Theoretical Chemistry

Lund, Sweden

Theoretical Chemistry

Lund, Sweden

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Forsman J.,Theoretical Chemistry
Current Opinion in Colloid and Interface Science | Year: 2017

Studies of interactions between surfaces immersed in a solution containing oppositely charged polyions are reviewed. Experimental as well as theoretical progress is discussed, focusing on underlying molecular mechanisms. © 2016 Elsevier Ltd


"Innovations in theoretical and computational chemistry underpin our understanding of biological interactions, chemical dynamics and structure, as well as many beneficial chemical technologies. Michele Parrinello is a giant in the field, whose innovations are widely used in chemistry, biology, materials science, and engineering," stated Matthew Tirrell, Chair of the Dreyfus Foundation Scientific Affairs Committee and Founding Pritzker Director of the Institute for Molecular Engineering at the University of Chicago. The impact of Parrinello's work is such that he is one of the most cited scientists in the present day. He is renowned for co-devising the Car–Parrinello method for computer simulation of the movements of atoms and molecules. This work brought together, for the first time, the classical approach of molecular dynamics with a quantum theoretical approach for electron densities. This enabled the realistic exploration of a wide range of physical situations. Prior to this Parrinello had become distinguished for developing the Parrinello–Rahman method to study phase transitions in crystals. More recently, he has developed what is called metadynamics and subsequently announced an efficient variational sampling process. This has allowed the calculation of complicated phenomena such as protein folding, crystallization from a liquid, or the binding of drugs to protein receptors. Henry C. Walter, President of the Dreyfus Foundation, said, "Michele Parrinello's contributions to chemistry are immense. The Dreyfus Foundation is proud to honor him with the Dreyfus Prize, and as the first recipient from outside the United States." "I am overjoyed and humbled by the honor," said Parrinello. "I would like to dedicate this prize to my mentor Anees Rahman, the founder of modern atomistic molecular dynamics, a superb scientist, and a great human being. It was my good fortune to have met him as well as the very many talented colleagues and students with whom I had the pleasure to collaborate." Born in Messina, Italy, Parrinello received his Italian Laurea in physics from the University of Bologna in 1968. He has received many international honors including the Dirac Medal, the Rahman Prize, the Hewlett-Packard Europhysics Prize (all with Roberto Car), the Schroedinger Medal, the Enrico Fermi Prize, and the American Chemical Society Award in Theoretical Chemistry. He is a Fellow of the American Physical Society, Socio corrispondente of the Accademia Nazionale dei Lincei (Italy), and a Member of the Royal Society (UK), the European Academy of Sciences, the National Academy of Sciences, the American Academy of Arts and Sciences, and others. The Camille and Henry Dreyfus Foundation (www.dreyfus.org), based in New York, is a leading non-profit organization devoted to the advancement of the chemical sciences. It was established in 1946 by chemist, inventor, and businessman Camille Dreyfus, who directed that the Foundation's purpose be "to advance the science of chemistry, chemical engineering, and related sciences as a means of improving human relations and circumstances throughout the world." In broad terms, the Foundation programs advance young faculty of early accomplishment, develop leadership in environmental chemistry, and fund lectureships at primarily undergraduate institutions. To view the original version on PR Newswire, visit:http://www.prnewswire.com/news-releases/michele-parrinello-wins-the-dreyfus-prize-for-advances-in-theoretical-and-computational-chemistry-300456587.html


