Computational Investigation of BMAA and Its Carbamate Adducts as Potential GluR2 Modulators.

Beta-N-methylamino-l-alanine (BMAA) is a potential neurotoxic nonprotein amino acid, which can reach the human body through the food chain. When BMAA interacts with bicarbonate in the human body, carbamate adducts are produced, which share a high structural similarity with the neurotransmitter glutamate. It is believed that BMAA and its l-carbamate adducts bind in the glutamate binding site of ionotropic glutamate receptor 2 (GluR2). Chronic exposure to BMAA and its adducts could cause neurological illness such as neurodegenerative diseases. However, the mechanism of BMAA action and its carbamate adducts bound to GluR2 has not yet been elucidated. Here, we investigate the binding modes and the affinity of BMAA and its carbamate adducts to GluR2 in comparison to the natural agonist, glutamate, to understand whether these can act as GluR2 modulators. Initially, we perform molecular dynamics simulations of BMAA and its carbamate adducts bound to GluR2 to examine the stability of the ligands in the S1/S2 ligand-binding core of the receptor. In addition, we utilize alchemical free energy calculations to compute the difference in the free energy of binding of the beta-carbamate adduct of BMAA to GluR2 compared to that of glutamate. Our findings indicate that carbamate adducts of BMAA and glutamate remain stable in the binding site of the GluR2 compared to BMAA. Additionally, alchemical free energy results reveal that glutamate and the beta-carbamate adduct of BMAA have comparable binding affinity to the GluR2. These results provide a rationale that BMAA carbamate adducts may be, in fact, the modulators of GluR2 and not BMAA itself.

Structure Distribution of Gaseous Ions in Strong Electrostatic Fields.

In drift tube experiments, where ions move in gases under the action of an electrostatic field, collision excitation is implemented for the study of the energy partitioning in the molecular degrees of freedom and the corresponding relaxation rates when the excitation is turned off. In the case of flexible ions, the vibration modes related to metastable molecular structures have been activated in ion mobility spectrometry and their population has been probed with respect to the field strength and the gas temperature. Here, we study the angular vibrational excitation and relaxation of such systems by examining the motion of molecular ions with one bending mode at strong fields using a nonequilibrium molecular dynamics simulation method. The relatively stable structures are introduced through the use of an intramolecular angular potential with minima at the position of the most stable conformations. We calculate the first few moments of the velocity and angular velocity distribution functions as well as the distribution of the conformers, and find that they follow unified curves when plotted with respect to the relative ion-atom collision energy. At high field strengths, the angular vibration is excited and a portion of the ions interchanges conformations continuously in time with the populations of the molecular structures to attain limiting values. In addition, orientational alignment, with the perpendicular angular momentum being greater than the one parallel to the field, is observed. Our observations, although based on a specific system, must be rather general for the case of large flexible molecular ions.

Molecular Dynamics Simulation for the Dynamics and Kinetics of Folding Peptides in the Gas Phase.

The conformations of flexible molecular species, such as oligomers and oligopeptides, and their interconversion in the gas phase have been probed by ion mobility spectrometry measurements. The ion motion is interpreted through the calculation of effective cross sections in the case of stable conformations of the macromolecules. However, when the molecular structures transform to each other as the ions collide with gas atoms during their flight through the drift tube, the introduction of an average cross section is required. To provide a direct way for the reproduction of the ion motion, we employ a nonequilibrium molecular dynamics simulation method and consider a molecular model that consists of two connected stiff cylindrical bodies interacting through an intramolecular model potential. With this procedure we have calculated the ion mobility as a function of temperature for a prototype peptide that converts between a helical and an extended globular form. The results are in good agreement with ion mobility spectrometry data confirming that an angular vibration coordinate can be used for the interpretation of the shifting of the drift-time distributions at high temperatures. The approach produces mean kinetic energies as well as various combined distributions of the ion degrees of freedom. It is easily applied to flexible macromolecular ions and can be extended to include additional degrees of freedom.

Kinetic and theoretical studies on the protonation of [Ni(2-SC6H4N){PhP(CH2CH2PPh2)2}]+: nitrogen versus sulfur as the protonation site.

