Elemi reakciók dinamikájának és kinetikájának elméleti vizsgálata = Theoretical studies of the dynamics and kinetics of elementary reactions

Elemi kémiai reakciók dinamikáját tanulmányoztuk kváziklasszikus trajektória módszerrel. Főbb eredményeink a következők: 1. Direkt dinamikai úton megállapítottuk, hogy a metán és H atom reakciójában a nagy ütközési paraméterrel induló ütközések dominálnak és határozzák meg a termékeknek a kísérletekben megfigyelt szórási szög szerinti eloszlását; 2. a triplett oxigénatom és etén reakciójában a termékek kb. fele nemadiabatikus átmenet következtében szingulett állapotban képződik; 3. az O + O2 és a H + O2 reakcióban keletkező komplex élettartam-eloszlása nem exponenciális, egyik reakció sem írható le statisztikus reakciókinetikai elméletekkel; 4. a H + O2 reakció sebességét jelentősen megnöveli az O2 molekula rotációs gerjesztése; 5. a H + HX(v) (X=F,Cl) reakcióban nagy rezgési gerjesztettség esetén a reaktív hatáskeresztmetszet divergál a reaktánsok relatív kinetikus energiájának csökkenésével, amit a HX rotációs gerjesztése megakadályoz. Nagy rezgési kvantumszám esetén a reakció negatív aktiválási energiával jellemezhető. Alacsony ütközési energiáknál a reakcióban jelentős a "roaming atom" mechanizmus szerepe. Meghatároztuk és jellemeztük az acetonilgyök + O2, a CH3OOH + OH, a C6H5SO3H + OH és a triplett (C6H5)2CO + (CH3)2CHOH reakciók potenciálfelületének stacionárius pontjait. | Dynamics of elementary chemical reactions were studied in quasiclassical trajectory calculations. The main conclusions are: 1. using the direct dynamics method we found that in the reaction of methane and H atoms the large impact parameter collisions play a dominant role and determine the shape of the experimentally observed product angular distribution. 2. Using the trajectory surface hopping method we established that in the reaction of triplet oxygen atoms with ethene, about 50% of the products correlate with the singlet reactant because of nonadiabatic transitions. 3. In the O + O2 and H + O2 reactions the lifetime distribution of the complex formed initially is not exponential, these two reactions can not be described by statistical theories. 4. The rate of the H + O2 reaction is the significantly enhanced by rotational excitation of the O2 molecule. 5. In the H + HX reactions (X=F, Cl) at large reactant vibrational excitation the reactive cross section diverges as the initial collision energy tends to zero. Rotational excitation of the HX reactant prevents the divergence of cross sections. The reaction is characterized by negative activation energy if the reactant vibrational excitation is large. At low collision energies the 'roaming atom' mechanism plays a significant role. We have determined and characterized the stationary points on the potential surfaces of the following reactions: acetonyl + O2; CH3OOH + OH; C6H5SO3H + OH; (C6H5)2CO(triplet) + (CH3)2CHOH

Szabadgyök - molekula és molekula - molekula komplexek keletkezése és szerepük gázfázisú elemi reakciók kinetikájában és dinamikájában = Formation and role of radical-molecule and molecule-molecule complexes in the kinetics and dynamics of gas phase elementary reactions

Kutatásaink legáltalánosabb megállapítása az, hogy az elemi reakciók körében jóval gyakoribbak a reakció-köztiterméken keresztül lezajló változások, mint korábban feltételezték. Közülük is a hidrogénhidas komplexek közbejöttével végbeemenő elemi reakciók állnak az érdeklődés középpontjában, ezekkel kapcsolatban értük el a legfontosabb eredményeinket: 1. Az OH-gyök reakciója acetonnal hattagú gyűrűs hidrogénhidas komplexen keresztül megy végbe, ami a reakció szokatlan, nem Arrhenius tipusú hőmérsékletfüggését eredményezi. Reakciókinetikai eredményeink szerint az OH+aceton reakció szerepe lényegesen nagyobb a légkörben mint korábban gondolták. 2. Az R+HBr reakciók negatív hőmérsékletfüggését (R = szerves szabadgyök) H-hidas komplexek keletkezése okozza. A negatív T-függés igazolása azt jelenti, hogy a kinetikai módszerrel meghatározott szabadgyök képződési entalpiák megbízhatóak. 3. A H-hidas ''reakció komplexek'' csökkentik a reakciók energiagátját és növelik a kvantumkémiai alagúthatást, így elősegitik a reakciók végbemenetelét. | The most general conclusion from our reported research is that complex-forming elementary reactions occur much more frequently among elementary reactions than thought previously. Complexes formed with H-bonds on along the reaction path have been the focus of interest about which we have obtained our most important results: 1. The reaction of OH radicals with acetone takes place via a six-membered hydrogen bonded complex that gives rise to an unusual, non-Arrhenius type temperature dependence. 2. The negative temperature dependence of the R + HBr reactions (R = organic free radical) is caused by the formation of H-bridged complexes. A verification of the negative temperature dependence means that the enthalpy of formation values, determined for free radicals by the kinetic method, are reliable. 3. The hydrogen-bonded ''reaction complexes'' reduce the barriers of the elementary reaction, increase the quantum chemical tunneling effect, thus facilitate the progress of the reaction