News Article | May 18, 2017
Site: phys.org

The ability to assemble electronic building blocks consisting of individual molecules is an important objective in nanotechnology. An interdisciplinary research group at Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) is now significantly closer to achieving this goal. The team of researchers headed by Prof. Dr. Sabine Maier, Prof. Dr. Milan Kivala and Prof. Dr. Andreas Görling has successfully assembled and tested conductors and networks made up of individual, newly developed building block molecules. These could in future serve as the basis of components for optoelectronic systems, such as flexible flat screens or sensors. The FAU researchers have published their results in the journal Nature Communications. Lithographic techniques in which the required structures are cut from existing blocks are mainly employed at present to produce micro- and nano-electronic components. 'This is not unlike how a sculptor creates an object from existing material by cutting away what they do not need. How small we can make these structures is determined by the quality of the material and our mechanical skills,' explains Prof. Dr. Sabine Maier from the Chair of Experimental Physics. "We now have something like a set of Lego bricks for use in the nanoelectronic field; this enables us to fabricate the required objects 'bottom-up', in other words, we start from the base and place the tiny units one on top of the other." The researchers can now use these building blocks to produce the smallest one-dimensional structures -conductors - and two-dimensional structures -networks - under precision-controlled conditions. The structures are characterised by their extreme regularity with no structural flaws. Flawless structures of this kind are essential for producing minuscule nanoelectronic components with various properties. The basis of these synthetic organic semiconductors - the Lego bricks as it were - was synthesised at the Institute for Organic Chemistry at FAU. 'Our basic building block is a triangle consisting of 21 carbon atoms with one nitrogen atom at its centre, with either hydrogen, iodine or bromine deposited at the corners depending on the desired structure' clarifies Prof. Dr. Milan Kivala from the Chair of Organic Chemistry I. The FAU researchers attach the corresponding molecules to a carrier surface made of gold and this is then heated to 150 - 270°C. This process initially forms hexagons or chains. When the samples reach a temperature of 270°C, the molecular building blocks form chemically bound, flat and honeycomb-like meshes that are similar in structure to that of the Nobel Prize-winning material graphene. The research group has already managed to determine one of the major electrical properties - the so-called 'band gap'. 'We have established that the band gap of two-dimensional structures is smaller than that of one-dimensional arrangements of the same molecular building blocks,' adds Prof. Dr. Andreas Görling from the Chair of Theoretical Chemistry. 'These insights will help us in the future to predict the properties of these structures and adjust them to the desired values for specific optoelectronic applications.' This research has opened up the possibility of fabricating ever-smaller nanoelectronic components. The current lithographic techniques used in the commercial production of microchips can only create structures larger than 14 nanometres. The conductors generated in Erlangen are only a little wider than one nanometre and therefore around fifty thousand times thinner than a human hair. However, a number of additional developments are necessary before they can be used in technological applications. For example, it is still necessary to find a suitable electrically non-conductive carrier material. More information: Christian Steiner et al, Hierarchical on-surface synthesis and electronic structure of carbonyl-functionalized one- and two-dimensional covalent nanoarchitectures, Nature Communications (2017). DOI: 10.1038/ncomms14765


News Article | May 18, 2017
Site: www.sciencedaily.com

The ability to assemble electronic building blocks consisting of individual molecules is an important objective in nanotechnology. An interdisciplinary research group at Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) is now significantly closer to achieving this goal. The team of researchers headed by Prof. Dr. Sabine Maier, Prof. Dr. Milan Kivala and Prof. Dr. Andreas Görling has successfully assembled and tested conductors and networks made up of individual, newly developed building block molecules. These could in future serve as the basis of components for optoelectronic systems, such as flexible flat screens or sensors. The FAU researchers have published their results in the journal Nature Communications. Lithographic techniques in which the required structures are cut from existing blocks are mainly employed at present to produce micro- and nano-electronic components. 'This is not unlike how a sculptor creates an object from existing material by cutting away what they do not need. How small we can make these structures is determined by the quality of the material and our mechanical skills,' explains Prof. Dr. Sabine Maier from the Chair of Experimental Physics. "We now have something like a set of Lego bricks for use in the nanoelectronic field; this enables us to fabricate the required objects 'bottom-up', in other words, we start from the base and place the tiny units one on top of the other." The researchers can now use these building blocks to produce the smallest one-dimensional structures -conductors -- and two-dimensional structures -networks -- under precision-controlled conditions. The structures are characterised by their extreme regularity with no structural flaws. Flawless structures of this kind are essential for producing minuscule nanoelectronic components with various properties. The basis of these synthetic organic semiconductors -- the Lego bricks as it were -- was synthesised at the Institute for Organic Chemistry at FAU. 'Our basic building block is a triangle consisting of 21 carbon atoms with one nitrogen atom at its centre, with either hydrogen, iodine or bromine deposited at the corners depending on the desired structure' clarifies Prof. Dr. Milan Kivala from the Chair of Organic Chemistry I. The FAU researchers attach the corresponding molecules to a carrier surface made of gold and this is then heated to 150 -- 270°C. This process initially forms hexagons or chains. When the samples reach a temperature of 270°C, the molecular building blocks form chemically bound, flat and honeycomb-like meshes that are similar in structure to that of the Nobel Prize-winning material graphene. The research group has already managed to determine one of the major electrical properties -- the so-called 'band gap'. 'We have established that the band gap of two-dimensional structures is smaller than that of one-dimensional arrangements of the same molecular building blocks,' adds Prof. Dr. Andreas Görling from the Chair of Theoretical Chemistry. 'These insights will help us in the future to predict the properties of these structures and adjust them to the desired values for specific optoelectronic applications.' This research has opened up the possibility of fabricating ever-smaller nanoelectronic components. The current lithographic techniques used in the commercial production of microchips can only create structures larger than 14 nanometres. The conductors generated in Erlangen are only a little wider than one nanometre and therefore around fifty thousand times thinner than a human hair. However, a number of additional developments are necessary before they can be used in technological applications. For example, it is still necessary to find a suitable electrically non-conductive carrier material.