The complexes [Ni(4-Spy)(triphos)]BPh(4) and [Ni(2-Spy)(triphos)]BPh(4) {triphos = PhP(CH(2)CH(2)PPh(2))(2), 4-Spy = 4-pyridinethiolate, 2-Spy = 2-pyridinethiolate} have been prepared and characterized both spectroscopically and using X-ray crystallography. In both complexes the triphos is a tridentate ligand. However, [Ni(4-Spy)(triphos)](+) comprises a 4-coordinate, square-planar nickel with the 4-Spy ligand bound to the nickel through the sulfur while [Ni(2-Spy)(triphos)](+) contains a 5-coordinate, trigonal-bipyramidal nickel with a bidentate 2-Spy ligand bound to the nickel through both sulfur and nitrogen. The kinetics of the reactions of [Ni(4-Spy)(triphos)](+) and [Ni(2-Spy)(triphos)](+) with lutH(+) (lut = 2,6-dimethylpyridine) in MeCN have been studied using stopped-flow spectrophotometry, and the two complexes show very different reactivities. The reaction of [Ni(4-Spy)(triphos)](+) with lutH(+) is complete within the deadtime of the stopped-flow apparatus (2 ms) and corresponds to protonation of the nitrogen. However, upon mixing [Ni(2-Spy)(triphos)](+) and lutH(+) a reaction is observed (on the seconds time scale) to produce an equilibrium mixture. The mechanistic interpretation of the rate law has been aided by the application of MSINDO semiempirical and ADF calculations. The kinetics and calculations are consistent with the reaction between [Ni(2-Spy)(triphos)](+) and lutH(+) involving initial protonation of the sulfur followed by dissociation of the nitrogen and subsequent transfer of the proton from sulfur to nitrogen. The factors affecting the position of protonation and the coupling of the coordination state of the 2-pyridinethiolate ligand to the site of protonation are discussed.

Transport and dynamic properties of O2+(X2Πg) in Kr under the action of an electrostatic field: single or multiple potential energy surface treatment.

Ion transport and dynamic properties are calculated through molecular dynamics simulation of the motion of O(2)(+) in Kr under the action of an electrostatic field. The two lower potential energy surfaces X̃(2)A(") and Ã(2)A(') are considered for the interaction of the Π ground state of the ion with a closed shell noble gas. First, we study the reproduction of experimental mobility data through the use of single and multiple potential energy surfaces and establish the contribution of both lower energy states to the interactions. Further, we obtain mean energies and components of the diffusion coefficient parallel and perpendicular to the field, the latter through calculation of the velocity correlation functions. We also calculate components of the angular momentum which provide a measure of the collisional rotational alignment of the ions at high field strength.

Computational modeling of the adsorption and (*)OH initiated photochemical and photocatalytic primary oxidation of nitrobenzene.

The adsorption and primary oxidation step for the photodegradation of nitrobenzene (NB) have been studied computationally using MSINDO SCF MO method. The method performs efficiently for extended surface models such as Ti(36)O(90)H(36). Molecular dynamics simulations have revealed that NB is linked to TiO(2) surface at the titanium ion via the oxygen atoms of NO(2) group. In addition, the computed vibrational density of states for the adsorbed NB molecule is in reasonably good agreement with the available experimental data and theoretical results. In order to identify the primary photochemical and photocatalytic (*)OH initiated photooxidation intermediates, we have employed two different theoretical approaches, frontier orbital theory and Wheland localization theory. It has been found that the meta- hydroxynitrocyclohexadienyl radical is energetically more favored than para- and ortho-hydroxynitrocyclohexadienyl radicals for the photochemical photolysis, whereas in the case of photocatalysis, the (*)OH radical attack is unselective and all three possible isomers have comparable stabilities.

Mixed quantum-classical molecular dynamics simulation of vibrational relaxation of ions in an electrostatic field.

The vibrational relaxation of ions in low-density gases under the action of an electrostatic field is reproduced through a molecular dynamics simulation method. The vibration is treated though quantum mechanics and the remaining degrees of freedom are considered classical. The procedure is tested through comparison against analytic results for a two-dimensional quantum model and by studying energy exchange during binary ion-atom collisions. Finally, the method has been applied successfully to the calculation of the mobility and the vibrational relaxation rate of O2+ in Kr as a function of the mean collision energy using a model interaction potential that reproduces the potential minimum of a previously known ab initio potential surface. The calculation of the steady mean vibrational motion of the ions in (flow) drift tubes seems straightforward, though at the expense of large amounts of computer time.