainable technologies that significantly increase the resource efficiency of chemical processes and reduce the operation time of such technologies. In addition, these new technologies should be accomplished in chemical industries by the introduction of chemical processes that do not produce contaminants, but only non-toxic commodities and recyclable or easily degradable materials. Industries should be based on ideal processes that start from non-polluting starting materials, lead to no secondary or concomitant products and require no solvents in order to carry out any chemical conversion or to isolate and purify the product. Such intrinsically clean processes seem still hardly attainable at present. But it is expected from the ingenuity and resourcefulness of chemists that the chemical industry replaces many existing processes with new technologies aiming at a zero environmental footprint. This is important for fine and pharmaceutical industries which use energy [7] and generate a significant amount of chemical waste. However it is probably even more important for large chemical industries which a few minutes carbon footprint equals a yearly carbon footprint of pharma enterprise [8]. The waste and energy problems must be solved in the near future because the waste generation and energy consumption are increasing strongly due to growth of the world population and increasing standards of living in emerging economies [9]."
The electronic version of this article is the complete one and can be found online at: http://www.sustainablechemicalprocesses.com/content/1/1/18
Image source: http://wastebiorefining.blogspot.hk/2011_10_01_archive.html
Laboratório Nacional de Energia e Geologia, Unidade de Bioenergia, 1649-038, Lisboa, Portugal
[more about author]
Sustainable Chemical Processes 2013, 1:18 doi:10.1186/2043-7129-1-18
Excerpt
"Among the several definitions of biorefinery, the most widely used and recently accomplished by International Energy Agency (IEA) Bioenergy Task 42 is “Biorefining is the sustainable processing of biomass into a spectrum of marketable products and energy”. The biorefinery is an industrial facility (or network of facilities) that cover an extensive range of combined technologies aiming to full sustainable transformation of biomass into their building blocks with the concomitant production of biofuels, energy, chemicals and materials, preferably of added-value [4]. The biorefinery concept embraces a whole crop approach of biomass conversion pathways leading to a whole portfolio of valuable products, drawing direct similarities to today’s fossil oil refineries, in which multiple fuels, basic chemicals, intermediate products and sophisticated products are produced from petroleum [5,6]. To accomplish these needs science developed many less energy-requiring and less waste-generation technologies. However, still need of a new investment requirements and a perceived high risk of adoption of new technologies are slowing down the implementation of new processes. The solution of this problem is the development of more sustainable technologies that significantly increase the resource efficiency of chemical processes and reduce the operation time of such technologies. In addition, these new technologies should be accomplished in chemical industries by the introduction of chemical processes that do not produce contaminants, but only non-toxic commodities and recyclable or easily degradable materials. Industries should be based on ideal processes that start from non-polluting starting materials, lead to no secondary or concomitant products and require no solvents in order to carry out any chemical conversion or to isolate and purify the product. Such intrinsically clean processes seem still hardly attainable at present. But it is expected from the ingenuity and resourcefulness of chemists that the chemical industry replaces many existing processes with new technologies aiming at a zero environmental footprint. This is important for fine and pharmaceutical industries which use energy [7] and generate a significant amount of chemical waste. However it is probably even more important for large chemical industries which a few minutes carbon footprint equals a yearly carbon footprint of pharma enterprise [8]. The waste and energy problems must be solved in the near future because the waste generation and energy consumption are increasing strongly due to growth of the world population and increasing standards of living in emerging economies [9]."
The electronic version of this article is the complete one and can be found online at: http://www.sustainablechemicalprocesses.com/content/1/1/18
Image source: http://wastebiorefining.blogspot.hk/2011_10_01_archive.html
Why Systems Chemistry?
Corresponding author: Günter von Kiedrowski kiedro@rub.de
Bioorganic Chemistry, Ruhr University, Bochum, Germany
<More about author>
Journal of Systems Chemistry 2010, 1:1 doi:10.1186/1759-2208-1-1
Why Systems Chemistry?