News Article | May 18, 2017
Site: www.eurekalert.org

The ability to assemble electronic building blocks consisting of individual molecules is an important objective in nanotechnology. An interdisciplinary research group at Friedrich-Alexander Universität Erlangen-Nürnberg (FAU) is now significantly closer to achieving this goal. The team of researchers headed by Prof. Dr. Sabine Maier, Prof. Dr. Milan Kivala and Prof. Dr. Andreas Görling has successfully assembled and tested conductors and networks made up of individual, newly developed building block molecules. These could in future serve as the basis of components for optoelectronic systems, such as flexible flat screens or sensors. The FAU researchers have published their results in the journal Nature Communications. Lithographic techniques in which the required structures are cut from existing blocks are mainly employed at present to produce micro- and nano-electronic components. 'This is not unlike how a sculptor creates an object from existing material by cutting away what they do not need. How small we can make these structures is determined by the quality of the material and our mechanical skills,' explains Prof. Dr. Sabine Maier from the Chair of Experimental Physics. "We now have something like a set of Lego bricks for use in the nanoelectronic field; this enables us to fabricate the required objects 'bottom-up', in other words, we start from the base and place the tiny units one on top of the other." The researchers can now use these building blocks to produce the smallest one-dimensional structures -conductors - and two-dimensional structures -networks - under precision-controlled conditions. The structures are characterised by their extreme regularity with no structural flaws. Flawless structures of this kind are essential for producing minuscule nanoelectronic components with various properties. The basis of these synthetic organic semiconductors - the Lego bricks as it were - was synthesised at the Institute for Organic Chemistry at FAU. 'Our basic building block is a triangle consisting of 21 carbon atoms with one nitrogen atom at its centre, with either hydrogen, iodine or bromine deposited at the corners depending on the desired structure' clarifies Prof. Dr. Milan Kivala from the Chair of Organic Chemistry I. The FAU researchers attach the corresponding molecules to a carrier surface made of gold and this is then heated to 150 - 270°C. This process initially forms hexagons or chains. When the samples reach a temperature of 270°C, the molecular building blocks form chemically bound, flat and honeycomb-like meshes that are similar in structure to that of the Nobel Prize-winning material graphene. The research group has already managed to determine one of the major electrical properties - the so-called 'band gap'. 'We have established that the band gap of two-dimensional structures is smaller than that of one-dimensional arrangements of the same molecular building blocks,' adds Prof. Dr. Andreas Görling from the Chair of Theoretical Chemistry. 'These insights will help us in the future to predict the properties of these structures and adjust them to the desired values for specific optoelectronic applications.' This research has opened up the possibility of fabricating ever-smaller nanoelectronic components. The current lithographic techniques used in the commercial production of microchips can only create structures larger than 14 nanometres. The conductors generated in Erlangen are only a little wider than one nanometre and therefore around fifty thousand times thinner than a human hair. However, a number of additional developments are necessary before they can be used in technological applications. For example, it is still necessary to find a suitable electrically non-conductive carrier material. The results stem from an interdisciplinary collaboration within the Cluster of Excellence 'Engineering of Advanced Materials' and the Collaborative Research Centre 953 'Synthetic Carbon Allotropes' which has been published in an open access article entitled "Hierarchical on-surface synthesis and electronic structure of carbonyl-functionalized one- and two-dimensional covalent nanoarchitectures" in the scientific journal Nature Communications 8, 14765 (2017). (doi: 10.1038/ncomms14765).


