NONSTATISTICAL DYNAMICS IN THERMAL REACTIONS OF POLYATOMIC MOLECULES

Why nature really chose phosphate

Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and maintaining the integrity of the genetic material. On the surface, it would appear to be a simple nucleophile displacement reaction. However, this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalyzed reactions. To further complicate matters, while powerful, traditional experimental techniques such as the use of linear free-energy relationships (LFER) or measuring isotope effects cannot make unique distinctions between different potential mechanisms. A quarter of a century has passed since Westheimer wrote his seminal review, 'Why Nature Chose Phosphate' (Science 235 (1987), 1173), and a lot has changed in the field since then. The present review revisits this biologically crucial issue, exploring both relevant enzymatic systems as well as the corresponding chemistry in aqueous solution, and demonstrating that the only way key questions in this field are likely to be resolved is through careful theoretical studies (which of course should be able to reproduce all relevant experimental data). Finally, we demonstrate that the reason that nature really chose phosphate is due to interplay between two counteracting effects: on the one hand, phosphates are negatively charged and the resulting charge-charge repulsion with the attacking nucleophile contributes to the very high barrier for hydrolysis, making phosphate esters among the most inert compounds known. However, biology is not only about reducing the barrier to unfavorable chemical reactions. That is, the same charge-charge repulsion that makes phosphate ester hydrolysis so unfavorable also makes it possible to regulate, by exploiting the electrostatics. This means that phosphate ester hydrolysis can not only be turned on, but also be turned off, by fine tuning the electrostatic environment and the present review demonstrates numerous examples where this is the case. Without this capacity for regulation, it would be impossible to have for instance a signaling or metabolic cascade, where the action of each participant is determined by the fine-tuned activity of the previous piece in the production line. This makes phosphate esters the ideal compounds to facilitate life as we know it.

Chemical dynamics simulations of X- + CH3Y → XCH3 + Y- gas-phase S(N)2 nucleophilic substitution reactions. Nonstatistical dynamics and nontraditional reaction mechanisms

Extensive classical chemical dynamics simulations of gas-phase X(-) + CH(3)Y → XCH(3) + Y(-) S(N)2 nucleophilic substitution reactions are reviewed and discussed and compared with experimental measurements and predictions of theoretical models. The primary emphasis is on reactions for which X and Y are halogen atoms. Both reactions with the traditional potential energy surface (PES), which include pre- and postreaction potential energy minima and a central barrier, and reactions with nontraditional PESs are considered. These S(N)2 reactions exhibit important nonstatistical atomic-level dynamics. The X(-) + CH(3)Y → X(-)---CH(3)Y association rate constant is less than the capture model as a result of inefficient energy transfer from X(-)+ CH(3)Y relative translation to CH(3)Y rotation and vibration. There is weak coupling between the low-frequency intermolecular modes of the X(-)---CH(3)Y complex and higher frequency CH(3)Y intramolecular modes, resulting in non-RRKM kinetics for X(-)---CH(3)Y unimolecular decomposition. Recrossings of the [X--CH(3)--Y](-) central barrier is important. As a result of the above dynamics, the relative translational energy and temperature dependencies of the S(N)2 rate constants are not accurately given by statistical theory. The nonstatistical dynamics results in nonstatistical partitioning of the available energy to XCH(3) +Y(-) reaction products. Besides the indirect, complex forming atomic-level mechanism for the S(N)2 reaction, direct mechanisms promoted by X(-) + CH(3)Y relative translational or CH(3)Y vibrational excitation are possible, e.g., the roundabout mechanism.

Vibrationally induced dissociation of sulfuric acid (H2SO4)

One of the important reactive steps in Earth's atmosphere is the decomposition of H(2)SO(4) to H(2)O and SO(3). However, because the UV spectrum of H(2)SO(4) was not found up to 140 nm, alternative mechanisms, including vibrationally induced dissociation, were proposed. Using adiabatic reactive molecular dynamics (ARMD) simulations with validated force fields for the product and educt channels, it is shown through explicit atomistic simulation that by exciting the ν(9) (OH-stretching-) mode, photodissociation can occur on the picosecond time scale. With the potential energy surfaces used in the present work, ν(9) = 4 is sufficient for this process. From a statistically significant number of trajectories (several thousands), vibrationally induced dissociation times are found to follow Gamma-distributions with most likely reaction times between 40 and 200 ps by depositing energies ranging from 40 to 60 kcal/mol, corresponding to 4 and 6 vibrational quanta in the OH stretching vibration. Because ARMD simulations allow multiple and long-time simulations, both nonstatistical, impulsive H-transfer and statistical, IVR-regimes of the decomposition reaction can be discussed in detail at an atomistic level.

Ab initio direct classical trajectory investigation on the SN2 reaction of F- with NH2F: nonstatistical central barrier recrossing dynamics

The bimolecular nucleophilic substitution (S(N)2) reaction of F(a)(-) with NH(2)F(b) has been investigated with the ab initio direct classical trajectory method. According to our trajectory calculations, a dynamic behavior of nonstatistical central barrier recrossing is revealed. Among the 64 trajectories calculated in this work, 45 trajectories follow the dynamic reaction pathways as assumed by statistical theory and other 19 trajectories with central barrier recrossings are nonstatistical. For the nonstatistical trajectories, the central barrier recrossings may originate from the inefficient kinetic energy transfer from the intramolecular modes of the NH(2)F(a) moiety in the dynamic F(b)(-)…H-NH-F(a) complex to the intermolecular modes of the dynamic F(b)(-)…H-NH-F(a) complex on the exit-channel potential energy surface. With respect to the dynamic behavior of the nonstatistical central barrier recrossing, the statistical theories such as the Rice-Ramsperger-Kassel-Marcus and transition state theories without further corrections cannot be used to model the reaction kinetics for this S(N)2 reaction.

