The complex kinetics of protein folding in wide temperature ranges

The complex protein folding kinetics in wide temperature ranges is studied through diffusive dynamics on the underlying energy landscape. The well-known kinetic chevron rollover behavior is recovered from the mean first passage time, with the U-shape dependence on temperature. The fastest folding temperature T-0 is found to be smaller than the folding transition temperature T-f. We found that the fluctuations of the kinetics through the distribution of first passage time show rather universal behavior, from high-temperature exponential Poissonian kinetics to the relatively low-temperature highly nonexponential kinetics. The transition temperature is at T-k and T-0, T-k, T-f. In certain low-temperature regimes, a power law behavior at long time emerges. At very low temperatures ( lower than trapping transition temperature T< T-0/(4&SIM;6)), the kinetics is an exponential Poissonian process again.

Probing the kinetics of single molecule protein folding

We propose an approach to integrate the theory, simulations, and experiments in protein-folding kinetics. This is realized by measuring the mean and high-order moments of the first-passage time and its associated distribution. The full kinetics is revealed in the current theoretical framework through these measurements. In the experiments, information about the statistical properties of first-passage times can be obtained from the kinetic folding trajectories of single molecule experiments ( for example, fluorescence). Theoretical/simulation and experimental approaches can be directly related. We study in particular the temperature-varying kinetics to probe the underlying structure of the folding energy landscape. At high temperatures, exponential kinetics is observed; there are multiple parallel kinetic paths leading to the native state. At intermediate temperatures, nonexponential kinetics appears, revealing the nature of the distribution of local traps on the landscape and, as a result, discrete kinetic paths emerge. At very low temperatures, exponential kinetics is again observed; the dynamics on the underlying landscape is dominated by a single barrier.

Dominant kinetic paths on biomolecular binding-folding energy landscape

The identification of kinetic pathways is a central issue in understanding the nature of flexible binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. The kinetic time can be obtained through the contributions from the dominant paths and has a U-shape dependence on temperature.

Single-molecule dynamics reveals cooperative binding-folding in protein recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure ( the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state.

Study on dimeric ion of toluene in the gas phase by tandem mass spectrometry

The reaction character of m/z183 and 184 ions generated from ion -molecule reaction of toluene under self-chemical ionization was studied using Collision-Induced Dissociation (CID). The results Show that the m/z183 and 184 ions have several transition state structures; such as diphenyl methane derivative, alpha-bond structure formed between toluene and tropylium, pi-complex formed between toluene radical ion and toluene and pi-complex consisted of benzyl ion and toluene.

A STUDY ON CH5O+ IONS IN GAS PHASE CID EYPERIMENT AND QUANTUM CHEMISTRY CALCULATION

The structures of CH5O+ from two different reactions which are protonation of CH3OH from the above two pathways possess the same structures, CH3OH2+. The value of kinetic energy release for the metastable decomposition CH2OH3+-> CH2OH+ + H-2 determined from the experiment is in good agreement with that from theoretical calculations. The transition state of above reaction were disscussed.

Ab initio calculations of group 4 metallocene reaction mechanisms: atomic layer deposition and bond activation catalysis