News Article | February 15, 2017
Site: phys.org

The new method offers unprecedented detail in measuring molecular motion and energy – enabling better control and understanding of chemical reactions in the field of biotechnology research. The technique, which was recently published in Nature Communications, uses X-ray scattering to measure the specific movements of atoms in a molecule with extreme energy resolution. "The idea is based on exciting a molecule to a high-energy, localized state," says Victor Kimberg, a researcher in the department of Theoretical Chemistry and Biology, at KTH Royal Institute of Technology in Stockholm. The X-ray radiation that it emits then scans the energy landscape of the molecule with a level of precision that Kimberg compares to observing the movements of individual insects from on top of a mountain. Every molecule has its own energy "landscape", or the full multidimensional spectrum of motion that atoms undergo when the molecule is energized. These motions include bending and stretching of bonds. Expressed in geometric terms, the relationships of atoms to one another in a single molecule are among the key things scientists need to know in order to determine a molecule's potential energy surface (PES) – an important value in the study of molecular structures, properties and reactivity. "The PES is useful for processes such as catalysis and photochemistry," Kimberg says. For the first time, the technique enables scientists to break down the collective atomic motion in a molecule into elementary components, he says. "We can now go further than examining the collective multidimensional atomic motion in a molecule, and look at specific vibrations along selected reaction coordinates," he says. "We are not aware of any other way to do this, so it looks like our idea is new." Typically when a molecule is excited, the only measurements available show all atomic motion simultaneously. The full PES landscape is complex with all types of vibrations. Kimberg says that with the method they propose, x-ray photon energy can be tuned to excite vibrations of a singled-out type of nuclear motion – which he says can serve as a basis for developing methods of reaction control. "We show clearly that tuning the x-ray photon energy in resonance with one core-excited state induces only symmetric stretching motion; while tuning to another core-excited state excites exclusively the bending motion," he says. The measurements were conducted at the Swiss Light Source (SLS) synchrotron laboratory in Zurich, in collaboration with the KTH group, comprised of Kimberg, Faris Gel'mukhanov and Hans Ågren, who were responsible for the underlying theory and simulations. Explore further: High-energy electrons synced to ultrafast laser pulse to probe how vibrational states of atoms change in time More information: Rafael C. Couto et al. Selective gating to vibrational modes through resonant X-ray scattering, Nature Communications (2017). DOI: 10.1038/ncomms14165