Synthesis and design is per se a chemical endeavor - but the goal of synthesis in chemistry is usually a chemical structure. On the other hand, the design and synthesis of complex dynamic behavior in chemical systems is as much in its infant shoes as the reduction and reconstruction approach of synthetic biology. It is a challenge (if not the challenge) for the chemistry of the 21st century. Let us now try to generalize the challenges that face Systems Chemistry in the near future. Systems chemistry seeks to combine the "classical" knowledge of chemistry, viz. the language of molecules, their structures, their reactions and interactions, together with the "classical" knowledge derived from existing forms of life. One component of this approach, acting both as a translator and abstractor between these languages comes from the fields of theoretical biology and complex systems research; the other key component comes from a chemistry that is the offspring of both supramolecular and prebiotic chemistry, and adds a new dimension that has not been sufficiently addressed so far. Over the past decades more and more chemists have learned to design and implement chemical systems showing emergent behavior, such as simple self-replicating and self-reproducing systems, chiral symmetry breaking reactions, as well as far-from-equilibrium self-organizing systems (i.e. oscillating reactions , Turing patterns) and today we even have the first examples of systems chemistry making molecular motors [69]. For a more detailed description of some recent highlights in systems chemistry from a more supramolecular perspective, see ref [70]. What is missing here is a kind of generalization of "synthetic methods" based on the principles of autocatalysis, supramolecular self-organization, molecular information processing, and moreover, applicable in the range from small molecules via nano- to mesosystems. Before we will be able to come to such generalizations, many more studies of the complex/emergent behavior of chemical systems are required. The analytical tools have now become accessible to most chemists to be able to set off and explore the largely uncharted territory of chemistry at systems level. The discoveries and new insights that this territory holds in store require a forum for dissemination. The Journal of Systems Chemistry has been set up for this purpose at a time that Systems Chemistry starts to resonate with an increasingly large number of chemists, biologists, physicists and computer scientists.
⓿ The electronic version of this article is the complete one and can be found online at: http://www.jsystchem.com/content/1/1/1
Bioorganic Chemistry, Ruhr University, Bochum, Germany
<More about author>
Journal of Systems Chemistry 2010, 1:1 doi:10.1186/1759-2208-1-1
Why Systems Chemistry?
Synthesis and design is per se a chemical endeavor - but the goal of synthesis in chemistry is usually a chemical structure. On the other hand, the design and synthesis of complex dynamic behavior in chemical systems is as much in its infant shoes as the reduction and reconstruction approach of synthetic biology. It is a challenge (if not the challenge) for the chemistry of the 21st century. Let us now try to generalize the challenges that face Systems Chemistry in the near future. Systems chemistry seeks to combine the "classical" knowledge of chemistry, viz. the language of molecules, their structures, their reactions and interactions, together with the "classical" knowledge derived from existing forms of life. One component of this approach, acting both as a translator and abstractor between these languages comes from the fields of theoretical biology and complex systems research; the other key component comes from a chemistry that is the offspring of both supramolecular and prebiotic chemistry, and adds a new dimension that has not been sufficiently addressed so far. Over the past decades more and more chemists have learned to design and implement chemical systems showing emergent behavior, such as simple self-replicating and self-reproducing systems, chiral symmetry breaking reactions, as well as far-from-equilibrium self-organizing systems (i.e. oscillating reactions , Turing patterns) and today we even have the first examples of systems chemistry making molecular motors [69]. For a more detailed description of some recent highlights in systems chemistry from a more supramolecular perspective, see ref [70]. What is missing here is a kind of generalization of "synthetic methods" based on the principles of autocatalysis, supramolecular self-organization, molecular information processing, and moreover, applicable in the range from small molecules via nano- to mesosystems. Before we will be able to come to such generalizations, many more studies of the complex/emergent behavior of chemical systems are required. The analytical tools have now become accessible to most chemists to be able to set off and explore the largely uncharted territory of chemistry at systems level. The discoveries and new insights that this territory holds in store require a forum for dissemination. The Journal of Systems Chemistry has been set up for this purpose at a time that Systems Chemistry starts to resonate with an increasingly large number of chemists, biologists, physicists and computer scientists.