The taxadiene-forming carbocation cascade

A complete pathway (structures and energies of intermediates and transition state structures connecting them) from geranylgeranyl diphosphate to taxadiene, obtained using quantum chemical calculations, is described. This pathway is fully consistent with previous labeling experiments, despite differing in several subtle ways (in terms of conformations of certain carbocation intermediates and in the concertedness and synchronicity of certain bond-forming events) from previous mechanistic proposals. Also, on the basis of the theoretical results, it is proposed that the 2-fluoro-geranylgeranyl diphosphate substrate analogue in the recently reported X-ray crystal structure of taxadiene synthase is bound in a nonproductive orientation.

Differentiating mechanistic possibilities for the thermal, intramolecular [2 + 2] cycloaddition of allene-ynes

Intramolecular [2 + 2] cycloaddition reactions of allene-ynes offer a quick and efficient route to fused bicyclic ring structures. Insights into the mechanism and regiochemical preferences of this reaction are provided herein on the basis of the results of quantum chemical calculations (B3LYP/6-31+G(d,p)) and select experiments; both indicate that the reaction likely proceeds through a stepwise diradical pathway where one radical center is stabilized through allylic delocalization. The influences of the length of the tether connecting the alkyne and allene and substituent effects are also discussed.

Computational investigation of the mechanism of addition of singlet carbenes to bicyclobutanes

Singlet carbenes are known to react with bicyclobutanes to yield 1,4-diene products, as in the addition of dichlorocarbene to bicyclobutane to yield 1,1-dichloro-1,4-pentadiene. At least two mechanisms have been proposed to explain this unusual reaction: (1) a concerted process and (2) a stepwise process involving a zwitterionic intermediate. Ab initio electronic structure calculations have been performed in order to help distinguish between these two mechanistic possibilities. In the parent system, the concerted pathway and the corresponding transition structure are readily located. On the other hand, the hypothesized zwitterionic intermediate does not correspond to a minimum at most levels of theory, even in the presence of a polar medium representing the solvent. Instead, this structure corresponds to a transition state or, at best, an extremely shallow minimum. The two pathways--one unambiguously concerted, the other possibly leading through an extremely shallow minimum (intermediate)--have very similar barriers and are expected to be competitive. In the substituted 1,2,2-trimethylbicyclobutane system, five regioisomeric concerted pathways exist and lead to four different diene products. Two of these pathways lie well below the others in energy, and they alone are expected to play a significant role at ordinary temperatures. Of these two pathways, the one calculated to have the slightly lower barrier leads to the only product that is reported experimentally. In addition, a sixth geometry of approach exists, leading over a transition structure of comparable energy to a shallow minimum that corresponds to a zwitterionic intermediate. The calculated potential energy surface suggests that the reaction can proceed through this intermediate both to the observed diene product and to one of the other isomers. It therefore appears that the concerted and stepwise mechanisms are competitive in the substituted system. Taken together, the calculated pathways and barriers do not adequately account for the very pronounced regioselectivity observed experimentally; only modest regioselectivity would be predicted at best. Examination of a calculated potential energy surface defined over two relevant internal coordinates sheds further light on the reaction and suggests that the experimentally observed regioselectivity might derive in considerable part from dynamic effects.

Evidence for nonstatistical dynamics in the Wolff rearrangement of a carbene

Two (13)C-labeled isomers of the formal Diels-Alder adduct of acetylmethyloxirene to tetramethyl 1,2,4,5-benzenetetracarboxylate have been synthesized. Flash vacuum thermolysis of these adducts leads to various isotopic isomers of acetylmethylketene, the ratios of which have been determined by NMR. The surprising finding that the principal product comes from methylpyruvoyl carbene rather than its more stable isomer diacetylcarbene is explained by MPWB1K density functional calculations, which show that the reactant probably undergoes a unimolecular rearrangement to a norcaradiene derivative prior to its fragmentation. Coupled-cluster calculations on the methylpyruvoyl carbene show that it is capable of undergoing three unimolecular isomerizations. The fastest is 1,2-acetyl migration to give acetylmethylketene directly. The next is rearrangement via acetylmethyloxirene to diacetylcarbene and thence by Wolff rearrangement to acetylmethylketene. The least-favorable reaction is degenerate rearrangement via 1,3-dimethyl-2-oxabicyclo[1.1.0]butan-4-one (the epoxide of dimethylcyclopropenone). The combined experimental and computational results indicate that Wolff rearrangement of the diacetylcarbene occurs with a 2.5:1 ratio of the methyl groups despite the fact that they are related by a twofold axis of symmetry in the carbene. Preliminary molecular dynamics simulations are consistent with this conclusion. Taken together, the results suggest that the Wolff rearrangement is subject to the same kind of nonstatistical dynamical effects detected for other kinds of thermally generated reactive intermediates.