News Article | September 6, 2016
Site: www.rdmag.com

Using a unique computational approach to rapidly sample, in millisecond time intervals, proteins in their natural state of gyrating, bobbing, and weaving, a research team from UC San Diego and Monash University in Australia has identified promising drug leads that may selectively combat heart disease, from arrhythmias to cardiac failure. Reported in the September 5, 2016 Proceedings of the National Academy of Sciences (PNAS) Early Edition, the researchers used the computing power of Gordon and Comet, based at the San Diego Supercomputer Center (SDSC) at UC San Diego; and Stampede, at the Texas Advanced Computing Center at the University of Texas at Austin, to perform an unprecedented survey of protein structures using accelerated molecular dynamics or aMD - a method that performs a more complete sampling of the myriad shapes and conformations that a target protein molecule may go through. The computing resources were provided by the National Science Foundation-funded Extreme Science and Engineering Discovery Environment (XSEDE) program, one of the most advanced collections of integrated digital resources and services in the world. "The supercomputing power of Gordon, Comet, and Stampede allows us to run hundreds-of-nanosecond aMD simulations, which are able to capture millisecond timescale events in complex biomolecules," said the study's first author Yinglong Miao, a research specialist with the Howard Hughes Medical Institute at UC San Diego and research scientist with the UC San Diego Department of Pharmacology. Though effective in most cases, today's heart medications - many of which act on M2 muscarinic acetylcholine receptors or M2 mAChRs that decrease heart rate and reduce heart contractions - may carry side effects, sometimes serious. That's because the genetic sequence of M2 mAChR's primary 'orthosteric' binding site is "highly conserved," and found in at least four other receptor types that are widely spread in the body, yielding unwanted results. For this reason, drug designers are seeking a different approach, homing in on molecular targets or so-called "allosteric binding sites" that reside away from the receptor's primary binding site and are built around a more diverse genetic sequence and structure than their counterpart 'orthosteric' binding sites. Essentially, allosteric modulators act as a kind of cellular dimmer-switch that, once turned on, 'fine tunes' the activation and pharmacological profile of the target receptor. "Allosteric sites typically exhibit great sequence diversity and therefore present exciting new targets for designing selective therapeutics," said the study's co-investigator J. Andrew McCammon, the Joseph E. Mayer Chair of Theoretical Chemistry, a Howard Hughes Medical Institute investigator, and Distinguished Professor of Pharmacology, all at UC San Diego. In particular, drug designers have begun to aggressively search for allosteric modulators to fine-tune medications that bind to G protein-coupled receptors (GPCRs), the largest and most diverse group of membrane receptors in animals, plants, fungi and protozoa. These cell surface receptors act like an inbox for messages in the form of light energy, hormones and neurotransmitters, and perform an incredible array of functions in the human body. In fact, between one-third to one-half of all marketed drugs act by binding to GPCRs, treating diseases including cancer, asthma, schizophrenia, Alzheimer's and Parkinson's disease, and heart disease. Though many of the GPCR drugs have made their way to the medicine cabinet, most -- including M2 mAChR targeted drugs -- exhibit side effects owing to their lack of specificity. All these drugs target the orthosteric binding sites of receptors, thus creating the push to find more targeted therapies based on allosteric sites. "The problem here is that molecules that bind to these allosteric sites have proven extremely difficult to identify using conventional high-throughput screening techniques," said McCammon, also a chemistry and biochemistry professor in UC San Diego's Division of Physical Sciences. Enter accelerated molecular dynamics and supercomputing. As described in this latest study, called Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor, some 38 lead compounds were selected from a database of compounds from the National Cancer Institute, using computationally enhanced simulations to account for binding strength and receptor flexibility. About half of these compounds exhibited the hallmarks of an allosteric behavior in subsequent in vitro experiments, with about a dozen showing strong affinity to the M2 mAChR binding site. Of these, the researchers highlighted two showing both strong affinity and high selectivity in studies of cellular behavior. These cutting-edge experiments were performed by collaborators from the Monash Institute of Pharmaceutical Sciences. "To our knowledge, this study demonstrates for the first time an unprecedented successful structure-based approach to identify chemically diverse and selective GPCR allosteric modulators with outstanding potential for further structure-activity relationship studies," the researchers wrote. The next steps will involve an investigation of the chemical properties of these novel molecules by the molecular chemists from Monash, led by Celine Valant and her colleague Arthur Christopoulos. "This is just the beginning. We believe that it will be possible to apply our combined cutting-edge in silico and in vitro techniques to a wide array of receptor targets that are involved in some of the most devastating diseases," said Valant, the study's co-lead investigator from Monash.


Woodward C.E.,University of New South Wales | Forsman J.,Theoretical Chemistry
Langmuir | Year: 2015

We developed an analytical theory for the manybody potential of mean force (POMF) between N spheres immersed in a continuum chain fluid. The theory is almost exact for a Θ polymer solution in the protein limit (small particles, long polymers), where N-body effects are important. Polydispersity in polymer length according to a Schulz-Flory distribution emerges naturally from our analysis, as does the transition to the monodisperse limit. The analytical expression for the POMF allows for computer simulations employing the complete N-body potential (i.e., without n-body truncation; n


Segad M.,Theoretical Chemistry | Hanski S.,Aalto University | Olsson U.,Lund University | Ruokolainen J.,Aalto University | And 2 more authors.
Journal of Physical Chemistry C | Year: 2012

Aqueous dispersions of pure sodium and calcium smectite clays with platelet sizes on the order of a few hundred nanometers were characterized using a combination of cryo-transmission electron microscopy (cryo-TEM) and small-angle X-ray scattering (SAXS). With monovalent sodium counterions the clay is dispersed as individual platelets, as seen by cryo-TEM, that order into a nematic phase. From SAXS a one-dimensional swelling of the clay in water is observed with the characteristic spacing h s = Î́/ Ï• c, where h s is the separation between the platelets, Î́ = 1 nm is the effective platelet thickness, and Ï• c is the clay volume fraction in the sample. In calcium montmorillonite, on the other hand, cryo-TEM images clearly show the presence of tactoids, where the platelets have aggregated into stacks with a periodic spacing of 2 nm. From imaging a large number of tactoids the distribution function f(N) for the number of platelets per tactoid was estimated, and the average number â'̈Nâ'© â‰̂ 10. The characteristic 2 nm spacing as well as the small number of platelets per tactoid was also confirmed by SAXS. The present study demonstrates that cryo-TEM, with carefully prepared specimen, is a very useful technique to characterize clay dispersions, particularly in aggregated systems. © 2012 American Chemical Society.

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