Sodium-Assisted Formation of Binding and Traverse Conformations of the Substrate in a Neurotransmitter Sodium Symporter Model

Therapeutics designed to increase synaptic neurotransmitter levels by inhibiting neurotransmitter sodium sym- porters (NSSs) classify a strategic approach to treat brain disorders such as depression or epilepsy, however, the critical elementary steps that couple downhill flux of sodium to uphill transport of neurotransmitter are not disti nguished as yet. Here we present modelling of NSS member neuronal GAT1 with the substrate � -aminobutyric acid (GABA), the major inhibitory neurotransmitter. GABA binding is simulated with the occluded conformation of GAT1 homodimer in an ex- plicit lipid/water environment. Simulations performed in the 1-10 ns range of time elucidated persistent formation of half- extended minor and H-bridged major GABA conformations, referred to as binding and traverse conformations, respec- tively. The traverse GABA conformation was further stabilized by GAT1-bound Na + (1). We also observed Na + (1) trans- location to GAT1-bound Cl - as well as the appearance of water molecules at GABA and GAT1-bound Na + (2), conjectur- ing causality. Scaling dynamics suggest that the traverse GABA conformation may be valid for developing substrate in- hibitors with high efficacy. The potential for this finding is significant with impact not only in pharmacology but wherever understanding of the mechanism of neurotransmitter uptake is valuable

Hydrogen bond network topology in liquid water and methanol: a graph theory approach

Networks are increasingly recognized as important building blocks of various systems in nature and society. Water is known to possess an extended hydrogen bond network, in which the individual bonds are broken in the sub-picosecond range and still the network structure remains intact. We investigated and compared the topological properties of liquid water and methanol at various temperatures using concepts derived within the framework of graph and network theory (neighbour number and cycle size distribution, the distribution of local cyclic and local bonding coefficients, Laplacian spectra of the network, inverse participation ratio distribution of the eigenvalues and average localization distribution of a node) and compared them to small world and Erdős–Rényi random networks. Various characteristic properties (e.g. the local cyclic and bonding coefficients) of the network in liquid water could be reproduced by small world and/or Erdős–Rényi networks, but the ring size distribution of water is unique and none of the studied graph models could describe it. Using the inverse participation ratio of the Laplacian eigenvectors we characterized the network inhomogeneities found in water and showed that similar phenomena can be observed in Erdős–Rényi and small world graphs. We demonstrated that the topological properties of the hydrogen bond network found in liquid water systematically change with the temperature and that increasing temperature leads to a broader ring size distribution. We applied the studied topological indices to the network of water molecules with four hydrogen bonds, and showed that at low temperature (250 K) these molecules form a percolated or nearly-percolated network, while at ambient or high temperatures only small clusters of four-hydrogen bonded water molecules exist

Structural determinants of ligand binding in the ternary complex of human ileal bile acid binding protein with glycocholate and glycochenodeoxycholate obtained from solution NMR

Besides aiding digestion, bile salts are important signal molecules exhibiting a regulatory role in metabolic processes. Human ileal bile acid binding protein (I-BABP) is an intracellular carrier of bile salts in the epithelial cells of the distal small intestine and has a key role in the enterohepatic circulation of bile salts. Positive binding cooperativity combined with site selectivity of glycocholate and glycochenodeoxycholate, the two most abundant bile salts in the human body, make human I-BABP a unique member of the family of intracellular lipid binding proteins. Solution NMR structure of the ternary complex of human I-BABP with glycocholate and glycochenodeoxycholate reveals an extensive network of hydrogen bonds and hydrophobic interactions stabilizing the bound bile salts. Conformational changes accompanying bile salt binding affects four major regions in the protein including the C/D, E/F and G/H loops as well as the helical segment. Most of these protein regions coincide with a previously described network of millisecond time scale fluctuations in the apo protein, a motion absent in the bound state. Comparison of the heterotypic doubly ligated complex with the unligated form provides further evidence of a conformation selection mechanism of ligand entry. Structural and dynamic aspects of human I-BABP-bile salt interaction are discussed and compared with characteristics of ligand binding in other members of the intracellular lipid binding protein family. PROTEIN DATA BANK ACCESSION NUMBERS: The coordinates of the 10 lowest energy structures of the human I-BABP : GCDA : GCA complex as well as the distance restraints used to calculate the final ensemble have been deposited in the Brookhaven Protein Data Bank with accession number 2MM3