Thin film dielectrics based on titanium, zirconium or hafnium oxides are being introduced to increase the permittivity of insulating layers in transistors for micro/nanoelectronics and memory devices. Atomic layer deposition (ALD) is the process of choice for fabricating these films, as it allows for high control of composition and thickness in thin, conformal films which can be deposited on substrates with high aspect-ratio features. The success of this method depends crucially on the chemical properties of the precursor molecules. A successful ALD precursor should be volatile, stable in the gas-phase, but reactive on the substrate and growing surface, leading to inert by-products. In recent years, many different ALD precursors for metal oxides have been developed, but many of them suffer from low thermal stability. Much promise is shown by group 4 metal precursors that contain cyclopentadienyl (Cp = C5H5-xRx) ligands. One of the main advantages of Cp precursors is their thermal stability. In this work ab initio calculations were carried out at the level of density functional theory (DFT) on a range of heteroleptic metallocenes [M(Cp)4-n(L)n], M = Hf/Zr/Ti, L = Me and OMe, in order to find mechanistic reasons for their observed behaviour during ALD. Based on optimized monomer structures, reactivity is analyzed with respect to ligand elimination. The order in which different ligands are eliminated during ALD follows their energetics which was in agreement with experimental measurements. Titanocene-derived precursors, TiCp*(OMe)3, do not yield TiO2 films in atomic layer deposition (ALD) with water, while Ti(OMe)4 does. DFT was used to model the ALD reaction sequence and find the reason for the difference in growth behaviour. Both precursors adsorb initially via hydrogen-bonding. The simulations reveal that the Cp* ligand of TiCp*(OMe)3 lowers the Lewis acidity of the Ti centre and prevents its coordination to surface O (densification) during both of the ALD pulses. Blocking this step hindered further ALD reactions and for that reason no ALD growth is observed from TiCp*(OMe)3 and water. The thermal stability in the gas phase of Ti, Zr and Hf precursors that contain cyclopentadienyl ligands was also considered. The reaction that was found using DFT is an intramolecular α-H transfer that produces an alkylidene complex. The analysis shows that thermal stabilities of complexes of the type MCp2(CH3)2 increase down group 4 (M = Ti, Zr and Hf) due to an increase in the HOMO-LUMO band gap of the reactants, which itself increases with the electrophilicity of the metal. The reverse reaction of α-hydrogen abstraction in ZrCp2Me2 is 1,2-addition reaction of a C-H bond to a Zr=C bond. The same mechanism is investigated to determine if it operates for 1,2 addition of the tBu C-H across Hf=N in a corresponding Hf dimer complex. The aim of this work is to understand orbital interactions, how bonds break and how new bonds form, and in what state hydrogen is transferred during the reaction. Calculations reveal two synchronous and concerted electron transfers within a four-membered cyclic transition state in the plane between the cyclopentadienyl rings, one π(M=X)-to-σ(M-C) involving metal d orbitals and the other σ(C-H)-to-σ(X-H) mediating the transfer of neutral H, where X = C or N. The reaction of the hafnium dimer complex with CO that was studied for the purpose of understanding C-H bond activation has another interesting application, namely the cleavage of an N-N bond and resulting N-C bond formation. Analysis of the orbital plots reveals repulsion between the occupied orbitals on CO and the N-N unit where CO approaches along the N-N axis. The repulsions along the N-N axis are minimized by instead forming an asymmetrical intermediate in which CO first coordinates to one Hf and then to N. This breaks the symmetry of the N-N unit and the resultant mixing of MOs allows σ(NN) to be polarized, localizing electrons on the more distant N. This allowed σ(CO) and π(CO) donation to N and back-donation of π*(Hf2N2) to CO. Improved understanding of the chemistry of metal complexes can be gained from atomic-scale modelling and this provides valuable information for the design of new ALD precursors. The information gained from the model decomposition pathway can be additionally used to understand the chemistry of molecules in the ALD process as well as in catalytic systems.

Synthesis and Binding of Stable Bisubstrate Ligands for Phosphoglycerate Kinase

Stable bisubstrate ligands of phosphoglycerate kinase (PGK) have been synthesised with AMP or ADP conjugated to hydrolytically-stable, symmetrical analogues of 1,3-bisphosphoglycerate and their binding to yeast PGK evaluated. Their Kds decrease with net negative charge, with a penta-anionic analogue 7 showing highest affinity - in accordance with its approximation to the transition state for the reaction catalysed by PGK.

Bandstructure approach to near edge structure

We review the current state of the art in EELS fingerprinting by computer simulation, focusing on the bandstructure approach to the problem. Currently calculations are made using a one electron theory, but we describe in principle the way to go beyond this to include final state effects. We include these effects within the one electron framework using the Slater transition state formula and assess the errors involved. Two examples are then given which illustrate the use of the one electron approximation within density functional theory. Our approach is to combine predicted atomic structure with predicted electronic structure to assist in fingerprinting of complex crystal structures.

Effect of relaxation on the oxygen K-edge electron energy-loss near-edge structure in yttria-stabilized zirconia

The electron energy-loss near-edge structure (ELNES) at the oxygen K-edge has been investigated in a range of yttria-stabilized zirconia (YSZ) materials. The electronic structure of the three polymorphs of pure ZrO2 and of the doped YSZ structure close to the 33 mol %Y2O3 composition have been calculated using a full-potential linear muffin-tin orbital method (NFP-LMTO) as well as a pseudopotential based technique. Calculations of the ELNES dipole transition matrix elements in the framework of the NFP-LMTO scheme and inclusion of core hole screening within Slater's transition state theory enable the ELNES to be computed. Good agreement between the experimental and calculated ELNES is obtained for pure monoclinic ZrO2. The agreement is less good with the ideal tetragonal and cubic structures. This is because the inclusion of defects is essential in the calculation of the YSZ ELNES. If the model used contains ordered defects such as vacancies and metal Y planes, agreement between the calculated and experimental O K-edges is significantly improved. The calculations show how the five different O environments of Zr,Y,O, are connected with the features observed in the experimental spectra and demonstrate clearly the power of using ELNES to probe the stabilization mechanism in doped metal oxides.

