Posts Tagged ‘energy’
Tuesday, August 29th, 2017
The triennial conference is this year located in Munich. With 1500 participants and six parallel sessions, this report can give only a flavour of proceedings.
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Tags:bond dissociation energy, City: Aachen, City: Munich, Dieter Cremer, Edward Valeev, energy, Flavour, Jeremy Harvey, Ken Houk, Leo Radom, Peter Scheiner, Physics, Proceedings, Quark matter, Standard Model, Yitzhak Apeloig
Posted in Interesting chemistry, WATOC reports | No Comments »
Sunday, June 18th, 2017
The iron complex shown below forms the basis for many catalysts.[cite]10.1002/anie.200502985[/cite] With iron, the catalytic behaviour very much depends on the spin-state of the molecule, which for the below can be either high (hextet) or medium (quartet) spin, with a possibility also of a low spin (doublet) state. Here I explore whether structural information in crystal structures can reflect such spin states.
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Tags:catalysis, Catalysts, Chemistry, energy, energy separations, energy span, Fe complex, Homogeneous catalysis, Kumada coupling, Organometallic chemistry, spin-state energy separations, Synergistic catalysis
Posted in crystal_structure_mining | 1 Comment »
Saturday, April 15th, 2017
Back in the early 1990s, we first discovered the delights of searching crystal structures for unusual bonding features.[cite]10.1039/P29940000703[/cite] One of the first cases was a search for hydrogen bonds formed to the π-faces of alkenes and alkynes. In those days the CSD database of crystal structures was a lot smaller (<80,000 structures; it’s now ten times larger) and the search software less powerful. So here is an update.
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Tags:calculated energy, chemical bonding, Chemistry, Crystal, crystallography, energy, energy calculation, Intermolecular forces, Nature, search query, search software, Supramolecular chemistry
Posted in crystal_structure_mining | 2 Comments »
Monday, March 20th, 2017
The example a few posts back of how methane might invert its configuration by transposing two hydrogen atoms illustrated the reaction mechanism by locating a transition state and following it down in energy using an intrinsic reaction coordinate (IRC). Here I explore an alternative method based instead on computing a molecular dynamics trajectory (MD).
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Tags:animation, chemical reaction, Chemistry, computational chemistry, computed potential energy surface, energy, Gaseous signaling molecules, Hydrogen, kinetic energy, kinetic energy contributions, Methane, Molecular dynamics, Physical chemistry, Quantum chemistry, Reaction coordinate, simulation, Theoretical chemistry
Posted in reaction mechanism | 2 Comments »
Thursday, December 1st, 2016
Following on from a search for long C-C bonds, here is the same repeated for C=C double bonds.
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Tags:Chemical bond, chemical bonding, Chemical nomenclature, Chemistry, Conjugated system, double bond, energy, Nature, Nonmetal, Organic chemistry, Physical organic chemistry, search query, Substituent
Posted in crystal_structure_mining, Interesting chemistry | 2 Comments »
Thursday, September 1st, 2016
Bromoallene is a pretty simple molecule, with two non-equivalent double bonds. How might it react with an electrophile, say dimethyldioxirane (DMDO) to form an epoxide?[cite]10.1039/C6CC06395K[/cite] Here I explore the difference between two different and very simple approaches to predicting its reactivity. 
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Tags:chemical bonding, chemical reaction, Chemistry, Delocalized electron, double bond, energy, energy difference, HOMO/LUMO, lowest energy, Molecular orbital, Natural bond orbital, Nature, Physics, Quantum chemistry, stable HOMO-1
Posted in reaction mechanism | No Comments »
Friday, May 27th, 2016
In the previous post, I explored the mechanism for nucleophilic substitution at a silicon centre proceeding via retention of configuration involving a Berry-like pseudorotation. Here I probe an alternative route involving inversion of configuration at the Si centre. Both stereochemical modes are known to occur, depending on the leaving group, solvent and other factors.[cite]10.1016/S0040-4020(01)89077-3[/cite],[cite]10.1021/ja01006a024[/cite],[cite]10.1021/ja00784a081[/cite]
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Tags:Brook rearrangement, energy, free energy, Leaving group, Nucleophilic substitution, Pseudorotation, Si centre, SNi, Substitution reactions, Walden inversion
Posted in reaction mechanism | No Comments »
Wednesday, May 25th, 2016
The substitution of a nucleofuge (a good leaving group) by a nucleophile at a carbon centre occurs with inversion of configuration at the carbon, the mechanism being known by the term SN2 (a story I have also told in this post). Such displacement at silicon famously proceeds by a quite different mechanism, which I here quantify with some calculations.
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Tags:Berry mechanism, Elimination reaction, energy, energy barrier, energy profile, free energy, Leaving group, lower energy orientation, Molecular geometry, Organic reactions, overall free energy, Pseudorotation, search query, SN2 reaction, Stereochemistry, Trigonal bipyramidal molecular geometry
Posted in reaction mechanism | No Comments »
Sunday, April 24th, 2016
The autoionization of water involves two molecules transfering a proton to give hydronium hydroxide, a process for which the free energy of reaction is well known. Here I ask what might happen with the next element along in the periodic table, F.
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Tags:dielectric, energy, Equilibrium chemistry, Fluorides, free energy, free energy barrier, Hydrogen bond, Hydronium, Inorganic solvents, Lithium fluoride, low energy final geometry corresponds, Oxides, PH, Properties of water, Self-ionization of water, Water, Water model
Posted in Interesting chemistry | 10 Comments »
Friday, April 22nd, 2016
Earlier, I constructed a possible model of hydronium hydroxide, or H3O+.OH– One way of assessing the quality of the model is to calculate the free energy difference between it and two normal water molecules and compare the result to the measured difference. Here I apply a further test of the model using isotopes.
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Tags:dielectric, energy, free energy, Heat transfer, Heavy water, Kilocalorie per mole, model is to calculate the free energy difference, Properties of water, the free energy, thermodynamics, Tritiated water
Posted in Interesting chemistry | 4 Comments »