⓿ The electronic version of this article is the complete one and can be found online at: http://www.jsystchem.com/content/1/1/1
Valorisation of food residues: waste to wealth using green chemical technologies
Corresponding author: Emerson L Schultz emerson.schultz@embrapa.br
Embrapa Agroenergy, Parque Estação Biológica, PqEB s/n – Av.W3 Norte (final), Brasília, 70770-901, DF, Brazil
Chemical and Biological Technologies in Agriculture 2014, 1:7 doi:10.1186/s40538-014-0007-z
Abstract
According to estimates from the International Energy Agency, global energy consumption will increase by at least one third, between 2010 and 2035. The additional power required will be provided not only by fossil sources but also by renewables. While the world energy matrix is supplied only by 13.2% from renewable sources, Brazil has different scenery with renewables accounting for 42.4% of the energy matrix. This work aimed to evaluate the potential use of oleaginous in biorefineries considering the produced quantity, prices, and costs of raw materials and products. Considering the availability of these raw materials, the results showed significant opportunities that can be exploited in Brazil, within the biorefinery concept. Soybean oil is the main raw material for biodiesel production in Brazil, although there are many other vegetable oils with potential for this purpose. Related to the production costs, the soybean biodiesel has higher costs than diesel. Then, this biofuel is only produced due to Brazilian regulatory rules and public subsidies. In order to become this production favorable in the market environment, it is essential to aggregate value to all byproducts and residues generated along the biodiesel production chain. Glycerin is a byproduct of biodiesel that could be used, in a glycerol biorefinery concept, as raw material for the production of value-added products through chemical, biochemical, or thermochemical routes.
Keywords: Biorefinery; Oleaginous; Soybean; Biodiesel; Glycerin; Biofuels; Chemicals; Energy; Prices and costs
The electronic version of this article is the complete one and can be found online at: http://www.chembioagro.com/content/1/1/7
image source: Texas A&M And University of Arkansas Work Cooperatively To Improve Soybean Crops
Embrapa Agroenergy, Parque Estação Biológica, PqEB s/n – Av.W3 Norte (final), Brasília, 70770-901, DF, Brazil
Chemical and Biological Technologies in Agriculture 2014, 1:7 doi:10.1186/s40538-014-0007-z
Abstract
According to estimates from the International Energy Agency, global energy consumption will increase by at least one third, between 2010 and 2035. The additional power required will be provided not only by fossil sources but also by renewables. While the world energy matrix is supplied only by 13.2% from renewable sources, Brazil has different scenery with renewables accounting for 42.4% of the energy matrix. This work aimed to evaluate the potential use of oleaginous in biorefineries considering the produced quantity, prices, and costs of raw materials and products. Considering the availability of these raw materials, the results showed significant opportunities that can be exploited in Brazil, within the biorefinery concept. Soybean oil is the main raw material for biodiesel production in Brazil, although there are many other vegetable oils with potential for this purpose. Related to the production costs, the soybean biodiesel has higher costs than diesel. Then, this biofuel is only produced due to Brazilian regulatory rules and public subsidies. In order to become this production favorable in the market environment, it is essential to aggregate value to all byproducts and residues generated along the biodiesel production chain. Glycerin is a byproduct of biodiesel that could be used, in a glycerol biorefinery concept, as raw material for the production of value-added products through chemical, biochemical, or thermochemical routes.
Keywords: Biorefinery; Oleaginous; Soybean; Biodiesel; Glycerin; Biofuels; Chemicals; Energy; Prices and costs
The electronic version of this article is the complete one and can be found online at: http://www.chembioagro.com/content/1/1/7
image source: Texas A&M And University of Arkansas Work Cooperatively To Improve Soybean Crops