Concertedness and solvent effects in multiple proton transfer reactions: The formic acid dimer in solution

The issue of multiple proton transfer (PT) reactions in solution is addressed by performing molecular dynamics simulations for a formic acid dimer embedded in a water cluster. The reactant species is treated quantum mechanically, within a density functional approach, while the solvent is represented by a classical model. By constraining different distances within the dimer we analyze the PT process in a variety of situations representative of more complex environments. Free energy profiles are presented, and analyzed in terms of typical solvated configurations extracted from the simulations. A decrease in the PT barrier height upon solvation is rationalized in terms of a transition state which is more polarized than the stable states. The dynamics of the double PT process is studied in a low-barrier case and correlated with solvent polarization fluctuations. Cooperative effects in the motion of the two protons are observed in two different situations: when the solvent polarization does not favor the transfer of one of the two protons and when the motion of the two protons is not synchronized. This body of observations is correlated with local structural and dynamical properties of the solvent in the vicinity of the reactant. (C) 2000 American Institute of Physics. [S0021-9606(00)51121-0].

On the origin of the forward peak and backward oscillations in the F + H2(v = 0) to HF(v' = 2) + H reaction

We present a semiclassical complex angular momentum (CAM) analysis of the forward scattering peak which occurs at a translational collision energy around 32 meV in the quantum mechanical calculations for the F + H2(v = 0, j = 0) ? HF(v' = 2, j' = 0) + H reaction on the Stark–Werner potential energy surface. The semiclassical CAM theory is modified to cover the forward and backward scattering angles. The peak is shown to result from constructive/destructive interference of the two Regge states associated with two resonances, one in the transition state region and the other in the exit channel van der Waals well. In addition, we demonstrate that the oscillations in the energy dependence of the backward differential cross section are caused by the interference between the direct backward scattering and the decay of the two resonance complexes returning to the backward direction after one full rotation.

Chain growth mechanism in Fischer-Tropsch synthesis: A DFT study of C-C coupling over Ru, Fe, Rh, and Re surfaces

A quantitative approach is used to understand the chain growth mechanism in FT synthesis on the Ru, Fe, Rh, and Re surfaces. The C-C coupling reactions are extensively calculated on the stepped metal surfaces. Combining the coupling barriers and reactant stabilities, we investigate the reaction rates of all possible C, + C-1 coupling pathways on the metal surfaces. It is found that (i) all the transition-state structures are similar on these surfaces, while some coupling barriers are very different; (ii) the dominant chain growth pathways on these surfaces are different: C + CH and CH + CH on Rh and Ru surfaces, C + CH3 on Fe surface, and C + CH on Re surface. The common features of the major coupling reactions together with those on the Co surface are also discussed.

Comparative study of diastereoisomer interconversion in chiral BINOL-ate and diamine platinum complexes of conformationally flexible NUPHOS diphosphines

A thorough and detailed study of diastereointerconversion in the chiral platinum complexes [(NUPHOS)Pt{(S)-BINOL}] (3a-e) has been undertaken and compared with the results of a similar study with [(BIPHEP)Pt{(S)-BINOL}]. Rate data revealed that this process obeys first-order relaxation kinetics, and rate constants for conversion of the minor to the major diastereoisomer have been obtained. Eyring analysis of the data gave DeltaH(double dagger) and DeltaS(double dagger) values of 22-25 kcal mol(-1) and -1 to -16 eu, respectively. In combination with computational analysis, these studies indicate that atropinversion most likely occurs via an on-metal pathway involving a planar seven-membered transition state. Substitution of (S)-BINOL for (S,S)-DPEN results in a marked reduction in the barrier to atropinversion; a DeltaH(double dagger) value of 17 kcal mol(-1) has been determined for the conversion of delta-[(Ph-4-NUPHOS)Pt{(S,S)-DPEN}]Cl-2 to lambda-[(Ph-4-NUPHOS)Pt{(S,S)-DPEN}]Cl-2, which could indicate that an alternative mechanism operates.

The importance of hydrogen's potential-energy surface and the strength of the forming R-H bond in surface hydrogenation reactions

An understanding of surface hydrogenation reactivity is a prevailing issue in chemistry and vital to the rational design of future catalysts. In this density-functional theory study, we address hydrogenation reactivity by examining the reaction pathways for N+H -> NH and NH+H -> NH2 over the close-packed surfaces of the 4d transition metals from Zr-Pd. It is found that the minimum-energy reaction pathway is dictated by the ease with which H can relocate between hollow-site and top-site adsorption geometries. A transition state where H is close to a top site reduces the instability associated with bond sharing of metal atoms by H and N (NH) (bonding competition). However, if the energy difference between hollow-site and top-site adsorption energies (Delta E-H) is large this type of transition state is unfavorable. Thus we have determined that hydrogenation reactivity is primarily controlled by the potential-energy surface of H on the metal, which is approximated by Delta E-H, and that the strength of N (NH) chemisorption energy is of less importance. Delta E-H has also enabled us to make predictions regarding the structure sensitivity of these reactions. Furthermore, we have found that the degree of bonding competition at the transition state is responsible for the trend in reaction barriers (E-a) across the transition series. When this effect is quantified a very good linear correlation is found with E-a. In addition, we find that when considering a particular type of reaction pathway, a good linear correlation is found between the destabilizing effects of bonding competition at the transition state and the strength of the forming N-H (HN-H) bond. (c) 2006 American Institute of Physics.